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Garciaz S, Berton G, Hospital MA, Guille A, Adélaïde J, Saillard C, Hicheri Y, Mozziconacci MJ, Duprez E, Récher C, Alary AS, Birnbaum D, Vey N. Long-term survival of NPM1 AML treated with intensive chemotherapy with extensive molecular data available. Leuk Lymphoma 2024; 65:700-703. [PMID: 38329727 DOI: 10.1080/10428194.2024.2312430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Affiliation(s)
- Sylvain Garciaz
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Guillaume Berton
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Marie-Anne Hospital
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Center, INSERMUMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Center, INSERMUMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Colombe Saillard
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Yosr Hicheri
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | | | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Marseille Cancer Research Center, INSERMUMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Christian Récher
- Department of Hematology, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
- Université Toulouse III Paul Sabatier, Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, Toulouse, France
| | - Anne-Sophie Alary
- Department of Cancer Biology, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Center, INSERMUMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
| | - Norbert Vey
- Department of Hematology, Institut Paoli-Calmettes, INSERM UMR 1068, CNRS UMR725, CNRS, Aix-Marseille University, Marseille, France
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Bertucci F, de Nonneville A, Finetti P, Cohendet A, Guille A, Mamessier E. The co-expression of antigen targets as a rationale for ADC combination in urothelial cancer. Ann Oncol 2024; 35:477-478. [PMID: 38364991 DOI: 10.1016/j.annonc.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Affiliation(s)
- F Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille; Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.
| | - A de Nonneville
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille; Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - P Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille
| | - A Cohendet
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille
| | - A Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille
| | - E Mamessier
- Predictive Oncology Laboratory, Marseille Cancer Research Center (CRCM), Aix-Marseille University, U1068 INSERM, U7258 CNRS, Institut Paoli-Calmettes, Marseille
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3
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Bertucci F, Lerebours F, Ceccarelli M, Guille A, Syed N, Finetti P, Adélaïde J, Van Laere S, Goncalves A, Viens P, Birnbaum D, Mamessier E, Callens C, Bedognetti D. Mutational landscape of inflammatory breast cancer. J Transl Med 2024; 22:374. [PMID: 38637846 PMCID: PMC11025259 DOI: 10.1186/s12967-024-05198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is the most pro-metastatic form of BC. Better understanding of its enigmatic pathophysiology is crucial. We report here the largest whole-exome sequencing (WES) study of clinical IBC samples. METHODS We retrospectively applied WES to 54 untreated IBC primary tumor samples and matched normal DNA. The comparator samples were 102 stage-matched non-IBC samples from TCGA. We compared the somatic mutational profiles, spectra and signatures, copy number alterations (CNAs), HRD and heterogeneity scores, and frequencies of actionable genomic alterations (AGAs) between IBCs and non-IBCs. The comparisons were adjusted for the molecular subtypes. RESULTS The number of somatic mutations, TMB, and mutational spectra were not different between IBCs and non-IBCs, and no gene was differentially mutated or showed differential frequency of CNAs. Among the COSMIC signatures, only the age-related signature was more frequent in non-IBCs than in IBCs. We also identified in IBCs two new mutational signatures not associated with any environmental exposure, one of them having been previously related to HIF pathway activation. Overall, the HRD score was not different between both groups, but was higher in TN IBCs than TN non-IBCs. IBCs were less frequently classified as heterogeneous according to heterogeneity H-index than non-IBCs (21% vs 33%), and clonal mutations were more frequent and subclonal mutations less frequent in IBCs. More than 50% of patients with IBC harbored at least one high-level of evidence (LOE) AGA (OncoKB LOE 1-2, ESCAT LOE I-II), similarly to patients with non-IBC. CONCLUSIONS We provide the largest mutational landscape of IBC. Only a few subtle differences were identified with non-IBCs. The most clinically relevant one was the higher HRD score in TN IBCs than in TN non-IBCs, whereas the most intriguing one was the smaller intratumor heterogeneity of IBCs.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
| | - Florence Lerebours
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, USA
- Department of Public Health Sciences, University of Miami, Miami, USA
| | - Arnaud Guille
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Najeeb Syed
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Pascal Finetti
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - José Adélaïde
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Anthony Goncalves
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Daniel Birnbaum
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Emilie Mamessier
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Céline Callens
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Davide Bedognetti
- Tumor Biology and Immunology Laboratory, Research Branch, Sidra Medicine, Doha, Qatar
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Legrand S, Saifudeen A, Bordelet H, Vernerey J, Guille A, Bignaud A, Thierry A, Acquaviva L, Gaudin M, Sanchez A, Johnson D, Friedrich A, Schacherer J, Neale MJ, Borde V, Koszul R, Llorente B. Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri. Proc Natl Acad Sci U S A 2024; 121:e2312820121. [PMID: 38478689 PMCID: PMC10962940 DOI: 10.1073/pnas.2312820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/24/2024] [Indexed: 03/27/2024] Open
Abstract
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.
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Affiliation(s)
- Sylvain Legrand
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Asma Saifudeen
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Hélène Bordelet
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Julien Vernerey
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Arnaud Guille
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Laurent Acquaviva
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Maxime Gaudin
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Aurore Sanchez
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Anne Friedrich
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Valérie Borde
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Bertrand Llorente
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
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Udu-Ituma S, Adélaïde J, Le TK, Omabe K, Finetti P, Paris C, Guille A, Bertucci F, Birnbaum D, Rocchi P, Chaffanet M. ZNF703 mRNA-Targeting Antisense Oligonucleotide Blocks Cell Proliferation and Induces Apoptosis in Breast Cancer Cell Lines. Pharmaceutics 2023; 15:1930. [PMID: 37514116 PMCID: PMC10384502 DOI: 10.3390/pharmaceutics15071930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The luminal B molecular subtype of breast cancers (BC) accounts for more than a third of BCs and is associated with aggressive clinical behavior and poor prognosis. The use of endocrine therapy in BC treatment has significantly contributed to the decrease in the number of deaths in recent years. However, most BC patients with prolonged exposure to estrogen receptor (ER) selective modulators such as tamoxifen develop resistance and become non-responsive over time. Recent studies have implicated overexpression of the ZNF703 gene in BC resistance to endocrine drugs, thereby highlighting ZNF703 inhibition as an attractive modality in BC treatment, especially luminal B BCs. However, there is no known inhibitor of ZNF703 due to its nuclear association and non-enzymatic activity. Here, we have developed an antisense oligonucleotide (ASO) against ZNF703 mRNA and shown that it downregulates ZNF703 protein expression. ZNF703 inhibition decreased cell proliferation and induced apoptosis. Combined with cisplatin, the anti-cancer effects of ZNF703-ASO9 were improved. Moreover, our work shows that ASO technology may be used to increase the number of targetable cancer genes.
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Affiliation(s)
- Sandra Udu-Ituma
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
- Department of Biology, Alex Ekwueme Federal University Ndufu-Alike Ikwo, Abakaliki P.M.B. 1010, Ebonyi State, Nigeria
- European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France
| | - José Adélaïde
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Thi Khanh Le
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
- European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France
| | - Kenneth Omabe
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Pascal Finetti
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Clément Paris
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Arnaud Guille
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - François Bertucci
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Daniel Birnbaum
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Palma Rocchi
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
- European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France
| | - Max Chaffanet
- Equipe Labellisée Ligue Nationale Contre le Cancer, Predictive Oncology Laboratory, Marseille Research Cancer Center, INSERM U1068, CNRS U7258, Institut Paoli-Calmettes, Aix Marseille University, 13009 Marseille, France
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6
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Nigon E, Lefeuvre-Plesse C, Martinez A, Chauleur C, Lortholary A, Favier L, Bats AS, Guille A, AdélaÏde J, Finetti P, de Casteljac V, Provansal M, Mamessier E, Bertucci F, Ray-Coquard I, Sabatier R. Clinical, pathological, and comprehensive molecular analysis of the uterine clear cell carcinoma: a retrospective national study from TMRG and GINECO network. J Transl Med 2023; 21:408. [PMID: 37353806 PMCID: PMC10288685 DOI: 10.1186/s12967-023-04264-7] [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: 01/09/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND Uterine clear cell carcinomas (CCC) represent less than 5% of uterine cancers. Their biological characteristics and clinical management remain uncertain. A multicenter study to explore both clinical and molecular features of these rare tumors was conducted. METHODS This multicenter retrospective national study was performed within the French TMRG (Rare Gynecologic Malignant Tumors) network. Clinical data and, when available, FFPE blocks were collected. Clinical features, treatments, and outcome (progression-free survival (PFS) and overall survival (OS)) were analyzed and correlated to the protein (tissue micro-array), RNA (Nanostring nCounter® technology), and DNA (array-Comparative Genomic hybridization and target-next generation sequencing) levels using the tumor samples available. RESULTS Sixty-eight patients with uterine CCC were enrolled, 61 from endometrial localization and 5 with cervix localization. Median age at diagnosis was 68.9 years old (range 19-89.7). Most tumors were diagnosed at an early stage (78% FIGO stage I-II). Hysterectomy (performed in 90%) and lymph node dissection (80%) were the most frequent surgical treatment. More than 70% of patients received external beam radiotherapy and 57% received brachytherapy. Nearly half (46%) of the patients received chemotherapy. After a median follow-up of 24.7 months, median PFS was 64.8 months (95 CI [5.3-124.4]) and median OS was 79.7 (IC95 [31.0-128.4]). Low hormone receptor expression (13% estrogen-receptor positive), frequent PI3K pathway alterations (58% PTEN loss, 50% PIK3CA mutations), and P53 abnormalities (41%) were observed. Mismatch repair deficiency was identified in 20%. P16 expression was associated with shorter PFS (HR = 5.88, 95 CI [1.56-25], p = 0.009). Transcriptomic analyzes revealed a specific transcriptomic profile notably with a high expression of immune response-associated genes in uterine CCC displaying a very good overall prognosis. CONCLUSIONS Uterine CCC reported to be potentially MSI high, hormone receptors negative, and sometimes TP53 mutated. However, some patients with immune response-associated features and better prognosis may be candidate to treatment de-escalation and immunotherapy.
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Affiliation(s)
- Elsa Nigon
- Department of Medical Oncology, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, Marseille, France
| | | | - Alejandra Martinez
- Department of Surgical Oncology, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Céline Chauleur
- Department of Medical Oncology, Institut de Cancérologie de la Loire, Saint Etienne, France
| | - Alain Lortholary
- Hôpital privé du Confluent, Institut de Cancérologie Catherine de Sienne, Nantes, France
| | - Laure Favier
- Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Anne-Sophie Bats
- Department of Surgical Oncology, Hôpital Européen Georges Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Arnaud Guille
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France
| | - José AdélaÏde
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France
| | - Victoire de Casteljac
- Department of Medical Oncology, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, Marseille, France
| | - Emilie Mamessier
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France
| | - François Bertucci
- Department of Medical Oncology, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, Marseille, France
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France
| | - Isabelle Ray-Coquard
- Department of Medical Oncology, Centre Léon Bérard, University Claude Bernard Lyon 1, Lyon, France
| | - Renaud Sabatier
- Department of Medical Oncology, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, Marseille, France.
- CRCM, Predictive Oncology laboratory, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France.
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7
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Cervera N, Guille A, Adélaïde J, Hospital M, Garciaz S, Mozziconacci M, Vey N, Gelsi‐Boyer V, Birnbaum D. Erythroleukemia: Classification. EJHaem 2023; 4:450-453. [PMID: 37206278 PMCID: PMC10188454 DOI: 10.1002/jha2.676] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 05/21/2023]
Abstract
Acute erythroid leukemia (AEL) is a rare (2%-5%) form of acute myeloid leukemia (AML). Molecular alterations found in AEL resemble those of other AMLs. We report a classification of AELs in three major classes, with different prognosis and some specific features such as a tendency to mutual exclusion of mutations in epigenetic regulators and signaling genes.
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Affiliation(s)
- Nathalie Cervera
- Laboratoire d'Oncologie PrédictiveCentre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐CalmettesINSERM UMR 1068CNRS UMR725Aix‐Marseille UniversitéMarseilleFrance
| | - Arnaud Guille
- Laboratoire d'Oncologie PrédictiveCentre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐CalmettesINSERM UMR 1068CNRS UMR725Aix‐Marseille UniversitéMarseilleFrance
| | - José Adélaïde
- Laboratoire d'Oncologie PrédictiveCentre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐CalmettesINSERM UMR 1068CNRS UMR725Aix‐Marseille UniversitéMarseilleFrance
| | | | - Sylvain Garciaz
- Département d'HématologieInstitut Paoli‐CalmettesMarseilleFrance
| | | | - Norbert Vey
- Département d'HématologieInstitut Paoli‐CalmettesMarseilleFrance
| | - Véronique Gelsi‐Boyer
- Laboratoire d'Oncologie PrédictiveCentre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐CalmettesINSERM UMR 1068CNRS UMR725Aix‐Marseille UniversitéMarseilleFrance
- Département de BioPathologieInstitut Paoli‐CalmettesMarseilleFrance
| | - Daniel Birnbaum
- Laboratoire d'Oncologie PrédictiveCentre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐CalmettesINSERM UMR 1068CNRS UMR725Aix‐Marseille UniversitéMarseilleFrance
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8
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Velazquez C, Orhan E, Tabet I, Fenou L, Orsetti B, Adélaïde J, Guille A, Thézénas S, Crapez E, Colombo PE, Chaffanet M, Birnbaum D, Sardet C, Jacot W, Theillet C. BRCA1-methylated triple negative breast cancers previously exposed to neoadjuvant chemotherapy form RAD51 foci and respond poorly to olaparib. Front Oncol 2023; 13:1125021. [PMID: 37007122 PMCID: PMC10064050 DOI: 10.3389/fonc.2023.1125021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
BackgroundAbout 15% of Triple-Negative-Breast-Cancer (TNBC) present silencing of the BRCA1 promoter methylation and are assumed to be Homologous Recombination Deficient (HRD). BRCA1-methylated (BRCA1-Me) TNBC could, thus, be eligible to treatment based on PARP-inhibitors or Platinum salts. However, their actual HRD status is discussed, as these tumors are suspected to develop resistance after chemotherapy exposure.MethodsWe interrogated the sensitivity to olaparib vs. carboplatin of 8 TNBC Patient-Derived Xenografts (PDX) models. Four PDX corresponded to BRCA1-Me, of which 3 were previously exposed to NeoAdjuvant-Chemotherapy (NACT). The remaining PDX models corresponded to two BRCA1-mutated (BRCA1-Mut) and two BRCA1-wild type PDX that were respectively included as positive and negative controls. The HRD status of our PDX models was assessed using both genomic signatures and the functional BRCA1 and RAD51 nuclear foci formation assay. To assess HR restoration associated with olaparib resistance, we studied pairs of BRCA1 deficient cell lines and their resistant subclones.ResultsThe 3 BRCA1-Me PDX that had been exposed to NACT responded poorly to olaparib, likewise BRCA1-WT PDX. Contrastingly, 3 treatment-naïve BRCA1-deficient PDX (1 BRCA1-Me and 2 BRCA1-mutated) responded to olaparib. Noticeably, the three olaparib-responsive PDX scored negative for BRCA1- and RAD51-foci, whereas all non-responsive PDX models, including the 3 NACT-exposed BRCA1-Me PDX, scored positive for RAD51-foci. This suggested HRD in olaparib responsive PDX, while non-responsive models were HR proficient. These results were consistent with observations in cell lines showing a significant increase of RAD51-foci in olaparib-resistant subclones compared with sensitive parental cells, suggesting HR restoration in these models.ConclusionOur results thus support the notion that the actual HRD status of BRCA1-Me TNBC, especially if previously exposed to chemotherapy, may be questioned and should be verified using the BRCA1- and RAD51-foci assay.
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Affiliation(s)
- Carolina Velazquez
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Esin Orhan
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Imene Tabet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Lise Fenou
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Béatrice Orsetti
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - José Adélaïde
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Simon Thézénas
- Biometry Unit, Institut du Cancer de Montpellier, Montpellier, France
| | - Evelyne Crapez
- Unité de Recherche Translationnelle, Institut du Cancer de Montpellier, Montpellier, France
| | - Pierre-Emmanuel Colombo
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Oncological Surgery, Institut du Cancer de Montpellier, Montpellier, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - William Jacot
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Clinical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - Charles Theillet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- *Correspondence: Charles Theillet,
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9
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de Nonneville A, Salas S, Bertucci F, Sobinoff AP, Adélaïde J, Guille A, Finetti P, Noble JR, Churikov D, Chaffanet M, Lavit E, Pickett HA, Bouvier C, Birnbaum D, Reddel RR, Géli V. TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT. EMBO Mol Med 2022; 14:e15859. [PMID: 35920001 PMCID: PMC9549729 DOI: 10.15252/emmm.202215859] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high-grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild-type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT-positive ATRX-wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX-mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX-wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.
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Affiliation(s)
- Alexandre de Nonneville
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance,Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia,Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Sébastien Salas
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - François Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Pascal Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Jane R Noble
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Dimitri Churikov
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
| | - Max Chaffanet
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Elise Lavit
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Corinne Bouvier
- Department of PathologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Roger R Reddel
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
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10
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Sabatier R, Garnier S, Guille A, Carbuccia N, Pakradouni J, Adelaide J, Provansal M, Cappiello M, Rousseau F, Chaffanet M, Birnbaum D, Mamessier E, Gonçalves A, Bertucci F. Whole-genome/exome analysis of circulating tumor DNA and comparison to tumor genomics from patients with heavily pre-treated ovarian cancer: subset analysis of the PERMED-01 trial. Front Oncol 2022; 12:946257. [PMID: 35965534 PMCID: PMC9373051 DOI: 10.3389/fonc.2022.946257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionThe poor prognosis of ovarian carcinoma (OvC) is due to the advanced stage at diagnosis, a high risk of relapse after first-line therapies, and the lack of efficient treatments in the recurrence setting. Circulating tumor DNA (ctDNA) analysis is a promising tool to assess treatment-resistant OvC and may avoid iterative tissue biopsies. We aimed to evaluate the genomic profile of recurrent heavily pre-treated OvC.MethodsWe performed tumor panel-based sequencing as well as low-coverage whole-genome sequencing (LC-WGS) of tumor and plasma collected in patients with ovarian cancer included in the PERMED-01 trial. Whole-exome sequencing (WES) data of plasma samples were also analyzed and compared to mutation and copy number alteration (CNA) tumor profiles. The prognostic value [progression-free survival (PFS)] of these alterations was assessed in an exploratory analysis.ResultsTumor and plasma genomic analyses were done for 24 patients with heavily pretreated OvC [67% high-grade serous carcinoma (HGSC)]. Tumor mutation burden was low (median 2.04 mutations/Mb) and the most frequent mutated gene was TP53 (94% of HGSC). Tumor CNAs were frequent with a median of 50% of genome altered fraction. Plasma LC-WGS and WES detected ctDNA in 21/24 cases (88%) with a median tumor fraction of 12.7%. We observed a low correlation between plasma and tumor CNA profiles. However, this correlation was significant in cases with the highest circulating tumor fraction. Plasma genome altered fraction and plasma mutation burden (p = 0.011 and p = 0.041, respectively, log-rank tests) were associated with PFS.ConclusionsCombination of LC-WGS and WES can detect ctDNA in most pre-treated OvCs. Some ctDNA characteristics, such as genome altered fraction and plasma mutation burden, showed prognostic value. ctDNA assessment with LC-WGS may be a promising and non-expansive tool to evaluate disease evolution in this disease with high genomic instability.Clinical Trial Registrationhttps://clinicaltrials.gov/ct2/show/NCT02342158, identifier NCT02342158.
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Affiliation(s)
- Renaud Sabatier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
- *Correspondence: Renaud Sabatier,
| | - Séverine Garnier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Arnaud Guille
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Nadine Carbuccia
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Jihane Pakradouni
- Department of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - José Adelaide
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Magali Provansal
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
| | - Maria Cappiello
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
| | - Frédérique Rousseau
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
| | - Max Chaffanet
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Daniel Birnbaum
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Emilie Mamessier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
| | - Anthony Gonçalves
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
| | - François Bertucci
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM—Predictive Oncology Laboratory, Marseille, France
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes—Department of Medical Oncology, CRCM, Marseille, France
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11
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Cabaud O, Berger L, Crompot E, Adélaide J, Finetti P, Garnier S, Guille A, Carbuccia N, Farina A, Agavnian E, Chaffanet M, Gonçalves A, Charafe-Jauffret E, Mamessier E, Birnbaum D, Bertucci F, Lopez M. Overcoming Resistance to Anti-nectin-4 Antibody-Drug Conjugate. Mol Cancer Ther 2022; 21:1227-1235. [PMID: 35534238 DOI: 10.1158/1535-7163.mct-22-0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/14/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Antibody-drug conjugates (ADCs) represent a fast-growing drug class in oncology. However, ADCs are associated with resistance, and therapies able to overcome it are of utmost importance. Recently, enfortumab vedotin-ejfv (EV) was approved in nectin-4+ metastatic urothelial cancer. We previously described PVRL4/nectin-4, as a new therapeutic target in breast cancer (BC), and produced an efficient EV-like ADC comprising a human anti-nectin-4 monoclonal antibody conjugated to monomethyl auristatin-E (MMAE) named N41mab-vcMMAE. To study the consequence of the long-term treatment with this ADC, we developed a preclinical BC model in mice, and report a mechanism of resistance to N41mab-vcMMAE after a 9- months treatment and a way to reverse it. RNA-sequencing pointed to an upregulation in resistant tumors of ABCB1 expression, encoding the multidrug resistance protein MDR-1/P-glycoprotein (P-gp), associated with focal gene amplification and high protein expression. Sensitivity to N41mab-vcMMAE of the resistant model was restored in vitro by P-gp pharmacological inhibitors, like tariquidar. P-gp is expressed in a variety of normal tissues. By delivering the drug to the tumor more specifically than does classical chemotherapy, we hypothesized that the combined use of ADC with P-gp inhibitors might reverse resistance in vivo without toxicity. Indeed, we showed that the tariquidar/N41mab-vcMMAE combination was well tolerated and induced a rapid regression of ADC-resistant tumors in mice. By contrast, the tariquidar/docetaxel combination was toxic and poorly efficient. These results show that ABC transporter inhibitors can be safely used with ADC to reverse ADC-induced resistance and open new opportunities in the fight against multidrug resistance.
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Affiliation(s)
- Olivier Cabaud
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Ludovic Berger
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Emerence Crompot
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - José Adélaide
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Sèverine Garnier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Nadine Carbuccia
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Anne Farina
- ICEP Platform, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Agavnian
- ICEP Platform, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Anthony Gonçalves
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Emmanuelle Charafe-Jauffret
- ICEP Platform, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Mamessier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
| | - François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Marc Lopez
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université U105, Institut Paoli-Calmettes, Label « Ligue contre le cancer », Marseille, France
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12
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Sabatier R, Vicier C, Garnier S, Guille A, Carbuccia N, Isambert N, Dalenc F, Robert M, Levy C, Pakradouni J, Adelaïde J, Chaffanet M, Sfumato P, Mamessier E, Bertucci F, Goncalves A. Circulating tumor DNA predicts efficacy of a dual AKT/p70S6K inhibitor (LY2780301) plus paclitaxel in metastatic breast cancer: plasma analysis of the TAKTIC phase IB/II study. Mol Oncol 2022; 16:2057-2070. [PMID: 35122700 PMCID: PMC9120890 DOI: 10.1002/1878-0261.13188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
The phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway is frequently activated in HER2-negative breast cancer and may play a role in taxane resistance. The phase IB/II TAKTIC trial (NCT01980277) has shown that combining a dual AKT and p70 ribosomal protein S6 kinase (p70S6K) inhibitor (LY2780301) taken orally with weekly paclitaxel in HER2-negative advanced breast cancer is feasible, with preliminary evidence of efficacy. We wanted to explore whether circulating tumor DNA (ctDNA) may be a surrogate marker of treatment efficacy in this setting. Serial plasma samples were collected and cell-free DNA was sequenced using low-coverage whole-genome sequencing, and analysis was completed with droplet digital PCR for some patients with driver mutations. Baseline tumor fraction (TF) and TF after 7 weeks on treatment were compared to progression-free survival (PFS) and overall response rate. We also explored circulating copy number alterations associated with treatment failure. Of the 51 patients enrolled in the TAKTIC trial, at least one plasma sample was available for 44 cases (96 time points). All patients with tumor TP53, PI3KCA or AKT1 mutations harbored at least one of these alterations in plasma. TF at inclusion was correlated to PFS (6m-PFS was 92% for ctDNAneg patients vs 68% for ctDNApos cases; HR=3.45, 95%CI [1.34-8.90], p=0.007). ctDNA status at week 7 was not correlated to prognosis. Even though most circulating copy number alterations were conserved at disease progression, some genomic regions of interest were altered in post-progression samples. In conclusions, ctDNA detection at baseline was associated with shorter PFS in patients included in the TAKTIC trial. Plasma-based copy number analysis may help to identify alterations involved in resistance to treatment.
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Affiliation(s)
- Renaud Sabatier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France.,Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
| | - Cécile Vicier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
| | - Séverine Garnier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France
| | - Arnaud Guille
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France
| | - Nadine Carbuccia
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France
| | - Nicolas Isambert
- Drug Development Department, Centre Georges François Leclerc, Dijon, France
| | - Florence Dalenc
- Department of Medical Oncology, Institut Claudius Regaud, IUCT-Oncopole, CRCT, Inserm, Toulouse, France
| | - Marie Robert
- Institut de Cancérologie de l'Ouest-René Gauducheau, Saint-Herblain, France
| | - Christelle Levy
- Centre François Baclesse, Department of Medical Oncology, Caen, France
| | - Jihane Pakradouni
- Depatment of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - José Adelaïde
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France
| | - Max Chaffanet
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France
| | - Patrick Sfumato
- Depatment of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Mamessier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
| | - François Bertucci
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France.,Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
| | - Anthony Goncalves
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM-Predictive Oncology laboratory, Marseille, France.,Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
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13
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Azzoni V, Wicinski J, Macario M, Castagné M, Finetti P, Ambrosova K, Rouault CD, Sergé A, Farina A, Agavnian E, Coslet S, Josselin E, Guille A, Adelaide J, Zacharioudakis E, Castellano R, Bertucci F, Birnbaum D, Rodriguez R, Charafe-Jauffret E, Ginestier C. BMI1 nuclear location is critical for RAD51-dependent response to replication stress and drives chemoresistance in breast cancer stem cells. Cell Death Dis 2022; 13:96. [PMID: 35110528 PMCID: PMC8811067 DOI: 10.1038/s41419-022-04538-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
Abstract
Replication stress (RS) has a pivotal role in tumor initiation, progression, or therapeutic resistance. In this study, we depicted the mechanism of breast cancer stem cells’ (bCSCs) response to RS and its clinical implication. We demonstrated that bCSCs present a limited level of RS compared with non-bCSCs in patient samples. We described for the first time that the spatial nuclear location of BMI1 protein triggers RS response in breast cancers. Hence, in bCSCs, BMI1 is rapidly located to stalled replication forks to recruit RAD51 and activate homologous-recombination machinery, whereas in non-bCSCs BMI1 is trapped on demethylated 1q12 megasatellites precluding effective RS response. We further demonstrated that BMI1/RAD51 axis activation is necessary to prevent cisplatin-induced DNA damage and that treatment of patient-derived xenografts with a RAD51 inhibitor sensitizes tumor-initiating cells to cisplatin. The comprehensive view of replicative-stress response in bCSC has profound implications for understanding and improving therapeutic resistance.
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Affiliation(s)
- Violette Azzoni
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Julien Wicinski
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Manon Macario
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Martin Castagné
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Pascal Finetti
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Katerina Ambrosova
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Célia D Rouault
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Arnaud Sergé
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, leuko/stromal interactions in normal and pathological hematopoiesis Lab, Marseille, France
| | - Anne Farina
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Experimental Pathology Platform, Marseille, France
| | - Emilie Agavnian
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Experimental Pathology Platform, Marseille, France
| | - Sergiu Coslet
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Experimental Pathology Platform, Marseille, France
| | - Emmanuelle Josselin
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Plateform, Marseille, France
| | - Arnaud Guille
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - José Adelaide
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Emmanouil Zacharioudakis
- Institut Curie, CNRS, INSERM, PSL Research University, Chemical Cell Biology Group, Paris, France
| | - Rémy Castellano
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Plateform, Marseille, France
| | - Francois Bertucci
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Daniel Birnbaum
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Raphael Rodriguez
- Institut Curie, CNRS, INSERM, PSL Research University, Chemical Cell Biology Group, Paris, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France.
| | - Christophe Ginestier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France.
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14
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Laurent C, Hamon M, Syrykh C, Adélaï J, Guille A, Parrens M, Dartigues P, Bardet A, Mescam L, Schiano De Colella J, Sujobert P, Besson C, Birnbaum D, Xerri L. RESISTANCE OF B‐CELL LYMPHOMAS TO CAR‐T CELL THERAPY IS ASSOCIATED WITH HISTOPHENOTYPICAL AND GENOMIC TUMOR CHANGES WHICH CAN INDUCE PROFOUND TRANS‐DIFFERENTIATION. Hematol Oncol 2021. [DOI: 10.1002/hon.190_2880] [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: 11/07/2022]
Affiliation(s)
| | - M. Hamon
- Hopital André Mignot Pathology Versailles France
| | | | - J. Adélaï
- IPC, Predictive Oncology/ CRCM Inserm CNRS AMU Marseille France
| | - A. Guille
- CRCM Predictive oncology Marseille France
| | - M. Parrens
- Hopital haut‐Lévéque, Pathology Bordeaux France
| | | | - A. Bardet
- Institut Paoli‐Calmettes pathology Marseille France
| | - L. Mescam
- Institut Paoli‐Calmettes pathology Marseille France
| | | | - P. Sujobert
- CHU Lyon‐Sud, Hématology Pierre‐Bénite France
| | - C. Besson
- Hopital André Mignot Pathology Versailles France
| | | | - L. Xerri
- Institut Paoli‐Calmettes pathology Marseille France
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15
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Mari R, Pomel C, Colombo PE, Narducci F, Garnier S, Carbuccia N, Guille A, Provansal M, Cappiello MA, Rousseau F, Blache G, Lambaudie E, Birnbaum D, Bertucci F, Sabatier R. Circulating tumor DNA as a noninvasive marker of resectability in ovarian carcinomas. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.5548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5548 Background: Ovarian cancer is the leading cause of death by gynecological cancer. Complete surgery remains one of the main prognostic factors. Laparoscopic exploration is mandatory to assess surgical resectability at diagnosis or after neoadjuvant chemotherapy. However, there is no clinical or biological marker that can correctly predict resectability and may be able to avoid a second laparoscopic exploration for initially unresectable diseases. Our aim was to assess circulating tumor DNA (ctDNA) value as a predictive non-invasive marker of evolution towards resectability for patients with epithelial ovarian cancer receiving first-line chemotherapy. Methods: We explored in this work one of the secondary objectives of the CIDOC study (NCT03302884). CIDOC is a multicenter prospective study aiming to explore ctDNA value as early marker of disease relapse after first-line treatment for epithelial ovarian cancer. Patients with mucinous histology or early stages not requiring chemotherapy are excluded. Plasma samples are collected at diagnosis, during neoadjuvant chemotherapy, and during follow-up. After DNA extraction, panel-based next generation sequencing is performed on both tumor samples and germline DNA, and somatic mutations of interest are selected for ctDNA monitoring. ctDNA analyses are conducted using droplet digital PCR (BioRad QX200) by measuring the variant allele fraction (VAF) of previously identified mutations. Results: This intermediary analysis has included 47 patients diagnosed between March 2017 and December 2019. Median age was 69 years old (48 – 84). Most of the patients had advanced disease (89.4% stage FIGO III or IV), serous histology (94.8%), and high grade tumor (92.3%). Most of the patients underwent complete interval cytoreductive surgery (76.3% vs 17.4% complete upfront surgery). Most of the tumors had TP53 mutations (85.1%), following by alterations involving DNA repair genes (38.3%). Median cell-free DNA concentration at baseline was 0.38 ng/µL (0 – 12.8). ctDNA was identified in 92.1% of patients at baseline with a median VAF of 1.84% (0 – 42.52%). ctDNA VAF was correlated to the peritoneal dissemination ( p= 0.039) assessed with the peritoneal cancer index. ctDNA clearance after preoperative chemotherapy tended to be correlated to achievement of complete interval surgery for patients receiving neoadjuvant chemotherapy ( p= 0.108). Conclusions: ctDNA may be a promising non-invasive marker to assess peritoneal cancer spreading and to predict surgical resectability after neoadjuvant chemotherapy. If confirmed in larger populations, this may enable to avoid additional surgical explorations for patients who remain ctDNA positive after chemotherapy. Clinical trial information: NCT03302884.
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Affiliation(s)
- Roxane Mari
- Department of Medical Oncology, Institut Paoli Calmettes, Marseille, France
| | - Christophe Pomel
- Department of Surgical Oncology, Centre Jean Perrin, Clermont-Ferrand, France
| | - Pierre-Emmanuel Colombo
- Department of Surgical Oncology, Institut Regional du Cancer de Montpellier, Montpellier, France
| | - Fabrice Narducci
- Department of Surgical Oncology, Centre Oscar Lambret, Lille, France
| | - Séverine Garnier
- Aix-Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nadine Carbuccia
- Aix-Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Arnaud Guille
- Aix-Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli Calmettes, Marseille, France
| | | | | | - Guillaume Blache
- Department of Surgical Oncology, Institut Paoli Calmettes, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli Calmettes, Marseille, France
| | - Daniel Birnbaum
- Aix-Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Francois Bertucci
- Department of Medical Oncology, Institut Paoli Calmettes, Marseille, France
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli Calmettes, Marseille, France
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16
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Bertucci F, Gonçalves A, Guille A, Adelaïde J, Garnier S, Carbuccia N, Billon E, Finetti P, Sfumato P, Monneur A, Pécheux C, Khran M, Brunelle S, Mescam L, Thomassin-Piana J, Poizat F, Charafe-Jauffret E, Turrini O, Lambaudie E, Provansal M, Extra JM, Madroszyk A, Gilabert M, Sabatier R, Vicier C, Mamessier E, Chabannon C, Pakradouni J, Viens P, André F, Gravis G, Popovici C, Birnbaum D, Chaffanet M. Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial. Genome Med 2021; 13:87. [PMID: 34006291 PMCID: PMC8132379 DOI: 10.1186/s13073-021-00897-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults with advanced solid cancer, the feasibility and impact of extensive molecular profiling applied to newly biopsied tumor sample and based on targeted NGS (t-NGS) of the largest gene panel to date and whole-genome array-comparative genomic hybridization (aCGH) with assessment of single-gene alterations and clinically relevant genomic scores. METHODS Eligible patients with refractory cancer had one tumor lesion accessible to biopsy. Extracted tumor DNA was profiled by t-NGS and aCGH. We assessed alterations of 802 "candidate cancer" genes and global genomic scores, such as homologous recombination deficiency (HRD) score and tumor mutational burden. The primary endpoint was the number of patients with actionable genetic alterations (AGAs). Secondary endpoints herein reported included a description of patients with AGA who received a "matched therapy" and their clinical outcome, and a comparison of AGA identification with t-NGS and aCGH versus whole-exome sequencing (WES). RESULTS Between November 2014 and September 2019, we enrolled 550 patients heavily pretreated. An exploitable complete molecular profile was obtained in 441/550 patients (80%). At least one AGA, defined in real time by our molecular tumor board, was found in 393/550 patients (71%, two-sided 90%CI 68-75%). Only 94/550 patients (17%, 95%CI 14-21) received an "AGA-matched therapy" on progression. The most frequent AGAs leading to "matched therapy" included PIK3CA mutations, KRAS mutations/amplifications, PTEN deletions/mutations, ERBB2 amplifications/mutations, and BRCA1/2 mutations. Such "matched therapy" improved by at least 1.3-fold the progression-free survival on matched therapy (PFS2) compared to PFS on prior therapy (PFS1) in 36% of cases, representing 6% of the enrolled patients. Within patients with AGA treated on progression, the use of "matched therapy" was the sole variable associated with an improved PFS2/PFS1 ratio. Objective responses were observed in 19% of patients treated with "matched therapy," and 6-month overall survival (OS) was 62% (95%CI 52-73). In a subset of 112 metastatic breast cancers, WES did not provide benefit in term of AGA identification when compared with t-NGS/aCGH. CONCLUSIONS Extensive molecular profiling of a newly biopsied tumor sample identified AGA in most of cases, leading to delivery of a "matched therapy" in 17% of screened patients, of which 36% derived clinical benefit. WES did not seem to improve these results. TRIAL REGISTRATION ID-RCB identifier: 2014-A00966-41; ClinicalTrials.gov identifier: NCT02342158 .
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Affiliation(s)
- François Bertucci
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.
| | - Anthony Gonçalves
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - José Adelaïde
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Séverine Garnier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Nadine Carbuccia
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Emilien Billon
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Patrick Sfumato
- Biostatistics Unit, Institut Paoli-Calmettes, Marseille, France
| | - Audrey Monneur
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Christophe Pécheux
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
| | - Martin Khran
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
- Aix-Marseille University, Inserm, U1251-MMG, Marseille Medical Genetics, Marseille, France
| | - Serge Brunelle
- Department of Imaging, Institut Paoli-Calmettes, Marseille, France
| | - Lenaïg Mescam
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Flora Poizat
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Olivier Turrini
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Jean-Marc Extra
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Anne Madroszyk
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Marine Gilabert
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Christian Chabannon
- Biobank, Department of Hematology, Institut Paoli-Calmettes, Marseille, France
| | - Jihane Pakradouni
- Department of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Fabrice André
- Department of Medical Oncology, Gustave Roussy Cancer Campus, UMR981 Inserm, Villejuif, France
- Paris Sud University, Orsay, France
| | - Gwenaelle Gravis
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cornel Popovici
- Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Max Chaffanet
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
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17
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Raoul JL, Oziel-Taieb S, Lecomte T, Adelaide J, Guille A, Chaffanet M, Poizat F, Heymann MF, Barbier L, Bertucci F. Case Report: Two Cases of Metastatic Pancreatoblastoma in Adults: Efficacy of Folfirinox and Implication of the Wnt/β-Catenin Pathway in Genomic Analysis. Front Oncol 2021; 11:564506. [PMID: 33796447 PMCID: PMC8007973 DOI: 10.3389/fonc.2021.564506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/16/2021] [Indexed: 12/24/2022] Open
Abstract
Pancreatoblastomas are unfrequent tumors usually found in children. We report two cases of metastatic pancreatoblastomas observed in young women. A systemic chemotherapy (FOLFIRINOX regimen) was associated with a disease control in one case and a partial response in the second with an improvement of general status for both. A high-throughput sequencing of the tumor described in both cases alteration in the Wnt/β-catenin pathway: a mutation in CTNNB1 (exon 3, c.110C>G, p.S37C, reported as a hotspot in COSMIC) in one case and a homozygous loss associated with breakage targeting APC (5q22.2) in the second.
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Affiliation(s)
- Jean-Luc Raoul
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | | | - Thierry Lecomte
- Department of Hepatogastroenterology, CHU Tours, Tours, France
| | - José Adelaide
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Arnaud Guille
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Max Chaffanet
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Flora Poizat
- Department of Pathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Louise Barbier
- Department of Digestive Surgery, CHU Tours, Tours, France
| | - François Bertucci
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Marseille, France
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18
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Collignon A, Hospital MA, Montersino C, Courtier F, Charbonnier A, Saillard C, D'Incan E, Mohty B, Guille A, Adelaïde J, Carbuccia N, Garnier S, Mozziconacci MJ, Zemmour C, Pakradouni J, Restouin A, Castellano R, Chaffanet M, Birnbaum D, Collette Y, Vey N. A chemogenomic approach to identify personalized therapy for patients with relapse or refractory acute myeloid leukemia: results of a prospective feasibility study. Blood Cancer J 2020; 10:64. [PMID: 32488055 PMCID: PMC7266815 DOI: 10.1038/s41408-020-0330-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/26/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/05/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) and ex vivo drug sensitivity/resistance profiling (DSRP) have laid foundations defining the functional genomic landscape of acute myeloid leukemia (AML) and premises of personalized medicine to guide treatment options for patients with aggressive and/or chemorefractory hematological malignancies. Here, we have assessed the feasibility of a tailored treatment strategy (TTS) guided by systematic parallel ex vivo DSRP and tNGS for patients with relapsed/refractory AML (number NCT02619071). A TTS issued by an institutional personalized committee could be achieved for 47/55 included patients (85%), 5 based on tNGS only, 6 on DSRP only, while 36 could be proposed on the basis of both, yielding more options and a better rationale. The TSS was available in <21 days for 28 patients (58.3%). On average, 3 to 4 potentially active drugs were selected per patient with only five patient samples being resistant to the entire drug panel. Seventeen patients received a TTS-guided treatment, resulting in four complete remissions, one partial remission, and five decreased peripheral blast counts. Our results show that chemogenomic combining tNGS with DSRP to determine a TTS is a promising approach to propose patient-specific treatment options within 21 days.
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Affiliation(s)
- A Collignon
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - M A Hospital
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - C Montersino
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - F Courtier
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - A Charbonnier
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - C Saillard
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - E D'Incan
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - B Mohty
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - A Guille
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - J Adelaïde
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - N Carbuccia
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - S Garnier
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - M J Mozziconacci
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | - C Zemmour
- Department of Clinical Research & Innovation, Institut Paoli-Calmettes, Biostatistics & Methodology Unit, Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - J Pakradouni
- Department of Clinical Research & Innovation, Sponsor Unit, Institut Paoli-Calmettes, Marseille, France
| | - A Restouin
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - R Castellano
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - M Chaffanet
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - D Birnbaum
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France.
| | - Y Collette
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France.
| | - N Vey
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
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19
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Takedachi A, Despras E, Scaglione S, Guérois R, Guervilly JH, Blin M, Audebert S, Camoin L, Hasanova Z, Schertzer M, Guille A, Churikov D, Callebaut I, Naim V, Chaffanet M, Borg JP, Bertucci F, Revy P, Birnbaum D, Londoño-Vallejo A, Kannouche PL, Gaillard PHL. Publisher Correction: SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations. Nat Struct Mol Biol 2020; 27:604. [PMID: 32409716 DOI: 10.1038/s41594-020-0447-z] [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: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- A Takedachi
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France.,Inovarion, Paris, France.,Department of Chemistry, Faculty of Science, Fukuoka University, Fukuoka, Japan
| | - E Despras
- CNRS UMR9019, Université Paris-Saclay, Equipe labellisée Ligue contre le Cancer, Gustave Roussy, Villejuif, France
| | - S Scaglione
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - R Guérois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, cedex, France
| | - J H Guervilly
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - M Blin
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - S Audebert
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - L Camoin
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - Z Hasanova
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France.,Institute of Molecular Genetics, Prague, Czech Republic
| | - M Schertzer
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris, France
| | - A Guille
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - D Churikov
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - I Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - V Naim
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - M Chaffanet
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - J P Borg
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - F Bertucci
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - P Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - D Birnbaum
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - A Londoño-Vallejo
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris, France
| | - P L Kannouche
- CNRS UMR9019, Université Paris-Saclay, Equipe labellisée Ligue contre le Cancer, Gustave Roussy, Villejuif, France
| | - P H L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France.
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20
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Adélaïde J, Cervera N, Guille A, Murati A, Chaffanet M, Mozziconacci MJ, Vey N, Birnbaum D, Gelsi-Boyer V. Gains of EPOR and ERG genes in adult erythroleukaemia. Br J Haematol 2020; 189:e174-e177. [PMID: 32227335 DOI: 10.1111/bjh.16586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- José Adélaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Nathalie Cervera
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Anne Murati
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | | | - Norbert Vey
- Hématologie, Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Véronique Gelsi-Boyer
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France
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21
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Bertucci F, Rypens C, Finetti P, Guille A, Adélaïde J, Monneur A, Carbuccia N, Garnier S, Dirix P, Gonçalves A, Vermeulen P, Debeb BG, Wang X, Dirix L, Ueno NT, Viens P, Cristofanilli M, Chaffanet M, Birnbaum D, Van Laere S. NOTCH and DNA repair pathways are more frequently targeted by genomic alterations in inflammatory than in non-inflammatory breast cancers. Mol Oncol 2020; 14:504-519. [PMID: 31854063 PMCID: PMC7053236 DOI: 10.1002/1878-0261.12621] [Citation(s) in RCA: 20] [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] [Received: 11/13/2019] [Revised: 12/06/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Inflammatory breast cancer (IBC) is the most pro‐metastatic form of breast cancer. Better understanding of its pathophysiology and identification of actionable genetic alterations (AGAs) are crucial to improve systemic treatment. We aimed to define the DNA profiles of IBC vs noninflammatory breast cancer (non‐IBC) clinical samples in terms of copy number alterations (CNAs), mutations, and AGAs. We applied targeted next‐generation sequencing (tNGS) and array‐comparative genomic hybridization (aCGH) to 57 IBC and 50 non‐IBC samples and pooled these data with four public datasets profiled using NGS and aCGH, leading to a total of 101 IBC and 2351 non‐IBC untreated primary tumors. The respective percentages of each molecular subtype [hormone receptor‐positive (HR+)/HER2−, HER2+, and triple‐negative] were 68%, 15%, and 17% in non‐IBC vs 25%, 35%, and 40% in IBC. The comparisons were adjusted for both the molecular subtypes and the American Joint Committee on Cancer (AJCC) stage. The 10 most frequently altered genes in IBCs were TP53 (63%), HER2/ERBB2 (30%), MYC (27%), PIK3CA (21%), BRCA2 (14%), CCND1 (13%), GATA3 (13%), NOTCH1 (12%), FGFR1 (11%), and ARID1A (10%). The tumor mutational burden was higher in IBC than in non‐IBC. We identified 96 genes with an alteration frequency (p < 5% and q < 20%) different between IBC and non‐IBC, independently from the molecular subtypes and AJCC stage; 95 were more frequently altered in IBC, including TP53, genes involved in the DNA repair (BRCA2) and NOTCH pathways, and one (PIK3CA) was more frequently altered in non‐IBC. Ninety‐seven percent of IBCs displayed at least one AGA. This percentage was higher than in non‐IBC (87%), notably for drugs targeting DNA repair, NOTCH signaling, and CDK4/6, whose pathways were more frequently altered (DNA repair) or activated (NOTCH and CDK4/6) in IBC than in non‐IBC. The genomic landscape of IBC is different from that of non‐IBC. Enriched AGAs in IBC may explain its aggressiveness and provide clinically relevant targets.
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Affiliation(s)
- François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Charlotte Rypens
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - José Adélaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Audrey Monneur
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Nadine Carbuccia
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Séverine Garnier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Piet Dirix
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Anthony Gonçalves
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Peter Vermeulen
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Bisrat G Debeb
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoping Wang
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Dirix
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Naoto T Ueno
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrice Viens
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Steven Van Laere
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
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22
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Courtier F, Garnier S, Carbuccia N, Guille A, Adélaide J, Chaffanet M, Hirsch P, Paz DL, Slama B, Vey N, Ugo V, Delhommeau F, Rey J, Birnbaum D, Murati A. Targeted molecular characterization shows differences between primary and secondary myelofibrosis. Genes Chromosomes Cancer 2020; 59:30-39. [PMID: 31340059 DOI: 10.1002/gcc.22789] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 01/28/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 01/24/2023] Open
Abstract
INTRODUCTION In BCR-ABL1-negative myeloproliferative neoplasms, myelofibrosis (MF) is either primary (PMF) or secondary (SMF) to polycythemia vera or essential thrombocythemia. MF is characterized by an increased risk of transformation to acute myeloid leukemia (AML) and a shortened life expectancy. METHODS Because natural histories of PMF and SMF are different, we studied by targeted next generation sequencing the differences in the molecular landscape of 86 PMF and 59 SMF and compared their prognosis impact. RESULTS PMF had more ASXL1 (47.7%) and SRSF2 (14%) gene mutations than SMF (respectively 27.1% and 3.4%, P = .04). Poorer survival was associated with RNA splicing mutations (especially SRSF2) and TP53 in PMF (P = .0003), and with ASXL1 and TP53 mutations in SMF (P < .0001). These mutations of poor prognosis were associated with biological features of scoring systems (DIPSS and MYSEC-PM score). Mutations in TP53/SRSF2 in PMF or TP53/ASXL1 in SMF were more frequent as the risk of these scores increased. This allowed for a better stratification of MF patients, especially within the DIPSS intermediate-1 risk group (DIPSS) or the MYSEC-PM high risk group. AML transformation occurred faster in SMF than in PMF and patients who transformed to AML were more SRSF2-mutated and less CALR-mutated at MF sampling. CONCLUSIONS PMF and SMF have different but not specific molecular profiles and different prognosis depending on the molecular profile. This may be due to differences in disease history. Combining mutations and existing scores should improve prognosis assessment.
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Affiliation(s)
- Frédéric Courtier
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France.,Aix-Marseille Université, Marseille, France
| | - Séverine Garnier
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Nadine Carbuccia
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France
| | - José Adélaide
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France.,Aix-Marseille Université, Marseille, France
| | - Pierre Hirsch
- Centre de Recherche Saint-Antoine CRSA, APHP, Hôpital Saint-Antoine, Sorbonne Université, Inserm, Paris, France
| | | | - Bohrane Slama
- Centre Hospitalier Général d'Avignon, Service d'Onco-Hématologie, France
| | - Norbert Vey
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Aix-Marseille Université, Marseille, France.,Département d'Hématologie, IPC, Marseille, France
| | - Valérie Ugo
- Laboratoire d'Hématologie, CHU d'Angers, Angers, France
| | - François Delhommeau
- Centre de Recherche Saint-Antoine CRSA, APHP, Hôpital Saint-Antoine, Sorbonne Université, Inserm, Paris, France
| | - Jérome Rey
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Hématologie, IPC, Marseille, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France.,Aix-Marseille Université, Marseille, France
| | - Anne Murati
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, Marseille, France.,Département d'Oncologie Prédictive, Institut Paoli-Calmettes (IPC), Marseille, France.,Département de BioPathologie, IPC, Marseille, France
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23
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Sabatier R, Lopez M, Guille A, Billon E, Carbuccia N, Garnier S, Adelaide J, Extra JM, Cappiello MA, Charafe-Jauffret E, Pakradouni J, Viens P, Gonçalves A, Chaffanet M, Birnbaum D, Bertucci F. High Response to Cetuximab in a Patient With EGFR-Amplified Heavily Pretreated Metastatic Triple-Negative Breast Cancer. JCO Precis Oncol 2019; 3:1-8. [DOI: 10.1200/po.18.00310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Renaud Sabatier
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
| | - Marc Lopez
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Emilien Billon
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Nadine Carbuccia
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Séverine Garnier
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - José Adelaide
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | | | | | - Emmanuelle Charafe-Jauffret
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | | | - Patrice Viens
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Anthony Gonçalves
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
| | - François Bertucci
- Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, and Institut Paoli-Calmettes, Marseille, France
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24
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Seguin L, Chaffanet M, Garnier S, Adélaïde J, Carbuccia N, Guille A, Pakradouni J, Sabatier R, Popovici C, Birnbaum D, Bertucci F, Goncalves A. Major Response to Carboplatin in a Patient With Metastatic Triple-Negative Breast Cancer With Somatic Mutation of BRCA1 and Loss of RAD51B. JCO Precis Oncol 2019; 3:1-9. [DOI: 10.1200/po.18.00362] [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)
- Lorène Seguin
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - Séverine Garnier
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - José Adélaïde
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - Nadine Carbuccia
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | | | - Renaud Sabatier
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | | | - Daniel Birnbaum
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - François Bertucci
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
| | - Anthony Goncalves
- Aix-Marseille Université, Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Marseille, France
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25
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Cervera N, Lhoumeau AC, Adélaïde J, Guille A, Murati A, Mozziconacci MJ, Vey N, Birnbaum D, Gelsi-Boyer V. Acute erythroid leukemias have a distinct molecular hierarchy from non-erythroid acute myeloid leukemias. Haematologica 2019; 105:e340-e342. [PMID: 31601691 DOI: 10.3324/haematol.2019.231142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nathalie Cervera
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille
| | - Anne-Catherine Lhoumeau
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille
| | - José Adélaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille
| | - Anne Murati
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille
| | | | - Norbert Vey
- Département d'Hématologie, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille
| | - Véronique Gelsi-Boyer
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille
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26
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Chanez B, Appay R, Guille A, Lagarde A, Bequet C, Jiguet-Jiglaire C, Graillon T, Dufour H, Figarella-Branger D, Chinot O, Tabouret E. P13.09 Genomic analysis of paired IDHwt glioblastoma (GB) reveals recurrent alterations of MPDZ at relapse after radiotherapy and temozolomide (RTCT). Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz126.230] [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: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
GB are highly aggressive tumors which systematically relapse. Our objective was to identify disease progression mechanisms and genomic drivers of GB treatment resistance.
MATERIAL AND METHODS
Ten paired frozen tumors from initial and recurrent surgery after RTCT were screened by CGH Array. Next, NGS of the selected genes was performed on 19 paired tumors (38 samples). Molecular alterations were correlated with patient data. TCGA was used to characterize the molecular profile of MPDZ.
RESULTS
Nineteen IDHwt GB patients with a median age of 54.5 years (37.2–72.8) were included. Using CGH array, unsupervised analysis clustered the whole samples by paired of initial and recurrent tumors. However only 44% of CGH Array alterations were shared between initial and recurrent tumors (amplifications: 55%; deletions: 30%). The new alterations detected at relapse were amplifications in 25% and deletions in 23% of tumors. Two regions corresponding to 171 genes were lost at relapse (p=0.03): 19q13.33 and 19q13.41. Using DAVID genome, 3/171 genes (related to neutrophil chemotactic factors) were identified: FPR1, FPR2, FPR3. Moreover, 24 genes were lost (including MPDZ) and 2 genes were gained in 20% of recurrent tumors. Totally, 29 genes were analyzed by NGS and 4 genes showed pathogenic mutations shared by initial and recurrent tumors: FPR2, REL, TYRP1 and MPDZ. Only MPDZ showed, at relapse, an increasing rate of mutated variants and a new mutation affecting the splicing site. These alterations were independent from classical prognostic factors (age, sexe, karnofsky performans status, MMS and MGMT status) and from patient survivals. To explore MPDZ expression, we used TCGA initial dataset and observed that a lower RNA expression of MPDZ was associated with IDHwt (p<0.001) and grade IV (p<0.001) gliomas, reinforcing the potential pejorative impact of MPDZ loss.
CONCLUSION
Our results suggest that MPDZ is frequently altered at initial diagnosis with increased alterations in recurrent IDHwt GB after RTCT, suggesting that MPDZ impairment could contribute to the resistance/relapse mechanisms. Further investigations are needed to validate these results. Our results suggest that MPDZ is frequently altered at initial diagnosis with increased alterations in recurrent IDHwt GB after RTCT, suggesting that MPDZ impairment could contribute to the resistance/relapse mechanisms. Further investigations are needed to validate these results.
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Affiliation(s)
- B Chanez
- Timone Hospital- APHM, Marseille, France
| | - R Appay
- Timone Hospital- APHM, Marseille, France
| | - A Guille
- Timone Hospital- APHM, Marseille, France
| | - A Lagarde
- Timone Hospital- APHM, Marseille, France
| | - C Bequet
- Timone Hospital- APHM, Marseille, France
| | | | - T Graillon
- Timone Hospital- APHM, Marseille, France
| | - H Dufour
- Timone Hospital- APHM, Marseille, France
| | | | - O Chinot
- Timone Hospital- APHM, Marseille, France
| | - E Tabouret
- Timone Hospital- APHM, Marseille, France
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27
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Laurent C, Nicolae A, Laurent C, Le Bras F, Haioun C, Fataccioli V, Amara N, Adélaïde J, Guille A, Schiano De Colella J, Tesson B, Traverse-Glehen A, Chenard M, Mescam L, Moreau A, Chassagne-Clément C, Somja J, Escudié F, André M, Martin N, Hamy-Petit A, Reyal F, Croix M, Birnbaum D, Brousset P, Xerri L, Gaulard P. JAK-STAT PATHWAY AND EPIGENETIC REGULATORS ARE CRITICAL PLAYERS IN BI-ALCL PATHOGENESIS? Hematol Oncol 2019. [DOI: 10.1002/hon.16_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- C. Laurent
- Pathology Department; Institut Universitaire du Cancer Oncopole CHU Toulouse INSERM U1037; Toulouse France
| | - A. Nicolae
- Pathology; Hôpital de Hautepierre; Strasbourg France
| | - C. Laurent
- CALYM - LYSARC; Institut Carnot; Pierre-Bénite France
| | - F. Le Bras
- Lymphoid Malignancies Unit; AP-HP, Groupe Hospitalier Henri Mondor - Albert Chenevier; Créteil France
| | - C. Haioun
- Lymphoid Malignancies Unit; AP-HP, Groupe Hospitalier Henri Mondor-Albert Chenevier, INSERM U955, Université Paris-Est; Créteil France
| | - V. Fataccioli
- Department of Pathology; AP-HP, Groupe Hospitalier Henri Mondor-Albert Chenevier, INSERM U955, Université Paris-Est; Créteil France
| | - N. Amara
- Pathology Department; Institut Universitaire du Cancer Oncopole CHU Toulouse INSERM U1037; Toulouse France
| | - J. Adélaïde
- Department of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm U1068, CNRS UMR7258, Aix-Marseille University, UM 105; Institut Paoli-Calmettes; Marseille France
| | - A. Guille
- Department of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm U1068, CNRS UMR7258, Aix-Marseille University, UM 105; Institut Paoli-Calmettes; Marseille France
| | | | - B. Tesson
- CALYM - LYSARC; Institut Carnot; Pierre-Bénite France
| | - A. Traverse-Glehen
- Pathology Department; Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud; Pierre-Bénite France
| | - M. Chenard
- Pathology; Hôpital de Hautepierre; Strasbourg France
| | - L. Mescam
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
| | - A. Moreau
- Pathology; CHU Nantes; Nantes France
| | | | - J. Somja
- Pathology and Cytology Department; CHU de Liège; Liège Belgium
| | - F. Escudié
- Pathology Department; Institut Universitaire du Cancer Oncopole CHU Toulouse INSERM U1037; Toulouse France
| | - M. André
- Hematology; CHU UCL Namur; Yvoir Belgium
| | - N. Martin
- IMRB - Institut Mondor de Recherche Biomédicale; INSERM U955; Créteil France
| | - A. Hamy-Petit
- Residual Tumour & Response to Treatment Laboratory; RT2Lab, INSERM, U932, PSL Research University, Translational Research Department, Institut Curie; Paris France
| | - F. Reyal
- Department of Surgical Oncology; Institut Curie; Paris France
| | - M. Croix
- CALYM - LYSARC; Institut Carnot; Pierre-Bénite France
| | - D. Birnbaum
- Department of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm U1068, CNRS UMR7258, Aix-Marseille University, UM 105; Institut Paoli-Calmettes; Marseille France
| | - P. Brousset
- Pathology Department; Institut Universitaire du Cancer Oncopole CHU Toulouse INSERM U1037; Toulouse France
| | - L. Xerri
- Department of Bio-Pathology and Tumor Immunology, Aix-Marseille University, Centre de Recherche en Cancérologie de Marseille (CRCM); Institut Paoli-Calmettes; Marseille France
| | - P. Gaulard
- Department of Pathology; AP-HP, Groupe Hospitalier Henri Mondor-Albert Chenevier, INSERM U955, Université Paris-Est; Créteil France
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Chanez B, Appay R, Guille A, Lagarde A, Adelaide J, Denicolai E, Campello C, Tchoghandjian A, Petrirena G, Colin C, Barrie M, Baeza-Kallee N, Boucard C, Jiguet-Jiglaire C, Graillon T, Nanni-Metellus I, Dufour H, Figarella-Branger D, Chinot OL, Tabouret E. Genomic analysis of paired IDHwt glioblastoma (GB) to reveal recurrent alterations of MPDZ at relapse after radiotherapy and temozolomide (RTCT). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13535] [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
e13535 Background: GB are highly aggressive tumors which systematically relapse. Our objective was to identify disease progression mechanisms and genomic drivers of GB treatment resistance. Methods: Ten paired frozen tumors from initial and recurrent surgery after RTCT were screened by CGH Array. Next, NGS of the selected genes was performed on 19 paired tumors (38 samples). Molecular alterations were correlated with patient data. TCGA was used to characterize the molecular profile of MPDZ. Results: Nineteen IDHwt GB patients with a median age of 54.5 years (37.2-72.8) were included. Using CGH array, unsupervised analysis clustered the whole samples by paired of initial and recurrent tumors. However only 44% of CGH Array alterations were shared between initial and recurrent tumors (amplifications: 55%; deletions: 30%). The new alterations detected at relapse were amplifications in 25% and deletions in 23% of tumors. Two regions corresponding to 171 genes were lost at relapse (p = 0.03): 19q13.33 and 19q13.41. Using DAVID genome, 3/171 genes (related to neutrophil chemotactic factors) were identified: FPR1, FPR2, FPR3. Moreover, 24 genes were lost (including MPDZ) and 2 genes were gained in 20% of recurrent tumors. Totally, 29 genes were analyzed by NGS and 4 genes showed pathogenic mutations shared by initial and recurrent tumors: FPR2, REL, TYRP1 and MPDZ. Only MPDZ showed, at relapse, an increasing rate of mutated variants and a new mutation affecting the splicing site. These alterations were independent from classical prognostic factors (age, sexe, karnofsky performans status, MMS and MGMT status) and from patient survivals. To explore MPDZ expression, we used TCGA initial dataset and observed that a lower RNA expression of MPDZ was associated with IDHwt ( p< 0.001) and grade IV ( p< 0.001) gliomas, reinforcing the potential pejorative impact of MPDZ loss. Conclusions: Our results suggest that MPDZ is frequently altered at initial diagnosis with increased alterations in recurrent IDHwt GB after RTCT, suggesting that MPDZ impairment could contribute to the resistance/relapse mechanisms. Further investigations are needed to validate these results.
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Affiliation(s)
- Brice Chanez
- APHM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | | | | | | | | | | | - Chantal Campello
- Aix-Marseille University, AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | | | | | | | - Maryline Barrie
- AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | | | - Celine Boucard
- AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | | | - Thomas Graillon
- APHM, Service de Neurochirurgie, CHU Timone, Marseille, France
| | | | - Henry Dufour
- Aix-Marseille University, AP-HM, Service de Neuro-Chirurgie, CHU Timone, Marseille, France
| | - Dominique Figarella-Branger
- Aix-Marseille University, AP-HM, Service d'Anatomopathologie et de Neuropathologie, CHU Timone, Marseille, France
| | - Olivier L. Chinot
- Aix-Marseille University, AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | - Emeline Tabouret
- Aix-Marseille University, AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
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Vicier C, Isambert N, Dalenc F, Campone M, Levy C, Rezai K, Provansal M, Adelaide J, Garnier S, Guille A, Chaffanet M, Popovici C, Charafe-Jauffret E, Pakradouni J, Autret A, Goncalves A. TAKTIC: A prospective, multicenter, uncontrolled, phase IB/II study of LY2780301 (LY) in combination with weekly paclitaxel (wP) in HER2-negative locally advanced (LA) or metastatic breast cancer (MBC) patients. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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
1091 Background: Phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR)-pathway is frequently activated in HER2-negative breast cancer and may play a role in taxane-resistance. LY is a dual inhibitor of p70 S6 kinase and AKT. TAKTIC study aimed to determine the recommended phase II dose (RP2D) of the combination of LY with wP (phase Ib) and to estimate overall response rate (ORR) of this regimen (phase II) in HER2-negative LA or MBC patients, both in the overall patient population and in patients with activation of PI3K/AKT pathway (PI3KAKT+). Methods: HER2-negative inoperable LA or MBC patients (pts), with (phase Ib) or without (phase II) previous cytotoxic treatment for advanced disease were eligible. Oral LY (400 or 500mg) was administered daily in combination with intravenous wP (70 or 80mg/m2). A modified CRM using an adaptive Bayesian model guided the dose escalation of both agents. PI3KAKT+ was defined as activating mutation of PIK3CA and/or AKT by targeted NGS or homozygous loss of PTEN by array comparative genomic hybridization (aCGH) or loss of PTEN by immunohistochemistry, as evaluated on available fresh tumor tissue. Results: A total of 12 and 35 patients (pts) were included in the phase Ib and II, respectively. In phase Ib, only 1 dose-limiting toxicity (confusion) was observed at the last dose level (LY, 500 + wP, 80), which was determined as RP2D. Main drug-related adverse events (AE) in phase Ib were skin toxicity (92% of pts, G3-4 in 33%), and paresthesia (50% of pts, G3-4 in 8%). In the phase II study, ORR was 62.9 % [44.9,78.5] including 1 CR and 21 PR in the overall population and 55.6 % [30.8,78.5] in PI3KAKT+ pts (10 PR in 18 pts). Median progression-free survival was 12.4 months [7.9,17.9] and 6-month clinical benefit rate was 82.9% [66.4,93.4]. AEs in phase II were similar to phase I part, except that 17% of pts experienced pneumonia (G3-4 in 9%). Conclusions: Combining LY and wP in HER2-negative LA or MBC was feasible with preliminary evidences of efficacy, independently of PI3K/AKT activation. Clinical trial information: NCT01980277.
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Affiliation(s)
- Cecile Vicier
- Aix-Marseille Univ, CNRS,INSERM, Institut-Paoli-Calmettes, Department of Medical Oncology,CRCM, Marseille, France, Marseille, France
| | - Nicolas Isambert
- Drug Development Department, Centre Georges François Leclerc, Dijon, France
| | - Florence Dalenc
- Department of Medicalo Oncology, Institut Claudius Regaud, IUCT-Oncopole, CRCT, Inserm, Toulouse, France
| | - Mario Campone
- Institut de Cancérologie de l'Ouest-René Gauducheau, Saint-Herblain, France
| | - Christelle Levy
- Centre François Baclesse, Department of Medical Oncology, Caen, France
| | - Keyvan Rezai
- Department of Radio-Pharmacology,Institut Curie-Hôpital René Huguenin, St Cloud, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | | | - Séverine Garnier
- Aix-Marseille Uni,CNRS, INSERM, Institut Paoli-Calmettes, Dêpartment of Predictive Oncology, Marseille, France, Marseille, France
| | | | | | - Cornel Popovici
- Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, Department of Pathology, CRCM, Marseille, France
| | - Jihane Pakradouni
- Department of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - Aurelie Autret
- Department of Clinical Research and Innovation, Institut Paoli Calmettes, Marseille, France
| | - Anthony Goncalves
- Aix-Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, Department of Medical Oncology, CRCM, Marseille, France
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Tyran M, Carbuccia N, Garnier S, Guille A, Adelaïde J, Finetti P, Toulzian J, Viens P, Tallet A, Goncalves A, Metellus P, Birnbaum D, Chaffanet M, Bertucci F. A Comparison of DNA Mutation and Copy Number Profiles of Primary Breast Cancers and Paired Brain Metastases for Identifying Clinically Relevant Genetic Alterations in Brain Metastases. Cancers (Basel) 2019; 11:cancers11050665. [PMID: 31086113 PMCID: PMC6562582 DOI: 10.3390/cancers11050665] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 12/15/2022] Open
Abstract
Improving the systemic treatment of brain metastases (BM) in primary breast cancer (PBC) is impaired by the lack of genomic characterization of BM. To estimate the concordance of DNA copy-number-alterations (CNAs), mutations, and actionable genetic alterations (AGAs) between paired samples, we performed whole-genome array-comparative-genomic-hybridization, and targeted-next-generation-sequencing on 14 clinical PBC–BM pairs. We found more CNAs, more mutations, and higher tumor mutational burden, and more AGAs in BM than in PBC; 92% of the pairs harbored at least one AGA in the BM not observed in the paired PBC. This concerned various therapeutic classes, including tyrosine-kinase-receptor-inhibitors, phosphatidylinositol 3-kinase/AKT/ mammalian Target of Rapamycin (PI3K/AKT/MTOR)-inhibitors, poly ADP ribose polymerase (PARP)-inhibitors, or cyclin-dependent kinase (CDK)-inhibitors. With regards to the PARP-inhibitors, the homologous recombination defect score was positive in 79% of BM, compared to 43% of PBC, discordant in 7 out of 14 pairs, and positive in the BM in 5 out of 14 cases. CDK-inhibitors were associated with the largest percentage of discordant AGA appearing in the BM. When considering the AGA with the highest clinical-evidence level, for each sample, 50% of the pairs harbored an AGA in the BM not detected or not retained from the analysis of the paired PBC. Thus, the profiling of BM provided a more reliable opportunity, than that of PBC, for diagnostic decision-making based on genomic analysis. Patients with BM deserve an investigation of several targeted therapies.
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Affiliation(s)
- Marguerite Tyran
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département de Radiothérapie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Nadine Carbuccia
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Séverine Garnier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - José Adelaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Julien Toulzian
- Département d'Anatomopathologie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Patrice Viens
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
| | - Agnès Tallet
- Département de Radiothérapie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Anthony Goncalves
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
| | - Philippe Metellus
- Département de Neurochirurgie et de Neuro-oncologie, Hôpital Privé Clairval, Ramsay-Générale de Santé and Institut de Neurophysiopathologie Equipe 10, UMR0751, CNRS, 13009 Marseille, France.
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
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Xerri L, Adélaïde J, Avenin M, Guille A, Taix S, Bonnet N, Carbuccia N, Garnier S, Mescam L, Murati A, Chaffanet M, Coso D, Bouabdallah R, Bertucci F, Birnbaum D. Common origin of sequential cutaneous CD30+ lymphoproliferations with nodal involvement evidenced by genome-wide clonal evolution. Histopathology 2019; 74:654-662. [DOI: 10.1111/his.13783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Luc Xerri
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
- Aix-Marseille University; Marseille France
- Inserm-CNRS; CRCM; Marseille France
| | - José Adélaïde
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Morgan Avenin
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
- Aix-Marseille University; Marseille France
| | - Arnaud Guille
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Sebastien Taix
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
| | - Nathalie Bonnet
- Department of Haematology; Institut Paoli-Calmettes; Marseille France
| | - Nadine Carbuccia
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Séverine Garnier
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Lenaïg Mescam
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
| | - Anne Murati
- Department of Bio-Pathology; Institut Paoli-Calmettes; Marseille France
| | - Max Chaffanet
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Diane Coso
- Department of Haematology; Institut Paoli-Calmettes; Marseille France
| | - Reda Bouabdallah
- Department of Haematology; Institut Paoli-Calmettes; Marseille France
| | - François Bertucci
- Aix-Marseille University; Marseille France
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
| | - Daniel Birnbaum
- Aix-Marseille University; Marseille France
- Inserm-CNRS; CRCM; Marseille France
- Department of Predictive Oncology; Institut Paoli-Calmettes; Marseille France
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Wanquet A, Courtier F, Guille A, Carbuccia N, Garnier S, Adélaide J, Gelsi-Boyer V, Mozziconacci MJ, Rey J, Vey N, Birnbaum D, Murati A. Mutation patterns in essential thrombocythemia, polycythemia vera and secondary myelofibrosis. Leuk Lymphoma 2019; 60:1289-1293. [PMID: 30601073 DOI: 10.1080/10428194.2018.1522437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anne Wanquet
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France.,b Aix-Marseille Université , Marseille , France.,c Département d'Hématologie , Institut Paoli-Calmettes , Marseille , France
| | - Frédéric Courtier
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France.,b Aix-Marseille Université , Marseille , France
| | - Arnaud Guille
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France
| | - Nadine Carbuccia
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France
| | - Séverine Garnier
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France
| | - José Adélaide
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France
| | - Véronique Gelsi-Boyer
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France.,b Aix-Marseille Université , Marseille , France.,d Département de BioPathologie , Institut Paoli-Calmettes , Marseille , France
| | | | - Jérôme Rey
- c Département d'Hématologie , Institut Paoli-Calmettes , Marseille , France
| | - Norbert Vey
- b Aix-Marseille Université , Marseille , France.,c Département d'Hématologie , Institut Paoli-Calmettes , Marseille , France
| | - Daniel Birnbaum
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France.,b Aix-Marseille Université , Marseille , France
| | - Anne Murati
- a Laboratoire d'Oncologie Prédictive , Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille , Inserm U1068 CNRS UMR 7258 , Marseille , France.,b Aix-Marseille Université , Marseille , France.,d Département de BioPathologie , Institut Paoli-Calmettes , Marseille , France
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Chanez B, Chaffanet M, Adélaide J, Thomassin J, Garnier S, Carbuccia N, Guille A, Charrier N, Brenot-Rossi I, Walz J, Pignot G, Pakradouni J, Gonçalvès A, Eisinger F, Bertucci F, Birnbaum D, Gravis G. Poly (ADP-Ribose) Polymerase Inhibitors for De Novo BRCA2-Null Small-Cell Prostate Cancer. JCO Precis Oncol 2018; 2:1-8. [DOI: 10.1200/po.18.00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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)
- Brice Chanez
- All authors: Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- All authors: Institut Paoli-Calmettes, Marseille, France
| | - José Adélaide
- All authors: Institut Paoli-Calmettes, Marseille, France
| | | | | | | | - Arnaud Guille
- All authors: Institut Paoli-Calmettes, Marseille, France
| | | | | | - Jochen Walz
- All authors: Institut Paoli-Calmettes, Marseille, France
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Sabatier R, Pomel C, Colombo PE, Narducci F, Garnier S, Carbuccia N, Guille A, Birnbaum D, Zemmour C, Lambaudie E. Circulating tumour DNA as an early marker of recurrence and treatment efficacy in ovarian carcinoma, the CIDOC study. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy316.007] [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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35
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Sabatier R, Garnier S, Carbuccia N, Guille A, Tarpin C, Goncalves A, Birnbaum D. RETROSPHER. ERBB2 amplification detection in the plasma at diagnosis for early high-risk HER2-positive breast cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy316.001] [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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Seguin L, Chaffanet M, Sabatier R, Jose A, Garnier S, Carbuccia N, Guille A, Birnbaum D, Bertucci F, Goncalves A. A major response to carboplatin in a metastatic triple-negative breast cancer patient with somatic mutation of BRCA1 and RAD51B: When chemotherapy meets precision medicine. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy314.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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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37
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Gonçalves A, Bertucci F, Guille A, Garnier S, Adelaide J, Carbuccia N, Cabaud O, Finetti P, Brunelle S, Piana G, Tomassin-Piana J, Paciencia M, Lambaudie E, Popovici C, Sabatier R, Tarpin C, Provansal M, Extra JM, Eisinger F, Sobol H, Viens P, Lopez M, Ginestier C, Charafe-Jauffret E, Chaffanet M, Birnbaum D. Targeted NGS, array-CGH, and patient-derived tumor xenografts for precision medicine in advanced breast cancer: a single-center prospective study. Oncotarget 2018; 7:79428-79441. [PMID: 27765906 PMCID: PMC5346725 DOI: 10.18632/oncotarget.12714] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 09/29/2016] [Indexed: 12/30/2022] Open
Abstract
Background Routine feasibility and clinical impact of genomics-based tumor profiling in advanced breast cancer (aBC) remains to be determined. We conducted a pilot study to evaluate whether precision medicine could be prospectively implemented for aBC patients in a single center and to examine whether patient-derived tumor xenografts (PDX) could be obtained in this population. Results Thirty-four aBC patients were included. Actionable targets were found in 28 patients (82%). A targeted therapy could be proposed to 22 patients (64%), either through a clinical trial (n=15) and/or using already registered drugs (n=21). Ten patients (29%) eventually received targeted treatment, 2 of them deriving clinical benefit. Of 22 patients subjected to mouse implantation, 10 had successful xenografting (45%), mostly in triple-negative aBC. Methods aBC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Genomic profiling was established by whole-genome array comparative genomic hybridization (aCGH) and targeted next-generation sequencing (NGS) of 365 candidate cancer genes. For a subset of patients, a sample of fresh tumor was orthotopically implanted in humanized cleared fat pads of NSG mice for establishing PDX. Conclusions Precision medicine can be implemented in a single center in the context of clinical practice and may allow genomic-driven treatment in approximately 30% of aBC patients. PDX may be obtained in a significant fraction of cases.
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Affiliation(s)
- Anthony Gonçalves
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - François Bertucci
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Severine Garnier
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - José Adelaide
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Nadine Carbuccia
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Oliver Cabaud
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Serge Brunelle
- Department of Imaging, Institut Paoli-Calmettes, Marseille, France
| | - Gilles Piana
- Department of Imaging, Institut Paoli-Calmettes, Marseille, France
| | | | - Maria Paciencia
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cornel Popovici
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Carole Tarpin
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Jean-Marc Extra
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - François Eisinger
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Hagay Sobol
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Marc Lopez
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Christophe Ginestier
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France.,Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | - Max Chaffanet
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Aix Marseille Univ, CNRS U7258, INSERM U1068, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Molecular Oncology, Institut Paoli-Calmettes, Marseille, France
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Charafe-Jauffret E, Wicinski J, Cabaud O, Lopez M, Audebert S, Adelaide J, Chaffanet M, Guille A, Goncalves A, Bertucci F, Birnbaum D, Ginestier C. Abstract P5-06-02: Ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-06-02] [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: 11/16/2022]
Abstract
Abstract
In the developing area of personalized medicine, targeted therapies are mainly based on genomic characterization of each tumor, and is currently proposed as promising strategies for advanced breast cancer (ABC). Despite the promises of advanced genome sequencing, many patients still fail therapy, resulting in disease progression, recurrence, and metastases. Cancer stem cells (CSCs) concept illustrates the non-genetic intrinsic resistance, recapitulates tumor heterogeneity that creates hierarchically organized tumor tissues where a subpopulation of self-renewing cancer stem cells (CSCs) sustains the long- term clonal maintenance of the neoplasm. Evidences indicate that CSCs survive many commonly employed cancer therapeutics. Patient-derived tumor xenograft (PDXs) models recapitulate tumor complexity and heterogeneity at cellular and molecular level.
We aimed to specifically address the therapeutic sensitivity in ABC, by using an ex vivo assay based on PDX prospective collection, fully characterized for genomic alterations.
In this work, we aim at defining for each tumor the best therapy to target breast cancer intratumor heterogeneity, the CSC component. For that, we defined a panel of 44 FDA-approved compounds used for cancer treatment, including breast and other types of cancer, cancer stem cell drugs, chemo or targeted therapies. For each drug, we screened the differential sensitivity of the bulk tumor cells and the CSC components for 12 PDX models using an ex vivo screening approach on short term culture. To assess intra tumor heterogeneity, we set up an original dual strategy: for the bulk cells, an ex vivo assay based on IC50, and for breast CSC component a miniaturized Aldefluor assay. First, we demonstrate that bulk cells and CSCs sensitivity may be dissociated for the same drug in the same PDX models. Then, we observed that whereas bulk cell sensitivity may be correlated to tumor genomic abnormalities, CSC drug sensitivity seems not to follow the rule.CSC are selectively sensitive to specific compounds. We are exploring the pathways that sustain this selective sensitivity in the CSCs components. We are currently identifying targets using mass spectrometry in CSCs and bulk cells.Then, we validated the hits predicted from ex vivo screening assays by in vivo treatment of using PDX models for the selected drugs, and in a patient with ABC.
In that work, we demonstrated that CSCs display different sensitivity profiles than bulk cells to the same agents, irrespective to their genomic background and are identifying the CSC specific targets. Here, we propose a new model of precision medicine based on ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer.
Citation Format: Charafe-Jauffret E, Wicinski J, Cabaud O, Lopez M, Audebert S, Adelaide J, Chaffanet M, Guille A, Goncalves A, Bertucci F, Birnbaum D, Ginestier C. Ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-06-02.
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Affiliation(s)
| | - J Wicinski
- CRCM, Marseille, France; IPC, Marseille, France
| | - O Cabaud
- CRCM, Marseille, France; IPC, Marseille, France
| | - M Lopez
- CRCM, Marseille, France; IPC, Marseille, France
| | - S Audebert
- CRCM, Marseille, France; IPC, Marseille, France
| | - J Adelaide
- CRCM, Marseille, France; IPC, Marseille, France
| | - M Chaffanet
- CRCM, Marseille, France; IPC, Marseille, France
| | - A Guille
- CRCM, Marseille, France; IPC, Marseille, France
| | - A Goncalves
- CRCM, Marseille, France; IPC, Marseille, France
| | - F Bertucci
- CRCM, Marseille, France; IPC, Marseille, France
| | - D Birnbaum
- CRCM, Marseille, France; IPC, Marseille, France
| | - C Ginestier
- CRCM, Marseille, France; IPC, Marseille, France
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Cervera N, Carbuccia N, Mozziconacci MJ, Adélaïde J, Garnier S, Guille A, Murati A, Chaffanet M, Vey N, Birnbaum D, Gelsi-Boyer V. Revisiting gene mutations and prognosis of ex-M6a-acute erythroid leukemia with regard to the new WHO classification. Blood Cancer J 2017; 7:e594. [PMID: 28841205 PMCID: PMC5596380 DOI: 10.1038/bcj.2017.68] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- N Cervera
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - N Carbuccia
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - M-J Mozziconacci
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France
| | - J Adélaïde
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - S Garnier
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - A Guille
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - A Murati
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France
| | - M Chaffanet
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - N Vey
- Département d'Hématologie, Institut Paoli-Calmettes, Marseille, France.,Aix-Marseille Université, Marseille, France
| | - D Birnbaum
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France
| | - V Gelsi-Boyer
- Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR7258, Aix-Marseille Université UM105, Marseille, France.,Département de BioPathologie, Institut Paoli-Calmettes, Marseille, France
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Courtier F, Carbuccia N, Garnier S, Guille A, Adélaïde J, Cervera N, Gelsi-Boyer V, Mozziconacci MJ, Rey J, Vey N, Chaffanet M, Birnbaum D, Murati A. Genomic analysis of myeloproliferative neoplasms in chronic and acute phases. Haematologica 2016; 102:e11-e14. [PMID: 27742771 DOI: 10.3324/haematol.2016.152363] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Frédéric Courtier
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Nadine Carbuccia
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France
| | - Séverine Garnier
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France
| | - José Adélaïde
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France
| | - Nathalie Cervera
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France
| | - Véronique Gelsi-Boyer
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,IPC, Département de Biopathologie, Marseille, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Marie-Joelle Mozziconacci
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,IPC, Département de Biopathologie, Marseille, UM 105, Marseille, F-13284, France
| | - Jérôme Rey
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,IPC, Département d'Hématologie, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Norbert Vey
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,IPC, Département d'Hématologie, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France.,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
| | - Anne Murati
- Centre de Recherche en Cancérologie de Marseille, (CRCM), Inserm, U1068, CNRS UMR7258, France .,Institut Paoli-Calmettes (IPC), Département d'Oncologie Moléculaire, UM 105, Marseille, F-13284, France.,IPC, Département de Biopathologie, Marseille, UM 105, Marseille, F-13284, France.,Aix-Marseille Université, UM 105, Marseille, F-13284, France
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Charafe-Jauffret E, Ginestier C, Cabaud O, Wicinski J, Guille A, Garnier S, Chaffanet M, Goncalves A, Bertucci F, Birnbaum D. Abstract 4790: Breast cancer stem cells: The next step in the area of personalized medicine. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4790] [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: 11/16/2022]
Abstract
Abstract
In the developping area of personnalized medicine, targeted therapies are mainly based on genomic characterization of each tumor, and is currently proposed as promising strategies for resistant breast cancer (RBC). Despite the promises of advanced genome sequencing, many patients still fail therapy, resulting in disease progression, recurrence, and metastases. Cancer stem cells (CSCs) concept illustrates the non-genetic intrinsic resistance, recapitulates tumor heterogeneity that creates hierarchically organized tumor tissues where a subpopulation of self-renewing cancer stem cells (CSCs) sustains the long- term clonal maintenance of the neoplasm. Evidences indicate that CSCs survive many commonly employed cancer therapeutics. Patient-derived tumor xenograft (PDXs) models recapitulate tumor complexity and heterogeneity at cellular, and molecular level. We aimed to specifically address the therapeutic sensitivity in RBC, by using a PDX prospective collection, fully characterized for genomic alterations.
In this work, we aim at defining for each tumor the best therapy to target breast cancer intratumor heterogeneity, the CSC component. For that, we defined a panel of 44 FDA-approved compounds used for cancer treatment, including breast and other types of cancer, cancer stem cell drugs, chemo or targeted therapies. For each drug, we screened the differential sensitivity of the bulk tumor cells and the CSC components for 12 PDX models using an ex vivo screening approach on short term culture. To assess intra tumor heterogeneity, we set up an original dual strategy: for the bulk cells, an ex vivo assay based on IC50, and for breast CSC component a miniaturized Aldefluor assay. First, we demonstrate that bulk cells and CSCs sensitivity may be dissociated for the same drug in the same PDX models. Then, we observed that bulk cell sensitivity is often correlated to tumor genomic abnormalities. By opposite, CSC sensitivity seems not to follow the rule and displays selectivively sensitivity to specific targeted compounds belonging to Tyrosine Kinase Inhibitors family. We are exploring the pathways that sustain this selective sensitivity in the CSCs components. Then, we validated the hits predicted from ex vivo screening assays by treating different PDX models for selected drugs. As a Proof-of-concept, we have already validated one CSC targeted strategy for one PDX model.
In that work, we demonstrated that CSCs and bulks cells are not sensitive to same treatment, independently to their genomic abnormalities. This result highlights the need for differential testing on the two tumor components, proposes a dual-screening strategy to evaluate the differential drugs sensitivity, validated in PDX models. Afterall, we emphasized the importance of integrating CSC drug sensitivity in the new area of personnalized medicine currently focused on genomic-based strategies and irrespective of intra tumor heterogeneity.
Citation Format: Emmanuelle Charafe-Jauffret, Christophe Ginestier, Olivier Cabaud, Julien Wicinski, Arnaud Guille, Severine Garnier, Max Chaffanet, Anthony Goncalves, Francois Bertucci, Daniel Birnbaum. Breast cancer stem cells: The next step in the area of personalized medicine. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4790.
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Gonçalves A, Bertucci F, Chaffanet M, Guille A, Garnier S, Adelaide J, Carbuccia N, Brunelle S, Piana G, Cabaud O, Thomassin-Piana J, Paciencia-Gros M, Chereau-Ewald E, Lambaudie E, Sabatier R, Tarpin C, Provansal M, Jalaguier-Coudray A, Extra JM, Sarran A, Pakradouni J, Viens P, Lopez M, Ginestier C, Charafe-Jauffret E, Birnbaum D. Abstract P4-13-23: Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH) and patient-derived tumor xenograft (PDX) for precision medicine in advanced breast cancer: A single-center prospective study. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p4-13-23] [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: 11/16/2022]
Abstract
Abstract
Background
Genomic-based approaches in advanced breast cancer (ABC) were recently demonstrated as feasible in the clinical practice, but only a limited number of patients were actually treated with targeted therapies matching genomic alterations, with low antitumor activity. We conducted a pilot study to evaluate whether precision medicine using NGS and aCGH could be implemented prospectively at a single center in ABC patients. In addition, we examined whether PDX could be derived from ABC and thus could help inform therapeutic decision.
Methods
ABC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Tumor tissue from locally recurrent or metastatic disease was immediately frozen after dedicated biopsy. Genomic profiling included high-resolution 4x180K aCGH (Agilent Technologies, Massy, France) and DNA sequencing, using a library of 365 cancer candidate genes (HaloPlex target enrichment kit, Agilent technologies, Santa Clara, CA, USA) and MiSeq analyzer (Illumina, San Diego, CA, USA) with 2x150-bp, paired-end at about 300x coverage. In a subset of patients, fresh tumor was implanted orthotopically in humanized cleared fat pads of NSG mice for establishing xenotransplants.
Results
A total of 34 ABC patients were included, with the following characteristics: median age 54 years (35-77); molecular subtypes: 11 triple-negative (32%), 12 luminal non-HER2 (35%), 4 luminal HER2 (12%), 3 HER2 non-luminal (9%), and 4 unknown (12%); 33 with previous chemotherapy (97%); 22 with previous endocrine treatment (35%); 7 with previous anti-HER2 (21%). Tumor biopsies were obtained from liver (15), skin (6), peritoneum (4), breast (3), node (3), lung (1), pleura (1), and ascitis (1), with a median tumor cellularity of 70% (range 10-90%). aCGH and NGS were available from 34 and 33 patients, respectively. An actionable target was found in 28 patients (82%), corresponding to 66 targets, including 37 mutations (8 in PIK3CA, 7 TP53, 4 ESR1, 2 AKT1, 2 BRCA2, 2 HER2), 22 amplifications (7 for CCND1, 2 CCNE1, 2 FGFR1, 2 IGF1R) and 7 homozygous deletions (3 for PTEN, 2 CDKN2A/B,1 BRCA2, 1 STK11). A targeted therapeutic proposal was possible, either in a clinical trial (N=18, 52%) or using already registered drugs (N=17, 50%). Ten patients actually received a targeted treatment, 1 of them experienced objective response and 1 showed stable disease for more than 6 months. Of 26 patients subjected to mouse implantation, 10 had successful xenografting (6 triple-negative, 2 HER2, 1 luminal non-HER2, 1 subtype non-attributed), with a median time to reach 10 mm of 148 days. These PDX will be used as models to understand the patient's therapeutic response.
Conclusion
Precision medicine using high-throughput DNA sequencing and aCGH can be implemented at a single center in the context of clinical practice and may allow direct therapeutic proposal in 1/3 of patients, but antitumor activity was minimal. PDX may be obtained in a significant fraction of patients, especially in triple-negative and HER2 subtypes, and could phenotypically complement genomic data.
Citation Format: Gonçalves A, Bertucci F, Chaffanet M, Guille A, Garnier S, Adelaide J, Carbuccia N, Brunelle S, Piana G, Cabaud O, Thomassin-Piana J, Paciencia-Gros M, Chereau-Ewald E, Lambaudie E, Sabatier R, Tarpin C, Provansal M, Jalaguier-Coudray A, Extra J-M, Sarran A, Pakradouni J, Viens P, Lopez M, Ginestier C, Charafe-Jauffret E, Birnbaum D. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH) and patient-derived tumor xenograft (PDX) for precision medicine in advanced breast cancer: A single-center prospective study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-13-23.
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Affiliation(s)
- A Gonçalves
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - F Bertucci
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - M Chaffanet
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - A Guille
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - S Garnier
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - J Adelaide
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - N Carbuccia
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - S Brunelle
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - G Piana
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - O Cabaud
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - J Thomassin-Piana
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - M Paciencia-Gros
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - E Chereau-Ewald
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - E Lambaudie
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - R Sabatier
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - C Tarpin
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - M Provansal
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - A Jalaguier-Coudray
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - J-M Extra
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - A Sarran
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - J Pakradouni
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - P Viens
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - M Lopez
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - C Ginestier
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - E Charafe-Jauffret
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
| | - D Birnbaum
- Institut Paoli-Calmettes, Marseille, France; Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS U7258, Marseille, France; Aix-Marseille Universite, Marseille, France
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El Helou R, Wicinski J, Guille A, Adélaïde J, Finetti P, Bertucci F, Chaffanet M, Birnbaum D, Charafe-Jauffret E, Ginestier C. Brief Reports: A Distinct DNA Methylation Signature Defines Breast Cancer Stem Cells and Predicts Cancer Outcome. Stem Cells 2014; 32:3031-6. [DOI: 10.1002/stem.1792] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 06/02/2014] [Accepted: 06/11/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Rita El Helou
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Julien Wicinski
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Arnaud Guille
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Jose Adélaïde
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Pascal Finetti
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - François Bertucci
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Max Chaffanet
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Daniel Birnbaum
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Emmanuelle Charafe-Jauffret
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
| | - Christophe Ginestier
- CRCM, Molecular Oncology; “Equipe labellisée Ligue Contre le Cancer,” Inserm, U1068; Marseille France
- Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
- CNRS, UMR7258; Marseille France
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Sabatier R, Finetti P, Guille A, Adelaide J, Chaffanet M, Viens P, Birnbaum D, Bertucci F. Claudin-low breast cancers: clinical, pathological, molecular and prognostic characterization. Mol Cancer 2014; 13:228. [PMID: 25277734 PMCID: PMC4197217 DOI: 10.1186/1476-4598-13-228] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [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: 04/08/2014] [Accepted: 09/22/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The lastly identified claudin-low (CL) subtype of breast cancer (BC) remains poorly described as compared to the other molecular subtypes. We provide a comprehensive characterization of the largest series of CL samples reported so far. METHODS From a data set of 5447 invasive BC profiled using DNA microarrays, we identified 673 CL samples (12,4%) that we describe comparatively to the other molecular subtypes at several levels: clinicopathological, genomic, transcriptional, survival, and response to chemotherapy. RESULTS CL samples display profiles different from other subtypes. For example, they differ from basal tumors regarding the hormone receptor status, with a lower frequency of triple negative (TN) tumors (52% vs 76% for basal cases). Like basal tumors, they show high genomic instability with many gains and losses. At the transcriptional level, CL tumors are the most undifferentiated tumors along the mammary epithelial hierarchy. Compared to basal tumors, they show enrichment for epithelial-to-mesenchymal transition markers, immune response genes, and cancer stem cell-like features, and higher activity of estrogen receptor (ER), progesterone receptor (PR), EGFR, SRC and TGFβ pathways, but lower activity of MYC and PI3K pathways. The 5-year disease-free survival of CL cases (67%) and the rate of pathological complete response (pCR) to primary chemotherapy (32%) are close to those of poor-prognosis and good responder subtypes (basal and ERBB2-enriched). However, the prognostic features of CL tumors are closer to those observed in the whole BC series and in the luminal A subtype, including proliferation-related gene expression signatures (GES). Immunity-related GES valuable in basal breast cancers are not significant in CL tumors. By contrast, the GES predictive for pCR in CL tumors resemble more to those of basal and HER2-enriched tumors than to those of luminal A tumors. CONCLUSIONS Many differences exist between CL and the other subtypes, notably basal. An unexpected finding concerns the relatively high numbers of ER-positive and non-TN tumors within CL subtype, suggesting a larger heterogeneity than in basal and luminal A subtypes.
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Affiliation(s)
| | | | | | | | | | | | | | - François Bertucci
- Department of Molecular Oncology, Centre de Recherche en Cancérologie de Marseille, UMR1068 Inserm, Institut Paoli-Calmettes (IPC), Marseille, France.
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Helou RE, Wicinski J, Guille A, Adelaide J, Finetti P, Bertucci F, Chaffanet M, Birnbaum D, Charafe-Jauffret E, Ginestier C. Abstract 3881: A distinct DNA methylation signature defines breast cancer stem cells and predict cancer outcome. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pluripotency of stem cells depends on epigenetic programs that regulate self-renewal and differentiation. During oncogenesis, dysregulation of these two programs leads to the development of cancer stem cells (CSCs). Recent evidence suggests that CSCs are relatively resistant to conventional therapies and responsible for metastasis formation. Deciphering these processes will help gain insight into oncogenesis and allow the development of new targeted therapies. We used a whole-genomic promoter microarray to establish the DNA methylation portrait of breast cancer stem cells (bCSC) and compared it to non-bCSC. bCSC from five breast cancer cell lines were isolated using the ALDEFLUOR assay. We identified a DNA methylation signature with 68 differentially methylated regions (DMRs) that were hypomethylated in bCSCs as compared to non-bCSCs. Using a differentiation assay we demonstrated that DMRs are rapidly hypermethylated within the first six hours following induction of CSC differentiation whereas the cells reached the steady-state within 6 days, suggesting that these DMRs are linked to early CSC epigenetic regulation. DMRs were enriched in genes coding for TGFβ signaling-related proteins. Interestingly, overexpression of TGFβ signaling genes was correlated to DMRs hypomethylation in a series of 109 breast tumors. Moreover, the tumors harboring the bCSC DMRs signature had a worse evolution than the ones with the non-bCSC DMRs signature. Our results provide evidence that bCSCs harbor a distinct DNA methylation landscape with TGFβ signaling as a key epigenetic regulator of bCSCs differentiation.
Note: This abstract was not presented at the meeting.
Citation Format: Rita El Helou, Julien Wicinski, Arnaud Guille, Jose Adelaide, Pascal Finetti, Francois Bertucci, Max Chaffanet, Daniel Birnbaum, Emmanuelle Charafe-Jauffret, Christophe Ginestier. A distinct DNA methylation signature defines breast cancer stem cells and predict cancer outcome. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3881. doi:10.1158/1538-7445.AM2014-3881
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Affiliation(s)
- Rita E. Helou
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Julien Wicinski
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Jose Adelaide
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Pascal Finetti
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Francois Bertucci
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille-U891-Inserm, Marseille, France
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Finetti P, Guille A, Adelaide J, Birnbaum D, Chaffanet M, Bertucci F. ESPL1 is a candidate oncogene of luminal B breast cancers. Breast Cancer Res Treat 2014; 147:51-9. [PMID: 25086634 DOI: 10.1007/s10549-014-3070-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/19/2014] [Indexed: 11/26/2022]
Abstract
ESPL1/separase is a putative oncogene of luminal B breast cancers. Histoclinical correlations of its expression have never been explored in large series of breast tumors, and specifically in the luminal subtype. In a pooled series of invasive breast carcinomas profiled using DNA microarrays, we identified 3,074 luminal cases, including 1,307 luminal B tumors, in which we searched for correlations between ESPL1 mRNA expression and molecular and histoclinical features. Compared to normal breast samples, ESPL1 was overexpressed in 52 % of luminal tumors, and much more frequently in luminal B (83 %) than luminal A tumors (29 %). In luminal breast cancers, higher ESPL1 expression was associated with poor-prognosis criteria (age ≤ 50 years, ductal type, advanced stage, large tumor size, lymph node-positive status, high grade, PR-negative status, luminal B subtype) and with poor metastasis-free survival in both uni- and multivariate analyses. This independent prognostic value was also observed in luminal B tumors only, and persisted when compared with gene expression signatures (PAM50, Recurrence Score, Mammaprint, EndoPredict) currently proposed to refine the indications of adjuvant chemotherapy in hormone receptor-positive/HER2-negative breast cancer. We also confirmed the observations made with experimental mouse models: ESPL1-overexpressing luminal tumors showed complex genomic profiles and molecular features of chromosomal instability and loss of tumor suppressor genes (P53 and Rb). Our results reinforce the idea that ESPL1 is a candidate oncogene in luminal B cancers. Its expression may help improve the prognostication. Inhibiting ESPL1 may represent a promising therapeutic approach for these poor-prognosis tumors.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/mortality
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/mortality
- Carcinoma, Lobular/pathology
- Female
- Follow-Up Studies
- Gene Dosage
- Humans
- Mice
- Middle Aged
- Neoplasm Grading
- Neoplasm Invasiveness
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Neoplasm Staging
- Oligonucleotide Array Sequence Analysis
- Prognosis
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptor, ErbB-2/genetics
- Receptors, Estrogen/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Separase/genetics
- Survival Rate
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Affiliation(s)
- Pascal Finetti
- Department of Molecular Oncology, U1068 Inserm, Institut Paoli-Calmettes (IPC), Marseille, France
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47
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Brecqueville M, Rey J, Devillier R, Guille A, Gillet R, Adélaide J, Gelsi-Boyer V, Arnoulet C, Chaffanet M, Mozziconacci MJ, Vey N, Birnbaum D, Murati A. Array comparative genomic hybridization and sequencing of 23 genes in 80 patients with myelofibrosis at chronic or acute phase. Haematologica 2013; 99:37-45. [PMID: 23996481 DOI: 10.3324/haematol.2013.091454] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Myelofibrosis is a myeloproliferative neoplasm that occurs de novo (primary myelofibrosis) or results from the progression of polycythemia vera or essential thrombocytemia (hereafter designated as secondary myelofibrosis or post-polycythemia vera/ essential thrombocythemia myelofibrosis). To progress in the understanding of myelofibrosis and to find molecular prognostic markers we studied 104 samples of primary and secondary myelofibrosis at chronic (n=68) and acute phases (n=12) from 80 patients, by using array-comparative genomic hybridization and sequencing of 23 genes (ASXL1, BMI1, CBL, DNMT3A, EZH2, IDH1/2, JAK2, K/NRAS, LNK, MPL, NF1, PPP1R16B, PTPN11, RCOR1, SF3B1, SOCS2, SRSF2, SUZ12, TET2, TP53, TRPS1). We found copy number aberrations in 54% of samples, often involving genes with a known or potential role in leukemogenesis. We show that cases carrying a del(20q), del(17) or del(12p) evolve in acute myeloid leukemia (P=0.03). We found that 88% of the cases were mutated, mainly in signaling pathway (JAK2 69%, NF1 6%) and epigenetic genes (ASXL1 26%, TET2 14%, EZH2 8%). Overall survival was poor in patients with more than one mutation (P=0.001) and in patients with JAK2/ASXL1 mutations (P=0.02). Our study highlights the heterogeneity of myelofibrosis, and points to several interesting copy number aberrations and genes with diagnostic and prognostic impact.
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Abstract
Next generation sequencing studies have drawn the general landscape of breast cancers and identified hundreds of new, actual therapeutic targets. Two major signaling pathways seem to be altered in a vast proportion of breast cancers. The PI3 kinase/AKT pathway is activated and the JUN/MAPK pathway is repressed. Via the regulation of the cell cycle this metabolic switch impacts on the balance between self-renewal, proliferation and differentiation of the tumor-initiating cells
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Affiliation(s)
- Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille, Oncologie Moléculaire, "Equipe labellisée Ligue Contre le Cancer", UMR1068 Inserm, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 27 bd, Leï Roure, BP 30059, Marseille 13273, France.
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49
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Stahl O, Duvergey H, Guille A, Blondin F, Vecchio AD, Finetti P, Granjeaud S, Vigy O, Bidaut G. Djeen (Database for Joomla!'s Extensible Engine): a research information management system for flexible multi-technology project administration. BMC Res Notes 2013; 6:223. [PMID: 23742665 PMCID: PMC3679982 DOI: 10.1186/1756-0500-6-223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 04/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today. FINDINGS We developed Djeen (Database for Joomla!'s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance. CONCLUSION Djeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.
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Affiliation(s)
- Olivier Stahl
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Hugo Duvergey
- Plate-forme de Protéomique Fonctionnelle, c/o Institut de Génomique Fonctionnelle, Montpellier, F-34000, France,CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, F-34094, France,INSERM, U661, Montpellier, F-34094, France,Universités de Montpellier 1 & 2, UMR-5203, Montpellier, F-34094, France
| | - Arnaud Guille
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Fanny Blondin
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Alexandre Del Vecchio
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Pascal Finetti
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Samuel Granjeaud
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
| | - Oana Vigy
- Plate-forme de Protéomique Fonctionnelle, c/o Institut de Génomique Fonctionnelle, Montpellier, F-34000, France,CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, F-34094, France,INSERM, U661, Montpellier, F-34094, France,Universités de Montpellier 1 & 2, UMR-5203, Montpellier, F-34094, France
| | - Ghislain Bidaut
- Aix-Marseille Univ, Marseille, F-13284, France,Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France,Institut Paoli-Calmettes, Marseille, F-13009, France,CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, F-13009, France
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50
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Ginestier C, Monville F, Wicinski J, Cabaud O, Cervera N, Josselin E, Finetti P, Guille A, Larderet G, Viens P, Sebti S, Bertucci F, Birnbaum D, Charafe-Jauffret E. Mevalonate metabolism regulates Basal breast cancer stem cells and is a potential therapeutic target. Stem Cells 2012; 30:1327-37. [PMID: 22605458 DOI: 10.1002/stem.1122] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is increasing evidence that breast tumors are organized in a hierarchy, with a subpopulation of tumorigenic cancer cells, the cancer stem cells (CSCs), which sustain tumor growth. The characterization of protein networks that govern CSC behavior is paramount to design new therapeutic strategies targeting this subpopulation of cells. We have sought to identify specific molecular pathways of CSCs isolated from 13 different breast cancer cell lines of luminal or basal/mesenchymal subtypes. We compared the gene expression profiling of cancer cells grown in adherent conditions to those of matched tumorsphere cultures. No specific pathway was identified to be commonly regulated in luminal tumorspheres, resulting from a minor CSC enrichment in tumorsphere passages from luminal cell lines. However, in basal/mesenchymal tumorspheres, the enzymes of the mevalonate metabolic pathway were overexpressed compared to those in cognate adherent cells. Inhibition of this pathway with hydroxy-3-methylglutaryl CoA reductase blockers resulted in a reduction of breast CSC independent of inhibition of cholesterol biosynthesis and of protein farnesylation. Further modulation of this metabolic pathway demonstrated that protein geranylgeranylation (GG) is critical to breast CSC maintenance. A small molecule inhibitor of the geranylgeranyl transferase I (GGTI) enzyme reduced the breast CSC subpopulation both in vitro and in primary breast cancer xenografts. We found that the GGTI effect on the CSC subpopulation is mediated by inactivation of Ras homolog family member A (RHOA) and increased accumulation of P27(kip1) in the nucleus. The identification of protein GG as a major contributor to CSC maintenance opens promising perspectives for CSC targeted therapy in basal breast cancer.
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Affiliation(s)
- Christophe Ginestier
- Département d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, Marseille, France.
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