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Fléchon L, Arib I, Dutta AK, Hasan Bou Issa L, Sklavenitis-Pistofidis R, Tilmont R, Stewart C, Dubois R, Poulain S, Copin MC, Javed S, Nudel M, Cavalieri D, Escure G, Gower N, Chauvet P, Gazeau N, Saade C, Thiam MB, Ouelkite-Oumouchal A, Gaggero S, Cailliau É, Faiz S, Carpentier O, Duployez N, Idziorek TB, Mortier L, Figeac M, Preudhomme C, Quesnel B, Mitra S, Morschhauser F, Getz G, Ghobrial IM, Manier S. Genomic profiling of Mycosis Fungoides identifies patients at high risk of disease progression. Blood Adv 2024:bloodadvances.2023012125. [PMID: 38513135 DOI: 10.1182/bloodadvances.2023012125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/23/2024] Open
Abstract
Mycosis fungoides (MF) is the most prevalent primary cutaneous T-cell lymphoma, with an indolent or aggressive course and poor survival. The pathogenesis of MF remains unclear, and prognostic factors in the early stages are not well-established. Here, we characterized the most recurrent genomic alterations using whole-exome sequencing of 67 samples from 48 patients from Lille University Hospital (France), including 18 sequential samples drawn across stages of the malignancy. Genomic data were analyzed on the Broad Institute's Terra bioinformatics platform. We found that gain7q, gain10p15.1 (IL2RA and IL15RA), del10p11.22 (ZEB1), or mutations in JUNB and TET2 are associated with high-risk disease stages. Furthermore, gain7q, gain10p15.1 (IL2RA and IL15RA), del10p11.22 (ZEB1), and del6q16.3 (TNFAIP3) are coupled with shorter survival. Del6q16.3 (TNFAIP3) was a risk factor for progression in low-risk patients. By analyzing the clonal heterogeneity and the clonal evolution of the cohort, we defined different phylogenetic pathways of the disease with acquisition of JUNB, gain10p15.1 (IL2RA and IL15RA), or del12p13.1 (CDKN1B) at progression. These results establish the genomics and clonality of MF and identify potential patients at risk of progression, independent of their clinical stage.
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Affiliation(s)
- Léa Fléchon
- Canther, INSERM UMR-S1277, CNRS UMR9020, Lille University, Lille, France
| | - Inès Arib
- Canther, INSERM UMR-S1277, CNRS UMR9020, Lille University, Lille, France
| | - Ankit K Dutta
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | | | | | | | - Chip Stewart
- Broad Institute, Cambridge, Massachusetts, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suman Mitra
- UMR 9020-UMR-S 1277-Canther, Institut de Recherche contre le Cancer de Lille, University Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France, Lille, France
| | | | - Gad Getz
- Broad Institute, Mass General Hospital, Cambridge, Massachusetts, United States
| | - Irene M Ghobrial
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Salomon Manier
- Canther, INSERM UMR-S1277, CNRS UMR9020, Lille University, Lille, France
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Lionet A, Van Triempon M, Figeac M, Fages V, Gibier JB, Provot F, Maanaoui M, Pottier N, Cauffiez C, Glowacki F. Extracorporeal Photopheresis Reduces Fibrotic and Inflammatory Transcriptomic Biological Marker of Chronic Antibody-mediated Kidney Rejection. Transplant Direct 2024; 10:e1587. [PMID: 38380348 PMCID: PMC10876237 DOI: 10.1097/txd.0000000000001587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/22/2024] Open
Abstract
Background The benefit of extracorporeal photopheresis on the course of kidney transplant rejection is unknown. The aim of our study was to investigate the variations in transcriptomics on graft biopsies when extracorporeal photopheresis was used to treat chronic humoral rejection after kidney transplantation. Methods We retrospectively analyzed the mRNA expression of 770 genes of interest in graft biopsies performed before and after treatment. Eight patients received an average of 23 extracorporeal photopheresis sessions over 4 mo between the 2 biopsies. Results Transcriptomic analysis of the graft biopsies identified a significant (adjusted P < 0.05) increase in CAV1 mRNA in all patients and a significant decrease in CD19, IL21, PAX5, and SFTPA2 mRNAs in 7 of 8 patients. Conclusions In patients treated with extracorporeal photopheresis for chronic humoral rejection after renal transplantation, omic analysis of repeated biopsies shows a reduction in fibrotic and inflammatory transcriptomic biologicals markers.
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Affiliation(s)
- Arnaud Lionet
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277—CANTHER, University of Lille, Lille, France
| | - Marine Van Triempon
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
| | - Martin Figeac
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014—PLBS, University of Lille, Lille, France
| | - Victor Fages
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
| | | | - François Provot
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
| | - Mehdi Maanaoui
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMRU1190 Translational Research for Diabetes, University of Lille, Lille, France
| | - Nicolas Pottier
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277—CANTHER, University of Lille, Lille, France
| | - Christelle Cauffiez
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277—CANTHER, University of Lille, Lille, France
| | - François Glowacki
- Department of Nephrology and Kidney Transplantation, University Hospital Huriez, CHU-Lille, Lille, France
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277—CANTHER, University of Lille, Lille, France
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Guérin C, Vinchent A, Fernandes M, Damour I, Laratte A, Tellier R, Estevam GO, Meneboo JP, Villenet C, Descarpentries C, Fraser JS, Figeac M, Cortot AB, Rouleau E, Tulasne D. MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation. bioRxiv 2023:2023.11.03.565283. [PMID: 37965202 PMCID: PMC10635098 DOI: 10.1101/2023.11.03.565283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
In hereditary papillary renal cell carcinoma (HPRCC), the MET receptor tyrosine kinase (RTK) mutations recorded to date are located in the kinase domain and lead to constitutive MET activation. This contrasts with MET mutations recently identified in non-small cell lung cancer (NSCLC), which lead to exon 14 skipping and deletion of a regulatory domain: in this latter case, the mutated receptor still requires ligand stimulation. Sequencing of MET in samples from 158 HPRCC and 2808 NSCLC patients revealed ten uncharacterized mutations. Four of these, all found in HPRCC and leading to amino acid substitutions in the N-lobe of the MET kinase, proved able to induce cell transformation, further enhanced by HGF stimulation: His1086Leu, Ile1102Thr, Leu1130Ser, and Cis1125Gly. Similar to the variant resulting in MET exon14 skipping, the two N-lobe MET variants His1086Leu, Ile1102Thr further characterized were found to require stimulation by HGF in order to strongly activate downstream signaling pathways and epithelial cell motility. The Ile1102Thr mutation displayed also transforming potential, promoting tumor growth in a xenograft model. In addition, the N-lobe-mutated MET variants were found to trigger a common HGF-stimulation-dependent transcriptional program, consistent with an observed increase in cell motility and invasion. Altogether, this functional characterization revealed that N-lobe variants still require ligand stimulation, in contrast to other RTK variants. This suggests that HGF expression in the tumor microenvironment is important for tumor growth. The sensitivity of these variants to MET TKIs opens the way for use of targeted therapies for patients harboring the corresponding mutations.
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Fernandes M, Hoggard B, Jamme P, Paget S, Truong M, Grégoire V, Vinchent A, Descarpentries C, Morabito A, Stanislovas J, Farage E, Meneboo J, Sebda S, Bouchekioua‐Bouzaghou K, Nollet M, Humez S, Perera T, Fromme P, Grumolato L, Figeac M, Copin M, Tulasne D, Cortot AB, Kermorgant S, Kherrouche Z. MET exon 14 skipping mutation is a hepatocyte growth factor (HGF)-dependent oncogenic driver in vitro and in humanised HGF knock-in mice. Mol Oncol 2023; 17:2257-2274. [PMID: 36799689 PMCID: PMC10620121 DOI: 10.1002/1878-0261.13397] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
Exon skipping mutations of the MET receptor tyrosine kinase (METex14), increasingly reported in cancers, occur in 3-4% of non-small-cell lung cancer (NSCLC). Only 50% of patients have a beneficial response to treatment with MET-tyrosine kinase inhibitors (TKIs), underlying the need to understand the mechanism of METex14 oncogenicity and sensitivity to TKIs. Whether METex14 is a driver mutation and whether it requires hepatocyte growth factor (HGF) for its oncogenicity in a range of in vitro functions and in vivo has not been fully elucidated from previous preclinical models. Using CRISPR/Cas9, we developed a METex14/WT isogenic model in nontransformed human lung cells and report that the METex14 single alteration was sufficient to drive MET-dependent in vitro anchorage-independent survival and motility and in vivo tumorigenesis, sensitising tumours to MET-TKIs. However, we also show that human HGF (hHGF) is required, as demonstrated in vivo using a humanised HGF knock-in strain of mice and further detected in tumour cells of METex14 NSCLC patient samples. Our results also suggest that METex14 oncogenicity is not a consequence of an escape from degradation in our cell model. Thus, we developed a valuable model for preclinical studies and present results that have potential clinical implication.
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Affiliation(s)
- Marie Fernandes
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | | | - Philippe Jamme
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | - Sonia Paget
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | - Marie‐José Truong
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | | | - Audrey Vinchent
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | | | - Angela Morabito
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | | | - Enoir Farage
- Barts Cancer InstituteQueen Mary University of LondonUK
| | - Jean‐Pascal Meneboo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, LilleFrance
| | - Shéhérazade Sebda
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, LilleFrance
| | | | - Marie Nollet
- Barts Cancer InstituteQueen Mary University of LondonUK
| | - Sarah Humez
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
- Univ LilleDepartment of Pathology, CHU LilleFrance
| | | | - Paul Fromme
- Department of Mechanical EngineeringUniversity College LondonUK
| | - Luca Grumolato
- Univ Rouen Normandie, Inserm, NorDiC UMR 1239, 76000 RouenFrance
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, LilleFrance
| | - Marie‐Christine Copin
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
- Univ LilleDepartment of Pathology, CHU LilleFrance
| | - David Tulasne
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
| | - Alexis B. Cortot
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
- Univ. LilleThoracic Oncology Department, CHU LilleFrance
| | | | - Zoulika Kherrouche
- Univ. Lille, CNRS, Inserm, CHU LilleInstitut Pasteur de Lille, UMR9020 – UMR1277 - Canther – Cancer Heterogeneity, Plasticity and Resistance to TherapiesFrance
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Thorel L, Morice PM, Paysant H, Florent R, Babin G, Thomine C, Perréard M, Abeilard E, Giffard F, Brotin E, Denoyelle C, Villenet C, Sebda S, Briand M, Joly F, Dolivet E, Goux D, Blanc-Fournier C, Jeanne C, Villedieu M, Meryet-Figuiere M, Figeac M, Poulain L, Weiswald LB. Comparative analysis of response to treatments and molecular features of tumor-derived organoids versus cell lines and PDX derived from the same ovarian clear cell carcinoma. J Exp Clin Cancer Res 2023; 42:260. [PMID: 37803448 PMCID: PMC10559504 DOI: 10.1186/s13046-023-02809-8] [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: 03/03/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND In the era of personalized medicine, the establishment of preclinical models of cancer that faithfully recapitulate original tumors is essential to potentially guide clinical decisions. METHODS We established 7 models [4 cell lines, 2 Patient-Derived Tumor Organoids (PDTO) and 1 Patient-Derived Xenograft (PDX)], all derived from the same Ovarian Clear Cell Carcinoma (OCCC). To determine the relevance of each of these models, comprehensive characterization was performed based on morphological, histological, and transcriptomic analyses as well as on the evaluation of their response to the treatments received by the patient. These results were compared to the clinical data. RESULTS Only the PDX and PDTO models derived from the patient tumor were able to recapitulate the patient tumor heterogeneity. The patient was refractory to carboplatin, doxorubicin and gemcitabine, while tumor cell lines were sensitive to these treatments. In contrast, PDX and PDTO models displayed resistance to the 3 drugs. The transcriptomic analysis was consistent with these results since the models recapitulating faithfully the clinical response grouped together away from the other classical 2D cell culture models. We next investigated the potential of drugs that have not been used in the patient clinical management and we identified the HDAC inhibitor belinostat as a potential effective treatment based on PDTO response. CONCLUSIONS PDX and PDTO appear to be the most relevant models, but only PDTO seem to present all the necessary prerequisites for predictive purposes and could constitute relevant tools for therapeutic decision support in the context of these particularly aggressive cancers refractory to conventional treatments.
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Affiliation(s)
- Lucie Thorel
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Pierre-Marie Morice
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Hippolyte Paysant
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Romane Florent
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- Université de Caen Normandie, Services Unit PLATON, ORGAPRED Core Facility, Caen, France
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Guillaume Babin
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Department of Surgery, Caen, France
| | - Cécilia Thomine
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Marion Perréard
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Edwige Abeilard
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Florence Giffard
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Emilie Brotin
- Université de Caen Normandie, Services Unit PLATON, ImpedanCell Core Facility, Caen, France
| | - Christophe Denoyelle
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
- Université de Caen Normandie, Services Unit PLATON, ImpedanCell Core Facility, Caen, France
| | - Céline Villenet
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Shéhérazade Sebda
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Mélanie Briand
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Biological Resources Center 'OvaRessources', Caen, France
| | - Florence Joly
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Clinical Research Department, Caen, France
| | - Enora Dolivet
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Department of Surgery, Caen, France
| | - Didier Goux
- Université de Caen Normandie, Services Unit EMERODE, « Centre de Microscopie Appliquée À La Biologie » CMAbio3, Caen, France
| | - Cécile Blanc-Fournier
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Biological Resources Center 'OvaRessources', Caen, France
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Department of Biopathology, Caen, France
| | - Corinne Jeanne
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Department of Biopathology, Caen, France
| | - Marie Villedieu
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
| | - Matthieu Meryet-Figuiere
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Martin Figeac
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Laurent Poulain
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.
- Université de Caen Normandie, Services Unit PLATON, ORGAPRED Core Facility, Caen, France.
- UNICANCER, Comprehensive Cancer Center Francois Baclesse, Biological Resources Center 'OvaRessources', Caen, France.
| | - Louis-Bastien Weiswald
- Université de Caen Normandie, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.
- Université de Caen Normandie, Services Unit PLATON, ORGAPRED Core Facility, Caen, France.
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.
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6
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Divoux J, Florent R, Jacobs M, Lequesne J, Grellard JM, San C, Grossi S, Kerdja K, Clarisse B, Boudier G, Cherifi F, Briand M, Dolivet E, Johnson A, Dubois B, Harter V, Lacroix J, Raboutet C, Marie B, Rousseau N, Blanc-Fournier C, Vaur D, Figeac M, Poulain L, Weiswald LB, Emile G. The TRIPLEX study: use of patient-derived tumor organoids as an innovative tool for precision medicine in triple-negative breast cancer. BMC Cancer 2023; 23:883. [PMID: 37726786 PMCID: PMC10508010 DOI: 10.1186/s12885-023-11362-8] [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: 07/17/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Triple negative breast cancers (TNBC) account for approximately 15% of all breast cancers and are associated with a shorter median survival mainly due to locally advanced tumor and high risk of metastasis. The current neoadjuvant treatment for TNBC consists of a regimen of immune checkpoint blocker and chemotherapy (chemo-ICB). Despite the frequent use of this combination for TNBC treatment, moderate results are observed and its clinical benefit in TNBC remains difficult to predict. Patient-derived tumor organoids (PDTO) are 3D in vitro cellular structures obtained from patient's tumor samples. More and more evidence suggest that these models could predict the response of the tumor from which they are derived. PDTO may thus be used as a tool to predict chemo-ICB efficacy in TNBC patients. METHOD The TRIPLEX study is a single-center observational study conducted to investigate the feasibility of generating PDTO from TNBC and to evaluate their ability to predict clinical response. PDTO will be obtained after the dissociation of biopsies and embedding into extra cellular matrix. PDTO will be cultured in a medium supplemented with growth factors and signal pathway inhibitors. Molecular and histological analyses will be performed on established PDTO lines to validate their phenotypic proximity with the original tumor. Response of PDTO to chemo-ICB will be assessed using co-cultures with autologous immune cells collected from patient blood samples. PDTO response will finally be compared with the response of the patient to evaluate the predictive potential of the model. DISCUSSION This study will allow to assess the feasibility of using PDTO as predictive tools for the evaluation of the response of TNBC patients to treatments. In the event that PDTO could faithfully predict patient response in clinically relevant time frames, a prospective clinical trial could be designed to use PDTO to guide clinical decision. This study will also permit the establishment of a living biobank of TNBC PDTO usable for future innovative strategies evaluation. TRIAL REGISTRATION The clinical trial (version 1.2) has been validated by local research ethic committee on December 30th 2021 and registered at ClinicalTrials.gov with the identifier NCT05404321 on June 3rd 2022, version 1.2.
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Affiliation(s)
- Jordane Divoux
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- US PLATON, ORGAPRED Core Facility, Université de Caen Normandie, Caen, France
| | - Romane Florent
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- US PLATON, ORGAPRED Core Facility, Université de Caen Normandie, Caen, France
| | - Margaux Jacobs
- Comprehensive Cancer Center François Baclesse, Breast Cancer Unit, UNICANCER, Institut Normand du Sein, Caen, France
| | - Justine Lequesne
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Jean-Michel Grellard
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Chankannira San
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Sara Grossi
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Katia Kerdja
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Bénédicte Clarisse
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Gwenaelle Boudier
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - François Cherifi
- Comprehensive Cancer Center François Baclesse, Breast Cancer Unit, UNICANCER, Institut Normand du Sein, Caen, France
| | - Mélanie Briand
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- US PLATON, Biological Resource Center 'OvaRessources', Université de Caen Normandie, Caen, France
| | - Enora Dolivet
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- Comprehensive Cancer Center François Baclesse, Department of Surgery, UNICANCER, Caen, France
| | - Alisson Johnson
- Comprehensive Cancer Center François Baclesse, Breast Cancer Unit, UNICANCER, Institut Normand du Sein, Caen, France
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France
| | - Brice Dubois
- Comprehensive Cancer Center François Baclesse, North-West Canceropole Data Center, UNICANCER, Caen, France
| | - Valentin Harter
- Comprehensive Cancer Center François Baclesse, North-West Canceropole Data Center, UNICANCER, Caen, France
| | - Joëlle Lacroix
- Comprehensive Cancer Center François Baclesse, Department of Radiology, UNICANCER, Caen, France
| | - Charlotte Raboutet
- Comprehensive Cancer Center François Baclesse, Department of Radiology, UNICANCER, Caen, France
| | - Brigitte Marie
- Comprehensive Cancer Center François Baclesse, Department of Radiology, UNICANCER, Caen, France
| | - Nathalie Rousseau
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- Biological Resource Center 'Tumorotheque de Caen Basse-Normandie', IRCBN Institut Régional du Cancer Basse Normandie, Caen, France
| | - Cécile Blanc-Fournier
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- US PLATON, Biological Resource Center 'OvaRessources', Université de Caen Normandie, Caen, France
- Biological Resource Center 'Tumorotheque de Caen Basse-Normandie', IRCBN Institut Régional du Cancer Basse Normandie, Caen, France
- Comprehensive Cancer Center François Baclesse, Department of Biopathology, UNICANCER, Caen, France
| | - Dominique Vaur
- Comprehensive Cancer Center François Baclesse, Department of Cancer Biology and Genetics, UNICANCER, Caen, France
| | - Martin Figeac
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, University of Lille, Lille, France
| | - Laurent Poulain
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France
- US PLATON, ORGAPRED Core Facility, Université de Caen Normandie, Caen, France
- US PLATON, Biological Resource Center 'OvaRessources', Université de Caen Normandie, Caen, France
| | - Louis-Bastien Weiswald
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA Laboratory (Precision Medicine for Ovarian Cancers), Université de Caen Normandie, Caen, France.
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France.
- US PLATON, ORGAPRED Core Facility, Université de Caen Normandie, Caen, France.
- INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, Caen Cedex 05, 14 076, France.
| | - George Emile
- Comprehensive Cancer Center François Baclesse, Breast Cancer Unit, UNICANCER, Institut Normand du Sein, Caen, France.
- Comprehensive Cancer Center François Baclesse, Clinical Research Department, UNICANCER, Caen, France.
- Breast Cancer Unit, Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, Caen Cedex 05, 14 076, France.
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7
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Fernandes M, Paget S, Kherrouche Z, Truong MJ, Vinchent A, Meneboo JP, Sebda S, Werkmeister E, Descarpentries C, Figeac M, Cortot AB, Tulasne D. Transforming properties of MET receptor exon 14 skipping can be recapitulated by loss of the CBL ubiquitin ligase binding site. FEBS Lett 2023; 597:2301-2315. [PMID: 37468447 DOI: 10.1002/1873-3468.14702] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
MET is a receptor tyrosine kinase that is activated in many cancers through various mechanisms. MET exon 14 (Ex14) skipping occurs in 3% of nonsmall cell lung tumors. However, the contribution of the regulatory sites lost upon this skipping, which include a phosphorylated serine (S985) and a binding site for the E3 ubiquitin ligase CBL (Y1003), remains elusive. Sequencing of 2808 lung tumors revealed 71 mutations leading to MET exon 14 skipping and three mutations affecting Y1003 or S985. In addition, MET exon 14 skipping and MET Y1003F induced similar transcriptional programs, increased the activation of downstream signaling pathways, and increased cell mobility. Therefore, the MET Y1003F mutation is able to fully recapitulate responses induced by MET exon 14 skipping, suggesting that loss of the CBL binding site is the main contributor of cell transformation induced by MET Ex14 mutations.
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Affiliation(s)
- Marie Fernandes
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
| | - Sonia Paget
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
| | - Zoulika Kherrouche
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
| | - Marie-José Truong
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
| | - Audrey Vinchent
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
| | - Jean-Pascal Meneboo
- Plateau de Génomique Fonctionnelle et Structurale, CHU Lille, Univ. Lille, France
| | - Shéhérazade Sebda
- Plateau de Génomique Fonctionnelle et Structurale, CHU Lille, Univ. Lille, France
| | - Elisabeth Werkmeister
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US41 - UMS2014 - PLBS, Univ. Lille, France
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, France
| | | | - Martin Figeac
- Plateau de Génomique Fonctionnelle et Structurale, CHU Lille, Univ. Lille, France
| | - Alexis B Cortot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
- Thoracic Oncology Department, CHU Lille, Univ. Lille, France
| | - David Tulasne
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, France
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8
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Darlington M, Sujobert P, Kosmider O, Luque Paz D, Kaltenbach S, Figeac M, Hayette S, Mezaour N, Coquerelle S, Alary AS, Bidet A, Le Bris Y, Delabesse E, Davi F, Preudhomme C, Durand-Zaleski I, Macintyre E, Alame M, Baran-Marzak F, Berger MG, Bories D, Caye-Eude A, Cayuela JM, Cornillet-Lefebvre P, Delhommeau F, Estienne-Felix MH, Etancelin P, Flandrin-Gresta P, Lippert E, Marzac C, Miguet L, Pastoret C, Raynaud S, Rizzo D. Targeted High-throughput Sequencing for Hematological Malignancies: A GBMHM Survey of Practice and Cost Evaluation in France. Hemasphere 2023; 7:e943. [PMID: 37637995 PMCID: PMC10455455 DOI: 10.1097/hs9.0000000000000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
The objective of this study was to assess the clinical impact and financial costs of next-generation sequencing (NGS) in 5 categories of pediatric and adult hematological cancers. NGS prescriptions were prospectively collected from 26 laboratories, with varied technical and reporting practice (all or only significant targets). Impact was defined by the identification of (1) an actionable mutation, (2) a mutation with prognostic and/or theranostic value, and/or (3) a mutation allowing nosological refinement, reported by local investigators. A microcosting study was undertaken in 4 laboratories, identifying the types and volumes of resources required for each procedural step. Individual index prescriptions for 3961 patients were available for impact analysis on the management of myeloid disorders (two thirds) and, mainly mature B, lymphoid disorders (one third). NGS results were considered to impact the management for 73.4% of prescriptions: useful for evaluation of prognostic risk in 34.9% and necessary for treatment adaptation (actionable) in 19.6%, but having no immediate individual therapeutic impact in 18.9%. The average overall cost per sample was 191 € for the restricted mature lymphoid amplicon panel. Capture panel costs varied from 369 € to 513 €. Unit costs varied from 0.5 € to 5.7 € per kb sequenced, from 3.6 € to 11.3 € per target gene/hot-spot sequenced and from 4.3 € to 73.8 € per target gene/hot-spot reported. Comparable costs for the Amplicon panels were 5-8 € per kb and 10.5-14.7 € per target gene/hot-spot sequenced and reported, demonstrating comparable costs with greater informativity/flexibility for capture strategies. Sustainable funding of precision medicine requires a transparent discussion of its impact on care pathways and its financial aspects.
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Affiliation(s)
- Meryl Darlington
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Pierre Sujobert
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
| | - Olivier Kosmider
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
| | - Damien Luque Paz
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
| | - Sophie Kaltenbach
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
| | - Sandrine Hayette
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
| | - Nadia Mezaour
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Séverine Coquerelle
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Anne-Sophie Alary
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
| | - Audrey Bidet
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
| | - Yannick Le Bris
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
| | - Eric Delabesse
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
| | - Frédéric Davi
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
| | - Claude Preudhomme
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
| | | | - Elizabeth Macintyre
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Université Paris Cité, CNRS, Inserm, France
| | - Mélissa Alame
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Fanny Baran-Marzak
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Marc G. Berger
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Dominique Bories
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Aurélie Caye-Eude
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Jean-Michel Cayuela
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascale Cornillet-Lefebvre
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - François Delhommeau
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Marie-Hélène Estienne-Felix
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascaline Etancelin
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascale Flandrin-Gresta
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Eric Lippert
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Christophe Marzac
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Laurent Miguet
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Cédric Pastoret
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Sophie Raynaud
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - David Rizzo
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
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9
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Vasseur L, Fenwarth L, Lambert J, de Botton S, Figeac M, Villenet C, Heiblig M, Dumas PY, Récher C, Berthon C, Lemasle E, Lebon D, Lambert J, Terré C, Celli-Lebras K, Dombret H, Preudhomme C, Cheok M, Itzykson R, Duployez N. LSC17 score complements genetics and measurable residual disease in acute myeloid leukemia: an ALFA study. Blood Adv 2023; 7:4024-4034. [PMID: 37205853 PMCID: PMC10410128 DOI: 10.1182/bloodadvances.2023010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023] Open
Abstract
Whether the LSC17 gene expression can improve risk stratification in the context of next generation sequencing-based risk stratification and measurable residual disease (MRD) in patients with intensively treated AML has not been explored. We analyzed LSC17 in 504 adult patients prospectively treated in the ALFA-0702 trial. RUNX1 or TP53 mutations were associated with higher LSC1 scores while CEBPA and NPM1 mutations were associated with lower scores. Patients with high LSC17 scores had a lower rate of complete response (CR) in a multivariable analysis (odds ratio, 0.41; P = .0007), accounting for European LeukemiaNet 2022 (ELN22), age, and white blood cell count (WBC). LSC17-high status was associated with shorter overall survival (OS) (3-year OS: 70.0% vs 52.7% in patients with LSC17-low status; P < .0001). In a multivariable analysis considering ELN22, age, and WBC, patients with LSC17-high status had shorter disease-free survival (DFS) (hazard ratio [HR], 1.36; P = .048) than those with LSC17-low status. In 123 patients with NPM1-mutated AML in CR, LSC17-high status predicted poorer DFS (HR, 2.34; P = .01), independent of age, WBC, ELN22 risk, and NPM1-MRD. LSC-low status and negative NPM1-MRD identified a subset comprising 48% of patients with mutated NPM1 with a 3-year OS from CR of 93.1% compared with 60.7% in those with LSC17-high status and/or positive NPM1-MRD (P = .0001). Overall, LSC17 assessment refines genetic risk stratification in adult patients with AML treated intensively. Combined with MRD, LSC17 identifies a subset of patients with NPM1-mutated AML with excellent clinical outcome.
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Affiliation(s)
- Loïc Vasseur
- Adolescents and Young Adults Hematology Department, St-Louis University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
- Biostatistical Department, St-Louis University Hospital, AP-HP, Paris, France
| | - Laurène Fenwarth
- CNRS, INSERM, CHU Lille, UMR9020-U1277 - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, Lille, France
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
| | - Jérôme Lambert
- Biostatistical Department, St-Louis University Hospital, AP-HP, Paris, France
| | - Stéphane de Botton
- Département d’hématologie et Département d’innovation thérapeutique, Gustave Roussy, Villejuif, France
| | - Martin Figeac
- CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, University of Lille, Lille, France
| | - Céline Villenet
- CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, University of Lille, Lille, France
| | - Maël Heiblig
- Hematology Department, Lyon-Sud University Hospital, Hospices Civils de Lyon, Pierre-Benite, France
| | - Pierre-Yves Dumas
- Department of Clinical Hematology, Bordeaux University Hospital, PESSAC, France
| | - Christian Récher
- Service d'Hématologie, CHU de Toulouse - Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | | | - Emilie Lemasle
- Hematology Department, Henri-Becquerel Cancer Center, Rouen, France
| | - Delphine Lebon
- Service d’Hématologie Clinique et Thérapie cellulaire, CHU d’Amiens, Amiens, France
| | - Juliette Lambert
- Service d'Hématologie et Oncologie, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Christine Terré
- Laboratory of Hematology, Centre Hospitalier de Versailles, Le Chesnay, France
| | | | - Hervé Dombret
- Department of Hematology, St-Louis University Hospital, AP-HP, Paris, France
| | - Claude Preudhomme
- CNRS, INSERM, CHU Lille, UMR9020-U1277 - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, Lille, France
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
| | - Meyling Cheok
- CNRS, INSERM, CHU Lille, UMR9020-U1277 - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, Lille, France
| | - Raphael Itzykson
- Department of Hematology, St-Louis University Hospital, AP-HP, Paris, France
- Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Nicolas Duployez
- CNRS, INSERM, CHU Lille, UMR9020-U1277 - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, Lille, France
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
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10
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Perréard M, Florent R, Divoux J, Grellard JM, Lequesne J, Briand M, Clarisse B, Rousseau N, Lebreton E, Dubois B, Harter V, Lasne-Cardon A, Drouet J, Johnson A, Le Page AL, Bazille C, Jeanne C, Figeac M, Goardon N, Vaur D, Micault E, Humbert M, Thariat J, Babin E, Poulain L, Weiswald LB, Bastit V. ORGAVADS: establishment of tumor organoids from head and neck squamous cell carcinoma to assess their response to innovative therapies. BMC Cancer 2023; 23:223. [PMID: 36894916 PMCID: PMC9999487 DOI: 10.1186/s12885-023-10692-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Radiotherapy is one of the cornerstones of the treatment of Head and Neck Squamous Cell Carcinomas (HNSCC). However, radioresistance is associated with a high risk of recurrence. To propose strategies (such as combinations with drugs) that could over intrinsic radioresistance, it is crucial to predict the response to treatment. Patient-Derived Tumor Organoids (PDTO) are in vitro tridimensional microtumors obtained from patient' own cancer samples. They have been shown to serve as reliable surrogates of the tumor response in patients. METHODS The ORGAVADS study is a multicenter observational trial conducted to investigate the feasibility of generating and testing PDTO derived from HNSCC for the evaluation of sensitivity to treatments. PDTO are obtained after dissociation of resected tumors remaining from tissues necessary for the diagnosis. Embedding of tumor cells is then performed in extracellular matrix and culture in medium supplemented with growth factors and inhibitors. Histological and immunohistochemical characterizations are performed to validate the resemblance between PDTO and their original tumor. Response of PDTO to chemotherapy, radiotherapy and innovating combinations are assessed, as well as response to immunotherapy using co-cultures of PDTO with autologous immune cells collected from patient blood samples. Transcriptomic and genetic analyses of PDTO allow validation of the models compared to patients' own tumor and identification of potential predictive biomarkers. DISCUSSION This study is designed to develop PDTO models from HNSCC. It will allow comparing the response of PDTO to treatment and the clinical response of the patients from whom they are derived. Our aim is to study the PDTO ability to predict the clinical response to treatment for each patient in view of a personalized medicine as well as to establish a collection of HNSCC models that will be useful for future innovative strategies evaluation. TRIAL REGISTRATION NCT04261192, registered February 7, 2020, last amendment v4 accepted on June, 2021.
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Affiliation(s)
- Marion Perréard
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Head and Neck Surgery, Caen University Hospital, Caen, France
| | - Romane Florent
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Normandy University, UNICAEN, SF Normandy Oncology, US PLATON, ORGAPRED core facility, Caen, France
| | - Jordane Divoux
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Normandy University, UNICAEN, SF Normandy Oncology, US PLATON, ORGAPRED core facility, Caen, France
| | - Jean-Michel Grellard
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Clinical Research Department, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Justine Lequesne
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Clinical Research Department, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Mélanie Briand
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Biological Resource Center 'OvaRessources', Caen, France
| | - Bénédicte Clarisse
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Clinical Research Department, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Nathalie Rousseau
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,IRCBN Institut Régional du cancer Basse Normandie, Biological Resource Center 'Tumorotheque de Caen Basse-Normandie', Caen, France
| | - Esther Lebreton
- Clinical Research Department, Caen University Hospital, Caen, France
| | - Brice Dubois
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, North-West Canceropole Data Center, Caen, France
| | - Valentin Harter
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, North-West Canceropole Data Center, Caen, France
| | - Audrey Lasne-Cardon
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Head and Neck Surgery, UNICANCER, Comprehensive Cancer Center François Baclesse, 3 avenue du Général Harris, Caen, 14000, France
| | - Julien Drouet
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Oral and Maxillofacial Surgery, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Alisson Johnson
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Medical Oncology Surgery, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | | | - Céline Bazille
- Department of Pathology, Caen University Hospital, Caen, France
| | - Corinne Jeanne
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Biopathology, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Martin Figeac
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Nicolas Goardon
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Cancer Biology and Genetics, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Dominique Vaur
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Department of Cancer Biology and Genetics, UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France
| | - Emmanuel Micault
- Department of Head and Neck Surgery, Caen University Hospital, Caen, France
| | - Maxime Humbert
- Department of Head and Neck Surgery, Caen University Hospital, Caen, France
| | - Juliette Thariat
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,LPC Caen ENSICAEN/CNRS UMR6534, Caen, France
| | - Emmanuel Babin
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,Department of Head and Neck Surgery, Caen University Hospital, Caen, France
| | - Laurent Poulain
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France.,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France.,Normandy University, UNICAEN, SF Normandy Oncology, US PLATON, ORGAPRED core facility, Caen, France
| | - Louis-Bastien Weiswald
- Normandy University, UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancers Prevention and Treatment), BioTICLA laboratory (Precision medicine for ovarian cancers), Comprehensive Cancer Center François Baclesse, 3 Avenue du Général Harris, BP 45026, 14 076, Caen, Cedex 05, France. .,UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France. .,Normandy University, UNICAEN, SF Normandy Oncology, US PLATON, ORGAPRED core facility, Caen, France.
| | - Vianney Bastit
- UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France. .,Department of Head and Neck Surgery, UNICANCER, Comprehensive Cancer Center François Baclesse, 3 avenue du Général Harris, Caen, 14000, France.
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11
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Boudry A, Darmon S, Duployez N, Figeac M, Geffroy S, Bucci M, Celli-Lebras K, Duchmann M, Joudinaud R, Fenwarth L, Nibourel O, Goursaud L, Itzykson R, Dombret H, Hunault M, Preudhomme C, Salson M. Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics 2022; 23:533. [PMID: 36494771 PMCID: PMC9732984 DOI: 10.1186/s12859-022-05079-x] [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: 12/13/2022] Open
Affiliation(s)
- Augustin Boudry
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Sasha Darmon
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France ,grid.15140.310000 0001 2175 9188ENS Lyon, Lyon, France
| | - Nicolas Duployez
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Martin Figeac
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Sandrine Geffroy
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Maxime Bucci
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Karine Celli-Lebras
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Matthieu Duchmann
- grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Romane Joudinaud
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Laurène Fenwarth
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Olivier Nibourel
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Laure Goursaud
- grid.410463.40000 0004 0471 8845Hematology Department, CHU LILLE, Lille, France
| | - Raphael Itzykson
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France ,grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Hervé Dombret
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Mathilde Hunault
- grid.7252.20000 0001 2248 3363Univ Angers, Université de Nantes, CHU Angers, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Claude Preudhomme
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Mikaël Salson
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
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12
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Djouina M, Waxin C, Leprêtre F, Tardivel M, Tillement O, Vasseur F, Figeac M, Bongiovanni A, Sebda S, Desreumaux P, Launay D, Dubuquoy L, Body-Malapel M, Vignal C. Gene/environment interaction in the susceptibility of Crohn's disease patients to aluminum. Sci Total Environ 2022; 850:158017. [PMID: 35973536 DOI: 10.1016/j.scitotenv.2022.158017] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND & AIM The key role of environmental factors in the pathogenesis of Inflammatory Bowel Diseases (IBD) is recognized. Aluminum is suspected to be a risk factor for IBD. However, mechanisms linking aluminum exposure to disease development are unknown. We examined the role of aluminum transport and subcellular localisation on human colon susceptibility to aluminum-induced inflammation. METHODS Human colon biopsies isolated from Crohn's disease (CD) or control patients and Caco-2 cells were incubated with aluminum. The effects of aluminum were evaluated on cytokine secretion and transporter expression. The role of aluminum kinetics parameters was studied in Caco-2 using transport inhibitors and in human colon biopsies by assessing genetic polymorphisms of transporters. RESULTS Aluminum exposure was shown to induce cytokine secretion in colon of CD but not healthy patients. In Caco-2 cells, aluminum internalisation was correlated with inflammatory status. In human colon, analysis of genetic polymorphisms and expression of ABCB1 and SLC26A3 transporters showed that their decreased activity was involved in aluminum-induced inflammation. CONCLUSIONS We hypothesize that alteration in detoxifying response would lead to a deregulation of intestinal homeostasis and to the expression of IBD. Our study emphasizes the complexity of gene/environment interaction for aluminum adverse health effect, highlighting at risk populations or subtypes of patients. A better understanding of correlations between gene expression or SNP and xenobiotic kinetics parameters would shift the medical paradigm to more personalized disease management and treatment.
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Affiliation(s)
- Madjid Djouina
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Christophe Waxin
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Meryem Tardivel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Olivier Tillement
- Institut Lumière Matière, Université Claude Bernard Lyon 1, CNRS UMR 5306, 69622 Villeurbanne, France
| | - Francis Vasseur
- Univ. Lille, CHU Lille, ULR 2694-METRICS : Évaluation des technologies de santé et des pratiques médicales, F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Pierre Desreumaux
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Mathilde Body-Malapel
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Cécile Vignal
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France.
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13
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Boudry A, Darmon S, Duployez N, Figeac M, Geffroy S, Bucci M, Celli-Lebras K, Duchmann M, Joudinaud R, Fenwarth L, Nibourel O, Goursaud L, Itzykson R, Dombret H, Hunault M, Preudhomme C, Salson M. Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics 2022; 23:448. [PMID: 36307762 PMCID: PMC9617311 DOI: 10.1186/s12859-022-04983-6] [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: 06/02/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data. RESULTS Our algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. CONCLUSION FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r . The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.
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Affiliation(s)
- Augustin Boudry
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Sasha Darmon
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France ,grid.15140.310000 0001 2175 9188ENS Lyon, Lyon, France
| | - Nicolas Duployez
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Martin Figeac
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Sandrine Geffroy
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Maxime Bucci
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Karine Celli-Lebras
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Duchmann
- grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Romane Joudinaud
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Laurène Fenwarth
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Olivier Nibourel
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Laure Goursaud
- grid.410463.40000 0004 0471 8845Hematology Department, CHU LILLE, Lille, France
| | - Raphael Itzykson
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France ,grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Hervé Dombret
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Mathilde Hunault
- grid.7252.20000 0001 2248 3363Univ Angers, Université de Nantes, CHU Angers, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Claude Preudhomme
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Mikaël Salson
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
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14
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Smol T, Brunelle P, Caumes R, Boute-Benejean O, Thuillier C, Figeac M, Ait-Yahya E, Bonte F, Mau-Them FT, Thauvin-Robinet C, Faivre L, Roche-Lestienne C, Manouvrier-Hanu S, Petit F, Ghoumid J. TRIT1 deficiency: Two novel patients with four novel variants. Eur J Med Genet 2022; 65:104603. [PMID: 36049610 DOI: 10.1016/j.ejmg.2022.104603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
TRIT1 encodes a tRNA isopentenyl transferase that allows a strong interaction between the mini helix and the codon. Recent reports support the TRIT1 bi-allelic alterations as the cause of an autosomal recessive disorder, named combined oxydative phophorylation deficiency 35, with microcephaly, developmental disability, and epilepsy. The phenotype is due to decreased mitochondrial function, with deficit of i6A37 in cytosolic and mitochondrial tRNA. Only 10 patients have been reported. We report on two new patients with four novel variants, and confirm the published clinical TRIT1 deficient phenotype stressing the possibility of both very severe, with generalized pharmaco-resistant seizures, and mild phenotypes.
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Affiliation(s)
- Thomas Smol
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Institut de Génaffnoétique Médicale, F-59000, Lille, France
| | - Perrine Brunelle
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Institut de Génaffnoétique Médicale, F-59000, Lille, France
| | - Roseline Caumes
- CHU Lille, Clinique de Génétique « Guy Fontaine », F-59000, Lille, France
| | - Odile Boute-Benejean
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique « Guy Fontaine », F-59000, Lille, France
| | | | - Martin Figeac
- Université de Lille, Functional and Structural Plaform, F-59000, Lille, France
| | - Emilie Ait-Yahya
- Université de Lille, Functional and Structural Plaform, F-59000, Lille, France
| | - Fabrice Bonte
- Université de Lille, Functional and Structural Plaform, F-59000, Lille, France
| | - Frederic Tran Mau-Them
- CHU Dijon, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, F-21000, Dijon, France; Université de Bourgogne Franche-Comté, UMR Inserm 1231 Génétique des Anomalies du Développement, F-21000, Dijon, France; Unité Fonctionnelle 6254 d'Innovation en diagnostique génomique des Maladies Rares, CHU, Dijon, France
| | - Christel Thauvin-Robinet
- CHU Dijon, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, F-21000, Dijon, France; Université de Bourgogne Franche-Comté, UMR Inserm 1231 Génétique des Anomalies du Développement, F-21000, Dijon, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU, Dijon, France
| | - Laurence Faivre
- CHU Dijon, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, F-21000, Dijon, France; Université de Bourgogne Franche-Comté, UMR Inserm 1231 Génétique des Anomalies du Développement, F-21000, Dijon, France; Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU, Dijon, France
| | | | - Sylvie Manouvrier-Hanu
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique « Guy Fontaine », F-59000, Lille, France
| | - Florence Petit
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique « Guy Fontaine », F-59000, Lille, France
| | - Jamal Ghoumid
- Univ Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique « Guy Fontaine », F-59000, Lille, France.
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15
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Ledoult E, Jendoubi M, Collet A, Guerrier T, Largy A, Speca S, Vivier S, Bray F, Figeac M, Hachulla E, Labalette M, Leprêtre F, Sebda S, Sanges S, Rolando C, Sobanski V, Dubucquoi S, Launay D. Simple gene signature to assess murine fibroblast polarization. Sci Rep 2022; 12:11748. [PMID: 35817787 PMCID: PMC9273630 DOI: 10.1038/s41598-022-15640-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 02/11/2022] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
We provide an original multi-stage approach identifying a gene signature to assess murine fibroblast polarization. Prototypic polarizations (inflammatory/fibrotic) were induced by seeded mouse embryonic fibroblasts (MEFs) with TNFα or TGFß1, respectively. The transcriptomic and proteomic profiles were obtained by RNA microarray and LC-MS/MS. Gene Ontology and pathways analysis were performed among the differentially expressed genes (DEGs) and proteins (DEPs). Balb/c mice underwent daily intradermal injections of HOCl (or PBS) as an experimental murine model of inflammation-mediated fibrosis in a time-dependent manner. As results, 1456 and 2215 DEGs, and 289 and 233 DEPs were respectively found in MEFs in response to TNFα or TGFß1, respectively. Among the most significant pathways, we combined 26 representative genes to encompass the proinflammatory and profibrotic polarizations of fibroblasts. Based on principal component analysis, this signature deciphered baseline state, proinflammatory polarization, and profibrotic polarization as accurately as RNA microarray and LC-MS/MS did. Then, we assessed the gene signature on dermal fibroblasts isolated from the experimental murine model. We observed a proinflammatory polarization at day 7, and a mixture of a proinflammatory and profibrotic polarizations at day 42 in line with histological findings. Our approach provides a small-size and convenient gene signature to assess murine fibroblast polarization.
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Affiliation(s)
- Emmanuel Ledoult
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France. .,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France. .,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France.
| | - Manel Jendoubi
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France
| | - Aurore Collet
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France
| | - Thomas Guerrier
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Laboratoire d'Immunologie, Pole Biologie et d'Anatomopathologie, CHU Lille, 59000, Lille, France
| | - Alexis Largy
- INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France
| | - Silvia Speca
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France
| | - Solange Vivier
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France
| | - Fabrice Bray
- CNRS, UAR 3290 - MSAP - Miniaturisation Pour La Synthèse, Univ. Lille, l'Analyse et la Protéomique, 59000, Lille, France
| | - Martin Figeac
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Univ. Lille, 59000, Lille, France
| | - Eric Hachulla
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France
| | - Myriam Labalette
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Laboratoire d'Immunologie, Pole Biologie et d'Anatomopathologie, CHU Lille, 59000, Lille, France
| | - Frédéric Leprêtre
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Univ. Lille, 59000, Lille, France
| | - Shéhérazade Sebda
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Univ. Lille, 59000, Lille, France
| | - Sébastien Sanges
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France
| | - Christian Rolando
- CNRS, UAR 3290 - MSAP - Miniaturisation Pour La Synthèse, Univ. Lille, l'Analyse et la Protéomique, 59000, Lille, France.,Shrieking Sixties, 1-3 Allée Lavoisier, 59650, Villeneuve-d'Ascq, France
| | - Vincent Sobanski
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France.,Institut Universitaire de France (IUF), 75005, Paris, France
| | - Sylvain Dubucquoi
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Laboratoire d'Immunologie, Pole Biologie et d'Anatomopathologie, CHU Lille, 59000, Lille, France
| | - David Launay
- Inserm, U1286, 4Ème Étage Centre, Place Verdun, 59000, Lille, France.,INFINITE - Institute for Translational Research in Inflammation, Univ. Lille, 59000, Lille, France.,Service de Médecine Interne et d'Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, 59000, Lille, France
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16
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Chepy A, Vivier S, Bray F, Ternynck C, Meneboo JP, Figeac M, Filiot A, Guilbert L, Jendoubi M, Rolando C, Launay D, Dubucquoi S, Marot G, Sobanski V. Effects of Immunoglobulins G From Systemic Sclerosis Patients in Normal Dermal Fibroblasts: A Multi-Omics Study. Front Immunol 2022; 13:904631. [PMID: 35844491 PMCID: PMC9276964 DOI: 10.3389/fimmu.2022.904631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Autoantibodies (Aabs) are frequent in systemic sclerosis (SSc). Although recognized as potent biomarkers, their pathogenic role is debated. This study explored the effect of purified immunoglobulin G (IgG) from SSc patients on protein and mRNA expression of dermal fibroblasts (FBs) using an innovative multi-omics approach. Dermal FBs were cultured in the presence of sera or purified IgG from patients with diffuse cutaneous SSc (dcSSc), limited cutaneous SSc or healthy controls (HCs). The FB proteome and transcriptome were explored using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and microarray assays, respectively. Proteomic analysis identified 3,310 proteins. SSc sera and purified IgG induced singular protein profile patterns. These FB proteome changes depended on the Aab serotype, with a singular effect observed with purified IgG from anti-topoisomerase-I autoantibody (ATA) positive patients compared to HC or other SSc serotypes. IgG from ATA positive SSc patients induced enrichment in proteins involved in focal adhesion, cadherin binding, cytosolic part, or lytic vacuole. Multi-omics analysis was performed in two ways: first by restricting the analysis of the transcriptomic data to differentially expressed proteins; and secondly, by performing a global statistical analysis integrating proteomics and transcriptomics. Transcriptomic analysis distinguished 764 differentially expressed genes and revealed that IgG from dcSSc can induce extracellular matrix (ECM) remodeling changes in gene expression profiles in FB. Global statistical analysis integrating proteomics and transcriptomics confirmed that IgG from SSc can induce ECM remodeling and activate FB profiles. This effect depended on the serotype of the patient, suggesting that SSc Aab might play a pathogenic role in some SSc subsets.
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Affiliation(s)
- Aurélien Chepy
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
| | - Solange Vivier
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, USR 3290, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Camille Ternynck
- Univ. Lille, CHU Lille, ULR 2694, METRICS: Évaluation des Technologies de Santé et des Pratiques Médicales, Lille, France
| | - Jean-Pascal Meneboo
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
| | - Martin Figeac
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
| | - Alexandre Filiot
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Lucile Guilbert
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Lille, France
| | - Manel Jendoubi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
- *Correspondence: David Launay,
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Lille, France
| | - Guillemette Marot
- Univ. Lille, CHU Lille, ULR 2694, METRICS: Évaluation des Technologies de Santé et des Pratiques Médicales, Lille, France
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
- Inria, Models for Data Analysis and Learning, Lille, France
| | - Vincent Sobanski
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
- Institut Universitaire de France, Paris, France
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17
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Mopin A, Leprêtre F, Sebda S, Villenet C, Ben Khoud M, Figeac M, Quesnel B, Brinster C. Detection of residual and chemoresistant leukemic cells in an immune-competent mouse model of acute myeloid leukemia: Potential for unravelling their interactions with immunity. PLoS One 2022; 17:e0267508. [PMID: 35486629 PMCID: PMC9053800 DOI: 10.1371/journal.pone.0267508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/08/2022] [Indexed: 11/23/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by blocked differentiation and extensive proliferation of hematopoietic progenitors/precursors. Relapse is often observed after chemotherapy due to the presence of residual leukemic cells, which is also called minimal residual disease (MRD). Subclonal heterogeneity at diagnosis was found to be responsible for MRD after treatment. Patient xenograft mouse models are valuable tools for studying MRD after chemotherapy; however, the contribution of the immune system in these models is usually missing. To evaluate its role in leukemic persistence, we generated an immune-competent AML mouse model of persistence after chemotherapy treatment. We used well-characterized (phenotypically and genetically) subclones of the murine C1498 cell line stably expressing the ZsGreen reporter gene and the WT1 protein, a valuable antigen. Accordingly, these subclones were also selected due to their in vitro aracytidine (Ara-c) sensitivity. A combination of 3 subclones (expressing or not expressing WT1) was found to lead to prolonged mouse survival after Ara-c treatment (as long as 150 days). The presence of residual leukemic cells in the blood and BM of surviving mice indicated their persistence. Thus, a new mouse model that may offer insights into immune contributions to leukemic persistence was developed.
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Affiliation(s)
- Alexia Mopin
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
- Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, UAR2014 - US 41 - Plateformes Lilloises en Biologie & Santé- Plateau de génomique fonctionnelle, Centre de biologie Pathologie Génétique - CHU Lille, Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, UAR2014 - US 41 - Plateformes Lilloises en Biologie & Santé- Plateau de génomique fonctionnelle, Centre de biologie Pathologie Génétique - CHU Lille, Lille, France
| | - Céline Villenet
- Univ. Lille, UAR2014 - US 41 - Plateformes Lilloises en Biologie & Santé- Plateau de génomique fonctionnelle, Centre de biologie Pathologie Génétique - CHU Lille, Lille, France
| | - Meriem Ben Khoud
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
- Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Martin Figeac
- Univ. Lille, UAR2014 - US 41 - Plateformes Lilloises en Biologie & Santé- Plateau de génomique fonctionnelle, Centre de biologie Pathologie Génétique - CHU Lille, Lille, France
| | - Bruno Quesnel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
- Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Carine Brinster
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
- Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
- * E-mail:
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18
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Puy L, Perbet R, Figeac M, Duchêne B, Deramecourt V, Cordonnier C, Bérézowski V. Brain Peri-Hematomal Area, a Strategic Interface for Blood Clearance: A Human Neuropathological and Transcriptomic Study. Stroke 2022; 53:2026-2035. [DOI: 10.1161/strokeaha.121.037751] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Enhancing the blood clearance process is a promising therapeutic strategy for intracerebral hemorrhage (ICH). We aimed to investigate the kinetic of this process after ICH in human brain tissue through the monocyte-macrophage scavenger receptor (CD163)/HO-1 (hemoxygenase-1) pathway.
Methods:
We led a cross-sectional post-mortem study including 22 consecutive ICH cases (2005–2019) from the Lille Neurobank. Cases were grouped according to the time of death: ≤72 hours, 4 to 7 days, 8 to 15 days, 16 to 90 days, and >90 days after ICH onset. Paraffin-embedded tissue was extracted from 4 strategic areas, including hematoma core and peri-hematomal area to perform histological investigations. Additionally, we extracted RNA from the peri-hematomal area of 6 cases to perform transcriptomic analysis.
Results:
We included 19 ICH cases (median age: 79 [71–89] years; median delay ICH-death: 13 [5–41] days). The peri-hematomal area concentrated most of reactive microglia, CD163/HO-1 and iron deposits as compared with other brain areas. We found a surge in the blood clearance process from day 8 to day 15 after ICH onset. Transcriptomic analysis showed that HO-1 was the most upregulated gene (2.81±0.39, adjusted
P
=1.11×10
–10
) and CD163 the sixth (1.49±0.29, adjusted
P
=1.68×10
–
5
). We also identified several upregulated genes that exert a beneficial role in terminating inflammation and enhancing tissue repair.
Conclusions:
We provide histological and transcriptomic-based evidence in humans for the key role of peri-hematomal area in endogenous blood clearance process through the CD163/HO-1 pathway, especially from day 8 after ICH and favored by an anti-inflammatory environment. Our findings contribute to identify innovative therapeutic strategies for ICH.
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Affiliation(s)
- Laurent Puy
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
| | - Romain Perbet
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
- Alzheimer Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown (R.P.)
- Harvard Medical School, Boston, MA (R.P.)
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, France (M.F.)
| | - Bélinda Duchêne
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France (B.D.)
| | - Vincent Deramecourt
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
- Université d’Artois, Lens, France (V.B.)
| | - Charlotte Cordonnier
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
| | - Vincent Bérézowski
- Univ. Lille, Inserm, CHU-Lille, Lille Neuroscience & Cognition research Center UMR-S1172, Degenerative and Vascular Cognitive Disorders, France (L.P., R.P., V.D., C.C., V.B.)
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19
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Salvador F, Deramoudt L, Leprêtre F, Figeac M, Guerrier T, Boucher J, Bas M, Journiac N, Peters A, Mars LT, Zéphir H. A Spontaneous Model of Experimental Autoimmune Encephalomyelitis Provides Evidence of MOG-Specific B Cell Recruitment and Clonal Expansion. Front Immunol 2022; 13:755900. [PMID: 35185870 PMCID: PMC8850296 DOI: 10.3389/fimmu.2022.755900] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/11/2022] [Indexed: 01/02/2023] Open
Abstract
The key role of B cells in the pathophysiology of multiple sclerosis (MS) is supported by the presence of oligoclonal bands in the cerebrospinal fluid, by the association of meningeal ectopic B cell follicles with demyelination, axonal loss and reduction of astrocytes, as well as by the high efficacy of B lymphocyte depletion in controlling inflammatory parameters of MS. Here, we use a spontaneous model of experimental autoimmune encephalomyelitis (EAE) to study the clonality of the B cell response targeting myelin oligodendrocyte glycoprotein (MOG). In particular, 94% of SJL/j mice expressing an I-As: MOG92-106 specific transgenic T cell receptor (TCR1640) spontaneously develop a chronic paralytic EAE between the age of 60-500 days. The immune response is triggered by the microbiota in the gut-associated lymphoid tissue, while there is evidence that the maturation of the autoimmune demyelinating response might occur in the cervical lymph nodes owing to local brain drainage. Using MOG-protein-tetramers we tracked the autoantigen-specific B cells and localized their enrichment to the cervical lymph nodes and among the brain immune infiltrate. MOG-specific IgG1 antibodies were detected in the serum of diseased TCR1640 mice and proved pathogenic upon adoptive transfer into disease-prone recipients. The ontogeny of the MOG-specific humoral response preceded disease onset coherent with their contribution to EAE initiation. This humoral response was, however, not sufficient for disease induction as MOG-antibodies could be detected at the age of 69 days in a model with an average age of onset of 197 days. To assess the MOG-specific B cell repertoire we FACS-sorted MOG-tetramer binding cells and clonally expand them in vitro to sequence the paratopes of the IgG heavy chain and kappa light chains. Despite the fragility of clonally expanding MOG-tetramer binding effector B cells, our results indicate the selection of a common CDR-3 clonotype among the Igk light chains derived from both disease-free and diseased TCR1640 mice. Our study demonstrates the pre-clinical mobilization of the MOG-specific B cell response within the brain-draining cervical lymph nodes, and reiterates that MOG antibodies are a poor biomarker of disease onset and progression.
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Affiliation(s)
- Florent Salvador
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Laure Deramoudt
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Frédéric Leprêtre
- UMS2014-US51, Genomics and Structural Platform, Lille University, Lille, France
| | - Martin Figeac
- UMS2014-US51, Genomics and Structural Platform, Lille University, Lille, France
| | - Thomas Guerrier
- Univ. Lille, Inserm, CHU Lille, U1286, INFINITE-Institute for Translational Research in Inflammation, Lille, France
| | - Julie Boucher
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Mathilde Bas
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Nathalie Journiac
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Anneli Peters
- Institute of Clinical Neuroimmunology, Hospital and Biomedical Center of the Ludwig-Maximilian University (LMU), Martinsried, Germany
| | - Lennart T Mars
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France
| | - Hélène Zéphir
- Univ. Lille, Inserm, CHU Lille, Laboratory of Neuroinflammation and Multiple Sclerosis (NEMESIS), UMR-S1172, Lille Neuroscience & Cognition, LICEND, FHU Imminent, Lille, France.,Institute of Clinical Neuroimmunology, Hospital and Biomedical Center of the Ludwig-Maximilian University (LMU), Martinsried, Germany.,CRC-SEP of Lille, CHU of Lille, Lille, France
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20
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Touil Y, Latreche-Carton C, Bouazzati HE, Nugues AL, Jouy N, Thuru X, Laine W, Lepretre F, Figeac M, Tardivel M, Kluza J, Idziorek T, Quesnel B. p65/RelA NF-κB fragments generated by RIPK3 activity regulate tumorigenicity, cell metabolism, and stemness characteristics. J Cell Biochem 2021; 123:543-556. [PMID: 34927768 PMCID: PMC9299825 DOI: 10.1002/jcb.30198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/17/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Receptor‐interacting protein kinase 3 (RIPK3) can induce necroptosis, apoptosis, or cell proliferation and is silenced in several hematological malignancies. We previously reported that RIPK3 activity independent of its kinase domain induces caspase‐mediated p65/RelA cleavage, resulting in N‐terminal 1‐361 and C‐terminal 362‐549 fragments. We show here that a noncleavable p65/RelA D361E mutant expressed in DA1‐3b leukemia cells decreases mouse survival times and that coexpression of p65/RelA fragments increases the tumorigenicity of B16F1 melanoma cells. This aggressiveness in vivo did not correlate with NF‐κB activity measured in vitro. The fragments and p65/RelA D361E mutant induced different expression profiles in DA1‐3b and B16F1 cells. Stemness markers were affected: p65/RelA D361E increased ALDH activity in DA1‐3b cells, and fragment expression increased melanoma sphere formation in B16/F1 cells. p65/RelA fragments and the D361E noncleavable mutant decreased oxidative or glycolytic cell metabolism, with differences observed between models. Thus, p65/RelA cleavage initiated by kinase‐independent RIPK3 activity in cancer cells is not neutral and induces pleiotropic effects in vitro and in vivo that may vary across tumor types.
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Affiliation(s)
- Yasmine Touil
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Céline Latreche-Carton
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Hassiba El Bouazzati
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Anne-Lucie Nugues
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Nathalie Jouy
- UMS 2014 CNRS/US 41 Inserm, University of Lille, Lille, France
| | - Xavier Thuru
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - William Laine
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | | | - Martin Figeac
- UMS 2014 CNRS/US 41 Inserm, University of Lille, Lille, France
| | - Meryem Tardivel
- UMS 2014 CNRS/US 41 Inserm, University of Lille, Lille, France
| | - Jérôme Kluza
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Thierry Idziorek
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France
| | - Bruno Quesnel
- CANTHER, UMR 1277 Inserm - 9020 CNRS, University of Lille, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, UMR 1277 Inserm - 9020 CNRS, Lille, France.,Service des Maladies du Sang, CHU Lille, Lille, France
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21
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Casilag F, Matarazzo L, Franck S, Figeac M, Michelet R, Kloft C, Carnoy C, Sirard JC. The Biosynthetic Monophosphoryl Lipid A Enhances the Therapeutic Outcome of Antibiotic Therapy in Pneumococcal Pneumonia. ACS Infect Dis 2021; 7:2164-2175. [PMID: 34260199 DOI: 10.1021/acsinfecdis.1c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alternative treatment strategies against bacterial infections are required to decrease the use of antibiotics. This study tested the hypothesis that stimulation of the innate immune receptor Toll-like receptor 4 can be combined with antibiotics to improve the treatment of invasive pneumonia. The efficacy of the biosynthetic monophosphoryl lipid A (MPLA), a clinically approved Toll-like receptor 4 activator, was tested in a mouse model of Streptococcus pneumoniae respiratory infection. Interestingly, administration of amoxicillin or MPLA decreased 400- to 11 000-fold the bacterial load in the lungs and spleen but did not enhance survival compared to mock treatment. The single administration of a combination of MPLA and amoxicillin further reduced 10- to 18-fold the bacterial colonization and invasion and significantly improved protection against lethal disease. The combined administration of MPLA and amoxicillin in a context of infection was associated with transient increase of the serum concentrations of amoxicillin and pro-inflammatory cytokines and chemokines as well as the expression of immune genes in lung tissue. Remarkably, the systemic and lung immune activation extended beyond amoxicillin elimination, suggesting a two-step and cooperative anti-infective effect, i.e., rapid antibiotic-mediated alteration of bacteria and a long-lasting impact through mucosal and systemic immunity. Our proof-of-concept study demonstrated for the first time that boosting Toll-like receptor 4 signaling can synergize with antibiotics in order to increase the efficacy of therapy of bacterial pneumonia, thereby in fine reducing the dose or regimen of antibiotics.
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Affiliation(s)
- Fiordiligie Casilag
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Laura Matarazzo
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sebastian Franck
- Freie Universitaet Berlin, Institute of Pharmacy, Department of Clinical Pharmacy & Biochemistry, D-12169 Berlin, Germany
| | - Martin Figeac
- Univ. Lille, Plateforme de Génomique Fonctionnelle et Structurale, F-59000 Lille, France
| | - Robin Michelet
- Freie Universitaet Berlin, Institute of Pharmacy, Department of Clinical Pharmacy & Biochemistry, D-12169 Berlin, Germany
| | - Charlotte Kloft
- Freie Universitaet Berlin, Institute of Pharmacy, Department of Clinical Pharmacy & Biochemistry, D-12169 Berlin, Germany
| | - Christophe Carnoy
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jean-Claude Sirard
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
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22
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Wambecke A, Ahmad M, Morice PM, Lambert B, Weiswald LB, Vernon M, Vigneron N, Abeilard E, Brotin E, Figeac M, Gauduchon P, Poulain L, Denoyelle C, Meryet-Figuiere M. The lncRNA 'UCA1' modulates the response to chemotherapy of ovarian cancer through direct binding to miR-27a-5p and control of UBE2N levels. Mol Oncol 2021; 15:3659-3678. [PMID: 34160887 PMCID: PMC8637575 DOI: 10.1002/1878-0261.13045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 06/22/2021] [Indexed: 01/28/2023] Open
Abstract
Ovarian cancer (OC) is the leading cause of death in patients with gynecologic cancers. Due to late diagnosis and resistance to chemotherapy, the 5‐year survival rate in patients with OC is below 40%. We observed that UCA1, a lncRNA previously reported to play an oncogenic role in several malignancies, is overexpressed in the chemoresistant OC cell line OAW42‐R compared to their chemotherapy‐sensitive counterpart OAW42. Additionally, UCA1 overexpression was related to poor prognosis in two independent patient cohorts. Currently, the molecular mechanisms through which UCA1 acts in OC are poorly understood. We demonstrated that downregulation of the short isoform of UCA1 sensitized OC cells to cisplatin and that UCA1 acted as competing endogenous RNA to miR‐27a‐5p. Upon UCA1 downregulation, miR‐27a‐5p downregulated its direct target UBE2N leading to the upregulation of BIM, a proapoptotic protein of the Bcl2 family. The upregulation of BIM is the event responsible for the sensitization of OC cells to cisplatin. In order to model response to therapy in patients with OC, we used several patient‐derived organoid cultures, a model faithfully mimicking patient’s response to therapy. Inhibition of UBE2N sensitized patient‐derived organoids to platinum salts. In conclusion, response to treatment in patients with OC is regulated by the UCA1/miR‐27a‐5p/UBE2N axis, where UBE2N inhibition could potentially represent a novel therapeutic strategy to counter chemoresistance in OC.
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Affiliation(s)
- Anaïs Wambecke
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Mohammad Ahmad
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Pierre-Marie Morice
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Bernard Lambert
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France.,CNRS, Normandy Regional Delegation, Caen, France
| | - Louis-Bastien Weiswald
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Mégane Vernon
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Nicolas Vigneron
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Edwige Abeilard
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Emilie Brotin
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France.,ImpedanCELL Core Facility, Federative Structure 4206 ICORE, UNICAEN, Caen, France
| | - Martin Figeac
- Functional and structural genomics platform, Institute for Cancer Research, Lille Univ, France
| | - Pascal Gauduchon
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Laurent Poulain
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Christophe Denoyelle
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France.,ImpedanCELL Core Facility, Federative Structure 4206 ICORE, UNICAEN, Caen, France
| | - Matthieu Meryet-Figuiere
- UNICAEN, Inserm U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie Univ, Caen, France.,Cancer Centre François Baclesse, UNICANCER, Caen, France
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23
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Pérès L, Monedero Alonso D, Nudel M, Figeac M, Bruge J, Sebda S, Picard V, El Nemer W, Preudhomme C, Rose C, Egée S, Bouyer G. Characterisation of Asp669Tyr Piezo1 cation channel activity in red blood cells: an unexpected phenotype. Br J Haematol 2021; 194:e51-e55. [PMID: 33973227 DOI: 10.1111/bjh.17467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Laurent Pérès
- Sorbonne Université, CNRS, UMR8227, Station Biologique de Roscoff, Roscoff, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - David Monedero Alonso
- Sorbonne Université, CNRS, UMR8227, Station Biologique de Roscoff, Roscoff, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Morgane Nudel
- Hôpital Saint Vincent de Paul, Université Catholique, Lille, France
| | - Martin Figeac
- Univ-Lille, Plate-forme de Génomique Fonctionnelle et Structurale, Lille, France.,CHU Lille, cellule bioinformatique, plateau commun de séquençage, Lille, France
| | - Judith Bruge
- Hôpital Saint Vincent de Paul, Université Catholique, Lille, France
| | - Shéhérazade Sebda
- Univ-Lille, Plate-forme de Génomique Fonctionnelle et Structurale, Lille, France
| | | | - Wassim El Nemer
- Inserm, UMR_S 1134, Institut National de la Transfusion Sanguine INTS, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Claude Preudhomme
- Univ-Lille, Plate-forme de Génomique Fonctionnelle et Structurale, Lille, France
| | - Christian Rose
- Hôpital Saint Vincent de Paul, Université Catholique, Lille, France
| | - Stéphane Egée
- Sorbonne Université, CNRS, UMR8227, Station Biologique de Roscoff, Roscoff, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Guillaume Bouyer
- Sorbonne Université, CNRS, UMR8227, Station Biologique de Roscoff, Roscoff, France.,Laboratoire d'Excellence GR-Ex, Paris, France
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24
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Galiègue‐Zouitina S, Fu Q, Carton‐Latreche C, Poret N, Cheok M, Leprêtre F, Figeac M, Quesnel B, El Bouazzati H, Shelley CS. Bimodal expression of
RHOH
during myelomonocytic differentiation: Implications for the expansion of AML differentiation therapy. eJHaem 2021; 2:196-210. [PMID: 35845268 PMCID: PMC9175762 DOI: 10.1002/jha2.128] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/09/2020] [Accepted: 10/26/2020] [Indexed: 11/06/2022]
Abstract
RhoH is an unusual member of the Rho family of small GTP‐binding proteins in that it lacks GTPase activity. Since the RhoH protein is constantly bound by GTP, it is constitutively active and controlled predominantly by changes in quantitative expression. Abnormal levels of RHOH gene transcripts have been linked to a range of malignancies including acute myeloid leukemia (AML). One of the hallmarks of AML is a block in the normal program of myeloid differentiation. Here we investigate how myeloid differentiation is controlled by the quantitative expression of RHOH. Our analysis demonstrates that increasingly mature myeloid cells express progressively lower levels of RHOH. However, as monocytic myeloid cells terminally differentiate into macrophages, RHOH expression is up‐regulated. This up‐regulation is not apparent in AML where myeloid differentiation is blocked at stages of low RHOH expression. Nevertheless, when the up‐regulation of RHOH is forced, then terminal macrophage differentiation is induced and the Cdc42 and Wnt intracellular signalling pathways are repressed. These results indicate that RHOH induction is a driver of terminal differentiation and might represent a means of effecting AML differentiation therapy. The potential of this therapeutic strategy is supported by forced up‐regulation of RHOH reducing the ability of AML cells to produce tumours in vivo.
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Affiliation(s)
- Sylvie Galiègue‐Zouitina
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
| | - Qiangwei Fu
- California Institute for Biomedical Research La Jolla California USA
| | - Céline Carton‐Latreche
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
| | - Nicolas Poret
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
| | - Meyling Cheok
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
- Canther UMR 1277 Inserm‐9020 CNRS Lille University Lille France
| | - Frédéric Leprêtre
- UMS 2014 ‐ US 41 Plateau de Génomique Fonctionnelle et Structurale Lille University Lille France
| | - Martin Figeac
- UMS 2014 ‐ US 41 Plateau de Génomique Fonctionnelle et Structurale Lille University Lille France
| | - Bruno Quesnel
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
- Canther UMR 1277 Inserm‐9020 CNRS Lille University Lille France
- CHU Lille Service des Maladies du Sang Lille France
| | - Hassiba El Bouazzati
- JPARC UMRS 1172 Inserm Lille University Lille France
- Place de Verdun Institut pour la Recherche sur le Cancer de Lille Lille Cedex France
- Canther UMR 1277 Inserm‐9020 CNRS Lille University Lille France
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25
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Dessein R, Bauduin M, Grandjean T, Le Guern R, Figeac M, Beury D, Faure K, Faveeuw C, Guery B, Gosset P, Kipnis E. Antibiotic-related gut dysbiosis induces lung immunodepression and worsens lung infection in mice. Crit Care 2020; 24:611. [PMID: 33076936 PMCID: PMC7574210 DOI: 10.1186/s13054-020-03320-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gut dysbiosis due to the adverse effects of antibiotics affects outcomes of lung infection. Previous murine models relied on significant depletion of both gut and lung microbiota, rendering the analysis of immune gut-lung cross-talk difficult. Here, we study the effects of antibiotic-induced gut dysbiosis without lung dysbiosis on lung immunity and the consequences on acute P. aeruginosa lung infection. METHODS C57BL6 mice received 7 days oral vancomycin-colistin, followed by normal regimen or fecal microbial transplant or Fms-related tyrosine kinase 3 ligand (Flt3-Ligand) over 2 days, and then intra-nasal P. aeruginosa strain PAO1. Gut and lung microbiota were studied by next-generation sequencing, and lung infection outcomes were studied at 24 h. Effects of vancomycin-colistin on underlying immunity and bone marrow progenitors were studied in uninfected mice by flow cytometry in the lung, spleen, and bone marrow. RESULTS Vancomycin-colistin administration induces widespread cellular immunosuppression in both the lung and spleen, decreases circulating hematopoietic cytokine Flt3-Ligand, and depresses dendritic cell bone marrow progenitors leading to worsening of P. aeruginosa lung infection outcomes (bacterial loads, lung injury, and survival). Reversal of these effects by fecal microbial transplant shows that these alterations are related to gut dysbiosis. Recombinant Flt3-Ligand reverses the effects of antibiotics on subsequent lung infection. CONCLUSIONS These results show that gut dysbiosis strongly impairs monocyte/dendritic progenitors and lung immunity, worsening outcomes of P. aeruginosa lung infection. Treatment with a fecal microbial transplant or immune stimulation by Flt3-Ligand both restore lung cellular responses to and outcomes of P. aeruginosa following antibiotic-induced gut dysbiosis.
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Affiliation(s)
- Rodrigue Dessein
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Marvin Bauduin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Teddy Grandjean
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Rémi Le Guern
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Martin Figeac
- CHU Lille, Institut Pasteur de Lille, Inserm, CNRS, UMR2014-US41-PLBS-6 Plateformes Lilloises de Biologie & Santé, University Lille, F-59000, Lille, France
| | - Delphine Beury
- CHU Lille, Institut Pasteur de Lille, Inserm, CNRS, UMR2014-US41-PLBS-6 Plateformes Lilloises de Biologie & Santé, University Lille, F-59000, Lille, France
| | - Karine Faure
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Christelle Faveeuw
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Benoit Guery
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe Gosset
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France
| | - Eric Kipnis
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France, University Lille, F-59000, Lille, France.
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26
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Fernandes M, Jamme P, Paget S, Morabito A, Leprêtre F, Figeac M, Descarpentries C, Escande F, Baldacci S, Chotteau-Lelièvre A, Grumolato L, Copin MC, Kherrouche Z, Cortot AB, Tulasne D. Abstract 3683: MET exon 14 skipping mutations in lung cancer: Screening, functional and clinical impact. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3683] [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
Mutations affecting exon 14 splice sites of the gene encoding the MET receptor have been recently revealed in non-small cell lung cancer (NSCLC). These mutations induce MET exon 14 skipping (METex14), leading to receptor activation through deletion of a regulatory domain. Importantly, these mutations represent a promising therapeutic opportunity since MET tyrosine kinase inhibitors (TKI) are available. Nevertheless, these mutations raise several scientific and clinical questions. (i) Their functional consequences are still poorly understood,(ii) these mutations are highly heterogeneous which makes them difficult to detect, and (iii) efficacy of MET-TKI seems limited by largely unknown resistances. To address these issues, we first created by genome editing a panel of pulmonary cells expressing either METex14 or MET receptor mutated in each known active site of the regulatory domain. Comparison of signalling pathways, transcriptional landscapes and cellular responses revealed that METex14 activation is recapitulated by mutation of the CBL binding site involved in MET internalization, but provide also an unexpected resistance to apoptosis through abrogating its caspase cleavage. Second, in order to detect METex14 mutations in clinical routine practice, we developed an optimized targeted next generation sequencing panel covering the METex14 in addition to the usual targets. This panel revealed METex14 alterations in 2.2% NSCLC patients and presence of various concurrent alterations. Third, by further characterization of the concurrent alterations, we found high rate of PI3K pathway alterations in METex14 patients. In addition, MET-TKI treatment in 3 patients harboring these alterations had shown progressive disease, suggesting their involvement in resistance. Using a patient-derived cell line with primary resistance and cell lines in which MET or PI3K alterations were inserted, we confirmed involvement of PI3K activation in the resistance process, which was overcome with PI3K inhibitor. Overall, our integrated study reveals that METex14 mutations induce an original activation involving cooperation between regulatory mechanisms, but offering sensitivity to MET-TKI. Therefore, these mutations, now detectable in routine practice, are druggable by MET-TKI providing a novel therapeutic line for NSCLC, but have to face to innate resistance including PI3K alterations.
Citation Format: Marie Fernandes, Philippe Jamme, Sonia Paget, Angela Morabito, Frédéric Leprêtre, Martin Figeac, Clotilde Descarpentries, Fabienne Escande, Simon Baldacci, Anne Chotteau-Lelièvre, Luca Grumolato, Marie-Christine Copin, Zoulika Kherrouche, Alexis B. Cortot, David Tulasne. MET exon 14 skipping mutations in lung cancer: Screening, functional and clinical impact [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3683.
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Affiliation(s)
- Marie Fernandes
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
| | - Philippe Jamme
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
| | - Sonia Paget
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
| | - Angela Morabito
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
| | | | | | | | | | | | | | | | | | - Zoulika Kherrouche
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
| | | | - David Tulasne
- 1CNRS, INSERM, University of Lille, Institut Pasteur de Lille, Lille, France
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27
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Keo A, Mahfouz A, Ingrassia AMT, Meneboo JP, Villenet C, Mutez E, Comptdaer T, Lelieveldt BPF, Figeac M, Chartier-Harlin MC, van de Berg WDJ, van Hilten JJ, Reinders MJT. Transcriptomic signatures of brain regional vulnerability to Parkinson's disease. Commun Biol 2020; 3:101. [PMID: 32139796 PMCID: PMC7058608 DOI: 10.1038/s42003-020-0804-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/28/2020] [Indexed: 01/11/2023] Open
Abstract
The molecular mechanisms underlying caudal-to-rostral progression of Lewy body pathology in Parkinson's disease remain poorly understood. Here, we identified transcriptomic signatures across brain regions involved in Braak Lewy body stages in non-neurological adults from the Allen Human Brain Atlas. Among the genes that are indicative of regional vulnerability, we found known genetic risk factors for Parkinson's disease: SCARB2, ELOVL7, SH3GL2, SNCA, BAP1, and ZNF184. Results were confirmed in two datasets of non-neurological subjects, while in two datasets of Parkinson's disease patients we found altered expression patterns. Co-expression analysis across vulnerable regions identified a module enriched for genes associated with dopamine synthesis and microglia, and another module related to the immune system, blood-oxygen transport, and endothelial cells. Both were highly expressed in regions involved in the preclinical stages of the disease. Finally, alterations in genes underlying these region-specific functions may contribute to the selective regional vulnerability in Parkinson's disease brains.
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Affiliation(s)
- Arlin Keo
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Angela M T Ingrassia
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Jean-Pascal Meneboo
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
- University lille. Bilille, F-59000, Lille, France
| | - Celine Villenet
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
| | - Eugénie Mutez
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France
- University Lille, Service de Neurologie et Pathologie du mouvement, centre expert Parkinson, F-59000, Lille, France
| | - Thomas Comptdaer
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France
| | - Boudewijn P F Lelieveldt
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martin Figeac
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
- University lille. Bilille, F-59000, Lille, France
| | - Marie-Christine Chartier-Harlin
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France.
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France.
| | - Wilma D J van de Berg
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands.
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
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28
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Baldacci S, Figeac M, Antoine M, Descarpentries C, Kherrouche Z, Jamme P, Copin MC, Tulasne D, Nanni I, Beau-Faller M, Melaabi S, Levallet G, Quoix E, Moro-Sibilot D, Friard S, Missy P, Barlesi F, Cadranel J, Cortot AB. High MET Overexpression Does Not Predict the presence of MET exon 14 Splice Mutations in NSCLC: Results From the IFCT PREDICT.amm study. J Thorac Oncol 2019; 15:120-124. [PMID: 31605799 DOI: 10.1016/j.jtho.2019.09.196] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
INTRODUCTION MET proto-oncogene (MET) exon 14 splice site (METex14) mutations were recently described in NSCLC and has been reported to correlate with efficacy of MET tyrosine kinase inhibitors. High diversity of these alterations makes them hard to detect by DNA sequencing in clinical practice. Because METex14 mutations induce increased stabilization of the MET receptor, it is anticipated that these mutations are associated with MET overexpression. We aim to determine whether NSCLC with high MET overexpression could define a subset of patients with a high rate of METex14 mutations. METHODS From The French Cooperative Thoracic Intergroup PREDICT.amm cohort of 843 consecutive patients with a treatment-naive advanced NSCLC who were eligible for a first-line therapy, 108 NSCLC samples with high MET overexpression defined by an immunochemistry score 3+ were tested for METex14 mutations using fragment length analysis combined with optimized targeted next-generation sequencing. MET copy number analysis was also derived from the sequencing data. RESULTS METex14 mutations were detected in two patients (2.2%) who also displayed a TP53 mutation and a PIK3CA mutation, respectively. An MET gene copy number increase was observed in seven additional patients (7.7%). Next-generation sequencing analysis revealed inactivating mutations in TP53 (52.7%) and PTEN (1.1%), and oncogenic mutations in KRAS (28.6%), EGFR (7.7%), PIK3CA (4.4%), BRAF (4.4%), NRAS (2.2%), GNAS (1.1%), and IDH1 (1.1%). CONCLUSIONS The rate of METex14 mutations in NSCLC with high MET overexpression was similar to that found in unselected NSCLC. Moreover, we observed a high frequency of driver alterations in other oncogenes. Consequently these findings do not support the use of MET immunohistochemistry as a surrogate marker for METex14 mutations.
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Affiliation(s)
- Simon Baldacci
- Lille University Hospital, CHU Lille, Thoracic Oncology Department, Lille, France
| | - Martin Figeac
- University Lille, Functional and Structural Platform, CHU Lille, Lille, France
| | - Martine Antoine
- Department of Pathology, Hospital Tenon, AP-HP, Paris, France
| | - Clotilde Descarpentries
- Department of Biochemistry and Molecular Biology, Hormonology Metabolism Nutrition Oncology, CHU Lille, Lille, France
| | - Zoulika Kherrouche
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Philippe Jamme
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Marie-Christine Copin
- University Lille, CHU Lille, Institute of Pathology, UMR8161 CNRS, Institute of Biology of Lille, F-59000 Lille, France
| | - David Tulasne
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Isabelle Nanni
- Department of Molecular Oncology, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Michèle Beau-Faller
- Department of Molecular Biology, Strasbourg University Hospital, Strasbourg, France
| | - Samia Melaabi
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | | | - Elisabeth Quoix
- Department of Pneumology, Nouvel Hôpital Civil, University Hospital, Strasbourg, France
| | - Denis Moro-Sibilot
- Department of Pneumology, Grenoble University Hospital, Grenoble, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Pascale Missy
- Clinical Research Unit, French Cooperative Thoracic Intergroup (IFCT), Paris, France
| | - Fabrice Barlesi
- Aix Marseille University, Assistance Publique Hôpitaux de Marseille, Multidisciplinary Oncology & Therapeutic Innovations Department, Marseille, France
| | - Jacques Cadranel
- Chest Department-Thoracic Oncology Expert Center, AP-HP, Groupe Hospitalier HUEP, Hopital Tenon, Paris, France, and Sorbonne University, Paris, France
| | - Alexis B Cortot
- Lille University Hospital, CHU Lille, Thoracic Oncology Department, Lille, France.
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29
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Baldacci S, Figeac M, Antoine M, Descarpentries C, Kherrouche Z, Jamme P, Copin M, Tulasne D, Nanni I, Beau-Faller M, Melaabi S, Levallet G, Quoix E, Moro-Sibilot D, Friard S, Missy P, Barlesi F, Cadranel J, Cortot A. P2.14-53 High MET Overexpression Does Not Predict the Presence of MET Exon 14 Splice Mutations in NSCLC: Results from the IFCT Predict.amm Study. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1838] [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: 10/25/2022]
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30
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Tian L, Truong MJ, Lagadec C, Adriaenssens E, Bouchaert E, Bauderlique-Le Roy H, Figeac M, Le Bourhis X, Bourette RP. s-SHIP Promoter Expression Identifies Mouse Mammary Cancer Stem Cells. Stem Cell Reports 2019; 13:10-20. [PMID: 31204299 PMCID: PMC6626869 DOI: 10.1016/j.stemcr.2019.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/27/2022] Open
Abstract
During normal mammary gland development, s-SHIP promoter expression marks a distinct type of mammary stem cells, at two different stages, puberty and early mid-pregnancy. To determine whether s-SHIP is a marker of mammary cancer stem cells (CSCs), we generated bitransgenic mice by crossing the C3(1)-SV40 T-antigen transgenic mouse model of breast cancer, and a transgenic mouse (11.5kb-GFP) expressing green fluorescent protein from the s-SHIP promoter. Here we show that in mammary tumors originating in these bitransgenic mice, s-SHIP promoter expression enriches a rare cell population with CSC activity as demonstrated by sphere-forming assays in vitro and limiting dilution transplantation in vivo. These s-SHIP-positive CSCs are characterized by lower expression of Delta-like non-canonical Notch ligand 1 (DLK1), a negative regulator of the Notch pathway. Inactivation of Dlk1 in s-SHIP-negative tumor cells increases their tumorigenic potential, suggesting a role for DLK1 in mammary cancer stemness.
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Affiliation(s)
- Lu Tian
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, Institut de Biologie de Lille, 1 rue du Professeur Calmette, CS 54447, Lille Cedex 59000/59021, France
| | - Marie-José Truong
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, Institut de Biologie de Lille, 1 rue du Professeur Calmette, CS 54447, Lille Cedex 59000/59021, France
| | - Chann Lagadec
- Université de Lille, INSERM U908 - CPAC - Cell Plasticity and Cancer, Lille 59000, France
| | - Eric Adriaenssens
- Université de Lille, INSERM U908 - CPAC - Cell Plasticity and Cancer, Lille 59000, France
| | | | | | - Martin Figeac
- Functional Genomics Platform, Université de Lille, Lille 59000, France
| | - Xuefen Le Bourhis
- Université de Lille, INSERM U908 - CPAC - Cell Plasticity and Cancer, Lille 59000, France
| | - Roland P Bourette
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, Institut de Biologie de Lille, 1 rue du Professeur Calmette, CS 54447, Lille Cedex 59000/59021, France.
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31
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Blanquart S, Borowiec AS, Delcourt P, Figeac M, Emerling CA, Meseguer AS, Roudbaraki M, Prevarskaya N, Bidaux G. Evolution of the human cold/menthol receptor, TRPM8. Mol Phylogenet Evol 2019; 136:104-118. [PMID: 30980935 DOI: 10.1016/j.ympev.2019.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 10/27/2022]
Abstract
Genes showing versatile functions or subjected to fast expansion and contraction during the adaptation of species to specific ecological conditions, like sensory receptors for odors, pheromones and tastes, are characterized by a great plasticity through evolution. One of the most fascinating sensory receptors in the family of TRP channels, the cold and menthol receptor TRPM8, has received significant attention in the literature. Recent studies have reported the existence of TRPM8 channel isoforms encoded by alternative mRNAs transcribed from alternative promoters and processed by alternative splicing. Since the first draft of the human genome was accomplished in 2000, alternative transcription, alternative splicing and alternative translation have appeared as major sources of gene product diversity and are thought to participate in the generation of complexity in higher organisms. In this study, we investigate whether alternative transcription has been a driving force in the evolution of the human forms of the cold receptor TRPM8. We identified 33 TRPM8 alternative mRNAs (24 new sequences) and their associated protein isoforms in human tissues. Using comparative genomics, we described the evolution of the human TRPM8 sequences in eight ancestors since the origin of Amniota, and estimated in which ancestors the new TRPM8 variants originated. In order to validate the estimated origins of this receptor, we performed experimental validations of predicted exons in mouse tissues. Our results suggest a first diversification event of the cold receptor in the Boreoeutheria ancestor, and a subsequent divergence at the origin of Simiiformes.
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Affiliation(s)
| | - Anne-Sophie Borowiec
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Philippe Delcourt
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Martin Figeac
- Université de Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France; CHRU de Lille, Cellule de bioinformatique du plateau commun de séquençage du CHRU de Lille, F-59000 Lille, France
| | - Christopher A Emerling
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554, Montpellier, France
| | - Andrea S Meseguer
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554, Montpellier, France
| | - Morad Roudbaraki
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Natalia Prevarskaya
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Gabriel Bidaux
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France; Univ Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, 69550 Bron, France; Hospices Civils de Lyon, Groupement Hospitalier EST, Département de Cardiologie, IHU-OPERA Bâtiment B13, 69550 Bron, France.
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32
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Duplaquet L, Figeac M, Leprêtre F, Frandemiche C, Villenet C, Sebda S, Sarafan-Vasseur N, Bénozène M, Vinchent A, Goormachtigh G, Wicquart L, Rousseau N, Beaussire L, Truant S, Michel P, Sabourin JC, Galateau-Sallé F, Copin MC, Zalcman G, De Launoit Y, Fafeur V, Tulasne D. Functional Analysis of Somatic Mutations Affecting Receptor Tyrosine Kinase Family in Metastatic Colorectal Cancer. Mol Cancer Ther 2019; 18:1137-1148. [PMID: 30926633 DOI: 10.1158/1535-7163.mct-18-0582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/08/2018] [Accepted: 03/21/2019] [Indexed: 11/16/2022]
Abstract
Besides the detection of somatic receptor tyrosine kinases (RTK) mutations in tumor samples, the current challenge is to interpret their biological relevance to give patients effective targeted treatment. By high-throughput sequencing of the 58 RTK exons of healthy tissues, colorectal tumors, and hepatic metastases from 30 patients, 38 different somatic mutations in RTKs were identified. The mutations in the kinase domains and present in both tumors and metastases were reconstituted to perform an unbiased functional study. Among eight variants found in seven RTKs (EPHA4-Met726Ile, EPHB2-Val621Ile, ERBB4-Thr731Met, FGFR4-Ala585Thr, VEGFR3-Leu1014Phe, KIT-Pro875Leu, TRKB-Leu584Val, and NTRK2-Lys618Thr), none displayed significantly increased tyrosine kinase activity. Consistently, none of them induced transformation of NIH3T3 fibroblasts. On the contrary, two RTK variants (FGFR4-Ala585Thr and FLT4-Leu1014Phe) caused drastic inhibition of their kinase activity. These findings indicate that these RTK variants are not suitable targets and highlight the importance of functional studies to validate RTK mutations as potential therapeutic targets.
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Affiliation(s)
- Leslie Duplaquet
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Martin Figeac
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Charline Frandemiche
- TCBN - Tumorothèque Caen Basse-Normandie, Caen, France.,Réseau Régional de Cancérologie, OncoBasseNormandie, Caen, France
| | - Céline Villenet
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Mélanie Bénozène
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Audrey Vinchent
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | | | | | | | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Stéphanie Truant
- Department of Digestive Surgery and Transplantation, CHU Lille, Univ Lille, Lille Cedex, France
| | - Pierre Michel
- Department of Hepato-Gastroenterology, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandy University, INSERM 1245, Rouen University Hospital, Rouen, France
| | | | - Marie-Christine Copin
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France.,Tumorothèque du C2RC de Lille, Lille, France
| | - Gérard Zalcman
- Thoracic Oncology Department, CIC1425/CLIP2 Paris-Nord, Hôpital Bichat-Claude Bernard, Paris, France
| | - Yvan De Launoit
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Véronique Fafeur
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - David Tulasne
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France.
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Depauw S, Lambert M, Jambon S, Paul A, Peixoto P, Nhili R, Marongiu L, Figeac M, Dassi C, Paul-Constant C, Billoré B, Kumar A, Farahat AA, Ismail MA, Mineva E, Sweat DP, Stephens CE, Boykin DW, Wilson WD, David-Cordonnier MH. Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model. J Med Chem 2019; 62:1306-1329. [PMID: 30645099 DOI: 10.1021/acs.jmedchem.8b01448] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most transcription factors were for a long time considered as undruggable targets because of the absence of binding pockets for direct targeting. HOXA9, implicated in acute myeloid leukemia, is one of them. To date, only indirect targeting of HOXA9 expression or multitarget HOX/PBX protein/protein interaction inhibitors has been developed. As an attractive alternative by inhibiting the DNA binding, we selected a series of heterocyclic diamidines as efficient competitors for the HOXA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence. Selected DB818 and DB1055 compounds altered HOXA9-mediated transcription in luciferase assays, cell survival, and cell cycle, but increased cell death and granulocyte/monocyte differentiation, two main HOXA9 functions also highlighted using transcriptomic analysis of DB818-treated murine Hoxa9-transformed hematopoietic cells. Altogether, these data demonstrate for the first time the propensity of sequence-selective DNA ligands to inhibit HOXA9/DNA binding both in vitro and in a murine Hoxa9-dependent leukemic cell model.
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Affiliation(s)
- Sabine Depauw
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Mélanie Lambert
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Samy Jambon
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Ananya Paul
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Paul Peixoto
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Raja Nhili
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Laura Marongiu
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Martin Figeac
- Functional and Structural Genomic Platform , Lille University , F-59000 Lille , France
| | - Christelle Dassi
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Charles Paul-Constant
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Benjamin Billoré
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
| | - Arvind Kumar
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Abdelbasset A Farahat
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Mohamed A Ismail
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Ekaterina Mineva
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Daniel P Sweat
- Department of Chemistry and Physics , Augusta University , Augusta , Georgia 30904 , United States
| | - Chad E Stephens
- Department of Chemistry and Physics , Augusta University , Augusta , Georgia 30904 , United States
| | - David W Boykin
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la Recherche sur le Cancer de Lille (IRCL) , F-59045 Lille , France
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34
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Faivre E, Coelho JE, Zornbach K, Malik E, Baqi Y, Schneider M, Cellai L, Carvalho K, Sebda S, Figeac M, Eddarkaoui S, Caillierez R, Chern Y, Heneka M, Sergeant N, Müller CE, Halle A, Buée L, Lopes LV, Blum D. Beneficial Effect of a Selective Adenosine A 2A Receptor Antagonist in the APPswe/PS1dE9 Mouse Model of Alzheimer's Disease. Front Mol Neurosci 2018; 11:235. [PMID: 30050407 PMCID: PMC6052540 DOI: 10.3389/fnmol.2018.00235] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023] Open
Abstract
Consumption of caffeine, a non-selective adenosine A2A receptor (A2AR) antagonist, reduces the risk of developing Alzheimer’s disease (AD) and mitigates both amyloid and Tau lesions in transgenic mouse models of the disease. While short-term treatment with A2AR antagonists have been shown to alleviate cognitive deficits in mouse models of amyloidogenesis, impact of a chronic and long-term treatment on the development of amyloid burden, associated neuroinflammation and memory deficits has never been assessed. In the present study, we have evaluated the effect of a 6-month treatment of APPsw/PS1dE9 mice with the potent and selective A2AR antagonist MSX-3 from 3 to 9-10 months of age. At completion of the treatment, we found that the MSX-3 treatment prevented the development of memory deficits in APP/PS1dE9 mice, without significantly altering hippocampal and cortical gene expressions. Interestingly, MSX-3 treatment led to a significant decrease of Aβ1-42 levels in the cortex of APP/PS1dE9 animals, while Aβ1-40 increased, thereby strongly affecting the Aβ1-42/Aβ1-40 ratio. Together, these data support the idea that A2AR blockade is of therapeutic value for AD.
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Affiliation(s)
- Emilie Faivre
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Joana E Coelho
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Katja Zornbach
- Center of Advanced European Studies and Research, Bonn, Germany
| | - Enas Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Younis Baqi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany.,Department of Chemistry, Faculty of Science, Sultan Qaboos University, Muscat, Oman
| | - Marion Schneider
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Lucrezia Cellai
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Kevin Carvalho
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Shéhérazade Sebda
- Plateau de Génomique Fonctionnelle et Structurale, CHU Lille, University of Lille, Lille, France
| | - Martin Figeac
- Plateau de Génomique Fonctionnelle et Structurale, CHU Lille, University of Lille, Lille, France
| | - Sabiha Eddarkaoui
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Raphaëlle Caillierez
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Yijuang Chern
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Michael Heneka
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geropsychiatry/Neurology, University of Bonn Medical Center, Bonn, Germany
| | - Nicolas Sergeant
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Annett Halle
- Center of Advanced European Studies and Research, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Luc Buée
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
| | - Luisa V Lopes
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - David Blum
- Université de Lille, Inserm, CHU-Lille, LabEx DISTALZ, Jean-Pierre Aubert Research Centre UMR-S1172, Alzheimer & Tauopathies, Lille, France
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35
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Mareschal S, Ruminy P, Alcantara M, Villenet C, Figeac M, Dubois S, Bertrand P, Bouzelfen A, Viailly PJ, Penther D, Tilly H, Bastard C, Jardin F. Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. Bioinformatics 2018; 33:2977-2985. [PMID: 28481978 DOI: 10.1093/bioinformatics/btx309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Motivation Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyze such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. Results The cghRA framework combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas. New algorithms for copy-number calling, polymorphism detection and minimal common region prioritization were also developed and validated. While their performances will only be demonstrated with aCGH, these algorithms could actually prove useful to any copy-number analysis, whatever the technique used. Availability and implementation R package and source for Linux, MS Windows and MacOS are freely available at http://bioinformatics.ovsa.fr/cghRA. Contact mareschal@ovsa.fr or fabrice.jardin@chb.unicancer.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylvain Mareschal
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Ruminy
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Marion Alcantara
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Céline Villenet
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France
| | - Martin Figeac
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France.,Cellule de Bioinformatique du Plateau Commun de Séquençage, CHRU de Lille, 59000 Lille, France
| | - Sydney Dubois
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Bertrand
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Abdelilah Bouzelfen
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Pierre-Julien Viailly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Dominique Penther
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Hervé Tilly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France
| | - Christian Bastard
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Fabrice Jardin
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
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36
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Fumery M, Speca S, Langlois A, Davila AM, Dubuquoy C, Grauso M, Martin Mena A, Figeac M, Metzger D, Rousseaux C, Colombel JF, Dubuquoy L, Desreumaux P, Bertin B. Peroxisome proliferator-activated receptor gamma (PPARγ) regulates lactase expression and activity in the gut. EMBO Mol Med 2018; 9:1471-1481. [PMID: 28947679 PMCID: PMC5666307 DOI: 10.15252/emmm.201707795] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Lactase (LCT) deficiency affects approximately 75% of the world's adult population and may lead to lactose malabsorption and intolerance. Currently, the regulation of LCT gene expression remains poorly known. Peroxisome proliferator activator receptorγ (PPARγ) is a key player in carbohydrate metabolism. While the intestine is essential for carbohydrate digestion and absorption, the role of PPARγ in enterocyte metabolic functions has been poorly investigated. This study aims at characterizing PPARγ target genes involved in intestinal metabolic functions. In microarray analysis, the LCT gene was the most upregulated by PPARγ agonists in Caco-2 cells. We confirmed that PPARγ agonists were able to increase the expression and activity of LCT both in vitro and in vivo in the proximal small bowel of rodents. The functional response element activated by PPARγ was identified in the promoter of the human LCT gene. PPARγ modulation was able to improve symptoms induced by lactose-enriched diet in weaned rats. Our results demonstrate that PPARγ regulates LCT expression, and suggest that modulating intestinal PPARγ activity might constitute a new therapeutic strategy for lactose malabsorption.
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Affiliation(s)
- Mathurin Fumery
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France.,Service d'Hépatogastroentérologie, Centre Hospitalier Universitaire d'Amiens Université de Picardie Jules Verne, Amiens, France
| | - Silvia Speca
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France
| | - Audrey Langlois
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France
| | - Anne-Marie Davila
- UMR0914, Institut National de la Recherche Agronomique/AgroParisTech, Université Paris-Saclay, Paris, France
| | | | - Marta Grauso
- UMR0914, Institut National de la Recherche Agronomique/AgroParisTech, Université Paris-Saclay, Paris, France
| | - Anthony Martin Mena
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Université de Lille, Lille, France
| | - Daniel Metzger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS, UMR7104/INSERM U964/Université de Strasbourg Collège de France, Paris, France
| | | | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurent Dubuquoy
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France
| | - Pierre Desreumaux
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France.,Inserm, U995, Lille, France.,CHU Lille, Service des Maladies de l'Appareil Digestif et de la Nutrition, Hôpital Claude Huriez, Lille, France
| | - Benjamin Bertin
- U995-LIRIC-Lille Inflammation Research International Center, Univ. Lille, Lille, France .,Inserm, U995, Lille, France
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Saad C, Noé L, Richard H, Leclerc J, Buisine MP, Touzet H, Figeac M. DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. BMC Bioinformatics 2018; 19:223. [PMID: 29890948 PMCID: PMC5996464 DOI: 10.1186/s12859-018-2215-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 05/21/2018] [Indexed: 12/30/2022] Open
Abstract
Background Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. However, it remains a difficult challenge, especially with the huge quantity of data generated by high throughput sequencing technologies. To overcome this problem, existing tools use greedy algorithms and probabilistic approaches to find motifs in reasonable time. Nevertheless these approaches lack sensitivity and have difficulties coping with rare and subtle motifs. Results We developed DiNAMO (for DNA MOtif), a new software based on an exhaustive and efficient algorithm for IUPAC motif discovery. We evaluated DiNAMO on synthetic and real datasets with two different applications, namely ChIP-seq peaks and Systematic Sequencing Error analysis. DiNAMO proves to compare favorably with other existing methods and is robust to noise. Conclusions We shown that DiNAMO software can serve as a tool to search for degenerate motifs in an exact manner using IUPAC models. DiNAMO can be used in scanning mode with sliding windows or in fixed position mode, which makes it suitable for numerous potential applications. Availability https://github.com/bonsai-team/DiNAMO. Electronic supplementary material The online version of this article (10.1186/s12859-018-2215-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chadi Saad
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France. .,Univ. Lille, Inserm, Lille University Hospital, UMR-S 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT, Lille, F-59000, France.
| | - Laurent Noé
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Hugues Richard
- Sorbonne Université, UMR7238, Laboratory Computational and Quantitative Biology, LCQB, Paris, F-75005, France
| | - Julie Leclerc
- Univ. Lille, Inserm, Lille University Hospital, UMR-S 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT, Lille, F-59000, France
| | - Marie-Pierre Buisine
- Univ. Lille, Inserm, Lille University Hospital, UMR-S 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT, Lille, F-59000, France
| | - Hélène Touzet
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Martin Figeac
- Univ. Lille. Plateau de génomique fonctionnelle et structurale, Lille, F-59000, France
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Jambon S, Lambert M, Depauw S, Figeac M, Perrais M, David-Cordonnier M. PO-133 Hoxa9 transcription factor: a potential novel therapeutic target in renal cell carcinoma (RCC). ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.174] [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: 11/04/2022] Open
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Petrella T, Copie-Bergman C, Brière J, Delarue R, Jardin F, Ruminy P, Thieblemont C, Figeac M, Canioni D, Feugier P, Fabiani B, Leroy K, Parrens M, André M, Haioun C, Salles GA, Gaulard P, Tilly H, Jais JP, Molina TJ. BCL2 expression but not MYC and BCL2 coexpression predicts survival in elderly patients with diffuse large B-cell lymphoma independently of cell of origin in the phase 3 LNH03-6B trial. Ann Oncol 2018; 28:1042-1049. [PMID: 28327893 DOI: 10.1093/annonc/mdx022] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Our aim was to evaluate whether the cell of origin (COO) as defined by the Hans algorithm and MYC/BCL2 coexpression, which are the two main biological risk factors in elderly patients treated with rituximab, cyclophosphamide, doxorubicin hydrochloride, vincristine, and prednisolone (R-CHOP), maintain their prognostic value in a large prospective clinical trial. Patients and methods We evaluated 285 paraffin-embedded samples from patients (60-80 years of age) enrolled in the Lymphoma Study Association trial LNH03-6B who were treated with R-CHOP. We correlated the COO defined by the transcriptome according to the Wright algorithm with that defined by the Hans algorithm in a subset of 62 tumors with available frozen tissue samples. Results The non-germinal center B-cell-like phenotype according to the Hans algorithm and BCL2 expression (but not MYC and BCL2 coexpression) predicted worse progression-free survival [hazard ratio (HR)=1.78, P = 0.003 and HR = 1.79, P = 0.003, respectively] and overall survival (HR = 1.85, P = 0.005 and HR = 1.67, P = 0.02, respectively) independently of the International Prognostic Index. The correlation between the Hans algorithm and the Wright algorithm was 91%, with an almost perfect concordance according to a kappa test (0.81). Conclusions Our results suggest that immunohistochemically defined COO remains a useful tool for predicting prognosis in diffuse large B-cell lymphoma when performed under optimized standardized conditions and that BCL2 expression may help to identify elderly patients at risk for relapse and who could potentially respond to anti-BCL2 targeted agents. In this prospective phase III trial, the coexpression of MYC and BCL2 does not appear to predict worse survival. Clinical trial Number NCT00144755.
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Affiliation(s)
| | - C Copie-Bergman
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - J Brière
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | - R Delarue
- Hematology, AP-HP, Necker Enfants-Malades, Paris
| | - F Jardin
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - P Ruminy
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - C Thieblemont
- Hemato-Oncology, AP-HP, Saint-Louis, Université Paris Diderot, Sorbonne Paris Cité and EA 7324, Paris Descartes, Sorbonne Paris Cité, Paris
| | - M Figeac
- Functional Genomic Platform, Cancer Research Institute, Lille
| | - D Canioni
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | | | - B Fabiani
- Pathology, AP-HP, Saint-Antoine, Paris
| | - K Leroy
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - M Parrens
- Pathology, CHU Bordeaux, Inserm U1053, Bordeaux, France
| | - M André
- Hematology, Université Catholique de Louvain, CHU UCL Namur, Yvoir, Belgium
| | - C Haioun
- Lymphoid Malignancies Unit, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil
| | - G A Salles
- Haematology, Hospices Civils de Lyon, Université Claude Bernard, Pierre Bénite
| | - P Gaulard
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - H Tilly
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - J P Jais
- Biostatistics, AP-HP, Necker Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | - T J Molina
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris.,EA7324, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Bobée V, Ruminy P, Marchand V, Viailly PJ, Abdel Sater A, Veresezan L, Drieux F, Bérard C, Bohers E, Mareschal S, Dubois S, Jais JP, Leroy K, Figeac M, Picquenot JM, Molina TJ, Salles G, Haioun C, Tilly H, Jardin F. Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier: A CALYM Study. J Mol Diagn 2017; 19:892-904. [PMID: 29054399 DOI: 10.1016/j.jmoldx.2017.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/11/2017] [Accepted: 07/28/2017] [Indexed: 11/16/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. It includes three major subtypes termed germinal center B-cell-like, activated B-cell-like, and primary mediastinal B-cell lymphoma. With the emergence of novel targeted therapies, accurate methods capable of interrogating this cell-of-origin classification should soon become essential in the clinics. To address this issue, we developed a novel gene expression profiling DLBCL classifier based on reverse transcriptase multiplex ligation-dependent probe amplification. This assay simultaneously evaluates the expression of 21 markers, to differentiate primary mediastinal B-cell lymphoma, activated B-cell-like, germinal center B-cell-like, and also Epstein-Barr virus-positive DLBCLs. It was trained using 70 paraffin-embedded biopsies and validated using >160 independent samples. Compared with a reference classification established from Affymetrix U133 + 2 data, reverse transcriptase multiplex ligation-dependent probe amplification classified 85.0% samples into the expected subtype, comparing favorably with current diagnostic methods. This assay also proved to be highly efficient in detecting the MYD88 L265P mutation, even in archival paraffin-embedded tissues. This reliable, rapid, and cost-effective method uses common instruments and reagents and could thus easily be implemented into routine diagnosis workflows, to improve the management of these aggressive tumors.
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Affiliation(s)
- Victor Bobée
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Biological Hematology, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France.
| | | | | | - Ahmad Abdel Sater
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; LITIS EA 4108, UNIROUEN, University of Normandie, Rouen, France
| | - Liana Veresezan
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fanny Drieux
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Caroline Bérard
- LITIS EA 4108, UNIROUEN, University of Normandie, Rouen, France
| | - Elodie Bohers
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | | | - Sydney Dubois
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | | | - Karen Leroy
- INSERM U955 Team 09, AP-HP Henri Mondor Hospital, Creteil, France
| | - Martin Figeac
- Functional Genomics Platform, Center for Biology and Pathology, University of Lille, Lille Cedex, France
| | - Jean-Michel Picquenot
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Thierry Jo Molina
- Department of Pathology, Necker Hospital, AP-HP, Université Paris Descartes Sorbonne Cité, Paris, France
| | - Gilles Salles
- Department of Hematology, University Claude Bernard Lyon 1, Hospices Civils de Lyon, Pierre-Benite, France
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Hospital Henri Mondor, Creteil, France
| | - Hervé Tilly
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
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Driss V, Leprêtre F, Briche I, Mopin A, Villenet C, Figeac M, Quesnel B, Brinster C. Sub-clonal analysis of the murine C1498 acute myeloid leukaemia cell line reveals genomic and immunogenic diversity. Immunol Lett 2017; 192:27-34. [PMID: 29030252 DOI: 10.1016/j.imlet.2017.10.004] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND In acute myeloid leukaemia (AML)-affected patients, the presence of heterogeneous sub-clones at diagnosis has been shown to be responsible for minimal residual disease and relapses. The role played by the immune system in this leukaemic sub-clonal hierarchy and maintenance remains unknown. As leukaemic sub-clone immunogenicity could not be evaluated in human AML xenograft models, we assessed the sub-clonal diversity of the murine C1498 AML cell line and the immunogenicity of its sub-clones in immune-competent syngeneic mice. METHODOLOGY The murine C1498 cell line was cultured in vitro and sub-clonal cells were generated after limiting dilution. The genomic profiles of 6 different sub-clones were analysed by comparative genomic hybridization arrays (CGH). The sub-clones were then injected into immune-deficient and - competent syngeneic mice. The immunogenicities of the sub-clones was evaluated through 1) assessment of mouse survival, 2) determination of leukaemic cell infiltration into organs by flow cytometry and the expression of a fluorescent reporter gene, 3) assessment of the CTL response ex vivo and 4) detection of residual leukaemic cells in the organs via amplification of the genomic reporter gene by real-time PCR (qPCR). RESULTS Genomic analyses revealed heterogeneity among the parental cell line and its derived sub-clones. When injected individually into immune-deficient mice, all sub-clones induced cases of AML with different kinetics. However, when administered into immune-competent animals, some sub-clones triggered AML in which no mice survived, whereas others elicited reduced lethality rates. The AML-surviving mice presented efficient anti-leukaemia CTL activity ex vivo and eliminated the leukaemic cells in vivo. CONCLUSION We showed that C1498 cell sub-clones presented genomic heterogeneity and differential immunogenicity resulting either in immune escape or elimination. Such findings could have potent implications for new immunotherapeutic strategies in patients with AML.
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Affiliation(s)
- Virginie Driss
- INSERM UMR-S-1172, Centre de Recherche Jean-Pierre Aubert (JPARC), France; Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France.
| | - Frédéric Leprêtre
- Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; IFR 114, IMPRT, Institut de Médecine Prédictive et de Recherche Thérapeutique, plate-forme génomique fonctionnelle et structurale, France; Université de Lille, Lille, France.
| | - Isabelle Briche
- INSERM UMR-S-1172, Centre de Recherche Jean-Pierre Aubert (JPARC), France; Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France.
| | - Alexia Mopin
- INSERM UMR-S-1172, Centre de Recherche Jean-Pierre Aubert (JPARC), France; Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; CHU Lille (Centre Hospitalier Universitaire de Lille), Service des Maladies du Sang, F-59000 Lille, France.
| | - Céline Villenet
- Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; IFR 114, IMPRT, Institut de Médecine Prédictive et de Recherche Thérapeutique, plate-forme génomique fonctionnelle et structurale, France; Université de Lille, Lille, France
| | - Martin Figeac
- Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; IFR 114, IMPRT, Institut de Médecine Prédictive et de Recherche Thérapeutique, plate-forme génomique fonctionnelle et structurale, France; Université de Lille, Lille, France.
| | - Bruno Quesnel
- INSERM UMR-S-1172, Centre de Recherche Jean-Pierre Aubert (JPARC), France; Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; CHU Lille (Centre Hospitalier Universitaire de Lille), Service des Maladies du Sang, F-59000 Lille, France.
| | - Carine Brinster
- INSERM UMR-S-1172, Centre de Recherche Jean-Pierre Aubert (JPARC), France; Institut pour la Recherche sur le Cancer de Lille (IRCL), 1, place de verdun, 59045 Lille Cedex, France; Université de Lille, Lille, France.
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Engelmann I, Alidjinou EK, Bertin A, Bossu J, Villenet C, Figeac M, Sane F, Hober D. Persistent coxsackievirus B4 infection induces microRNA dysregulation in human pancreatic cells. Cell Mol Life Sci 2017; 74:3851-3861. [DOI: 10.1007/s00018-017-2567-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/16/2017] [Accepted: 06/06/2017] [Indexed: 12/15/2022]
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Leblay N, Leprêtre F, Le Stang N, Gautier-Stein A, Villeneuve L, Isaac S, Maillet D, Galateau-Sallé F, Villenet C, Sebda S, Goracci A, Byrnes G, McKay JD, Figeac M, Glehen O, Gilly FN, Foll M, Fernandez-Cuesta L, Brevet M. BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas. J Thorac Oncol 2017; 12:724-733. [PMID: 28034829 DOI: 10.1016/j.jtho.2016.12.019] [Citation(s) in RCA: 54] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Malignant mesothelioma is a deadly disease that is strongly associated with asbestos exposure. Peritoneal mesotheliomas account for 10% of all the cases. BRCA1 associated protein 1 (BAP1) is a deubiquitinating hydrolase that plays a key role in various cellular processes. Germline and somatic inactivation of BRCA1 associated protein 1 gene (BAP1) is frequent in pleural mesothelioma; however, little is known about its status in peritoneal mesothelioma. METHODS Taking advantage of the extensive French National Network for the Diagnosis of Malignant Pleural Mesothelioma and Rare Peritoneal Tumors and the French National Network for the Treatment of Rare Peritoneal Surface Malignancies, we collected biological material and clinical and epidemiological data for 46 patients with peritoneal mesothelioma. The status of BAP1 was evaluated at the mutational and protein expression levels and combined with our previous data on copy number alterations assessed in the same samples. RESULTS We detected mutations in 32% of the malignant peritoneal mesotheliomas analyzed. In addition, we have previously reported that copy number losses occurred in 42% of the samples included in this series. Overall, 73% of the malignant peritoneal mesotheliomas analyzed carried at least one inactivated BAP1 allele, but only 57% had a complete loss of its protein nuclear expression. Better overall survival was observed for patients with BAP1 mutations (p = 0.04), protein expression loss (p = 0.016), or at least one of these alterations (p = 0.007) independently of tumor histological subtype, age, and sex. CONCLUSIONS As in pleural mesothelioma, inactivation of BAP1 is frequent in peritoneal mesotheliomas. We found that BAP1 protein nuclear expression is a good prognostic factor and a more reliable marker for the complete loss of BAP1 activity than mutation or copy number loss.
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Affiliation(s)
- Noémie Leblay
- International Agency for Research on Cancer, Lyon, France
| | - Frédéric Leprêtre
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Nolwenn Le Stang
- Department of Biopathology, Cancer Center Lyon Leon Berard, Lyon, France; National Cancer Institute, Research Unit 1086, Caen, France
| | | | - Laurent Villeneuve
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; University Hospital of Lyon, Lyon, France
| | - Sylvie Isaac
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Pathology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Denis Maillet
- Department of Oncology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Françoise Galateau-Sallé
- Department of Biopathology, Cancer Center Lyon Leon Berard, Lyon, France; National Cancer Institute, Research Unit 1086, Caen, France
| | - Céline Villenet
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Shéhérazade Sebda
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Alexandra Goracci
- Department of Radiology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Graham Byrnes
- International Agency for Research on Cancer, Lyon, France
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Martin Figeac
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France; Sequencing Platform, Research Cancer Institute, Lille, France
| | - Olivier Glehen
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Surgery, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - François-Noël Gilly
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Surgery, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Matthieu Foll
- International Agency for Research on Cancer, Lyon, France
| | | | - Marie Brevet
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Pathology, University Hospital of Lyon and Lyon1 University, Lyon, France
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Alidjinou EK, Engelmann I, Bossu J, Villenet C, Figeac M, Romond MB, Sané F, Hober D. Persistence of Coxsackievirus B4 in pancreatic ductal-like cells results in cellular and viral changes. Virulence 2017; 8:1229-1244. [PMID: 28112573 DOI: 10.1080/21505594.2017.1284735] [Citation(s) in RCA: 25] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Although known as cytolytic viruses, group B coxackieviruses (CVB) are able to establish a persistent infection in vitro and in vivo. Viral persistence has been reported as a key mechanism in the pathogenesis of CVB-associated chronic diseases such as type 1 diabetes (T1D). The impact of CVB4 persistence on human pancreas ductal-like cells was investigated. METHODS A persistent CVB4 infection was established in ductal-like cells. PDX-1 expression, resistance to CVB4-induced lysis and CAR expression were evaluated. The profile of cellular microRNAs (miRNAs) was investigated through miRNA-sequencing. Viral phenotypic changes were examined, and genomic modifications were assessed by sequencing of the viral genome. RESULTS The CVB4 persistence in ductal-like cells was productive, with continuous release of infectious particles. Persistently infected cells displayed a resistance to CVB4-induced lysis upon superinfection and expression of PDX-1 and CAR was decreased. These changes were maintained even after virus clearance. The patterns of cellular miRNA expression in mock-infected and in CVB4-persistently infected ductal-like cells were clearly different. The persistent infection-derived virus (PIDV) was still able to induce cytopathic effect but its plaques were smaller than the parental virus. Several mutations appeared in various PIDV genome regions, but amino acid substitutions did not affect the predicted site of interaction with CAR. CONCLUSION Cellular and viral changes occur during persistent infection of human pancreas ductal-like cells with CVB4. The persistence of cellular changes even after virus clearance supports the hypothesis of a long-lasting impact of persistent CVB infection on the cells.
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Affiliation(s)
- E K Alidjinou
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - I Engelmann
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - J Bossu
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - C Villenet
- b Plate-forme de Génomique Fonctionnelle et Structurale , CHU de Lille , France
| | - M Figeac
- b Plate-forme de Génomique Fonctionnelle et Structurale , CHU de Lille , France
| | - M-B Romond
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - F Sané
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
| | - D Hober
- a Univ Lille, CHU Lille, Laboratoire de Virologie EA3610 , Lille , France
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Dubois S, Viailly PJ, Bohers E, Bertrand P, Ruminy P, Marchand V, Maingonnat C, Mareschal S, Picquenot JM, Penther D, Jais JP, Tesson B, Peyrouze P, Figeac M, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Fabiani B, Delarue R, Peyrade F, André M, Ketterer N, Leroy K, Salles G, Molina TJ, Tilly H, Jardin F. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases. Clin Cancer Res 2016; 23:2232-2244. [PMID: 27923841 DOI: 10.1158/1078-0432.ccr-16-1922] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Purpose:MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of activated B-cell like (ABC) diffuse large B-cell lymphoma (DLBCL), leading to constitutive NFκB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88-mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants.Experimental Design: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next-generation sequencing (NGS) focusing on 34 genes to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses.Results: Importantly, we highlighted different genomic profiles for MYD88 L265P and MYD88 non-L265P-mutant DLBCL, shedding light on their divergent backgrounds. Clustering analysis also segregated subgroups according to associated genetic alterations among patients with the same MYD88 mutation. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFκB pathway activation, although the majority of MYD88 L265P-mutant cases harbors downstream NFκB alterations, which can predict BTK inhibitor resistance. Finally, although the MYD88 L265P variant was not an independent prognostic factor in ABC DLBCL, associated CD79B mutations significantly improved the survival of MYD88 L265P-mutant ABC DLBCL in our cohort.Conclusions: This study highlights the relative heterogeneity of MYD88-mutant DLBCL, adding to the field's knowledge of the theranostic importance of MYD88 mutations, but also of associated alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. Clin Cancer Res; 23(9); 2232-44. ©2016 AACR.
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Affiliation(s)
- Sydney Dubois
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Pierre-Julien Viailly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,LITIS EA 4108, Normandie Université, Rouen, France
| | - Elodie Bohers
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Bertrand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Ruminy
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Vinciane Marchand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Sylvain Mareschal
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Dominique Penther
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | | | | | | | | | | | - Corinne Haioun
- Unité Hémopathies Lymphoïdes, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | | | - Bettina Fabiani
- Laboratoire de Pathologie, AP-HP Hôpital Saint Antoine, Paris, France
| | - Richard Delarue
- Department of Hematology, AP-HP Hôpital Necker, Paris, France
| | | | - Marc André
- CHU Dinant Godinne, UcL Namur, Yvoir, Belgium
| | | | - Karen Leroy
- Inserm U955 Team 09, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | - Thierry J Molina
- Pathology, AP-HP Hôpital Necker, Université Paris Descartes, Paris, France
| | - Hervé Tilly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Fabrice Jardin
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.
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46
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Lambert M, Jambon S, Depauw S, Bouhlel M, Figeac M, David-Cordonnier M. HOXA9 transcription factor as a target in acute myeloid leukemia: Transcription, cellular and in vivo consequences of its invalidation. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32649-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Salson M, Giraud M, Caillault A, Grardel N, Duployez N, Ferret Y, Duez M, Herbert R, Rocher T, Sebda S, Quief S, Villenet C, Figeac M, Preudhomme C. High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones. Leuk Res 2016; 53:1-7. [PMID: 27930944 DOI: 10.1016/j.leukres.2016.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/28/2016] [Accepted: 11/11/2016] [Indexed: 01/22/2023]
Abstract
Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up. We assessed the clinical feasibility of using combined HTS and bioinformatics analysis with interactive visualization using Vidjil software. We discuss the advantages and drawbacks of HTS for monitoring MRD. HTS gives a more complete insight of the leukemic population than conventional real-time quantitative PCR (qPCR), and allows identification of new emerging clones at each time point of the monitoring. Thus, HTS monitoring of Ig/TR based MRD is expected to improve the management of patients with ALL.
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Affiliation(s)
- Mikaël Salson
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Mathieu Giraud
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Aurélie Caillault
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nathalie Grardel
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nicolas Duployez
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Yann Ferret
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Marc Duez
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ryan Herbert
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Tatiana Rocher
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Sabine Quief
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France; Univ. Lille, CHU Lille, Cellule bioinformatique, plateau commun de séquençage, F-59000 Lille, France
| | - Claude Preudhomme
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
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48
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Debarri H, Lebon D, Roumier C, Cheok M, Marceau-Renaut A, Nibourel O, Geffroy S, Helevaut N, Rousselot P, Gruson B, Gardin C, Chretien ML, Sebda S, Figeac M, Berthon C, Quesnel B, Boissel N, Castaigne S, Dombret H, Renneville A, Preudhomme C. IDH1/2 but not DNMT3A mutations are suitable targets for minimal residual disease monitoring in acute myeloid leukemia patients: a study by the Acute Leukemia French Association. Oncotarget 2016; 6:42345-53. [PMID: 26486081 PMCID: PMC4747230 DOI: 10.18632/oncotarget.5645] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/02/2015] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease. Even within the same NPM1-mutated genetic subgroup, some patients harbor additional mutations in FLT3, IDH1/2, DNMT3A or TET2. Recent studies have shown the prognostic significance of minimal residual disease (MRD) in AML but it remains to be determined which molecular markers are the most suitable for MRD monitoring. Recent advances in next-generation sequencing (NGS) have provided the opportunity to use multiple molecular markers. In this study, we used NGS technology to assess MRD in 31 AML patients enrolled in the ALFA-0701 trial and harboring NPM1 mutations associated to IDH1/2 or DNMT3A mutations. NPM1 mutation-based MRD monitoring was performed by RTqPCR. IDH1/2 and DNMT3A mutations were quantified by NGS using an Ion Torrent Proton instrument with high coverage (2 million reads per sample). The monitoringof IDH1/2 mutations showed that these mutations were reliable MRD markers that allowed the prediction of relapse in the majority of patients. Moreover, IDH1/2 mutation status predicted relapse or disease evolution in 100% of cases if we included the patient who developed myelodysplastic syndrome. In contrast, DNMT3A mutations were not correlated to the disease status, as we found that a preleukemic clone with DNMT3A mutation persisted in 40% of the patients who were in complete remission, reflecting the persistence of clonal hematopoiesis.
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Affiliation(s)
- Houria Debarri
- Hematology Department, Lille University Hospital, Lille, France.,Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France
| | - Delphine Lebon
- Hematology Department, Amiens University Hospital, Amiens, France
| | - Christophe Roumier
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Meyling Cheok
- UMR-S 1172, Team 3, INSERM, Lille, France.,Functional Genomic Platform, Cancer Research Institute, Lille, France
| | - Alice Marceau-Renaut
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Olivier Nibourel
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Sandrine Geffroy
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Nathalie Helevaut
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France
| | | | - Bérengère Gruson
- Hematology Department, Amiens University Hospital, Amiens, France
| | - Claude Gardin
- Hematology Department, Avicenne Hospital, APHP, University Paris 13, Bobigny, France
| | | | - Shéhérazade Sebda
- Functional Genomic Platform, Cancer Research Institute, Lille, France
| | - Martin Figeac
- Functional Genomic Platform, Cancer Research Institute, Lille, France
| | - Céline Berthon
- Hematology Department, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Bruno Quesnel
- Hematology Department, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Nicolas Boissel
- Hematology Department, Saint-Louis Hospital, APHP, Paris, France
| | | | - Hervé Dombret
- Hematology Department, Saint-Louis Hospital, APHP, Paris, France
| | - Aline Renneville
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
| | - Claude Preudhomme
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France.,UMR-S 1172, Team 3, INSERM, Lille, France
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49
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Nkiliza A, Mutez E, Simonin C, Leprêtre F, Duflot A, Figeac M, Villenet C, Semaille P, Comptdaer T, Genet A, Sablonnière B, Devos D, Defebvre L, Destée A, Chartier-Harlin MC. RNA-binding disturbances as a continuum from spinocerebellar ataxia type 2 to Parkinson disease. Neurobiol Dis 2016; 96:312-322. [PMID: 27663142 DOI: 10.1016/j.nbd.2016.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/07/2016] [Accepted: 09/17/2016] [Indexed: 12/13/2022] Open
Abstract
CAG triplet expansions in Ataxin-2 gene (ATXN2) cause spinocerebellar ataxia type 2 and have a role that remains to be clarified in Parkinson's disease (PD). To study the molecular events associated with these expansions, we sequenced them and analyzed the transcriptome from blood cells of controls and three patient groups diagnosed with spinocerebellar ataxia type 2 (herein referred to as SCA2c) or PD with or without ATXN2 triplet expansions (named SCA2p). The transcriptome profiles of these 40 patients revealed three main observations: i) a specific pattern of pathways related to cellular contacts, proliferation and differentiation associated with SCA2p group, ii) similarities between the SCA2p and sporadic PD groups in genes and pathways known to be altered in PD such as Wnt, Ephrin and Leukocyte extravasation signaling iii) RNA metabolism disturbances with "RNA-binding" and "poly(A) RNA-binding" as a common feature in all groups. Remarkably, disturbances of ALS signaling were shared between SCA2p and sporadic PD suggesting common molecular dysfunctions in PD and ALS including CACNA1, hnRNP, DDX and PABPC gene family perturbations. Interestingly, the transcriptome profiles of patients with parkinsonian phenotypes were prevalently associated with alterations of translation while SCA2c and PD patients presented perturbations of splicing. While ATXN2 RNA expression was not perturbed, its protein expression in immortalized lymphoblastoid cells was significantly decreased in SCA2c and SCA2p versus control groups assuming post-transcriptional biological perturbations. In conclusion, the transcriptome data do not exclude the role of ATXN2 mutated alleles in PD but its decrease protein expression in both SCA2c and SCA2p patients suggest a potential involvement of this gene in PD. The perturbations of "RNA-binding" and "poly(A) RNA-binding" molecular functions in the three patient groups as well as gene deregulations of factors not yet described in PD but known to be deleterious in other neurological conditions, suggest the existence of RNA-binding disturbances as a continuum between spinocerebellar ataxia type 2 and Parkinson's disease.
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Affiliation(s)
- Aurore Nkiliza
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Eugénie Mutez
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Clémence Simonin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Aurélie Duflot
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Pierre Semaille
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Thomas Comptdaer
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Alexandre Genet
- CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - Bernard Sablonnière
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - David Devos
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Luc Defebvre
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Alain Destée
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Marie-Christine Chartier-Harlin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France.
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50
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Choteau L, Vasseur F, Lepretre F, Figeac M, Gower-Rousseau C, Dubuquoy L, Poulain D, Colombel JF, Sendid B, Jawhara S. Corrigendum: Polymorphisms in the Mannose-Binding Lectin Gene are Associated with Defective Mannose-Binding Lectin Functional Activity in Crohn's Disease Patients. Sci Rep 2016; 6:33426. [PMID: 27633086 PMCID: PMC5025643 DOI: 10.1038/srep33426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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