Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma

Julien Calderaro; Narmin Ghaffari Laleh; Qinghe Zeng; Pascale Maille; Loetitia Favre; Anaïs Pujals; Christophe Klein; Céline Bazille; Lara Heij; Arnaud Uguen; Tom Luedde; Luca Di Tommaso; Aurélie Beaufrère; Augustin Chatain; Delphine Gastineau; Cong Trung Nguyen; Hiep Nguyen-Canh; Khuyen Nguyen Thi; Viviane Gnemmi; Rondell Graham; Frédéric Charlotte; Dominique Wendum; Mukul Vij; Daniela Allende; Federico Aucejo; Alba Diaz; Benjamin Rivière; Astrid Herrero; Katja Evert; Diego Francesco Calvisi; Jérémy Augustin; Wei Qiang Leow; Howard Ho Wai Leung; Emmanuel Boleslawski; Mohamed Rela; Arnaud François; Anthony Wing-Hung Cha; Alejandro Forner; Maria Reig; Manon Allaire; Olivier Scatton; Denis Chatelain; Camille Boulagnon-Rombi; Nathalie Sturm; Benjamin Menahem; Eric Frouin; Éric Frouin; David Tougeron; Christophe Tournigand; Emmanuelle Kempf; Haeryoung Kim; Massih Ningarhari; Sophie Michalak-Provost; Purva Gopal; Raffaele Brustia; Eric Vibert; Kornelius Schulze; Darius Rüther; Sören Weidemann; Rami Rhaiem; Jean-Michel Pawlotsky; Xuchen Zhang; Alain Luciani; Sébastien Mulé; Alexis Laurent; Giuliana Amaddeo; Hélène Regnault; Eleonora de Martin; Christine Sempoux; Pooja Navale; Maria Westerhoff; Regina Cheuk-Lam Lo; Jan Bednarsch; Annette Gouw; Catherine Guettier; Marie Lequoy; Kenichi Harada; Pimsiri Sripongpun; Poowadon Wetwittayaklang; Nicolas Loménie; Jarukit Tantipisit; Apichat Kaewdech; Jeanne Shen; Valérie Paradis; Stefano Caruso; Jakob Nikolas Kather

doi:10.1038/s41467-023-43749-3

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Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma

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Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma

Julien Calderaro, Narmin Ghaffari Laleh, Qinghe Zeng, Pascale Maille, Loetitia Favre, Anaïs Pujals, Christophe Klein, Céline Bazille, Lara Heij, Arnaud Uguen, …

Nature communications, Vol.14(1), pp.8290-10

14/12/2023

DOI: https://doi.org/10.1038/s41467-023-43749-3

PMID: 38092727

Résumé

Biochemistry, Molecular Biology

Cancer

Computer Science

Genomics

Human health and pathology

Hépatology and Gastroenterology

Life Sciences

Machine Learning

Quantitative Methods

Primary liver cancer arises either from hepatocytic or biliary lineage cells, giving rise to hepatocellular carcinoma (HCC) or intrahepatic cholangiocarcinoma (ICCA). Combined hepatocellular- cholangiocarcinomas (cHCC-CCA) exhibit equivocal or mixed features of both, causing diagnostic uncertainty and difficulty in determining proper management. Here, we perform a comprehensive deep learning-based phenotyping of multiple cohorts of patients. We show that deep learning can reproduce the diagnosis of HCC vs. CCA with a high performance. We analyze a series of 405 cHCC-CCA patients and demonstrate that the model can reclassify the tumors as HCC or ICCA, and that the predictions are consistent with clinical outcomes, genetic alterations and in situ spatial gene expression profiling. This type of approach could improve treatment decisions and ultimately clinical outcome for patients with rare and biphenotypic cancers such as cHCC-CCA.

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Titre: Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma
Créateurs - sans rôle: Julien Calderaro - Institut Mondor de Recherche Biomédicale
Narmin Ghaffari Laleh - Else Kroener Fresenius Center for Digital Health = Else Kröner Fresenius Zentrum für Digitale Gesundheit
Qinghe Zeng - Centre d'Histologie, d'Imagerie et de Cytométrie
Pascale Maille - Institut Mondor de Recherche Biomédicale
Loetitia Favre - Institut Mondor de Recherche Biomédicale
Anaïs Pujals - Institut Mondor de Recherche Biomédicale
Christophe Klein - Centre d'Histologie, d'Imagerie et de Cytométrie
Céline Bazille - Département de Pathologie [CHU Caen]
Lara Heij - RWTH Aachen University
Arnaud Uguen - CHRU Brest, Pôle de Biologie Pathologie
Tom Luedde - Klinik für Gastroenterologie, Hepatologie und Infektiologie
Luca Di Tommaso - IRCCS Humanitas Research Hospital
Aurélie Beaufrère - Service d'Anatomo-Pathologie
Augustin Chatain - IMRB - VHC/"Viruses-Hepatology-Cancers" [Créteil]
Delphine Gastineau - IMRB - VHC/"Viruses-Hepatology-Cancers" [Créteil]
Cong Trung Nguyen - Hanoï Medical University
Hiep Nguyen-Canh - Bach Mai Hospital [Hanoi]
Khuyen Nguyen Thi - National Cancer Hospital K1 [Hanoi, Vietnam]
Viviane Gnemmi - Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277
Rondell Graham - Department of Laboratory Medicine and Pathology (Mayo Clinic Rochester)
Frédéric Charlotte - CHU Pitié-Salpêtrière [AP-HP]
Dominique Wendum - CHU Saint-Antoine [AP-HP]
Mukul Vij - Dr. Rela Institute & Medical Centre [Chennai]
Daniela Allende - Gastrointestinal, Hepatic & Pancreatobiliary Pathology [Cleveland Clinic]
Federico Aucejo - Digestive Disease & Surgery Institute [Cleveland Clinic]
Alba Diaz - Barcelona Clínic Liver Cancer
Benjamin Rivière - Hôpital Gui de Chauliac
Astrid Herrero - Hôpital Gui de Chauliac [CHU Montpellier]
Katja Evert - Institut für Pathologie [Regensburg]
Diego Francesco Calvisi - Institut für Pathologie [Regensburg]
Jérémy Augustin - Institut Mondor de Recherche Biomédicale
Wei Qiang Leow - Department of Pathology [Singapour]
Howard Ho Wai Leung - The Chinese University of Hong Kong
Emmanuel Boleslawski - Hôpital Claude Huriez [Lille]
Mohamed Rela - Dr. Rela Institute & Medical Centre [Chennai]
Arnaud François - Département de Pathologie [CHU Rouen]
Anthony Wing-Hung Cha - The Chinese University of Hong Kong
Alejandro Forner - Barcelona Clínic Liver Cancer
Maria Reig - Barcelona Clínic Liver Cancer
Manon Allaire - CHU Pitié-Salpêtrière [AP-HP]
Olivier Scatton - CHU Pitié-Salpêtrière [AP-HP]
Denis Chatelain - Anatomie et Cytologie Pathologiques [CHU Amiens]
Camille Boulagnon-Rombi - Service d'Anatomie et de Cytologie Pathologiques
Nathalie Sturm - Anatomie et de Cytologie Pathologiques [CHU Grenoble]
Benjamin Menahem - Service de Chirurgie Viscérale et Digestive [CHU Caen]
Eric Frouin - Service de Pathologie [CHU Poitiers]
Éric Frouin - Laboratoire inflammation, tissus épithéliaux et cytokines [UR 15560]
David Tougeron - Service d'Hépato-Gastro-Enterologie et Nutrition [CHU Caen]
Christophe Tournigand - Service d'Oncologie médicale [CHU Henri Mondor]
Emmanuelle Kempf - Service d'Oncologie médicale [CHU Henri Mondor]
Haeryoung Kim - Department of Pathology [Seoul National University Hospital]
Massih Ningarhari - Service Hépato-gastroentérologie [Hôpital Claude Huriez, Lille]
Sophie Michalak-Provost - Département de Pathologie [CHU Angers]
Purva Gopal - Department of Pathology [Dallas]
Raffaele Brustia - Service de chirurgie digestive
Eric Vibert - Centre hépato-biliaire
Kornelius Schulze - Internal Medicine
Darius Rüther - Internal Medicine
Sören Weidemann - University Medical Center Hamburg-Eppendorf
Rami Rhaiem - Hôpital universitaire Robert Debré [Reims]
Jean-Michel Pawlotsky - Institut Mondor de Recherche Biomédicale
Xuchen Zhang - Department of Pathology [Yale]
Alain Luciani - Service d'imagerie médicale
Sébastien Mulé - Service d'imagerie médicale
Alexis Laurent - Service de chirurgie digestive
Giuliana Amaddeo - Service d'hépato-gastro-entérologie [APHP Henri Mondor]
Hélène Regnault - Service d'hépato-gastro-entérologie [APHP Henri Mondor]
Eleonora de Martin - Centre Hépato-Biliaire [Hôpital Paul Brousse]
Christine Sempoux - Institut de Pathologie
Pooja Navale - Department of Pathology and Immunology [Washington University in St. Louis]
Maria Westerhoff - Department of Pathology [University of Michigan Medical School, Ann Arbor]
Regina Cheuk-Lam Lo - Department of pathology [HKU]
Jan Bednarsch - RWTH Aachen University
Annette Gouw - Department of Pathology and Medical Biology
Catherine Guettier - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany]
Marie Lequoy - CHU Saint-Antoine [AP-HP]
Kenichi Harada - School of Medicine [Kanazawa Medical University]
Pimsiri Sripongpun - Department of Internal Medicine [Songkhla]
Poowadon Wetwittayaklang - Pathology Department [Songkla]
Nicolas Loménie - Laboratoire d'Informatique Paris Descartes
Jarukit Tantipisit - Pathology Department [Songkla]
Apichat Kaewdech - Department of Internal Medicine [Songkhla]
Jeanne Shen - Stanford Center for Artificial Intelligence in Medicine and Imaging
Valérie Paradis - Else Kroener Fresenius Center for Digital Health = Else Kröner Fresenius Zentrum für Digitale Gesundheit
Stefano Caruso - Institut Mondor de Recherche Biomédicale
Jakob Nikolas Kather
Détails de publication: Nature communications, Vol.14(1), pp.8290-10
Éditeur: Nature Publishing Group
Identifiants: 99141378009311
Unité académique: Institut de Recherche en Cancérologie de Montpellier - IRCM; Cell souches plasticité cellul régénérat tissulaire immuno des maladies inflamm - IRMB
Langue: English
Type de ressource: Journal article