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Alcala N, Leblay N, Gabriel AAG, Mangiante L, Hervas D, Giffon T, Sertier AS, Ferrari A, Derks J, Ghantous A, Delhomme TM, Chabrier A, Cuenin C, Abedi-Ardekani B, Boland A, Olaso R, Meyer V, Altmuller J, Le Calvez-Kelm F, Durand G, Voegele C, Boyault S, Moonen L, Lemaitre N, Lorimier P, Toffart AC, Soltermann A, Clement JH, Saenger J, Field JK, Brevet M, Blanc-Fournier C, Galateau-Salle F, Le Stang N, Russell PA, Wright G, Sozzi G, Pastorino U, Lacomme S, Vignaud JM, Hofman V, Hofman P, Brustugun OT, Lund-Iversen M, Thomas de Montpreville V, Muscarella LA, Graziano P, Popper H, Stojsic J, Deleuze JF, Herceg Z, Viari A, Nuernberg P, Pelosi G, Dingemans AMC, Milione M, Roz L, Brcic L, Volante M, Papotti MG, Caux C, Sandoval J, Hernandez-Vargas H, Brambilla E, Speel EJM, Girard N, Lantuejoul S, McKay JD, Foll M, Fernandez-Cuesta L. Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids. Nat Commun 2019; 10:3407. [PMID: 31431620 PMCID: PMC6702229 DOI: 10.1038/s41467-019-11276-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [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: 11/07/2018] [Accepted: 07/02/2019] [Indexed: 02/06/2023] Open
Abstract
The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identify therapeutically relevant molecular groups of pulmonary carcinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirm the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveil the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low- and high-grade lung neuroendocrine neoplasms.
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Affiliation(s)
- N Alcala
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - N Leblay
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - A A G Gabriel
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - L Mangiante
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - D Hervas
- Health Research Institute La Fe, Avenida Fernando Abril Martorell, Torre 106 A 7planta, 46026, Valencia, Spain
| | - T Giffon
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - A S Sertier
- Synergie Lyon Cancer, Centre Léon Bérard, 28 Rue Laennec, 69008, Lyon, France
| | - A Ferrari
- Synergie Lyon Cancer, Centre Léon Bérard, 28 Rue Laennec, 69008, Lyon, France
| | - J Derks
- Maastricht University Medical Centre (MUMC), GROW School for Oncology and Developmental Biology, P.O. Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - A Ghantous
- International Agency for Research on Cancer (IARC/WHO), Section of Mechanisms of Carcinogenesis, 150 Cours Albert Thomas, 69008, Lyon, France
| | - T M Delhomme
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - A Chabrier
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - C Cuenin
- International Agency for Research on Cancer (IARC/WHO), Section of Mechanisms of Carcinogenesis, 150 Cours Albert Thomas, 69008, Lyon, France
| | - B Abedi-Ardekani
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - A Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 2 rue Gaston Crémieux, CP 5706, 91057, Evry Cedex, France
| | - R Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 2 rue Gaston Crémieux, CP 5706, 91057, Evry Cedex, France
| | - V Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 2 rue Gaston Crémieux, CP 5706, 91057, Evry Cedex, France
| | - J Altmuller
- Cologne Centre for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115, 50931, Cologne, Germany
| | - F Le Calvez-Kelm
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - G Durand
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - C Voegele
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - S Boyault
- Translational Research and Innovation Department, Cancer Genomic Platform, 28 Rue Laennec, 69008, Lyon, France
| | - L Moonen
- Maastricht University Medical Centre (MUMC), GROW School for Oncology and Developmental Biology, P.O. Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - N Lemaitre
- Institute for Advanced Biosciences, Site Santé, Allée des Alpes, 38700, La Tronche, Grenoble, France
| | - P Lorimier
- Institute for Advanced Biosciences, Site Santé, Allée des Alpes, 38700, La Tronche, Grenoble, France
| | - A C Toffart
- Pulmonology-Physiology Unit, Grenoble Alpes University Hospital, 38700, La Tronche, France
| | - A Soltermann
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - J H Clement
- Department Hematology and Medical Oncology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - J Saenger
- Bad Berka Institute of Pathology, Robert-Koch-Allee 9, 99438, Bad Berka, Germany
| | - J K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6 West Derby Street, L7 8TX, Liverpool, UK
| | - M Brevet
- Pathology Institute, Hospices Civils de Lyon, University Claude Bernard Lyon 1, 59 Boulevard Pinel, 69677, BRON Cedex, France
| | - C Blanc-Fournier
- CLCC François Baclesse, 3 avenue du Général Harris, 14076, Caen Cedex 5, France
| | - F Galateau-Salle
- Department of Pathology, Centre Léon Bérard, 28, rue Laennec, 69373, Lyon Cedex 8, France
| | - N Le Stang
- Department of Pathology, Centre Léon Bérard, 28, rue Laennec, 69373, Lyon Cedex 8, France
| | - P A Russell
- St. Vincent's Hospital and University of Melbourne, Victoria Parade, Fitzroy, Melbourne, VIC, 3065, Australia
| | - G Wright
- St. Vincent's Hospital and University of Melbourne, Victoria Parade, Fitzroy, Melbourne, VIC, 3065, Australia
| | - G Sozzi
- Pathology Division Fondazione, IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133, Milan, Italy
| | - U Pastorino
- Pathology Division Fondazione, IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133, Milan, Italy
| | - S Lacomme
- Nancy Regional University Hospital, CHRU, CRB BB-0033-00035, INSERM U1256, 29 Avenue du Maréchal de Lattre de Tassigny, 54035, Nancy Cedex, France
| | - J M Vignaud
- Nancy Regional University Hospital, CHRU, CRB BB-0033-00035, INSERM U1256, 29 Avenue du Maréchal de Lattre de Tassigny, 54035, Nancy Cedex, France
| | - V Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Hospital, Biobank BB-0033-00025, IRCAN Inserm U1081 CNRS 7284, University Côte d'Azur, 30 avenue de la voie Romaine, CS, 51069-06001, Nice Cedex 1, France
| | - P Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Hospital, Biobank BB-0033-00025, IRCAN Inserm U1081 CNRS 7284, University Côte d'Azur, 30 avenue de la voie Romaine, CS, 51069-06001, Nice Cedex 1, France
| | - O T Brustugun
- Drammen Hospital, Vestre Viken Health Trust, Vestre Viken HF, Postboks 800, 3004, Drammen, Norway
- Institute of Cancer Research, Oslo University Hospital, Ullernchausseen 70, 0379, Oslo, Norway
| | - M Lund-Iversen
- Institute of Cancer Research, Oslo University Hospital, Ullernchausseen 70, 0379, Oslo, Norway
| | | | - L A Muscarella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo FG, Italy
| | - P Graziano
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo FG, Italy
| | - H Popper
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - J Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Pasterova 2, Belgrade, 11000, Serbia
| | - J F Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 2 rue Gaston Crémieux, CP 5706, 91057, Evry Cedex, France
| | - Z Herceg
- International Agency for Research on Cancer (IARC/WHO), Section of Mechanisms of Carcinogenesis, 150 Cours Albert Thomas, 69008, Lyon, France
| | - A Viari
- Synergie Lyon Cancer, Centre Léon Bérard, 28 Rue Laennec, 69008, Lyon, France
| | - P Nuernberg
- Cologne Centre for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Straße 26, 50931, Cologne, Germany
| | - G Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, and Inter-Hospital Pathology Division, IRCCS Multimedica, Via Gaudenzio Fantoli, 16/15, 20138, Milan, Italy
| | - A M C Dingemans
- Maastricht University Medical Centre (MUMC), GROW School for Oncology and Developmental Biology, P.O. Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - M Milione
- Pathology Division Fondazione, IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133, Milan, Italy
| | - L Roz
- Pathology Division Fondazione, IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133, Milan, Italy
| | - L Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - M Volante
- Department of Oncology, University of Turin, Pathology Division, Via Santena 7, 10126, Torino, Italy
| | - M G Papotti
- Department of Oncology, University of Turin, Pathology Division, Via Santena 7, 10126, Torino, Italy
| | - C Caux
- Department of Immunity, Virus, and Inflammation, Cancer Research Centre of Lyon (CRCL), 28 Rue Laennec, 69008, Lyon, France
| | - J Sandoval
- Health Research Institute La Fe, Avenida Fernando Abril Martorell, Torre 106 A 7planta, 46026, Valencia, Spain
| | - H Hernandez-Vargas
- Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Centre Léon Bérard, Université de Lyon, 28 Rue Laennec, 69008, Lyon, France
| | - E Brambilla
- Institute for Advanced Biosciences, Site Santé, Allée des Alpes, 38700, La Tronche, Grenoble, France
| | - E J M Speel
- Maastricht University Medical Centre (MUMC), GROW School for Oncology and Developmental Biology, P.O. Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - N Girard
- Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
- European Reference Network (ERN-EURACAN), 28 rue Laennec, 69008, Lyon, France
| | - S Lantuejoul
- Synergie Lyon Cancer, Centre Léon Bérard, 28 Rue Laennec, 69008, Lyon, France
- Translational Research and Innovation Department, Cancer Genomic Platform, 28 Rue Laennec, 69008, Lyon, France
- Department of Pathology, Centre Léon Bérard, 28, rue Laennec, 69373, Lyon Cedex 8, France
| | - J D McKay
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - M Foll
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France
| | - L Fernandez-Cuesta
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, 69008, Lyon, France.
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