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Limousin W, Laurent-Puig P, Ziol M, Ganne-Carrié N, Nahon P, Ait-Omar A, Seror O, Sidali S, Campani C, Blanc P, Lermine A, Marisa L, Zucman-Rossi J, Nault JC. Molecular-based targeted therapies in patients with hepatocellular carcinoma and hepato-cholangiocarcinoma refractory to atezolizumab/bevacizumab. J Hepatol 2023; 79:1450-1458. [PMID: 37647991 DOI: 10.1016/j.jhep.2023.08.017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND & AIMS The "French Medicine Genomic program 2025" has been designed to give patients with cancers that are refractory to systemic treatments access to off-label therapies adapted to their specific genomic profile. Herein, we reported the results of this program in patients with advanced hepatocellular carcinoma (HCC) and hepato-cholangiocarcinoma (H-CCK). METHODS In one center, all patients with HCC or H-CCK who progressed under atezolizumab/bevacizumab with available tumor frozen samples benefited from whole-genome/-exome and RNA sequencing. Targeted therapies were matched to genomic alterations following the recommendations of a molecular tumor board and radiological response and overall survival were assessed. RESULTS Among 135 patients with HCC and H-CCK treated by atezolizumab/bevacizumab, 20 patients benefited from genomic analysis after progression (16 HCC; 4 H-CCK). Nineteen patients had analyzable data, 70% were male, median age was 57 years, 65% had metastatic disease and 45% had vascular invasion. Among these 19 patients, 14 patients (76%) harbored at least one actionable genomic alteration and 9/14 received an adapted targeted therapy (45%). One patient with H-CCK showing CDK4 amplification was treated with palbociclib and achieved a partial radiological response for 16 months. Another patient with H-CCK, high HER2 overexpression and a high homologous recombination score was treated with trastuzumab/olaparib and had stable disease. One patient with an HCC and bi-allelic inactivation of TSC2 achieved a complete radiological response under everolimus. The remaining six treated patients (all HCC) had progressive disease, including three patients treated with trametinib, two with everolimus and one with olaparib. CONCLUSION Molecular-based guided therapy is feasible in patients with HCC/H-CCK progressing under atezolizumab/bevacizumab and may be useful in a small subset of patients. IMPACT AND IMPLICATIONS The use of whole-genome/-exome and RNA sequencing in clinical practice has not been reported in patients with hepatocellular carcinoma and hepato-cholangiocarcinoma. Herein, we performed a pilot study which suggested that whole-genome/-exome and RNA sequencing is feasible on tumor biopsies from patients refractory to atezolizumab/bevacizumab, with a small subset of patients exhibiting at least one actionable genomic alteration and receiving an adapted targeted therapy. This proof-of-concept study suggests that this clinical strategy could benefit a small subset of patients. Finally, validation of this approach will be required in a larger cohort of patients.
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Affiliation(s)
- Wendy Limousin
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
| | - Pierre Laurent-Puig
- Cordeliers Research Center, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, Paris, France; Multi-site Medical Biology Laboratory SeqOIA, Paris, France; Institut of Cancer Paris CARPEM, AP-HP-Hôpital Européen Georges Pompidou, Paris, France
| | - Marianne Ziol
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Pathology Department, and Centre de ressources biologiques (BB-0033-00027) Hôpitaux Universitaires Paris-Seine-Saint-Denis Avicenne Avicenne Hospital, APHP, Bobigny, France
| | - Nathalie Ganne-Carrié
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Liver Unit, Avicenne Hospital, APHP, Bobigny, France
| | - Pierre Nahon
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Institut of Cancer Paris CARPEM, AP-HP-Hôpital Européen Georges Pompidou, Paris, France
| | - Amal Ait-Omar
- Gastroenterology Unit, Avicenne Hospital, APHP, Bobigny, France
| | - Olivier Seror
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Interventional Radiology Unit, Avicenne Hospital, APHP, Bobigny, France
| | - Sabrina Sidali
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Liver Unit, Paris Cité University, Beaujon Hospital, APHP, DMU DIGEST, Clichy, France
| | - Claudia Campani
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Department of Experimental and Clinical Medicine, Internal Medicine and Hepatology Unit, University of Florence, Florence, Italy
| | - Pierre Blanc
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France
| | - Alban Lermine
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France
| | | | - Jessica Zucman-Rossi
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
| | - Jean-Charles Nault
- Cordeliers Research Center, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France; Liver Unit, Avicenne Hospital, APHP, Bobigny, France.
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Garinet S, Didelot A, Marisa L, Beinse G, Sroussi M, Le Pimpec-Barthes F, Fabre E, Gibault L, Laurent-Puig P, Mouillet-Richard S, Legras A, Blons H. A novel Chr1-miR-200 driven whole transcriptome signature shapes tumor immune microenvironment and predicts relapse in early-stage lung adenocarcinoma. J Transl Med 2023; 21:324. [PMID: 37189151 DOI: 10.1186/s12967-023-04086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/25/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND In Lung adenocarcinoma (LUAD), targeted therapies and immunotherapies have moved from metastatic to early stage and stratification of the relapse risk becomes mandatory. Here we identified a miR-200 based RNA signature that delineates Epithelial-to-mesenchymal transition (EMT) heterogeneity and predicts survival beyond current classification systems. METHODS A miR-200 signature was identified using RNA sequencing. We scored the miR-200 signature by WISP (Weighted In Silico Pathology), used GSEA to identify pathway enrichments and MCP-counter to characterize immune cell infiltrates. We evaluate the clinical value of this signature in our series of LUAD and using TCGA and 7 published datasets. RESULTS We identified 3 clusters based on supervised classification: I is miR-200-sign-down and enriched in TP53 mutations IIA and IIB are miR-200-sign-up: IIA is enriched in EGFR (p < 0.001), IIB is enriched in KRAS mutation (p < 0.001). WISP stratified patients into miR-200-sign-down (n = 65) and miR-200-sign-up (n = 42). Several biological processes were enriched in MiR-200-sign-down tumors, focal adhesion, actin cytoskeleton, cytokine/receptor interaction, TP53 signaling and cell cycle pathways. Fibroblast, immune cell infiltration and PDL1 expression were also significantly higher suggesting immune exhaustion. This signature stratified patients into high-vs low-risk groups, miR-200-sign-up had higher DFS, median not reached at 60 vs 41 months and within subpopulations with stage I, IA, IB, or II. Results were validated on TCGA data on 7 public datasets. CONCLUSION This EMT and miR-200-related prognostic signature refines prognosis evaluation independently of tumor stage and paves the way towards assessing the predictive value of this LUAD clustering to optimize perioperative treatment.
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Affiliation(s)
- Simon Garinet
- Assistance Publique-Hôpitaux de Paris, Department of Biochemistry, Pharmacogenetics and Molecular Oncology, European Georges Pompidou Hospital, Paris Cancer Institute CARPEM, 20 Rue Leblanc, 75015, Paris, France.
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France.
- Department of Genetics and Molecular Medicine, Georges Pompidou European Hospital, APHP Centre, Paris, France.
| | - Audrey Didelot
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France
| | - Laetitia Marisa
- Department of Genetics and Molecular Medicine, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Guillaume Beinse
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France
| | - Marine Sroussi
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France
| | | | - Elizabeth Fabre
- Department of Thoracic Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Laure Gibault
- Department of Pathology, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France
- Department of Genetics and Molecular Medicine, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France
| | - Antoine Legras
- Department of Thoracic Surgery, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Hélène Blons
- Assistance Publique-Hôpitaux de Paris, Department of Biochemistry, Pharmacogenetics and Molecular Oncology, European Georges Pompidou Hospital, Paris Cancer Institute CARPEM, 20 Rue Leblanc, 75015, Paris, France.
- Centre de Recherche des Cordeliers, INSERM, Team Personalized Medicine, Pharmacogenomics and Therapeutic Optimization (MEPPOT), Université de Paris, Sorbonne Université, Paris, France.
- Department of Genetics and Molecular Medicine, Georges Pompidou European Hospital, APHP Centre, Paris, France.
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3
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Evin C, Just PA, Borghese B, Fabiano E, Bennani S, Canny E, Marisa L, Derive N, Laurent-Puig P, Alexandre J, Durdux C. Adenoid cystic carcinoma of Bartholin's gland, a case report with genomic data and literature review. Cancer Radiother 2023:S1278-3218(23)00008-2. [PMID: 36759241 DOI: 10.1016/j.canrad.2023.01.001] [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: 01/11/2023] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
Adenoid cystic carcinoma of the Bartholin's gland (ACCBG) is a rare, slowly but aggressive malignancy. We reported the case of a 31-year-old woman who was treated by local excision and then hemi-vulvectomy, with positive margins and perineural invasion. Radiation therapy (RT) was then performed delivering 45Gy in 25 fractions in bilateral inguinal lymph nodes and 64.8Gy in 36 fractions on the vulvar area. After 30 months, there was no local relapse (LR) but the patient presented a histologically documented lung recurrence. Genomic profiling of the tumor showed a MYB-NFIB fusion transcript and a somatic mutation of PLCG1. A treatment by Lenvatinib was started. We conducted a literature review of 100 published cases. Patients were mainly treated by radical vulvectomy (30%), hemi-vulvectomy (17%), wide or local excision (21% and 24%, respectively) or other. Forty-four percent of patients received postoperative RT, more frequently in case of positive margin (71.9% versus 29.5%). RT may reduce the risk of LR regardless of margin status, with 15.4% vs. 41.9% of LR with or without RT, respectively, in patients with negative margins, and 13% vs. 33.3% of LR with or without RT, respectively, in patients with positive margins. The risk of relapse of any type was 40.9% in patients who received adjuvant RT vs. 48.2% in patients who did not. Median time to relapse was 24 months (range 6-156 months). The most frequent metastatic sites were lung (76.7%) and bone (26.7%). Optimal treatment for ACCBG is still not clearly defined but pooling the data from published case report help us better understand this rare disease and help in the therapeutic decision.
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Affiliation(s)
- C Evin
- Service d'oncologie radiothérapie, université Paris-Cité, centre, hôpital européen Georges-Pompidou, AP-HP, Paris, France.
| | - P-A Just
- Service de pathologie, université Paris-Cité, centre, hôpital Cochin, AP-HP, Paris, France
| | - B Borghese
- Service de chirurgie et cancérologie gynécologique, médecine de la reproduction, université Paris-Cité, centre, hôpital Cochin, AP-HP, Paris, France
| | - E Fabiano
- Service d'oncologie radiothérapie, université Paris-Cité, centre, hôpital européen Georges-Pompidou, AP-HP, Paris, France
| | - S Bennani
- Service de radiologie A, université Paris-Cité, centre, hôpital Cochin, AP-HP, Paris, France
| | - E Canny
- Service de chirurgie thoracique, université Paris-Cité, centre, hôpital Cochin, AP-HP, Paris, France
| | - L Marisa
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France
| | - N Derive
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France
| | - P Laurent-Puig
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France; Institut du cancer Paris CARPEM, centre, hôpital Européen Georges Pompidou, AP-HP, 75000 Paris, France
| | - J Alexandre
- Service d'oncologie médicale, université Paris-Cité, centre, hôpital Cochin, AP-HP, Paris, France
| | - C Durdux
- Service d'oncologie radiothérapie, université Paris-Cité, centre, hôpital européen Georges-Pompidou, AP-HP, Paris, France
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4
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Hamdan D, Marisa L, Tlemsani C, Angeli E, Soussan M, Derive N, Laurent-Puig P, Bousquet G. Olaparib in the Setting of Radiotherapy-Associated Sarcoma: What Can Precision Medicine Offer For Rare Cancers? JCO Precis Oncol 2023; 7:e2200582. [PMID: 36848605 DOI: 10.1200/po.22.00582] [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: 03/01/2023] Open
Affiliation(s)
- Diaddin Hamdan
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Medical Oncology Department, Hôpital La Porte Verte, Versailles, France
| | | | - Camille Tlemsani
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France.,Medical Oncology Department, Hôpital Cochin, AP-HP, Paris, France.,Université Paris Cité, Paris, France
| | - Eurydice Angeli
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Université Sorbonne Paris Nord, Villetaneuse, France.,Medical Oncology Department, AP-HP-Hôpital Avicenne, Bobigny, France
| | - Michael Soussan
- Université Sorbonne Paris Nord, Villetaneuse, France.,Nuclear Medicine Departments, AP-HP-Hôpital Avicenne, Bobigny, France
| | - Nicolas Derive
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France
| | - Pierre Laurent-Puig
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France.,Institut of Cancer Paris CARPEM, AP-HP-Hôpital Européen Georges Pompidou, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, Paris, France
| | - Guilhem Bousquet
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Université Sorbonne Paris Nord, Villetaneuse, France.,Medical Oncology Department, AP-HP-Hôpital Avicenne, Bobigny, France
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5
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Marisa L, Blum Y, Taieb J, Ayadi M, Pilati C, Le Malicot K, Lepage C, Salazar R, Aust D, Duval A, Blons H, Taly V, Gentien D, Rapinat A, Selves J, Mouillet-Richard S, Boige V, Emile JF, de Reyniès A, Laurent-Puig P. Intratumor CMS Heterogeneity Impacts Patient Prognosis in Localized Colon Cancer. Clin Cancer Res 2021; 27:4768-4780. [PMID: 34168047 PMCID: PMC8974433 DOI: 10.1158/1078-0432.ccr-21-0529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE The consensus molecular subtypes (CMS) represent a significant advance in the understanding of intertumor heterogeneity in colon cancer. Intratumor heterogeneity (ITH) is the new frontier for refining prognostication and understanding treatment resistance. This study aims at deciphering the transcriptomic ITH of colon cancer and understanding its potential prognostic implications. EXPERIMENTAL DESIGN We deconvoluted the transcriptomic profiles of 1,779 tumors from the PETACC8 trial and 155 colon cancer cell lines as weighted sums of the four CMSs, using the Weighted In Silico Pathology (WISP) algorithm. We assigned to each tumor and cell line a combination of up to three CMS subtypes with a threshold above 20%. RESULTS Over 55% of tumors corresponded to mixtures of at least two CMSs, demonstrating pervasive ITH in colon cancer. Of note, ITH was associated with shorter disease-free survival (DFS) and overall survival, [HR, 1.34; 95% confidence interval (CI; 1.12-1.59), 1.40, 95% CI (1.14-1.71), respectively]. Moreover, we uncovered specific combinations of CMS associated with dismal prognosis. In multivariate analysis, ITH represents the third parameter explaining DFS variance, after T and N stages. At a cellular level, combined WISP and single-cell transcriptomic analysis revealed that most colon cancer cell lines are a mixture of cells falling into different CMSs, indicating that ITH may correspond to distinct functional statuses of colon cancer cells. CONCLUSIONS This study shows that CMS-based transcriptomic ITH is frequent in colon cancer and impacts its prognosis. CMS-based transcriptomic ITH may correspond to distinct functional statuses of colon cancer cells, suggesting plasticity between CMS-related cell populations. Transcriptomic ITH deserves further assessment in the context of personalized medicine.
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Affiliation(s)
- Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Julien Taieb
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Camilla Pilati
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Karine Le Malicot
- Fédération Francophone de Cancérologie Digestive, INSERM, Université de Bourgogne et Franche Comté, Dijon, France
| | - Côme Lepage
- Fédération Francophone de Cancérologie Digestive, INSERM, Université de Bourgogne et Franche Comté, Dijon, France.,Hepatogastroenterology and Digestive Oncology department, CHU Dijon, Dijon, France
| | - Ramon Salazar
- Catalan Institute of Oncology (IDIBELL), Universitat de Barcelona, CIBERONC, Spanish Gastrointestinal Tumors TTD Group, Barcelona, Spain
| | - Daniela Aust
- Institute for Pathology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Alex Duval
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Equipe Instabilité des Microsatellites et Cancer, équipe labellisé par la Ligue Nationale contre le Cancer, Paris, France
| | - Hélène Blons
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Valérie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - David Gentien
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Audrey Rapinat
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Janick Selves
- Centre de Recherche en Cancérologie de Toulouse, INSERM, Université Toulouse III, Department of Pathology, CHU Toulouse, Toulouse, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France
| | - Valérie Boige
- Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France.,Department of Cancer Medicine, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean-François Emile
- Department of Pathology, AP-HP, Hôpital Ambroise Paré, Boulogne-Billancourt, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.,Corresponding Authors: Pierre Laurent-Puig, UMR-S1138, Université Paris Descartes, 15 rue de l'Ecole de Médecine, Paris 75006, France. Phone: 336-0843-7691; E-mail: ; and Aurélien de Reyniès,
| | - Pierre Laurent-Puig
- Institut du cancer Paris CARPEM, AP-HP, European Georges Pompidou Hospital, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris, Paris, France.,Corresponding Authors: Pierre Laurent-Puig, UMR-S1138, Université Paris Descartes, 15 rue de l'Ecole de Médecine, Paris 75006, France. Phone: 336-0843-7691; E-mail: ; and Aurélien de Reyniès,
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6
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Beck M, Baranger M, Moufok-Sadoun A, Bersuder E, Hinkel I, Mellitzer G, Martin E, Marisa L, Duluc I, de Reynies A, Gaiddon C, Freund JN, Gross I. The atypical cadherin MUCDHL antagonizes colon cancer formation and inhibits oncogenic signaling through multiple mechanisms. Oncogene 2020; 40:522-535. [PMID: 33188295 DOI: 10.1038/s41388-020-01546-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 01/24/2023]
Abstract
Cadherins form a large and pleiotropic superfamily of membranous proteins sharing Ca2+-binding repeats. While the importance of classic cadherins such as E- or N-cadherin for tumorigenesis is acknowledged, there is much less information about other cadherins that are merely considered as tissue-specific adhesion molecules. Here, we focused on the atypical cadherin MUCDHL that stood out for its unusual features and unique function in the gut. Analyses of transcriptomic data sets (n > 250) established that MUCDHL mRNA levels are down-regulated in colorectal tumors. Importantly, the decrease of MUCDHL expression is more pronounced in the worst-prognosis subset of tumors and is associated with decreased survival. Molecular characterization of the tumors indicated a negative correlation with proliferation-related processes (e.g., nucleic acid metabolism, DNA replication). Functional genomic studies showed that the loss of MUCDHL enhanced tumor incidence and burden in intestinal tumor-prone mice. Extensive structure/function analyses revealed that the mode of action of MUCDHL goes beyond membrane sequestration of ß-catenin and targets through its extracellular domain key oncogenic signaling pathways (e.g., EGFR, AKT). Beyond MUCDHL, this study illustrates how the loss of a gene critical for the morphological and functional features of mature cells contributes to tumorigenesis by dysregulating oncogenic pathways.
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Affiliation(s)
- Marine Beck
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Mathilde Baranger
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Ahlam Moufok-Sadoun
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Emilie Bersuder
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Isabelle Hinkel
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Georg Mellitzer
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | | | - Isabelle Duluc
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | | | - Christian Gaiddon
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Jean-Noel Freund
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France
| | - Isabelle Gross
- Université de Strasbourg, Inserm, IRFAC UMR-S1113, 67200, Strasbourg, France.
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7
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Le Corre D, Ghazi A, Balogoun R, Pilati C, Aparicio T, Martin-Lannerée S, Marisa L, Djouadi F, Poindessous V, Crozet C, Emile JF, Mulot C, Le Malicot K, Boige V, Blons H, de Reynies A, Taieb J, Ghiringhelli F, Bennouna J, Launay JM, Laurent-Puig P, Mouillet-Richard S. The cellular prion protein controls the mesenchymal-like molecular subtype and predicts disease outcome in colorectal cancer. EBioMedicine 2019; 46:94-104. [PMID: 31377347 PMCID: PMC6710984 DOI: 10.1016/j.ebiom.2019.07.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 05/27/2019] [Revised: 07/10/2019] [Accepted: 07/14/2019] [Indexed: 02/08/2023] Open
Abstract
Background Comprehensive transcriptomic analyses have shown that colorectal cancer (CRC) is heterogeneous and have led to the definition of molecular subtypes among which the stem-cell, mesenchymal-like group is associated with poor prognosis. The molecular pathways orchestrating the emergence of this subtype are incompletely understood. In line with the contribution of the cellular prion protein PrPC to stemness, we hypothesize that deregulation of this protein could lead to a stem-cell, mesenchymal-like phenotype in CRC. Methods We assessed the distribution of the PrPC-encoding PRNP mRNA in two large CRC cohorts according to molecular classification and its association with patient survival. We developed cell-based assays to explore the impact of gain and loss of PrPC function on markers of the mesenchymal subtype and to delineate the signalling pathways recruited by PrPC. We measured soluble PrPC in the plasmas of 325 patients with metastatic CRC and probed associations with disease outcome. Findings We found that PRNP gene expression is enriched in tumours of the mesenchymal subtype and is associated with poor survival. Our in vitro analyses revealed that PrPC controls the expression of genes that specify the mesenchymal subtype through the recruitment of the Hippo pathway effectors YAP and TAZ and the TGFß pathway. We showed that plasma levels of PrPC are elevated in metastatic CRC and are associated with poor disease control. Interpretation Our findings define PrPC as a candidate driver of the poor-prognosis mesenchymal subtype of CRC. They suggest that PrPC may serve as a potential biomarker for patient stratification in CRC. Funding Grant support was provided by the following: Cancéropôle Ile de France (grant number 2016-1-EMERG-36-UP 5-1), Association pour la Recherche sur le Cancer (grant number PJA 20171206220), SATT Ile de France Innov (grant number 415) as well as INSERM.
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Affiliation(s)
- Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Alexandre Ghazi
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Ralyath Balogoun
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Camilla Pilati
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Thomas Aparicio
- Department of Gastroenterology and Digestive Oncology, AP-HP, Hôpital Saint-Louis, Université Paris Diderot, F-75010 Paris, France
| | - Séverine Martin-Lannerée
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Laetitia Marisa
- Programme "Cartes d'Identité des Tumeurs", Ligue Nationale Contre le Cancer, F-75013 Paris, France
| | - Fatima Djouadi
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Virginie Poindessous
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Carole Crozet
- Institut de Médecine Régénératrice et de Biothérapie (I.M.R.B.), Université de Montpellier UMR-1183, Centre Hospitalo-Universitaire de Montpellier, F-34000 Montpellier, France
| | - Jean-François Emile
- Department of Pathology, AP-HP, Hôpital Ambroise Paré, F-92100 Boulogne-Billancourt, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Karine Le Malicot
- Fédération Francophone de Cancérologie Digestive, EPICAD INSERM LNC-UMR 1231, Université de Bourgogne et and Franche Comté, F-21000 Dijon, France
| | - Valérie Boige
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France; Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, F-94800 Villejuif, France
| | - Hélène Blons
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France; Department of Biology, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Aurélien de Reynies
- Programme "Cartes d'Identité des Tumeurs", Ligue Nationale Contre le Cancer, F-75013 Paris, France
| | - Julien Taieb
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France; Department of Gastroenterology and GI Oncology, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - François Ghiringhelli
- Department of Medical Oncology, Centre Georges-François Leclerc, F-21000 Dijon, France
| | - Jaafar Bennouna
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest, F-44800 Saint-Herblain, France
| | - Jean-Marie Launay
- Department of Biochemistry and Molecular Biology, INSERM U942, AP-HP, Hôpital Lariboisière, Université Paris Descartes, F-75010 Paris, France; Pharma Research Department, F. Hoffmann-La-Roche Ltd., CH-4070 Basel, Switzerland
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France; Department of Biology, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France.
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8
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Libanje F, Raingeaud J, Luan R, Thomas Z, Zajac O, Veiga J, Marisa L, Adam J, Boige V, Malka D, Goéré D, Hall A, Soazec J, Prall F, Gelli M, Dartigues P, Jaulin F. ROCK2 inhibition triggers the collective invasion of colorectal adenocarcinomas. EMBO J 2019; 38:e99299. [PMID: 31304629 PMCID: PMC6627234 DOI: 10.15252/embj.201899299] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 02/22/2018] [Revised: 04/19/2019] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
Abstract
The metastatic progression of cancer is a multi-step process initiated by the local invasion of the peritumoral stroma. To identify the mechanisms underlying colorectal carcinoma (CRC) invasion, we collected live human primary cancer specimens at the time of surgery and monitored them ex vivo. This revealed that conventional adenocarcinomas undergo collective invasion while retaining their epithelial glandular architecture with an inward apical pole delineating a luminal cavity. To identify the underlying mechanisms, we used microscopy-based assays on 3D organotypic cultures of Caco-2 cysts as a model system. We performed two siRNA screens targeting Rho-GTPases effectors and guanine nucleotide exchange factors. These screens revealed that ROCK2 inhibition triggers the initial leader/follower polarization of the CRC cell cohorts and induces collective invasion. We further identified FARP2 as the Rac1 GEF necessary for CRC collective invasion. However, FARP2 activation is not sufficient to trigger leader cell formation and the concomitant inhibition of Myosin-II is required to induce invasion downstream of ROCK2 inhibition. Our results contrast with ROCK pro-invasive function in other cancers, stressing that the molecular mechanism of metastatic spread likely depends on tumour types and invasion mode.
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Affiliation(s)
| | | | - Rui Luan
- INSERM U‐981Gustave RoussyVillejuifFrance
| | | | - Olivier Zajac
- INSERM U‐981Gustave RoussyVillejuifFrance
- Present address:
Department of Translational ResearchCurie InstituteParisFrance
| | - Joel Veiga
- Cell Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
- Present address:
Imagine InstituteParisFrance
| | - Laetitia Marisa
- Programme “Cartes d'Identité des Tumeurs”Ligue Nationale Contre le CancerParisFrance
| | - Julien Adam
- Pathology DepartmentGustave RoussyVillejuifFrance
| | | | - David Malka
- Digestive Cancer UnitGustave RoussyVillejuifFrance
| | - Diane Goéré
- Digestive Cancer UnitGustave RoussyVillejuifFrance
| | - Alan Hall
- Cell Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
| | | | - Friedrich Prall
- Institute of PathologyUniversity Medicine of RostockRostockGermany
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9
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Puleo F, Nicolle R, Blum Y, Cros J, Marisa L, Demetter P, Quertinmont E, Svrcek M, Elarouci N, Iovanna J, Franchimont D, Verset L, Galdon MG, Devière J, de Reyniès A, Laurent-Puig P, Van Laethem JL, Bachet JB, Maréchal R. Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features. Gastroenterology 2018; 155:1999-2013.e3. [PMID: 30165049 DOI: 10.1053/j.gastro.2018.08.033] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genomic studies have revealed subtypes of pancreatic ductal adenocarcinoma (PDA) based on their molecular features, but different studies have reported different classification systems. It is a challenge to obtain high-quality, freshly frozen tissue for clinical analysis and determination of PDA subtypes. We aimed to redefine subtypes of PDA using a large number of formalin-fixed and paraffin-embedded PDA samples, which are more amenable to routine clinical evaluation. METHODS We collected PDA samples from 309 consecutive patients who underwent surgery from September 1996 through December 2010 at 4 academic hospitals in Europe; nontumor tissue samples were not included. Samples were formalin fixed and paraffin embedded. DNA and RNA were isolated; gene expression, targeted DNA sequencing, and immunohistochemical analyses were performed. We used independent component analysis to deconvolute normal, tumor, and microenvironment transcriptome patterns in samples. We devised classification systems from an unsupervised analysis using a consensus clustering approach of our data set after removing normal contamination components. We associated subtypes with overall survival and disease-free survival of patients using Cox proportional hazards regression with estimation of hazard ratios and 95% confidence interval. We used The Cancer Genome Consortium and International Cancer Genome Consortium PDA data sets as validation cohorts. RESULTS We validated the previously reported basal-like and classical tumor-specific subtypes of PDAs. We identified features of the PDA, including microenvironment gene expression patterns, that allowed tumors to be categorized into 5 subtypes, called pure basal like, stroma activated, desmoplastic, pure classical, and immune classical. These PDA subtypes have features of cancer cells and immune cells that could be targeted by pharmacologic agents. Tumor subtypes were associated with patient outcomes, based on analysis of our data set and the International Cancer Genome Consortium and The Cancer Genome Consortium PDA data sets. We also observed an exocrine signal associated with acinar cell contamination (from pancreatic tissue). CONCLUSIONS We identified a classification system based on gene expression analysis of formalin-fixed PDA samples. We identified 5 PDA subtypes, based on features of cancer cells and the tumor microenvironment. This system might be used to select therapies and predict patient outcomes. We found evidence that the previously reported exocrine-like (called ADEX) tumor subtype resulted from contamination with pancreatic acinar cells. ArrayExpress accession number: E-MTAB-6134.
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Affiliation(s)
- Francesco Puleo
- Medical Oncology Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium.
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Jérôme Cros
- Department of Pathology, Beaujon Hospital-Paris Diderot University, Clichy, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | | | - Eric Quertinmont
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Svrcek
- Department of Pathology, Saint-Antoine Hospital, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Denis Franchimont
- Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Erasme Hospital, Brussels, Belgium
| | - Maria Gomez Galdon
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Devière
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Pierre Laurent-Puig
- Université Paris Descartes UMRS-1147; Assistance Publique Hopitaux de Paris Hopital Européen Georges Pompidou, Paris, France
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
| | - Jean-Baptiste Bachet
- Sorbonne Universités, UPMC Université, Department of Gastroenterology, Pitié-Salpetriére Hospital, Paris, France
| | - Raphaël Maréchal
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology and Digestive Oncology, Erasme Hospital, Brussels, Belgium
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10
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Weinstein AM, Giraldo NA, Petitprez F, Julie C, Lacroix L, Peschaud F, Emile JF, Marisa L, Fridman WH, Storkus WJ, Sautès-Fridman C. Association of IL-36γ with tertiary lymphoid structures and inflammatory immune infiltrates in human colorectal cancer. Cancer Immunol Immunother 2018; 68:109-120. [PMID: 30315348 DOI: 10.1007/s00262-018-2259-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [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: 02/23/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023]
Abstract
IL-1 family cytokines play a dual role in the gut, with different family members contributing either protective or pathogenic effects. IL-36γ is an IL-1 family cytokine involved in polarizing type-1 immune responses. However, its function in the gut, including in colorectal cancer pathogenesis, is not well appreciated. In a murine model of colon carcinoma, IL-36γ controls tertiary lymphoid structure formation and promotes a type-1 immune response concurrently with a decrease in expression of immune checkpoint molecules in the tumor microenvironment. Here, we demonstrate that IL-36γ plays a similar role in driving a pro-inflammatory phenotype in human colorectal cancer. We analyzed a cohort of 33 primary colorectal carcinoma tumors using imaging, flow cytometry, and transcriptomics to determine the pattern and role of IL-36γ expression in this disease. In the colorectal tumor microenvironment, we observed IL-36γ to be predominantly expressed by M1 macrophages and cells of the vasculature, including smooth muscle cells and high endothelial venules. This pattern of IL-36γ expression is associated with a CD4+ central memory T cell infiltrate and an increased density of B cells in tertiary lymphoid structures, as well as with markers of fibrosis. Conversely, expression of the antagonist to IL-36 signaling, IL-1F5, was associated with intratumoral expression of checkpoint molecules, including PD-1, PD-L1, and CTLA4, which can suppress the immune response. These data support a role for IL-36γ in the physiologic immune response to colorectal cancer by sustaining inflammation within the tumor microenvironment.
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Affiliation(s)
- Aliyah M Weinstein
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France.
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France.
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France.
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
| | - Nicolas A Giraldo
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Pathology Department, Johns Hopkins Hospital, Baltimore, MD, 21287, USA
| | - Florent Petitprez
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Programme Cartes d'Identités des Tumeurs, Ligue Nationale contre le Cancer, 75013, Paris, France
| | - Catherine Julie
- Laboratoire d'anatomie pathologique, Hopital Ambroise Paré, AP-HP, Boulogne, France
- EA4340, Université de Versailles SQY, Université Paris Saclay, Boulogne, France
| | - Laetitia Lacroix
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Frédérique Peschaud
- Laboratoire d'anatomie pathologique, Hopital Ambroise Paré, AP-HP, Boulogne, France
- EA4340, Université de Versailles SQY, Université Paris Saclay, Boulogne, France
| | - Jean-François Emile
- Laboratoire d'anatomie pathologique, Hopital Ambroise Paré, AP-HP, Boulogne, France
- EA4340, Université de Versailles SQY, Université Paris Saclay, Boulogne, France
| | - Laetitia Marisa
- Programme Cartes d'Identités des Tumeurs, Ligue Nationale contre le Cancer, 75013, Paris, France
| | - Wolf H Fridman
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Walter J Storkus
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Pathology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Bioengineering, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Catherine Sautès-Fridman
- INSERM, UMR_S 1138, Cordeliers Research Center, Team "Cancer, Immune Control and Escape", 75006, Paris, France
- University Paris Descartes, Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, 75006, Paris, France
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11
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Laurent-Puig P, Marisa L, Ayadi M, Blum Y, Balogoun R, Pilati C, Le Malicot K, Lepage C, Emile J, Salazar R, Aust D, Duval A, Selves J, Guenot D, Milano G, Seitz JF, Taieb J, Boige V, de Reyniès A. Colon cancer molecular subtype intratumoral heterogeneity and its prognostic impact: An extensive molecular analysis of the PETACC-8. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy269.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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12
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Jonchere V, Marisa L, Greene M, Guilloux A, Collura A, De Reynies A, Duval A. Identification of positively and negatively selected driver gene mutations associated with colorectal cancer with microsatellite instability. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy281.078] [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: 11/15/2022] Open
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13
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Uchuya-Castillo J, Aznar N, Frau C, Martinez P, Le Nevé C, Marisa L, Penalva LOF, Laurent-Puig P, Puisieux A, Scoazec JY, Samarut J, Ansieau S, Plateroti M. Increased expression of the thyroid hormone nuclear receptor TRα1 characterizes intestinal tumors with high Wnt activity. Oncotarget 2018; 9:30979-30996. [PMID: 30123421 PMCID: PMC6089551 DOI: 10.18632/oncotarget.25741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/12/2018] [Indexed: 01/10/2023] Open
Abstract
Our previous work demonstrated a key function of the thyroid hormone nuclear receptor TRα1, a T3-modulated transcription factor, in controlling intestinal development and homeostasis via the Wnt and Notch pathways. Importantly, increased expression of TRα1 in the intestinal epithelium in a mutated Apc genetic background (vil-TRα1/Apc+/1638N mice) accelerated tumorigenesis and contributed to a more aggressive tumor phenotype compared to that of the Apc mutants alone. Therefore, the aim of this study was to determine the relevance of this synergistic effect in human colorectal cancers and to gain insights into the mechanisms involved. We analyzed cohorts of patients by in silico and experimental approaches and observed increased TRα1 expression and a significant correlation between TRα1 levels and Wnt activity. TRα1 loss-of-function and gain-of-function in Caco2 cell lines not only confirmed that TRα1 levels control Wnt activity but also demonstrated the role of TRα1 in regulating cell proliferation and migration. Finally, upon investigation of the molecular mechanisms responsible for the Wnt-TRα1 association, we described the repression by TRα1 of several Wnt inhibitors, including Frzb, Sox17 and Wif1. In conclusion, our results underline an important functional interplay between the thyroid hormone nuclear receptor TRα1 and the canonical Wnt pathway in intestinal cancer initiation and progression. More importantly, we show for the first time that the expression of TRα1 is induced in human colorectal cancers.
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Affiliation(s)
- Joel Uchuya-Castillo
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Nicolas Aznar
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Carla Frau
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Pierre Martinez
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Clementine Le Nevé
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris 75000, France
| | - Luiz O F Penalva
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | | | - Alain Puisieux
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | | | - Jacques Samarut
- Institute de Génomique Fonctionnelle de Lyon, ENS de Lyon, Lyon 69342, France
| | - Stephane Ansieau
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
| | - Michelina Plateroti
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR5286, Université de Lyon, Université Lyon 1, Centre Léon Bérard, Département de la recherche, Lyon 69000, France
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14
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Jonchere V, Marisa L, Greene M, Virouleau A, Buhard O, Bertrand R, Svrcek M, Cervera P, Goloudina A, Guillerm E, Coulet F, Landman S, Ratovomanana T, Job S, Ayadi M, Elarouci N, Armenoult L, Merabtene F, Dumont S, Parc Y, Lefèvre JH, André T, Fléjou JF, Guilloux A, Collura A, de Reyniès A, Duval A. Identification of Positively and Negatively Selected Driver Gene Mutations Associated With Colorectal Cancer With Microsatellite Instability. Cell Mol Gastroenterol Hepatol 2018; 6:277-300. [PMID: 30116770 PMCID: PMC6089198 DOI: 10.1016/j.jcmgh.2018.06.002] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Recent studies have shown that cancers arise as a result of the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role, if any. However, these investigations were concerned with alterations at nonrepetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors showing microsatellite instability (MSI) resulting from mismatch repair deficiency investigated in the present study. METHODS We performed whole-exome sequencing of 47 MSI colorectal cancers (CRCs) and confirmed results in an independent cohort of 53 MSI CRCs. We used a probabilistic model of mutational events within microsatellites, while adapting pre-existing models to analyze nonrepetitive DNA sequences. Negatively selected coding alterations in MSI CRCs were investigated for their functional and clinical impact in CRC cell lines and in a third cohort of 164 MSI CRC patients. RESULTS Both positive and negative selection of somatic mutations in DNA repeats was observed, leading us to identify the expected true driver genes associated with the MSI-driven tumorigenic process. Several coding negatively selected MSI-related mutational events (n = 5) were shown to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations were observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio, 3; 95% CI, 1.1-7.9; P = .03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to a poor prognosis. CONCLUSIONS The present results identify the positive and negative driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation. Exome sequencing data have been deposited in the European genome-phenome archive (accession: EGAS00001002477).
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Key Words
- CRC, colorectal cancer
- Colorectal Cancer
- Driver Gene Mutations
- HR, hazard ratio
- MLH1, MutL Homolog 1
- MMR, mismatch repair
- MSH, MutS Homolog
- MSI, microsatellite instability
- Microsatellite Instability
- NR, nonrepetitive
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- Positive and Negative Selection
- R, repetitive
- RFS, relapse-free survival
- RTCA, Real-Time Cell Analyzer
- Tumorigenic Process
- UTR, untranslated region
- WES, whole-exome sequencing
- WGA, whole-genome amplification
- bp, base pair
- indel, insertion/deletion
- mRNA, messenger RNA
- shRNA, short hairpin RNA
- siRNA, small interfering RNA
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Affiliation(s)
- Vincent Jonchere
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Laetitia Marisa
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Malorie Greene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Alain Virouleau
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Olivier Buhard
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Romane Bertrand
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Magali Svrcek
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Pascale Cervera
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anastasia Goloudina
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Inovarion, Collaborative research Department Paris, France
| | - Erell Guillerm
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Florence Coulet
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Samuel Landman
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Toky Ratovomanana
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Lucile Armenoult
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Fatiha Merabtene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Sylvie Dumont
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Yann Parc
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Jérémie H. Lefèvre
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Thierry André
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Department of Oncology, Assistance publique - Hôpitaux de Paris, Hôpital Saint Antoine, Paris, France
| | - Jean-François Fléjou
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Agathe Guilloux
- Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Ada Collura
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Alex Duval
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Correspondence Address correspondence to: Alex Duval, MD, PhD, Sorbonne Universite, UPMC Univ Paris 06, Inserm, UMR938, Equipe Instabilite Des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France. fax: (33) 149284603.
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15
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Nicolle R, Blum Y, Marisa L, Dusetti N, Iovanna J. Des approches multi-omiques dévoilent de nouvelles cibles thérapeutiques pour le traitement du cancer du pancréas. Med Sci (Paris) 2018; 34:379-382. [DOI: 10.1051/medsci/20183405003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Romain B, Benbrika-Nehmar R, Marisa L, Legrain M, Lobstein V, Oravecz A, Poidevin L, Bour C, Freund JN, Duluc I, Guenot D, Pencreach E. Histone hypoacetylation contributes to CXCL12 downregulation in colon cancer: impact on tumor growth and cell migration. Oncotarget 2018; 8:38351-38366. [PMID: 28418886 PMCID: PMC5503537 DOI: 10.18632/oncotarget.16323] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 02/27/2017] [Indexed: 12/11/2022] Open
Abstract
CXCL12 has been shown to be involved in colon cancer metastasis, but its expression level and molecular mechanisms regulating its expression remain controversial. We thus evaluated CXCL12 expression in a large cohort of colon adenomas and carcinomas, investigated for an epigenetic mechanism controlling its expression and evaluated the impact of CXCL12 levels on cell migration and tumor growth. CXCL12 expression was measured in human colon adenomas and carcinomas with transcriptome array and RT-qPCR. The promoter methylation was analyzed with whole-genome DNA methylation chips and protein expression by immunohistochemistry. We confirm a reduced expression of CXCL12 in 75% of MSS carcinomas and show that the decrease is an early event as already present in adenomas. The methylome analysis shows that the CXCL12 promoter is methylated in only 30% of microsatellite-stable tumors. In vitro, treatments with HDAC inhibitors, butyrate and valproate restored CXCL12 expression in three colon cell lines, increased acetylation of histone H3 within the CXCL12 promoter and inhibited cell migration. In vivo, valproate diminished (65%) the number of intestinal tumors in APC mutant mice, slowed down xenograft tumor growth concomitant to restored CXCL12 expression. Finally we identified loss of PCAF expression in tumor samples and showed that forced expression of PCAF in colon cancer cell lines restored CXCL12 expression. Thus, reduced PCAF expression may participate to CXCL12 promoter hypoacetylation and its subsequent loss of expression. Our study is of potential clinical interest because agents that promote or maintain histone acetylation through HDAC inhibition and/or HAT stimulation, may help to lower colon adenoma/carcinoma incidence, especially in high-risk families, or could be included in therapeutic protocols to treat advanced colon cancer.
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Affiliation(s)
- Benoît Romain
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France.,Hôpitaux Universitaires de Strasbourg, Service de Chirurgie Générale et Digestive, Strasbourg, France
| | - Radhia Benbrika-Nehmar
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France
| | - Laetitia Marisa
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Michèle Legrain
- Hôpitaux Universitaires de Strasbourg, Laboratoire de Biochimie et Biologie Moléculaire, Strasbourg, France
| | - Viviane Lobstein
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France
| | - Attila Oravecz
- Université de Strasbourg, CNRS, Department of Computer Science, ICube, Strasbourg, France
| | - Laetitia Poidevin
- Université de Strasbourg, CNRS, Department of Computer Science, ICube, Strasbourg, France
| | - Cyril Bour
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France
| | | | - Isabelle Duluc
- Université de Strasbourg, INSERM Unit 1113, Strasbourg, France
| | - Dominique Guenot
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France
| | - Erwan Pencreach
- Université de Strasbourg, Progression Tumorale et Microenvironnement, Approches Translationnelles et Epidémiologie, Strasbourg, France.,Hôpitaux Universitaires de Strasbourg, Laboratoire de Biochimie et Biologie Moléculaire, Strasbourg, France.,Hôpitaux Universitaires de Strasbourg, Centre de Ressources Biologiques, Département de Pathologie, Strasbourg, France
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17
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Balbinot C, Armant O, Elarouci N, Marisa L, Martin E, De Clara E, Onea A, Deschamps J, Beck F, Freund JN, Duluc I. The Cdx2 homeobox gene suppresses intestinal tumorigenesis through non-cell-autonomous mechanisms. J Exp Med 2018; 215:911-926. [PMID: 29439001 PMCID: PMC5839756 DOI: 10.1084/jem.20170934] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/13/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
Balbinot et al. show that intestinal epithelial cells depleted in the homeobox gene Cdx2 acquire an imperfect gastric-type metaplastic phenotype that, through changes in the microenvironment, induces the tumorigenic evolution of adjacent Cdx2-intact cells without themselves becoming cancerous. Developmental genes contribute to cancer, as reported for the homeobox gene Cdx2 playing a tumor suppressor role in the gut. In this study, we show that human colon cancers exhibiting the highest reduction in CDX2 expression belong to the serrated subtype with the worst evolution. In mice, mosaic knockout of Cdx2 in the adult intestinal epithelium induces the formation of imperfect gastric-type metaplastic lesions. The metaplastic knockout cells do not spontaneously become tumorigenic. However, they induce profound modifications of the microenvironment that facilitate the tumorigenic evolution of adjacent Cdx2-intact tumor-prone cells at the surface of the lesions through NF-κB activation, induction of inducible nitric oxide synthase, and stochastic loss of function of Apc. This study presents a novel paradigm in that metaplastic cells, generally considered as precancerous, can induce tumorigenesis from neighboring nonmetaplastic cells without themselves becoming cancerous. It unveils the novel property of non–cell-autonomous tumor suppressor gene for the Cdx2 gene in the gut.
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Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Nabila Elarouci
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Marisa
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Elisabeth Martin
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Etienne De Clara
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Alina Onea
- Département de Pathologie, Centre Hospitalier Universitaire de Strasbourg, Strasbourg, France
| | - Jacqueline Deschamps
- Developmental Biology and Stem Cell Research, Hubrecht Institute, Utrecht, Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London, England, UK
| | - Jean-Noël Freund
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Isabelle Duluc
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
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18
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Nicolle R, Blum Y, Marisa L, Loncle C, Gayet O, Moutardier V, Turrini O, Giovannini M, Bian B, Bigonnet M, Rubis M, Elarouci N, Armenoult L, Ayadi M, Duconseil P, Gasmi M, Ouaissi M, Maignan A, Lomberk G, Boher JM, Ewald J, Bories E, Garnier J, Goncalves A, Poizat F, Raoul JL, Secq V, Garcia S, Grandval P, Barraud-Blanc M, Norguet E, Gilabert M, Delpero JR, Roques J, Calvo E, Guillaumond F, Vasseur S, Urrutia R, de Reyniès A, Dusetti N, Iovanna J. Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts. Cell Rep 2017; 21:2458-2470. [PMID: 29186684 PMCID: PMC6082139 DOI: 10.1016/j.celrep.2017.11.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023] Open
Abstract
Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC) xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively). Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.
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Affiliation(s)
- Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France.
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Celine Loncle
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Odile Gayet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Vincent Moutardier
- Hôpital Nord, Marseille, France; Aix Marseille Université, Marseille, France
| | - Olivier Turrini
- Aix Marseille Université, Marseille, France; Institut Paoli-Calmettes, Marseille, France
| | | | - Benjamin Bian
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Martin Bigonnet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Marion Rubis
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Lucile Armenoult
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Pauline Duconseil
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | - Aurélie Maignan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | | | | | - Jonathan Garnier
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Anthony Goncalves
- Aix Marseille Université, Marseille, France; Institut Paoli-Calmettes, Marseille, France
| | | | - Jean-Luc Raoul
- Aix Marseille Université, Marseille, France; Institut Paoli-Calmettes, Marseille, France
| | | | - Stephane Garcia
- Hôpital Nord, Marseille, France; Aix Marseille Université, Marseille, France
| | - Philippe Grandval
- Aix Marseille Université, Marseille, France; Hôpital de la Timone, Marseille, France
| | | | | | | | - Jean-Robert Delpero
- Aix Marseille Université, Marseille, France; Institut Paoli-Calmettes, Marseille, France
| | - Julie Roques
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Ezequiel Calvo
- Centre Génomique du Centre de Recherche du CHUL Research Center, Ville de Québec, QC, Canada
| | - Fabienne Guillaumond
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Sophie Vasseur
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Raul Urrutia
- Division of Research, Department of Surgery, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France.
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19
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Bian B, Bigonnet M, Gayet O, Loncle C, Maignan A, Gilabert M, Moutardier V, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Ouaissi M, Secq V, Poizat F, Nicolle R, Blum Y, Marisa L, Rubis M, Raoul JL, Bradner JE, Qi J, Lomberk G, Urrutia R, Saul A, Dusetti N, Iovanna J. Gene expression profiling of patient-derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts. EMBO Mol Med 2017; 9:482-497. [PMID: 28275007 PMCID: PMC5376755 DOI: 10.15252/emmm.201606975] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
c-MYC controls more than 15% of genes responsible for proliferation, differentiation, and cellular metabolism in pancreatic as well as other cancers making this transcription factor a prime target for treating patients. The transcriptome of 55 patient-derived xenografts show that 30% of them share an exacerbated expression profile of MYC transcriptional targets (MYC-high). This cohort is characterized by a high level of Ki67 staining, a lower differentiation state, and a shorter survival time compared to the MYC-low subgroup. To define classifier expression signature, we selected a group of 10 MYC target transcripts which expression is increased in the MYC-high group and six transcripts increased in the MYC-low group. We validated the ability of these markers panel to identify MYC-high patient-derived xenografts from both: discovery and validation cohorts as well as primary cell cultures from the same patients. We then showed that cells from MYC-high patients are more sensitive to JQ1 treatment compared to MYC-low cells, in monolayer, 3D cultured spheroids and in vivo xenografted tumors, due to cell cycle arrest followed by apoptosis. Therefore, these results provide new markers and potentially novel therapeutic modalities for distinct subgroups of pancreatic tumors and may find application to the future management of these patients within the setting of individualized medicine clinics.
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Affiliation(s)
- Benjamin Bian
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Martin Bigonnet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Odile Gayet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Celine Loncle
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Aurélie Maignan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Marine Gilabert
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Vincent Moutardier
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France.,Hôpital Nord, Marseille, France.,CIC1409, AP-HM-Hôpital Nord, Aix-Marseille Université, Marseille, France
| | - Stephane Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France.,Hôpital Nord, Marseille, France
| | - Olivier Turrini
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France.,Institut Paoli-Calmettes, Marseille, France
| | | | | | | | - Mohamed Gasmi
- Hôpital Nord, Marseille, France.,CIC1409, AP-HM-Hôpital Nord, Aix-Marseille Université, Marseille, France
| | | | | | | | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Marion Rubis
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | | | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gwen Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Departments of Biochemistry and Molecular Biology and Medicine, Mayo Clinic, Rochester, MN, USA
| | - Raul Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Departments of Biochemistry and Molecular Biology and Medicine, Mayo Clinic, Rochester, MN, USA
| | - Andres Saul
- Centre Interdisciplinaire de Nanoscience de Marseille-CNRS UMR 7325, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université, Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Parc Scientifique et Technologique de Luminy, Aix-Marseille Université and Institut Paoli-Calmettes, Marseille, France
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Marisa L, Svrcek M, Collura A, Becht E, Cervera P, Wanherdrick K, Buhard O, Goloudina A, Jonchère V, Selves J, Milano G, Guenot D, Cohen R, Colas C, Laurent-Puig P, Olschwang S, Lefèvre JH, Parc Y, Boige V, Lepage C, André T, Fléjou JF, Dérangère V, Ghiringhelli F, de Reynies A, Duval A. The Balance Between Cytotoxic T-cell Lymphocytes and Immune Checkpoint Expression in the Prognosis of Colon Tumors. J Natl Cancer Inst 2017; 110:4093940. [PMID: 28922790 DOI: 10.1093/jnci/djx136] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/05/2017] [Indexed: 12/18/2022] Open
Abstract
Background Immune checkpoint (ICK) expression might represent a surrogate measure of tumor-infiltrating T cell (CTL) exhaustion and therefore be a more accurate prognostic biomarker for colorectal cancer (CRC) patients than CTL enumeration as measured by the Immunoscore. Methods The expression of ICKs, Th1, CTLs, cytotoxicity-related genes, and metagenes, including Immunoscore-like metagenes, were evaluated in three independent cohorts of CRC samples (260 microsatellite instable [MSI], 971 non-MSI). Their associations with patient survival were analyzed by Cox models, taking into account the microsatellite instability (MSI) status and affiliation with various Consensus Molecular Subgroups (CMS). PD-L1 and CD8 expression were examined on a subset of tumors with immunohistochemistry. All statistical tests were two-sided. Results The expression of Immunoscore-like metagenes was statistically significantly associated with improved outcome in non-MSI tumors displaying low levels of both CTLs and immune checkpoints (ICKs; CMS2 and CMS3; hazard ratio [HR] = 0.63, 95% confidence interval [CI] = 0.43 to 0.92, P = .02; and HR = 0.55, 95% CI = 0.34 to 0.90, P = .02, respectively), but clearly had no prognostic relevance in CRCs displaying higher levels of CTLs and ICKs (CMS1 and CMS4; HR = 0.46, 95% CI = 0.10 to 2.10, P = .32; and HR = 1.13, 95% CI = 0.79 to 1.63, P = .50, respectively), including MSI tumors. ICK metagene expression was statistically significantly associated with worse prognosis independent of tumor staging in MSI tumors (HR = 3.46, 95% CI = 1.41 to 8.49, P = .007). ICK expression had a negative impact on the proliferation of infiltrating CD8 T cells in MSI neoplasms (median = 0.56 in ICK low vs median = 0.34 in ICK high, P = .004). Conclusions ICK expression cancels the prognostic relevance of CTLs in highly immunogenic colon tumors and predicts a poor outcome in MSI CRC patients.
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Affiliation(s)
- Laetitia Marisa
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Magali Svrcek
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Ada Collura
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Etienne Becht
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Pascale Cervera
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Kristell Wanherdrick
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Olivier Buhard
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Anastasia Goloudina
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Vincent Jonchère
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Janick Selves
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Gerard Milano
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Dominique Guenot
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Romain Cohen
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Chrystelle Colas
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Pierre Laurent-Puig
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Sylviane Olschwang
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Jérémie H Lefèvre
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Yann Parc
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Valérie Boige
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Côme Lepage
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Thierry André
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Jean-François Fléjou
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Valentin Dérangère
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - François Ghiringhelli
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Aurélien de Reynies
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
| | - Alex Duval
- Programme "Cartes d'Identité des Tumeurs," Ligue Nationale Contre le Cancer, Paris, France; INSERM, UMRS 938 - Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers," Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, UPMC Univ Paris 06, Paris, France; AP-HP, Hôpital Saint-Antoine, Service d'Anatomie et Cytologie Pathologiques, Paris, France; Centre de Recherche en Cancérologie de Toulouse, UMR 1037 INSERM - Université Toulouse III, Department of Pathology, CHU, Toulouse, France; Laboratoire d'Oncopharmacologie, EA 3836, Centre Antoine Lacassagne, Nice, France; INSERM, U682, Développement et Physiopathologie de l'Intestin et du Pancréas, Strasbourg, France; AP-HP, Hôpital Saint-Antoine, Service d'Oncologie Médicale, Paris, France; AP-HP, Laboratoire d'oncogénétique et d'Angiogénétique, GH Pitié-Salpétrière, Paris, France; INSERM, Unité Mixte de Recherche, Paris Sorbonne Cité, Université Paris Descartes, Paris, France; Aix Marseille Univ, INSERM, GMGF, Marseille, France and RGDS, HP Clairval, Marseille, France; AP-HP, Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Paris, France; Department of Oncologic Medicine, Gustave-Roussy, Villejuif, France; Université Paris Descartes, Paris Sorbonne Cité INSERM UMR-S775, Paris, France; INSERM, Burgundy Cancer Registry, U866, Burgundy University, Dijon University Hospital, BP 87900?21079 Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France; INSERM, UMR866, Burgundy University; Platform of transfer in oncology, Burgundy University, Centre Georges-François Leclerc, Dijon, France
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Nicolle R, Blum Y, Marisa L, Loncle C, Gayet O, Moutardier V, Turrini O, Giovannini M, Bian B, Bigonnet M, Rubis M, Elarouci N, Armenoult L, Ayadi M, Duconseil P, Gasmi M, Ouaissi M, Maignan A, Lomberk G, Boher JM, Ewald J, Bories E, Garnier J, Goncalves A, Poizat F, Raoul JL, Secq V, Garcia S, Grandval P, Barraud-Blanc M, Norguet E, Gilabert M, Delpero JR, Roques J, Calvo E, Guillaumond F, Vasseur S, Urrutia R, Reyniès AD, Dusetti N, Iovanna J. Abstract 4396: Multiomics assessment of the cancer and stromal compartments of patient-derived pancreatic xenografts reveals clinically-relevant subtypes and novel targeted therapies. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4396] [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
Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. In this work, 29 PDX were obtained from either surgery or endoscopic ultrasound-guided fine needle aspirate of pancreatic adenocarcinoma. The extensive genomic profiling of these pancreatic PDX, revealed two clinically-relevant subtypes having broad similarities with human primary tumors. These subtypes are defined by highly specific DNA methylation and transcriptomic profiles (mRNA, miRNA or lncRNA) but are not distinguishable by exonic mutations or copy number aberrations. Moreover, by specifically analyzing the stroma transcriptome, as defined by the expression of murine transcripts, we found that it is able to stratify the patients with the same efficiency than the analysis of grafted human tumor cells. This finding suggest that transformed pancreatic cells drive the composition of their own stroma. Finally, the multiomics analysis pinpoints novel therapeutic targets, one of which we demonstrate to be an efficient method for treating pancreatic cancer. Overall, we show that PDX are trustworthy pre-clinical models of pancreatic adenocarcinoma including of unresectable tumors. Their multiomics profiling allow the independent analysis of the uncontaminated cancer or stromal compartments and discloses several original therapeutics targets.
Citation Format: Remy Nicolle, Yuna Blum, Laetitia Marisa, Celine Loncle, Odile Gayet, Vincent Moutardier, Olivier Turrini, Marc Giovannini, Benjamin Bian, Martin Bigonnet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Aurélie Maignan, Gwen Lomberk, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Jonathan Garnier, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Julie Roques, Ezequiel Calvo, Fabienne Guillaumond, Sophie Vasseur, Raul Urrutia, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna. Multiomics assessment of the cancer and stromal compartments of patient-derived pancreatic xenografts reveals clinically-relevant subtypes and novel targeted therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4396. doi:10.1158/1538-7445.AM2017-4396
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Affiliation(s)
- Remy Nicolle
- 1Ligue Nationale Contre le Cancer, Paris, France
| | - Yuna Blum
- 1Ligue Nationale Contre le Cancer, Paris, France
| | | | - Celine Loncle
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Odile Gayet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | | | - Benjamin Bian
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Martin Bigonnet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Marion Rubis
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | - Mira Ayadi
- 1Ligue Nationale Contre le Cancer, Paris, France
| | - Pauline Duconseil
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | - Aurélie Maignan
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | | | | | - Jonathan Garnier
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | | | | | | | | | | | | | | | | | - Julie Roques
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | - Fabienne Guillaumond
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Sophie Vasseur
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | | | | | - Nelson Dusetti
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Juan Iovanna
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
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Marisa L, Ayadi M, Balogoun R, Pilati C, Le Malicot K, Lepage C, Emile JF, Salazar R, Aust DE, Duval A, Selves J, Guenot DE, Milano GA, Seitz JF, Taieb J, Boige V, De Reynies A, Laurent-Puig P. Clinical utility of colon cancer molecular subtypes: Validation of two main colorectal molecular classifications on the PETACC-8 phase III trial cohort. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.3509] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3509 Background: The molecular subtyping of colon cancers (CC) has been the subject of several recent publications, leading to an international consensus. The clinical relevance of these molecular classifications remains to be evaluated on large prospective patient cohorts using a tool that can be widely used on formalin-fixed paraffin-embedded (FFPE) samples. Methods: We aimed to evaluate the clinical relevance of two molecular subtyping systems, CMS (Guinney et al. 2015) and CCMST (Marisa et al. 2013), on the PETACC-8 cohort, a randomized phase III trial comparing adjuvant FOLFOX with or without cetuximab in patients with stage III CC. For each of these two classification systems, a predictor tool was developed and adapted to FFPE samples. The NanoString nCounter platform was used to screen 196 genes. Predictors were built from 249 frozen tumor samples previously used to build our classification system and 61 new paired FFPE/frozen samples. Both predictors were then applied to 1781 PETACC-8 FFPE samples. Subtypes associations to clinical and molecular features were analyzed. Results: The CMS predictor assigned 297 samples to CMS1 (17%), 585 to CMS2 (34%), 68 to CMS3 (4%) and 770 to CMS4 (45%). CMS were significantly associated with several molecular and clinical features, including MSI status (49% in CMS1, p < 0.001), CIMP status (47% in CMS1, p < 0.001), KRAS mutation (75% in CMS3, p < 0.001), BRAF mutation (34% in CMS1, p < 0.001), tumor location (less proximal tumors in CMS2, p < 0.001), validating the predictor tool developed. The classification was significantly associated to prognosis in multivariate analysis, CMS4 subtype having a shorter overall survival (hazard ratio = 1.7, p= 0.021). A deleterious effect of cetuximab was observed in CMS1 (p < 0.05). Similar results were obtained with the CCMST classification. Conclusions: We validated molecular CC subtyping predictors for both CMS and CCMST classifications on PETACC-8 FFPE samples. The prognostic value of CMS and CCMST classifications was confirmed, stem-like tumors being associated with a poor prognosis. These results pave the avenue for widely use of the CC molecular classification in clinical routine.
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Affiliation(s)
| | - Mira Ayadi
- Ligue Nationale Contre le Cancer, Paris, France
| | - Ralyath Balogoun
- Université Paris Descartes, Sorbonne Paris Cité, France; Assistance Publique Hôpitaux de Paris, Department of Biology, Hôpital Européen Georges Pompidou, INSERM UMR-S1147, Paris, France
| | | | | | - Come Lepage
- CHU Le Bocage HGE, INSERM U866, Dijon, France
| | | | - Ramon Salazar
- Institut Català D'Oncologia, L’Hospitalet de Llobregat, Barcelona, Spain
| | | | - Alex Duval
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | | | | | | | | | - Julien Taieb
- Hopital Européen Georges Pompidou, Paris, France
| | - Valerie Boige
- Service d'Oncologie Digestive, Gustave Roussy, Villejuif, France
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Pilati C, Taieb J, Balogoun R, Marisa L, de Reyniès A, Laurent-Puig P. CDX2 prognostic value in stage II/III resected colon cancer is related to CMS classification. Ann Oncol 2017; 28:1032-1035. [DOI: 10.1093/annonc/mdx066] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Nicolle R, Blum Y, Marisa L, Garnier J, Bian B, Loncle C, Bigonnet M, Gayet O, Moutardier V, Duconseil P, Gasmi M, Ouaissi M, Turrini O, Giovannini M, Maignan A, Boher JM, Ewald J, Bories E, Barthet M, Goncalves A, Poizat F, Raoul JL, Secq V, Garcia S, Grandval P, Barraud-Blanc M, Norguet E, Gilabert M, Delpero JR, Calvo E, Reyniès AD, Dusetti N, Iovanna J. Abstract A48: Multi-omics characterization of PDAC subtypes using PDX reveals that epigenetic but not genetic analysis permit a clinically relevant classification. Cancer Res 2016. [DOI: 10.1158/1538-7445.panca16-a48] [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
Genome-wide molecular profiles have been proven to be beneficial for the identification of clinically relevant tumor subtypes in many neoplastic diseases. While pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death, very few genomic and transcriptomic studies have been conducted. This is mainly due to the difficulty to obtain a suitable cohort of PDAC tumor samples. The major obstacle is the usually high proportion of non-transformed stromal cells, which can greatly hinder the analysis of carcinogenic-specific processes. Moreover, tumor cohorts requiring resection samples can be biased by the exclusion of inoperable patients, representing 85% of all patients presenting PDAC.
In this study, we generated Patient Derived Xenografts (PDX) with samples collected from 29 patients using either Endoscopic Ultrasound-Guided Fine-Needle Aspirates or, for operable patients, resections. The transcriptomic profiles, of both mRNA and miRNA, and the epigenetic landscape of early PDX passages consistently identified two tumor-specific molecular subtypes: a well differentiated group often referred to as classical, and an undifferentiated group previously recognized as Basal, Quasi-Mesenchymal or Squamous. Of all the genetic alterations determined by Copy Number analysis and exome sequencing, none were specific to any of the two subtypes, which therefore could not be discriminated solely on genetic basis.
These two PDAC subtypes are characterized by distinct epigenetic and transcriptomic profiles of which the analysis revealed the deregulation of several pathways previously imputed in PDAC development and carcinogenesis in general. In particular, we showed that the Wnt pathway as well as several metabolic pathways, including cytochrome P450 genes recently implicated in drug resistance, are both epigenetically and transcriptionally deregulated. Altogether, our results provide new insights on pancreatic carcinogenesis and suggest that PDAC phenotypical heterogeneity is mainly driven by epigenetic rather than genetic events.
Citation Format: Remy Nicolle, Yuna Blum, Laetitia Marisa, Jonathan Garnier, Benjamin Bian, Celine Loncle, Martin Bigonnet, Odile Gayet, Vincent Moutardier, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Olivier Turrini, Marc Giovannini, Aurélie Maignan, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Marc Barthet, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Ezequiel Calvo, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna.{Authors}. Multi-omics characterization of PDAC subtypes using PDX reveals that epigenetic but not genetic analysis permit a clinically relevant classification. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A48.
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Affiliation(s)
- Remy Nicolle
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Yuna Blum
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Laetitia Marisa
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Jonathan Garnier
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Benjamin Bian
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Celine Loncle
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Martin Bigonnet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Odile Gayet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | - Pauline Duconseil
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | | | | | | | - Aurélie Maignan
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ezequiel Calvo
- 6Centre Génomique du Centre de recherche du CHUL Research Center, QB, Canada
| | - Aurélien de Reyniès
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Nelson Dusetti
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Juan Iovanna
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
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Nicolle R, Blum Y, Marisa L, Garnier J, Bian B, Loncle C, Bigonnet M, Gayet O, Moutardier V, Duconseil P, Gasmi M, Ouaissi M, Turrini O, Giovannini M, Maignan A, Boher JM, Ewald J, Bories E, Barthet M, Goncalves A, Poizat F, Raoul JL, Secq V, Garcia S, Grandval P, Barraud-Blanc M, Norguet E, Gilabert M, Delpero JR, Calvo E, Reyniès AD, Iovanna J, Dusetti N. Abstract B72: Pancreatic cancer cell drives stroma composition. Cancer Res 2016. [DOI: 10.1158/1538-7445.panca16-b72] [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
The extensive desmoplasia in pancreatic ductal adenocarcinoma (PDAC) has raised major interrogations on its role and function in the carcinogenic process. Patient-derived xenograft (PDX) offers an ideal setting to distinguish and to study the interactions between the cancerous epithelial cells and its stroma. Indeed, sequencing profiles of a mix of cancerous/Human and stroma/Mouse cells can be analyzed separately in silico by unambiguously assigning each sequence to the human or mouse genome. Using RNA sequencing, we profiled 30 pancreatic tumor PDXs and extracted the transcriptome profiles of epithelial cancerous cells as well as their corresponding stroma. On average, 70% of RNA sequencing reads were specifically attributed to a human origin, and therefore an epithelial origin, while 22% of RNA sequencing reads were mouse-specific. Using the rate of mouse sequences as a surrogate of the proportion of non-transformed cells, we observe a high variability in the infiltration level from 7% to 60%. The estimation was also consistent in whole exome sequencing (using the same sequencing process) and with the histological quantification of fibrotic tissue.
By specifically analyzing the gene expression in mouse-stromal cells, we show that their transcriptomic profile is consistent with the recent description of human PDAC in situ tumors with high levels of genes of the reported activated-stroma and normal-stroma signatures. We also show that stromal cells over-express genes involved in the SLIT/ROBO axon guidance signalling pathway, in angiogenesis as well as a large number of collagens, cytokines and ligands associated with growth and developmental pathways.
Recent studies identified two major subtypes of PDAC from transcriptomic analysis: a well differentiated, often referred as classical, and an undifferentiated, previously recognized as Basal, Quasi-Mesenchymal or Squamous. The stroma characterized in this work broadly reflects this heterogeneity with stromal gene expression signatures predictive of each subtype. For instance, collagens are significantly over-expressed in the stroma of squamous tumors. The concomitant analysis of transcriptomic profiles of both subtypes shows potential cross-talks between cancerous and stromal cells. Particularly in Squamous tumors, genes implicated in the axon-guidance and Wnt pathways are significantly upregulated in both, stroma and transformed cells. On the other hand, the stroma and transformed cells of Classical tumors shows an upregulation of complementary genes associated with several metabolic pathways.
Taken together, our transcriptomic analysis reveals that human transformed pancreatic cells determine the composition, quantitatively and qualitatively, of stroma mouse cells in a PDX model. This model also reveals a broad variability of PDAC stromas and highlights potential cross-talks between them through known and novel pathways.
Citation Format: Rémy Nicolle, Yuna Blum, Laetitia Marisa, Jonathan Garnier, Benjamin Bian, Celine Loncle, Martin Bigonnet, Odile Gayet, Vincent Moutardier, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Olivier Turrini, Marc Giovannini, Aurélie Maignan, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Marc Barthet, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Ezequiel Calvo, Aurélien de Reyniès, Juan Iovanna, Nelson Dusetti.{Authors}. Pancreatic cancer cell drives stroma composition. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B72.
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Affiliation(s)
- Rémy Nicolle
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Yuna Blum
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Laetitia Marisa
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Jonathan Garnier
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Benjamin Bian
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Celine Loncle
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Martin Bigonnet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Odile Gayet
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | - Pauline Duconseil
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | | | | | | | - Aurélie Maignan
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ezequiel Calvo
- 6Centre Génomique du Centre de recherche du CHUL Research Center, Quebec, Canada
| | - Aurélien de Reyniès
- 1Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France,
| | - Juan Iovanna
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
| | - Nelson Dusetti
- 2Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Marseille, France,
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Nehmar RB, Romain B, Marisa L, Bour C, Duluc I, Pencreach E, Guenot D. Understanding loss of SDF1 expression in colon tumors. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61078-x] [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: 11/30/2022]
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Buhard O, Lagrange A, Guilloux A, Colas C, Chouchène M, Wanherdrick K, Coulet F, Guillerm E, Dorard C, Marisa L, Bokhari A, Greene M, El-Murr N, Bodo S, Muleris M, Sourouille I, Svrcek M, Cervera P, Blanché H, Lefevre JH, Parc Y, Lepage C, Chapusot C, Bouvier AM, Gaub MP, Selves J, Garrett K, Iacopetta B, Soong R, Hamelin R, Garrido C, Lascols O, André T, Fléjou JF, Collura A, Duval A. HSP110T17 simplifies and improves the microsatellite instability testing in patients with colorectal cancer. J Med Genet 2016; 53:377-84. [DOI: 10.1136/jmedgenet-2015-103518] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 01/09/2016] [Indexed: 11/04/2022]
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Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. The consensus molecular subtypes of colorectal cancer. Nat Med 2015; 21:1350-6. [PMID: 26457759 PMCID: PMC4636487 DOI: 10.1038/nm.3967] [Citation(s) in RCA: 3045] [Impact Index Per Article: 338.3] [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: 03/06/2015] [Accepted: 09/06/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression-based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMSs) with distinguishing features: CMS1 (microsatellite instability immune, 14%), hypermutated, microsatellite unstable and strong immune activation; CMS2 (canonical, 37%), epithelial, marked WNT and MYC signaling activation; CMS3 (metabolic, 13%), epithelial and evident metabolic dysregulation; and CMS4 (mesenchymal, 23%), prominent transforming growth factor-β activation, stromal invasion and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intratumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC-with clear biological interpretability-and the basis for future clinical stratification and subtype-based targeted interventions.
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Affiliation(s)
| | - Rodrigo Dienstmann
- Sage Bionetworks, Seattle, Washington, USA
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xin Wang
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | | | | | | | | | | | | | - Paolo Angelino
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Jeffrey S Morris
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Sarah Gerster
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Evelyn Fessler
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Felipe De Sousa E Melo
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | | | - Hena Ramay
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - David Barras
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Dipen Maru
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Ganiraju C Manyam
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Bradley Broom
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Beatriz Perez-Villamil
- Laboratorio de Genomica y Microarrays, Instituto de Investigación Sanitaria San Carlos, Hospital Clinico San Carlos, Madrid, Spain
| | | | - Ramon Salazar
- Institut Catala d'Oncologia, L'Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Joe W Gray
- Biomedical Engineering, Oregon Health Sciences University, Portland, Oregon, USA
| | - Douglas Hanahan
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Josep Tabernero
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rene Bernards
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | | | - Pierre Laurent-Puig
- Université Paris Descartes, Paris, France
- Department of Biology, Hôpital Européen Georges-Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | | | - Lodewyk Wessels
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Scott Kopetz
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
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Becht E, Giraldo NA, Beuselinck B, Job S, Marisa L, Vano Y, Oudard S, Zucman-Rossi J, Laurent-Puig P, Sautès-Fridman C, de Reyniès A, Fridman WH. Prognostic and theranostic impact of molecular subtypes and immune classifications in renal cell cancer (RCC) and colorectal cancer (CRC). Oncoimmunology 2015; 4:e1049804. [PMID: 26587318 PMCID: PMC4635888 DOI: 10.1080/2162402x.2015.1049804] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 02/08/2023] Open
Abstract
Molecular and immune classifications powerfully predict cancer patient's survival and response to therapies. We herein describe the immune tumor microenvironment of molecular subgroups of colorectal and renal cell cancers, revealing a strong correlation between tumor subtypes and distinct immune profiles.
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Affiliation(s)
- Etienne Becht
- INSERM UMR_S 1138 Cancer; Immune Control and Escape; Cordeliers Research Centre ; Paris, France ; Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Sorbonne Universités; UPMC Univ Paris 06; UMR_S 1138; Cordeliers Research Centre ; Paris, France
| | - Nicolas A Giraldo
- INSERM UMR_S 1138 Cancer; Immune Control and Escape; Cordeliers Research Centre ; Paris, France ; Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Sorbonne Universités; UPMC Univ Paris 06; UMR_S 1138; Cordeliers Research Centre ; Paris, France
| | - Benoit Beuselinck
- INSERM; UMR-1162; Génomique fonctionnelle des tumeurs solides ; Paris, France ; University Hospitals Leuven; KULeuven ; Leuven, Belgium
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs; Ligue Nationale Contre le Cancer ; Paris, France
| | - Laetitia Marisa
- Programme Cartes d'Identité des Tumeurs; Ligue Nationale Contre le Cancer ; Paris, France
| | - Yann Vano
- INSERM UMR_S 1138 Cancer; Immune Control and Escape; Cordeliers Research Centre ; Paris, France ; Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Sorbonne Universités; UPMC Univ Paris 06; UMR_S 1138; Cordeliers Research Centre ; Paris, France ; Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Department of Oncology , Paris, France
| | - Stéphane Oudard
- Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Department of Oncology , Paris, France
| | - Jessica Zucman-Rossi
- INSERM; UMR-1162; Génomique fonctionnelle des tumeurs solides ; Paris, France ; Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Department of Oncology , Paris, France
| | - Pierre Laurent-Puig
- Université Paris Descartes; Sorbonne Paris Cite; INSERM, UMR-S1147 ; Paris, France ; Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Department of Biology , Paris, France
| | - Catherine Sautès-Fridman
- INSERM UMR_S 1138 Cancer; Immune Control and Escape; Cordeliers Research Centre ; Paris, France ; Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Sorbonne Universités; UPMC Univ Paris 06; UMR_S 1138; Cordeliers Research Centre ; Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs; Ligue Nationale Contre le Cancer ; Paris, France
| | - Wolf Herman Fridman
- INSERM UMR_S 1138 Cancer; Immune Control and Escape; Cordeliers Research Centre ; Paris, France ; Université Paris Descartes; Sorbonne Paris Cité; UMR_S 1338; Cordeliers Research Centre ; Paris, France ; Sorbonne Universités; UPMC Univ Paris 06; UMR_S 1138; Cordeliers Research Centre ; Paris, France ; Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Department of Biology , Paris, France
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Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot B, Morris JS, Simon I, Gerster S, Fessler E, de Sousa e Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam G, Broom B, Boige V, Laderas T, Salazar R, Gray JW, Tabernero J, Bernards R, Friend S, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. Abstract 603: Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Gene expression-based subtyping is widely accepted as a relevant source of disease stratification. Despite the widespread use, its translational and clinical utility is hampered by discrepant results, likely related to differences in data processing and algorithms applied to diverse patient cohorts, sample preparation methods, and gene expression platforms. In the absence of a clear methodological gold standard to perform such analyses, a more general framework that integrates and compares multiple strategies is needed to define common disease patterns in a principled, unbiased manner.
Methods: We formed a consortium of 6 independent experts groups - each with a previously published CRC classifier, ranging from 3 to 6 subtypes - to understand similarities and differences of their subtyping systems. Sage Bionetworks functioned as neutral party to aggregate public and proprietary data (Synapse platform) and perform meta-analysis. Each group applied its CRC subtyping signature to the collection of data sets with gene expression (n = 4,151, predominantly stage II and III). Using the resulting subtype labels, we developed a network-based model and applied a Markov cluster algorithm to detect robust network substructures that would indicate recurring subtype patterns and therefore a consensus subtyping system. Correlative analyses using clinico-pathological, genomic and epigenomic features was performed to robustly characterize the identified subtypes.
Results: This analytical framework revealed significant interconnectivity between the six independent classification systems, leading to the identification of four biologically distinct consensus molecular subtypes (CMS) enriched for key pathway traits: CMS1 (MSI Immune), hypermutated, microsatellite unstable, with strong immune activation; CMS2 (Canonical), epithelial, chromosomally unstable, with marked WNT and MYC signaling activation; CMS3 (Metabolic), epithelial, with evident metabolic dysregulation; and CMS4 (Mesenchymal), prominent TGFβ activation, angiogenesis, stromal invasion. Patients diagnosed with MSI Immune tumors had worse survival after relapse and those with mesenchymal tumors had increased risk of metastasis and worse overall survival.
Discussion: We describe a novel methodological paradigm for deriving benchmarks of disease subtyping. Our work represents the first example of a community of experts identifying and advocating for a single reproducible model for cancer subtyping, effectively unifying previous classifiers. In the CRC domain, the uniformity afforded by this new classification system and its application to a large data set revealed important subtype-specific biological associations that were previously unnoticed or marginally significant, supporting a new taxonomy of the disease.
Citation Format: Justin Guinney, Rodrigo Dienstmann, Xin Wang, Aurelien de Reynies, Andreas Schlicker, Charlotte Soneson, Laetitia Marisa, Paul Roepman, Gift Nyamundanda, Paolo Angelino, Brian Bot, Jeffrey S. Morris, Iris Simon, Sarah Gerster, Evelyn Fessler, Felipe de Sousa e Melo, Edoardo Missiaglia, Hena Ramay, David Barras, Krisztian Homicsko, Dipen Maru, Ganiraju Manyam, Bradley Broom, Valerie Boige, Ted Laderas, Ramon Salazar, Joe W. Gray, Josep Tabernero, Rene Bernards, Stephen Friend, Pierre Laurent-Puig, Jan P. Medema, Anguraj Sadanandam, Lodewyk Wessels, Mauro Delorenzi, Scott Kopetz, Louis Vermeulen, Sabine Tejpar. Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 603. doi:10.1158/1538-7445.AM2015-603
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Affiliation(s)
| | | | - Xin Wang
- 2University of Amsterdam, Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hena Ramay
- 5SIB Swiss Institute of Bioinformatics, Switzerland
| | - David Barras
- 5SIB Swiss Institute of Bioinformatics, Switzerland
| | | | - Dipen Maru
- 8University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Ganiraju Manyam
- 8University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Bradley Broom
- 8University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | | | | | - Scott Kopetz
- 8University of Texas, MD Anderson Cancer Center, Houston, TX
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Manceau G, Marisa L, Boige V, Duval A, Gaub MP, Milano G, Selves J, Olschwang S, Jooste V, le Legrain M, Lecorre D, Guenot D, Etienne-Grimaldi MC, Kirzin S, Martin L, Lepage C, Bouvier AM, Laurent-Puig P. PIK3CA mutations predict recurrence in localized microsatellite stable colon cancer. Cancer Med 2015; 4:371-82. [PMID: 25641861 PMCID: PMC4380963 DOI: 10.1002/cam4.370] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/25/2022] Open
Abstract
PIK3CA, which encodes the p110α catalytic subunit of PI3Kα, is one of the most frequently altered oncogenes in colon cancer (CC), but its prognostic value is still a matter of debate. Few reports have addressed the association between PIK3CA mutations and survival and their results are controversial. In the present study, we aimed to clarify the prognostic impact of PIK3CA mutations in stage I-III CC according to mismatch repair status. Fresh frozen tissue samples from two independent cohorts with a total of 826 patients who underwent curative surgical resection of CC were analyzed for microsatellite instability and screened for activating point mutations in exon 9 and 20 of PIK3CA by direct sequencing. Overall, 693 tumors (84%) exhibited microsatellite stability (MSS) and 113 samples (14%) harbored PIK3CA mutation. In the retrospective training cohort (n = 433), patients with PIK3CA-mutated MSS tumors (n = 47) experienced a significant increased 5-year relapse-free interval compared with PIK3CA wild-type MSS tumors (n = 319) in univariate analysis (94% vs. 68%, Log-rank P = 0. 0003) and in multivariate analysis (HR = 0.12; 95% confidence interval, 0.029-0.48; P = 0.0027). In the prospective validation cohort (n = 393), the favorable prognostic impact of PIK3CA mutations in MSS tumors (n = 327) was confirmed (83% vs. 67%, Log-rank P = 0.04). Our study showed that PIK3CA mutations are associated with a good prognosis in patients with MSS stage I-III CC.
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Affiliation(s)
- Gilles Manceau
- Unité Mixte de Recherche S1147, Paris Sorbonne Cité, Université Paris Descartes, INSERM, Paris, France; Assistance Publique-Hôpitaux de Paris, Service de Chirurgie Digestive et Hépato-Bilio-Pancréatique, Hôpital Pitié-Salpêtrière, Paris, France; Institut Universitaire de Cancérologie, Université Pierre et Marie Curie-Paris 6, Paris, France
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Kirzin S, Marisa L, Guimbaud R, De Reynies A, Legrain M, Laurent-Puig P, Cordelier P, Pradère B, Bonnet D, Meggetto F, Portier G, Brousset P, Selves J. Sporadic early-onset colorectal cancer is a specific sub-type of cancer: a morphological, molecular and genetics study. PLoS One 2014; 9:e103159. [PMID: 25083765 PMCID: PMC4118858 DOI: 10.1371/journal.pone.0103159] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
Sporadic early onset colorectal carcinoma (EOCRC) which has by definition no identified hereditary predisposition is a growing problem that remains poorly understood. Molecular analysis could improve identification of distinct sub-types of colorectal cancers (CRC) with therapeutic implications and thus can help establish that sporadic EOCRC is a distinct entity. From 954 patients resected for CRC at our institution, 98 patients were selected. Patients aged 45–60 years were excluded to help define “young” and “old” groups. Thirty-nine cases of sporadic EOCRC (patients≤45 years with microsatellite stable tumors) were compared to both microsatellite stable tumors from older patients (36 cases, patients>60 years) and to groups of patients with microsatellite instability. Each group was tested for TP53, KRAS, BRAF, PIK3CA mutations and the presence of a methylator phenotype. Gene expression profiles were also used for pathway analysis. Compared to microsatellite stable CRC from old patients, sporadic EOCRC were characterized by distal location, frequent synchronous metastases and infrequent synchronous adenomas but did not have specific morphological characteristics. A familial history of CRC was more common in sporadic EOCRC patients despite a lack of identified hereditary conditions (p = 0.013). Genetic studies also showed the absence of BRAF mutations (p = 0.022) and the methylator phenotype (p = 0.005) in sporadic EOCRC compared to older patients. Gene expression analysis implicated key pathways such as Wnt/beta catenin, MAP Kinase, growth factor signaling (EGFR, HGF, PDGF) and the TNFR1 pathway in sporadic EOCRC. Wnt/beta catenin signaling activation was confirmed by aberrant nuclear beta catenin immunostaining (p = 0.01). This study strongly suggests that sporadic EOCRC is a distinct clinico-molecular entity presenting as a distal and aggressive disease associated with chromosome instability. Furthermore, several signaling pathways including the TNFR1 pathway have been identified as potential biomarkers for both the diagnosis and treatment of this disease.
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Affiliation(s)
- Sylvain Kirzin
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
- Department of Surgery, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Laetitia Marisa
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Rosine Guimbaud
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
- Department of Oncology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Aurélien De Reynies
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Michèle Legrain
- Laboratoire de Biochimie Biologie Moléculaire, Hôpitaux Universitaires de Hautepierre, Strasbourg, France
| | - Pierre Laurent-Puig
- Bases Moléculaires de la réponse aux xénobiotiques, Université Paris Descartes, INSERM, UMR-S775, Paris, France
| | - Pierre Cordelier
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
| | - Bernard Pradère
- Department of Surgery, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Delphine Bonnet
- Department of Oncology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Fabienne Meggetto
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
| | - Guillaume Portier
- Department of Surgery, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Pierre Brousset
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
- Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Janick Selves
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM – Université Toulouse III, Toulouse, France
- Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
- * E-mail:
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Dienstmann R, Guinney J, Delorenzi M, De Reynies A, Roepman P, Sadanandam A, Vermeulen L, Schlicker A, Missiaglia E, Soneson C, Marisa L, Homicsko K, Wang X, Simon I, Laurent-Puig P, Wessels L, Medema J, Kopetz S, Friend S, Tejpar S. Colorectal Cancer Subtyping Consortium (CRCSC) Identifies Consensus of Molecular Subtypes. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu193.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Dienstmann R, Guinney J, Delorenzi M, De Reynies A, Roepman P, Sadanandam A, Vermeulen L, Schlicker A, Missiaglia E, Soneson C, Marisa L, Homicsko K, Wang X, Simon I, Laurent-Puig P, Wessels LFA, Medema JP, Kopetz S, Friend SH, Tejpar S. Colorectal Cancer Subtyping Consortium (CRCSC) identification of a consensus of molecular subtypes. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.3511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics, Ludwig Center for Cancer Research and Department of Oncology, University Lausanne, Lausanne, Switzerland
| | | | - Paul Roepman
- Agendia NV Research and Development Dpt, Amsterdam, Netherlands
| | | | - Louis Vermeulen
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Schlicker
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | - Krisztian Homicsko
- Swiss Institute for Experimental Cancer Research, Swiss Federal Institute of Technology Lausanne, Department of Oncology Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Xin Wang
- Centre for Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Iris Simon
- Agendia NV Research and Development Dpt, Amsterdam, Netherlands
| | | | - Lodewyk F. A. Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Collura A, Lagrange A, Svrcek M, Marisa L, Buhard O, Guilloux A, Wanherdrick K, Dorard C, Taieb A, Saget A, Loh M, Soong R, Zeps N, Platell C, Mews A, Iacopetta B, De Thonel A, Seigneuric R, Marcion G, Chapusot C, Lepage C, Bouvier AM, Gaub MP, Milano G, Selves J, Senet P, Delarue P, Arzouk H, Lacoste C, Coquelle A, Bengrine-Lefèvre L, Tournigand C, Lefèvre JH, Parc Y, Biard DS, Fléjou JF, Garrido C, Duval A. Patients with colorectal tumors with microsatellite instability and large deletions in HSP110 T17 have improved response to 5-fluorouracil–based chemotherapy. Gastroenterology 2014; 146:401-11.e1. [PMID: 24512910 DOI: 10.1053/j.gastro.2013.10.054] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 10/11/2013] [Accepted: 10/21/2013] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Patients with colorectal tumors with microsatellite instability (MSI) have better prognoses than patients with tumors without MSI, but have a poor response to 5-fluorouracil–based chemotherapy. A dominant-negative form of heat shock protein (HSP)110 (HSP110DE9) expressed by cancer cells with MSI, via exon skipping caused by somatic deletions in the T(17) intron repeat, sensitizes the cells to 5-fluorouracil and oxaliplatin.We investigated whether HSP110 T(17) could be used to identify patients with colorectal cancer who would benefit from adjuvant chemotherapy with 5-fluorouracil and oxaliplatin. METHODS We characterized the interaction between HSP110 and HSP110DE9 using surface plasmon resonance. By using polymerase chain reaction and fragment analysis, we examined how the size of somatic allelic deletions in HSP110 T(17) affected the HSP110 protein expressed by tumor cells. We screened 329 consecutive patients with stage II–III colorectal tumors with MSI who underwent surgical resection at tertiary medical centers for HSP110 T(17). RESULTS HSP110 and HSP110DE9 interacted in a1:1 ratio. Tumor cells with large deletions in T(17) had increased ratios of HSP110DE9:HSP110, owing to the loss of expression of full-length HSP110. Deletions in HSP110 T(17) were mostly biallelic in primary tumor samples with MSI. Patients with stage II–III cancer who received chemotherapy and had large HSP110 T(17) deletions (≥5 bp; 18 of 77 patients, 23.4%) had longer times of relapse-free survival than patients with small or no deletions (≤4 bp; 59 of 77 patients, 76.6%) in multivariate analysis (hazard ratio, 0.16; 95% confidence interval, 0.012–0.8; P = .03). We found a significant interaction between chemotherapy and T17 deletion (P =.009). CONCLUSIONS About 25% of patients with stages II–III colorectal tumors with MSI have an excellent response to chemotherapy, due to large, biallelic deletions in the T(17) intron repeat of HSP110 in tumor DNA.
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36
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Bertucci F, Finetti P, Roche H, Le Doussal J, Marisa L, Martin A, Lacroix-Triki M, Blanc-Fournier C, Jacquemier J, Peyro-Saint-Paul H, Viens P, Sotiriou C, Birnbaum D, Penault-Llorca F. Comparison of the prognostic value of genomic grade index, Ki67 expression and mitotic activity index in early node-positive breast cancer patients. Ann Oncol 2013; 24:625-32. [DOI: 10.1093/annonc/mds510] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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37
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Marisa L, de Reyniès A, Duval A, Selves J, Gaub MP, Vescovo L, Etienne-Grimaldi MC, Schiappa R, Guenot D, Ayadi M, Kirzin S, Chazal M, Fléjou JF, Benchimol D, Berger A, Lagarde A, Pencreach E, Piard F, Elias D, Parc Y, Olschwang S, Milano G, Laurent-Puig P, Boige V. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med 2013; 10:e1001453. [PMID: 23700391 PMCID: PMC3660251 DOI: 10.1371/journal.pmed.1001453] [Citation(s) in RCA: 930] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 04/10/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colon cancer (CC) pathological staging fails to accurately predict recurrence, and to date, no gene expression signature has proven reliable for prognosis stratification in clinical practice, perhaps because CC is a heterogeneous disease. The aim of this study was to establish a comprehensive molecular classification of CC based on mRNA expression profile analyses. METHODS AND FINDINGS Fresh-frozen primary tumor samples from a large multicenter cohort of 750 patients with stage I to IV CC who underwent surgery between 1987 and 2007 in seven centers were characterized for common DNA alterations, including BRAF, KRAS, and TP53 mutations, CpG island methylator phenotype, mismatch repair status, and chromosomal instability status, and were screened with whole genome and transcriptome arrays. 566 samples fulfilled RNA quality requirements. Unsupervised consensus hierarchical clustering applied to gene expression data from a discovery subset of 443 CC samples identified six molecular subtypes. These subtypes were associated with distinct clinicopathological characteristics, molecular alterations, specific enrichments of supervised gene expression signatures (stem cell phenotype-like, normal-like, serrated CC phenotype-like), and deregulated signaling pathways. Based on their main biological characteristics, we distinguished a deficient mismatch repair subtype, a KRAS mutant subtype, a cancer stem cell subtype, and three chromosomal instability subtypes, including one associated with down-regulated immune pathways, one with up-regulation of the Wnt pathway, and one displaying a normal-like gene expression profile. The classification was validated in the remaining 123 samples plus an independent set of 1,058 CC samples, including eight public datasets. Furthermore, prognosis was analyzed in the subset of stage II-III CC samples. The subtypes C4 and C6, but not the subtypes C1, C2, C3, and C5, were independently associated with shorter relapse-free survival, even after adjusting for age, sex, stage, and the emerging prognostic classifier Oncotype DX Colon Cancer Assay recurrence score (hazard ratio 1.5, 95% CI 1.1-2.1, p = 0.0097). However, a limitation of this study is that information on tumor grade and number of nodes examined was not available. CONCLUSIONS We describe the first, to our knowledge, robust transcriptome-based classification of CC that improves the current disease stratification based on clinicopathological variables and common DNA markers. The biological relevance of these subtypes is illustrated by significant differences in prognosis. This analysis provides possibilities for improving prognostic models and therapeutic strategies. In conclusion, we report a new classification of CC into six molecular subtypes that arise through distinct biological pathways.
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Affiliation(s)
- Laetitia Marisa
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Aurélien de Reyniès
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Alex Duval
- Unité Mixte de Recherche S938, Centre de Recherche Hôpital Saint-Antoine, INSERM, Paris, France
- Université Pierre et Marie Curie–Paris 6, Paris, France
| | - Janick Selves
- Unité Mixte de Recherche 1037, Centre de Recherche en Cancérologie de Toulouse, Université de Toulouse III, INSERM, Toulouse, France
| | - Marie Pierre Gaub
- Unité de Recherche Physiopathologie et Médecine Translationnelle EA 4438, Université de Strasbourg, Strasbourg, France
- Laboratoire de Biochimie et Biologie Moléculaire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laure Vescovo
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | | | - Renaud Schiappa
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Dominique Guenot
- Unité de Recherche Physiopathologie et Médecine Translationnelle EA 4438, Université de Strasbourg, Strasbourg, France
| | - Mira Ayadi
- “Cartes d'Identité des Tumeurs” Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Sylvain Kirzin
- Unité Mixte de Recherche 1037, Centre de Recherche en Cancérologie de Toulouse, Université de Toulouse III, INSERM, Toulouse, France
| | | | - Jean-François Fléjou
- Unité Mixte de Recherche S938, Centre de Recherche Hôpital Saint-Antoine, INSERM, Paris, France
- Université Pierre et Marie Curie–Paris 6, Paris, France
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Anne Berger
- Hôpital Européen Georges Pompidou, Paris, France
| | - Arnaud Lagarde
- Unité Mixte de Recherche S910, Faculté de Médecine La Timone, INSERM, Marseille, France
| | - Erwan Pencreach
- Unité de Recherche Physiopathologie et Médecine Translationnelle EA 4438, Université de Strasbourg, Strasbourg, France
- Laboratoire de Biochimie et Biologie Moléculaire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Centre de Ressources Biologiques, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Françoise Piard
- Service de Pathologie, Centre Hospitalier Universitaire, Dijon, France
| | | | - Yann Parc
- Université Pierre et Marie Curie–Paris 6, Paris, France
- Service de Chirurgie Générale et Digestive, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sylviane Olschwang
- Unité Mixte de Recherche S910, Faculté de Médecine La Timone, INSERM, Marseille, France
- Pôle DACCORD, Hôpital La Timone, Marseille, France
- Département d'Oncologie, Hôpital Clairval, Marseille, France
- Département de Gastroentérologie, Hôpital Ambroise Paré, Marseille, France
| | - Gérard Milano
- Laboratoire d'Oncopharmacologie EA 3836, Centre Antoine Lacassagne, Nice, France
| | - Pierre Laurent-Puig
- Unité Mixte de Recherche S775, Paris Sorbonne Cité, Université Paris Descartes, INSERM, Paris, France
- * E-mail:
| | - Valérie Boige
- Institut Gustave Roussy, Villejuif, France
- Unité Mixte de Recherche S775, Paris Sorbonne Cité, Université Paris Descartes, INSERM, Paris, France
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Collura A, Marisa L, Trojan D, Buhard O, Lagrange A, Saget A, Bombled M, Méchighel P, Ayadi M, Muleris M, de Reynies A, Svrcek M, Fléjou JF, Florent JC, Mahuteau-Betzer F, Faussat AM, Duval A. Extensive characterization of sphere models established from colorectal cancer cell lines. Cell Mol Life Sci 2012; 70:729-42. [PMID: 23007843 DOI: 10.1007/s00018-012-1160-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 12/11/2022]
Abstract
Links between cancer and stem cells have been proposed for many years. As the cancer stem cell (CSC) theory became widely studied, new methods were developed to culture and expand cancer cells with conserved determinants of "stemness". These cells show increased ability to grow in suspension as spheres in serum-free medium supplemented with growth factors and chemicals. The physiological relevance of this phenomenon in established cancer cell lines remains unclear. Cell lines have traditionally been used to explore tumor biology and serve as preclinical models for the screening of potential therapeutic agents. Here, we grew cell-forming spheres (CFS) from 25 established colorectal cancer cell lines. The molecular and cellular characteristics of CFS were compared to the bulk of tumor cells. CFS could be isolated from 72 % of the cell lines. Both CFS and their parental CRC cell lines were highly tumorigenic. Compared to their parental cells, they showed similar expression of putative CSC markers. The ability of CRC cells to grow as CFS was greatly enhanced by prior treatment with 5-fluorouracil. At the molecular level, CFS and parental CRC cells showed identical gene mutations and very similar genomic profiles, although microarray analysis revealed changes in CFS gene expression that were independent of DNA copy-number. We identified a CFS gene expression signature common to CFS from all CRC cell lines, which was predictive of disease relapse in CRC patients. In conclusion, CFS models derived from CRC cell lines possess interesting phenotypic features that may have clinical relevance for drug resistance and disease relapse.
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MESH Headings
- Animals
- Antimetabolites, Antineoplastic/pharmacology
- Biomarkers, Tumor/genetics
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Colon/drug effects
- Colon/metabolism
- Colon/pathology
- Colorectal Neoplasms/diagnosis
- Colorectal Neoplasms/drug therapy
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Fluorouracil/pharmacology
- Gene Expression Regulation, Neoplastic
- Humans
- Mice
- Mice, Nude
- Neoplasm Recurrence, Local
- Rectum/drug effects
- Rectum/metabolism
- Rectum/pathology
- Spheroids, Cellular/drug effects
- Spheroids, Cellular/metabolism
- Spheroids, Cellular/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- Ada Collura
- Inserm, UMRS_938, Centre de Recherche Saint-Antoine, Equipe "Instabilité des Microsatellites et Cancers", 75012, Paris, France.
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39
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Letouzé E, Rosati R, Komechen H, Doghman M, Marisa L, Flück C, de Krijger RR, van Noesel MM, Mas JC, Pianovski MAD, Zambetti GP, Figueiredo BC, Lalli E. SNP array profiling of childhood adrenocortical tumors reveals distinct pathways of tumorigenesis and highlights candidate driver genes. J Clin Endocrinol Metab 2012; 97:E1284-93. [PMID: 22539591 DOI: 10.1210/jc.2012-1184] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Childhood adrenocortical tumors (ACT) are rare malignancies, except in southern Brazil, where a higher incidence rate is associated to a high frequency of the founder R337H TP53 mutation. To date, copy number alterations in these tumors have only been analyzed by low-resolution comparative genomic hybridization. OBJECTIVE We analyzed an international series of 25 childhood ACT using high-resolution single nucleotide polymorphism arrays to: 1) detect focal copy number alterations highlighting candidate driver genes; and 2) compare genetic alterations between Brazilian patients carrying the R337H TP53 mutation and non-Brazilian patients. RESULTS We identified 16 significantly recurrent chromosomal alterations (q-value < 0.05), the most frequent being -4q34, +9q33-q34, +19p, loss of heterozygosity (LOH) of chromosome 17 and 11p15. Focal amplifications and homozygous deletions comprising well-known oncogenes (MYC, MDM2, PDGFRA, KIT, MCL1, BCL2L1) and tumor suppressors (TP53, RB1, RPH3AL) were identified. In addition, eight focal deletions were detected at 4q34, defining a sharp peak region around the noncoding RNA LINC00290 gene. Although non-Brazilian tumors with a mutated TP53 were similar to Brazilian tumors, those with a wild-type TP53 displayed distinct genomic profiles, with significantly fewer rearrangements (P = 0.019). In particular, three alterations (LOH of chromosome 17, +9q33-q34, and -4q34) were significantly more frequent in TP53-mutated samples. Finally, two of four TP53 wild-type tumors displayed as sole rearrangement a copy-neutral LOH of the imprinted region at 11p15, supporting a major role for this region in ACT development. CONCLUSIONS Our findings highlight potential driver genes and cellular pathways implicated in childhood ACT and demonstrate the existence of different oncogenic routes in this pathology.
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Affiliation(s)
- Eric Letouzé
- Program Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, 14 rue Corvisart, 75013 Paris, France.
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Marisa L, Vescovo L, Reyniès A, Duval A, Etienne-Grimaldi MC, Gaub MP, Guenot D, Kirzin S, Milano G, Olschwang S, Selves J, Laurent-Puig P, Boige V. Abstract 5065: Gene expression profiling of colon adenocarcinomas reveals six prototypic molecular subtypes with distinct clinical and molecular characteristics. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5065] [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
Purpose: The purpose of our study was to build up a molecular classification of colon cancers (CC) and to further identify a molecular signature that correlated with disease outcome through a genome-wide DNA and mRNA expression analysis. Material: Fresh frozen tumor tissues from 750 patients with stage I to IV CC were analyzed for anatomo-clinical characteristics and common DNA alterations including KRAS, BRAF, TP53 mutations, MMR (Mismatch Repair system) and CIMP (CpG island methylator phenotype) status. Among the 750 tumors, 443 were screened for pangenomic alteration and expression profiles using Affymetrix U133P2 chips and CGH arrays. Results: A robust approach based on unsupervised hierarchical clusterings of the 443 tumors revealed six main prototypic molecular subtypes with distinct clinical/molecular correlations and outcomes. The first (C1), fifth (C5) and sixth (C6) subtypes were more frequently CIN+ (chromosomal instability assessed by CGHa), TP53 mutant and left-sided tumors, without any molecular or clinical annotation able to clearly discriminate these three subgroups except the low relapse rate observed in the C5 subgroup (21.6% versus 30.9% and 39.3% in C1 and C6 subgroups, respectively). C2 was enriched for patients with deficient MMR (80.7%), CIMP+ (62.5%), BRAF mutant (37.3%) and right-sided (71%) CC with low relapsing rate (19.7%). C3 was enriched for KRAS mutant (76.2%) and right-sided tumors (57.8%). C4 included more CIMP+ (35.4%), BRAF mutant (25%), right-sided (64.2%) and relapsing (47.2%) CC. Of those 6 subtypes, C4 and C2 (dMMR) appeared to be the most segregated subtypes, others being less distant to each other. Although not significant, there was a trend in favor of a prognostic value of the six-subgroup classification, with C1, C4 and C6 subgroups having a relative poor outcome, and C2 and C5 a relative good outcome (65%, 64%, 63%, 77% and 83% 5-year disease-free survival, respectively; p=0.12). Using the limited number of molecular features available from 6 public datasets, we validated the molecular and clinical characteristics of C2, as well as the higher rate of relapse observed in C4. The prognostic value of the six-subtype classification was significant when applied to one independent dataset of 304 CC (p=0.012), with a worse prognosis confirmed for C1 and C4, and a better prognosis for C2 and C5. Conclusion: Our results suggest that CC develop as distinct molecular entities evolving through multiple pathways on the basis of several molecular features that may not result in a single but in several prognostic signatures according to each molecular subtype.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5065. doi:1538-7445.AM2012-5065
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Affiliation(s)
| | | | | | - Alex Duval
- 2Hôpital Saint-Antoine INSERM, Paris, France
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41
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Dorard C, de Thonel A, Collura A, Marisa L, Svrcek M, Lagrange A, Jego G, Wanherdrick K, Joly AL, Buhard O, Gobbo J, Penard-Lacronique V, Zouali H, Tubacher E, Kirzin S, Selves J, Milano G, Etienne-Grimaldi MC, Bengrine-Lefèvre L, Louvet C, Tournigand C, Lefèvre JH, Parc Y, Tiret E, Fléjou JF, Gaub MP, Garrido C, Duval A. Expression of a mutant HSP110 sensitizes colorectal cancer cells to chemotherapy and improves disease prognosis. Nat Med 2011; 17:1283-9. [PMID: 21946539 DOI: 10.1038/nm.2457] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 08/01/2011] [Indexed: 12/26/2022]
Abstract
Heat shock proteins (HSPs) are necessary for cancer cell survival. We identified a mutant of HSP110 (HSP110ΔE9) in colorectal cancer showing microsatellite instability (MSI CRC), generated from an aberrantly spliced mRNA and lacking the HSP110 substrate-binding domain. This mutant was expressed at variable levels in almost all MSI CRC cell lines and primary tumors tested. HSP110ΔE9 impaired both the normal cellular localization of HSP110 and its interaction with other HSPs, thus abrogating the chaperone activity and antiapoptotic function of HSP110 in a dominant-negative manner. HSP110ΔE9 overexpression caused the sensitization of cells to anticancer agents such as oxaliplatin and 5-fluorouracil, which are routinely prescribed in the adjuvant treatment of people with CRC. The survival and response to chemotherapy of subjects with MSI CRCs was associated with the tumor expression level of HSP110ΔE9. HSP110 may thus constitute a major determinant for both prognosis and treatment response in CRC.
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Affiliation(s)
- Coralie Dorard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Paris, France
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42
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Guedj M, Marisa L, de Reynies A, Orsetti B, Schiappa R, Bibeau F, MacGrogan G, Lerebours F, Finetti P, Longy M, Bertheau P, Bertrand F, Bonnet F, Martin AL, Feugeas JP, Bièche I, Lehmann-Che J, Lidereau R, Birnbaum D, Bertucci F, de Thé H, Theillet C. A refined molecular taxonomy of breast cancer. Oncogene 2011; 31:1196-206. [PMID: 21785460 PMCID: PMC3307061 DOI: 10.1038/onc.2011.301] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The current histoclinical breast cancer classification is simple but imprecise. Several molecular classifications of breast cancers based on expression profiling have been proposed as alternatives. However, their reliability and clinical utility have been repeatedly questioned, notably because most of them were derived from relatively small initial patient populations. We analyzed the transcriptomes of 537 breast tumors using three unsupervised classification methods. A core subset of 355 tumors was assigned to six clusters by all three methods. These six subgroups overlapped with previously defined molecular classes of breast cancer, but also showed important differences, notably the absence of an ERBB2 subgroup and the division of the large luminal ER+ group into four subgroups, two of them being highly proliferative. Of the six subgroups, four were ER+/PR+/AR+, one was ER−/PR−/AR+ and one was triple negative (AR−/ER−/PR−). ERBB2-amplified tumors were split between the ER−/PR−/AR+ subgroup and the highly proliferative ER+ LumC subgroup. Importantly, each of these six molecular subgroups showed specific copy-number alterations. Gene expression changes were correlated to specific signaling pathways. Each of these six subgroups showed very significant differences in tumor grade, metastatic sites, relapse-free survival or response to chemotherapy. All these findings were validated on large external datasets including more than 3000 tumors. Our data thus indicate that these six molecular subgroups represent well-defined clinico-biological entities of breast cancer. Their identification should facilitate the detection of novel prognostic factors or therapeutical targets in breast cancer.
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Affiliation(s)
- M Guedj
- Ligue Nationale Contre le Cancer, Cartes d'Identité des Tumeurs program, Paris, France
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Jeanmougin M, de Reynies A, Marisa L, Paccard C, Nuel G, Guedj M. Should we abandon the t-test in the analysis of gene expression microarray data: a comparison of variance modeling strategies. PLoS One 2010; 5:e12336. [PMID: 20838429 PMCID: PMC2933223 DOI: 10.1371/journal.pone.0012336] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/24/2010] [Indexed: 02/07/2023] Open
Abstract
High-throughput post-genomic studies are now routinely and promisingly investigated in biological and biomedical research. The main statistical approach to select genes differentially expressed between two groups is to apply a t-test, which is subject of criticism in the literature. Numerous alternatives have been developed based on different and innovative variance modeling strategies. However, a critical issue is that selecting a different test usually leads to a different gene list. In this context and given the current tendency to apply the t-test, identifying the most efficient approach in practice remains crucial. To provide elements to answer, we conduct a comparison of eight tests representative of variance modeling strategies in gene expression data: Welch's t-test, ANOVA [1], Wilcoxon's test, SAM [2], RVM [3], limma [4], VarMixt [5] and SMVar [6]. Our comparison process relies on four steps (gene list analysis, simulations, spike-in data and re-sampling) to formulate comprehensive and robust conclusions about test performance, in terms of statistical power, false-positive rate, execution time and ease of use. Our results raise concerns about the ability of some methods to control the expected number of false positives at a desirable level. Besides, two tests (limma and VarMixt) show significant improvement compared to the t-test, in particular to deal with small sample sizes. In addition limma presents several practical advantages, so we advocate its application to analyze gene expression data.
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Affiliation(s)
- Marine Jeanmougin
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.
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Maunoury N, Redondo-Nieto M, Bourcy M, Van de Velde W, Alunni B, Laporte P, Durand P, Agier N, Marisa L, Vaubert D, Delacroix H, Duc G, Ratet P, Aggerbeck L, Kondorosi E, Mergaert P. Differentiation of symbiotic cells and endosymbionts in Medicago truncatula nodulation are coupled to two transcriptome-switches. PLoS One 2010; 5:e9519. [PMID: 20209049 PMCID: PMC2832008 DOI: 10.1371/journal.pone.0009519] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 02/12/2010] [Indexed: 12/16/2022] Open
Abstract
The legume plant Medicago truncatula establishes a symbiosis with the nitrogen-fixing bacterium Sinorhizobium meliloti which takes place in root nodules. The formation of nodules employs a complex developmental program involving organogenesis, specific cellular differentiation of the host cells and the endosymbiotic bacteria, called bacteroids, as well as the specific activation of a large number of plant genes. By using a collection of plant and bacterial mutants inducing non-functional, Fix(-) nodules, we studied the differentiation processes of the symbiotic partners together with the nodule transcriptome, with the aim of unravelling links between cell differentiation and transcriptome activation. Two waves of transcriptional reprogramming involving the repression and the massive induction of hundreds of genes were observed during wild-type nodule formation. The dominant features of this "nodule-specific transcriptome" were the repression of plant defense-related genes, the transient activation of cell cycle and protein synthesis genes at the early stage of nodule development and the activation of the secretory pathway along with a large number of transmembrane and secretory proteins or peptides throughout organogenesis. The fifteen plant and bacterial mutants that were analyzed fell into four major categories. Members of the first category of mutants formed non-functional nodules although they had differentiated nodule cells and bacteroids. This group passed the two transcriptome switch-points similarly to the wild type. The second category, which formed nodules in which the plant cells were differentiated and infected but the bacteroids did not differentiate, passed the first transcriptome switch but not the second one. Nodules in the third category contained infection threads but were devoid of differentiated symbiotic cells and displayed a root-like transcriptome. Nodules in the fourth category were free of bacteria, devoid of differentiated symbiotic cells and also displayed a root-like transcriptome. A correlation thus exists between the differentiation of symbiotic nodule cells and the first wave of nodule specific gene activation and between differentiation of rhizobia to bacteroids and the second transcriptome wave in nodules. The differentiation of symbiotic cells and of bacteroids may therefore constitute signals for the execution of these transcriptome-switches.
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Affiliation(s)
- Nicolas Maunoury
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Miguel Redondo-Nieto
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Marie Bourcy
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Willem Van de Velde
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Benoit Alunni
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Philippe Laporte
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Patricia Durand
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Nicolas Agier
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 3144 and Gif/Orsay DNA MicroArray Platform (GODMAP), Gif-sur-Yvette, France
| | - Laetitia Marisa
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 3144 and Gif/Orsay DNA MicroArray Platform (GODMAP), Gif-sur-Yvette, France
| | - Danièle Vaubert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Hervé Delacroix
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 3144 and Gif/Orsay DNA MicroArray Platform (GODMAP), Gif-sur-Yvette, France
- Université Paris-Sud 11, Orsay, France
| | - Gérard Duc
- Génétique et Ecophysiologie des Légumineuses à Graines, Institut National de la Recherche Agronomique, Dijon, France
| | - Pascal Ratet
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Lawrence Aggerbeck
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 3144 and Gif/Orsay DNA MicroArray Platform (GODMAP), Gif-sur-Yvette, France
| | - Eva Kondorosi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
- Bay Zoltan Foundation for Applied Research, Institute of Plant Genomics, Human Biotechnology and Bioenergy, Szeged, Hungary
| | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
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Narjoz C, Marisa L, Imbeaud S, Paris A, Delacroix H, Beaune P, De Waziers I. Genomic consequences of cytochrome P450 2C9 overexpression in human hepatoma cells. Chem Res Toxicol 2009; 22:779-87. [PMID: 19445531 DOI: 10.1021/tx800417u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cytochrome P450 2C9 (P450 2C9) is one of the most important P450 isoforms in the human liver, as it metabolizes numerous exogenous and endogenous substrates. Moreover, it is inducible by several compounds, such as rifampicin, phenobarbital, and NSAIDs (nonsteroidal anti-inflammatories). The aim of this study was to investigate the global cellular consequences of P450 2C9 overexpression at the transcriptional level using an untargeted approach: pangenomic microarrays. Recombinant adenovirus was used to express P450 2C9 instead of an inducer to prevent a per se effect of inducer or its metabolites. P450 2C9 overexpression induced endoplasmic reticulum (ER) stress and regulated genes implicated in the unfolded protein response (UPR) as heat shock protein (HSP) (we studied particurlarly HSPA5 and HSPB1) and in the endoplasmic reticulum associated degradation (ERAD) system as Sec61 and ubiquitin and proteasome pathways. UPR and ERAD are two mechanisms of adaptative response to ER stress. Moreover, activation of Akt was observed in HepG2 cells that overexpress P450 2C9 and might participate in the cellular adaptive response to stress, thus leading to the activation of cell survival pathways. UPR and ERAD should be caused by accumulation of native and misfolded P450 2C9 protein. Our results indicated that P450 2C9 overexpression did not lead to toxicity but induced an ER stress due to protein overexpression rather than mono-oxygenase activity. The ER stress triggered activation of the adaptative response and of pathways leading to cell survival.
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Affiliation(s)
- Céline Narjoz
- Université Paris Descartes and INSERM UMR U775, Paris, France
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Bertucci F, Le Doussal JM, Birnbaum D, Tagett R, Martinec A, Hermitte F, Marisa L, Martin AL, Geneve J, Roché H, Penault-Llorca F. Prognostic value of the genomic grade index (GGi) as compared to centrally measured Ki-67 IHC and mitotic index in early breast cancer patients. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.11094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11094 Background: Genomic grading has been proposed to improve tumor grading. The genomic grade index (GGi) is a 97-gene continuous measure which resolves 80% of histological grade 2 (HG 2) tumors into HG 1 and HG 3 risk categories. GGi has higher prognostic value than HG in patients treated with and without systemic adjuvant endocrine and chemotherapy. A key issue is whether the GGi adds prognostic information to centrally-determined mitotic index and Ki-67 IHC. Methods: The control arm of the PACS 01 trial included 996 women with node-positive (N+) early breast cancer treated with six cycles of fluorouracil, epirubicin, and cyclophosphamide (FEC) and tamoxifen as required. 128 genomic profiles could be obtained from available frozen tumor samples using Affymetrix U133 Plus 2.0 gene chips through the “Carte d'Identite des Tumeurs” program of the French Ligue Nationale contre le Cancer. The Genomic Grade index (GGi) was computed using Ipsogen MapQuant Dx(R). Central Elston-Ellis grade, mitotic index (mitosis / mm2), and Ki-67 IHC (% positive cells) were available for 125 patients. The GGi and histological parameters were correlated to the 5-year metastasis status (MFS-5) by ROC analysis and to the metastasis hazard (follow-up of 6.2 ± years) by Cox regression. Results: In ER+ patients (n=93), the GGi was the only significant correlate to metastasis hazard in multivariate Cox regression with histological parameters (HR = 3.5 [1.7–7.5], p<0.001). It was the best predictor of MFS-5 (ROC AUC = 0.83, p=1E-6) when compared to histological parameters (ROC AUC = 0.71, 0.72 and 0.66 resp. p=0.003 to 0.03). In HG 2 subgroup (n=43), the GGi was the only significant predictor of MFS-5 (ROC AUC = 0.81, p=0.016). Conclusions: In our sample of N+ ER+ breast cancer patients, the GGi improved prognostication compared to centrally-measured mitotic index and Ki-67 IHC used alone and in combination. Moreover, the GGi was the only prognostic factor in histological grade 2 patients. [Table: see text]
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Affiliation(s)
- F. Bertucci
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - J. M. Le Doussal
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - D. Birnbaum
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - R. Tagett
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - A. Martinec
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - F. Hermitte
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - L. Marisa
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - A. L. Martin
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - J. Geneve
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - H. Roché
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
| | - F. Penault-Llorca
- Institut Paoli Calmettes, Marseille, France; Ipsogen, Marseille, France; Ligue National Contre le Cancer, Paris, France; FNCLCC, Paris, France; Institut Claudius Regaud, Toulouse, France; Centre Jean Perrin, Clermont Ferrand, France
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Marisa L, Ichanté JL, Reymond N, Aggerbeck L, Delacroix H, Mucchielli-Giorgi MH. MAnGO: an interactive R-based tool for two-colour microarray analysis. Bioinformatics 2007; 23:2339-41. [PMID: 17586547 DOI: 10.1093/bioinformatics/btm321] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED MAnGO (Microarray Analysis at the Gif/Orsay platform) is an interactive R-based tool for the analysis of two-colour microarray experiments. It is a compilation of various methods, which allows the user (1) to control data quality by detecting biases with a large number of visual representations, (2) to pre-process data (filtering and normalization) and (3) to carry out differential analyses. MAnGO is not only a 'turn-key' tool, oriented towards biologists but also a flexible and adaptable R script oriented towards bioinformaticians. AVAILABILITY http://bioinfome.cgm.cnrs-gif.fr/.
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Affiliation(s)
- Laetitia Marisa
- Centre de Génétique Moléculaire, CNRS UPR2167 and Gif/Orsay DNA Microarray Platform, 91190 Gif-sur-Yvette, France
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Matsunaga F, Glatigny A, Mucchielli-Giorgi MH, Agier N, Delacroix H, Marisa L, Durosay P, Ishino Y, Aggerbeck L, Forterre P. Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res 2007; 35:3214-22. [PMID: 17452353 PMCID: PMC1904270 DOI: 10.1093/nar/gkm212] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of DNA replication (oriC) of the hyperthermophilic archaeon Pyrococcus abyssi contains multiple ORB and mini-ORB repeats that show sequence similarities to other archaeal ORB (origin recognition box). We report here that the binding of Cdc6/Orc1 to a 5 kb region containing oriC in vivo was highly specific both in exponential and stationary phases, by means of chromatin immunoprecipitation coupled with hybridization on a whole genome microarray (ChIP-chip). The oriC region is practically the sole binding site for the Cdc6/Orc1, thereby distinguishing oriC in the 1.8 M bp genome. We found that the 5 kb region contains a previously unnoticed cluster of ORB and mini-ORB repeats in the gene encoding the small subunit (dp1) for DNA polymerase II (PolD). ChIP and the gel retardation analyses further revealed that Cdc6/Orc1 specifically binds both of the ORB clusters in oriC and dp1. The organization of the ORB clusters in the dp1 and oriC is conserved during evolution in the order Thermococcales, suggesting a role in the initiation of DNA replication. Our ChIP-chip analysis also revealed that Mcm alters the binding specificity to the oriC region according to the growth phase, consistent with its role as a licensing factor.
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Affiliation(s)
- Fujihiko Matsunaga
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Annie Glatigny
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Marie-Hélène Mucchielli-Giorgi
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Nicolas Agier
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Hervé Delacroix
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Laetitia Marisa
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Patrice Durosay
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Yoshizumi Ishino
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Lawrence Aggerbeck
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
- *To whom correspondence should be addressed. Tel: +33 1 69 157489; Fax: +33 1 69 157808;
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Krin E, Chakroun N, Turlin E, Givaudan A, Gaboriau F, Bonne I, Rousselle JC, Frangeul L, Lacroix C, Hullo MF, Marisa L, Danchin A, Derzelle S. Pleiotropic role of quorum-sensing autoinducer 2 in Photorhabdus luminescens. Appl Environ Microbiol 2006; 72:6439-51. [PMID: 17021191 PMCID: PMC1610301 DOI: 10.1128/aem.00398-06] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial virulence is an integrative process that may involve quorum sensing. In this work, we compared by global expression profiling the wild-type entomopathogenic Photorhabdus luminescens subsp. laumondii TT01 to a luxS-deficient mutant unable to synthesize the type 2 quorum-sensing inducer AI-2. AI-2 was shown to regulate more than 300 targets involved in most compartments and metabolic pathways of the cell. AI-2 is located high in the hierarchy, as it controls the expression of several transcriptional regulators. The regulatory effect of AI-2 appeared to be dose dependent. The luxS-deficient strain exhibited decreased biofilm formation and increased type IV/V pilus-dependent twitching motility. AI-2 activated its own synthesis and transport. It also modulated bioluminescence by regulating the synthesis of spermidine. AI-2 was further shown to increase oxidative stress resistance, which is necessary to overcome part of the innate immune response of the host insect involving reactive oxygen species. Finally, we showed that the luxS-deficient strain had attenuated virulence against the lepidopteran Spodoptera littoralis. We concluded that AI-2 is involved mainly in early steps of insect invasion in P. luminescens.
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Affiliation(s)
- Evelyne Krin
- Unité de Génétique des Génomes Bactériens (URA2171), Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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