Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma
Nature Communications, vol. 14, pp. 8290
Abstract
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.
Authors 85
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Julien Caldéraro corresponding
Inserm · Université Paris-Est Créteil · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale · ERN RARE-LIVER
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France. julien.calderaro@aphp.fr
European Reference Network (ERN) RARE-LIVER, Créteil, France. julien.calderaro@aphp.fr
Inserm, U955, Team 18, Créteil, France. julien.calderaro@aphp.fr
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France. julien.calderaro@aphp.fr
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University
Affiliation as printed
Department of Medicine III, University Hospital RWTH Aachen, RWTH Aachen university, Aachen, Germany
Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
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Université Paris Cité · Centre de Recherche des Cordeliers · Laboratoire Informatique Paris Descartes
Affiliation as printed
Centre d'Histologie, d'Imagerie et de Cytométrie (CHIC), Centre de Recherche des Cordeliers, Paris, France
Laboratoire d'Informatique Paris Descartes (LIPADE), Université Paris Cité, Paris, France
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Inserm · Université Paris-Est Créteil · Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Inserm · Université Paris-Est Créteil · Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Inserm · Université Paris-Est Créteil · Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Inserm · Université Paris Cité · Sorbonne Université · Centre de Recherche des Cordeliers
Affiliation as printed
Centre d'Histologie, d'Imagerie et de Cytométrie (CHIC), Centre de Recherche des Cordeliers, Paris, France
INSERM, Sorbonne Université, Université Paris Cité, Paris, France
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Centre Hospitalier Universitaire de Caen Normandie
Affiliation as printed
Caen University Hospital, Department of Pathology, Caen, France
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
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Inserm · Centre Hospitalier Régional Universitaire de Brest
Affiliation as printed
CHRU Brest, Department of Pathology, Brest, 29220, France
Univ Brest, Inserm, CHU de Brest, LBAI, UMR1227, Brest, France
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Düsseldorf University Hospital · Heinrich Heine University Düsseldorf
Affiliation as printed
Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Affiliation as printed
Department of Pathology, Humanitas University, Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
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Centre National de la Recherche Scientifique · Inserm · Université Paris Cité · Hôpital Beaujon · Assistance Publique – Hôpitaux de Paris · Centre de Recherche sur l'Inflammation
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Beaujon University Hospital, Department of Pathology, F-92110, Clichy, France
Université de Paris, Inflammation Research Center, Inserm, U1149, CNRS, ERL8252, F-75018, Paris, France
Assistance Publique–Hôpitaux de Paris, Beaujon University Hospital, Department of Pathology, F-92110, Clichy, France
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Affiliation as printed
Inserm, U955, Team 18, Créteil, France
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Affiliation as printed
Inserm, U955, Team 18, Créteil, France
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Affiliation as printed
Department of Pathology, E Hospital, Hanoi Medical University, Hanoi, Vietnam
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Kanazawa University · Bạch Mai Hospital
Affiliation as printed
Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
Pathology Center, Bachmai Hospital, Hanoi, Vietnam
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Affiliation as printed
Pathology and Molecular biology Center, National Cancer Hospital, Hanoi, Vietnam
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Centre Hospitalier Universitaire de Lille · CANTHER - Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers
Affiliation as printed
CHU Lille, Institute of Pathology, Lille, France
University Lille, UMR9020-U1277, Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
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Affiliation as printed
Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
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Assistance Publique – Hôpitaux de Paris · Pitié-Salpêtrière Hospital
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Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Pathology, Paris, France
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Assistance Publique – Hôpitaux de Paris · Hôpital Saint-Antoine
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, Department of Pathology, Paris, France
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Affiliation as printed
Department of Pathology, Dr Rela Institute and Medical Centre, Bharath Institute of Higher Education and Research, Chennai, India
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Affiliation as printed
Department of Hepatobiliary Pathology, Cleveland Clinic Foundation, Cleveland, OH, USA
Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, L25, Cleveland, OH, 44195, USA
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Affiliation as printed
Department of Gastrointestinal and Hepatobiliary Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
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Hospital Clínic de Barcelona · Universitat de Barcelona
Affiliation as printed
Barcelona Clinic Liver Cancer (BCLC) Group, Department of Pathology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
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Affiliation as printed
Department of Pathology, Gui-de-Chauliac University Hospital, 80, avenue Augustin-Fliche, 34295, Montpellier, France
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Affiliation as printed
Department of Digestive and Hepatobiliary Surgery, Gui-de-Chauliac University Hospital, 80, avenue Augustin-Fliche, 34295, Montpellier, France
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Affiliation as printed
Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
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Affiliation as printed
Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
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Inserm · Université Paris-Est Créteil · Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Affiliation as printed
Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
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Chinese University of Hong Kong
Affiliation as printed
Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Centre Hospitalier Universitaire de Lille
Affiliation as printed
CHU Lille, Department of Digestive and Hepatobiliary Surgery, Lille, France
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Affiliation as printed
Dr Rela Institute and Medical Centre, Bharath Institute of Higher Education and Research, Chennai, India
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Affiliation as printed
Rouen University Hospital, Department of Pathology, Rouen, France
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Chinese University of Hong Kong
Affiliation as printed
Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Hospital Clínic de Barcelona · Consorci Institut D'Investigacions Biomediques August Pi I Sunyer · Universitat de Barcelona
Affiliation as printed
Barcelona Clinic Liver Cancer (BCLC), Liver Unit, Hospital Clinic of Barcelona, IDIBAPS, CIBEREHD, Universidad de Barcelona, Barcelona, Spain
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Hospital Clínic de Barcelona · Consorci Institut D'Investigacions Biomediques August Pi I Sunyer · Universitat de Barcelona
Affiliation as printed
Barcelona Clinic Liver Cancer (BCLC), Liver Unit, Hospital Clinic of Barcelona, IDIBAPS, CIBEREHD, Universidad de Barcelona, Barcelona, Spain
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Assistance Publique – Hôpitaux de Paris · Pitié-Salpêtrière Hospital
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Hepatology, Paris, France
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Assistance Publique – Hôpitaux de Paris · Pitié-Salpêtrière Hospital
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Digestive and Hepatobiliary Surgery, Paris, France
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Centre Hospitalier Universitaire Amiens-Picardie
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Centre Hospitalier Universitaire d'Amiens, Département de Pathologie, Amiens, France
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Centre Hospitalier Universitaire de Reims
Affiliation as printed
Reims University Hospital, Department of Pathology, Reims, France
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Centre National de la Recherche Scientifique · Centre Hospitalier Universitaire de Grenoble · Translational Innovation in Medicine and Complexity
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Department of Pathology, University Hospital, Grenoble, France
Translational Innovation in Medicine and Complexity, Centre National de la Recherche Scientifique UMR5525, La Tronche, France
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Centre Hospitalier Universitaire de Caen Normandie
Affiliation as printed
Caen University Hospital, Department of Digestive and Hepatobiliary Surgery, Caen, France
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Université de Poitiers · Centre Hospitalier Universitaire de Poitiers · Laboratoire Inflammation, Tissus Épithéliaux et Cytokines
Affiliation as printed
LITEC, Université de Poitiers, Poitiers, France
Poitiers University Hospital, Department of Pathology, Poitiers, France
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Centre Hospitalier Universitaire de Poitiers
Affiliation as printed
Poitiers University Hospital, Department of Hepatogastroenterology and Oncology, Poitiers, France
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Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Medical Oncology, Créteil, France
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Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Medical Oncology, Créteil, France
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Seoul National University · Seoul National University Hospital
Affiliation as printed
Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Centre Hospitalier Universitaire de Lille
Affiliation as printed
CHU Lille, Department of Hepatology, Lille, France
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Centre Hospitalier Universitaire d'Angers
Affiliation as printed
Angers University Hospital, Department of Pathology, Angers, France
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The University of Texas Southwestern Medical Center
Affiliation as printed
Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Digestive and Hepatobiliary Surgery, Créteil, France
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Assistance Publique – Hôpitaux de Paris
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Paul Brousse University Hospital, Department of Digestive and Hepatobiliary Surgery, Paris, France
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University Medical Center Hamburg-Eppendorf
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Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
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Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
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Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Centre Hospitalier Universitaire de Reims
Affiliation as printed
Reims University Hospital, Department of Digestive and Hepatobiliary Surgery, Reims, France
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Inserm · Université Paris-Est Créteil · Assistance Publique – Hôpitaux de Paris · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Paul Brousse University Hospital, Department of Digestive and Hepatobiliary Surgery, Paris, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Affiliation as printed
Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Medical Imaging, Créteil, France
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Medical Imaging, Créteil, France
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Digestive and Hepatobiliary Surgery, Créteil, France
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Hepatology, Créteil, France
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Hepatology, Créteil, France
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Assistance Publique – Hôpitaux de Paris
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Paul Brousse University Hospital, Department of Hepatology, Paris, France
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Centre Hospitalier Universitaire Vaudois · University of Lausanne
Affiliation as printed
Institute of Pathology, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland
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Washington University in St. Louis
Affiliation as printed
Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, 63110, USA
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Affiliation as printed
Department of Pathology University of Michigan, Ann Arbor, MI, USA
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Affiliation as printed
Department of Pathology, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
State Key Laboratory of Liver Research, (The University of Hong Kong), Pok Fu Lam, Hong Kong, China
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
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University Medical Center Groningen
Affiliation as printed
Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
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University Medical Center Groningen · Assistance Publique – Hôpitaux de Paris · Universitätsklinikum Aachen · Hôpital Paul-Brousse · RWTH Aachen University
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Paul Brousse University Hospital, Department of Pathology, Villejuif, France
Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
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Assistance Publique – Hôpitaux de Paris · Hôpital Saint-Antoine
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Saint Antoine University Hospital, Department of Hepatology, Paris, France
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Affiliation as printed
Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
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Affiliation as printed
Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
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Affiliation as printed
Prince of Songkla University, Department of Pathology, Hat Yai, Thailand
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Université Paris Cité · Laboratoire Informatique Paris Descartes
Affiliation as printed
Laboratoire d'Informatique Paris Descartes (LIPADE), Université Paris Cité, Paris, France
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Affiliation as printed
Prince of Songkla University, Department of Pathology, Hat Yai, Thailand
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Affiliation as printed
Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
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Stanford Medicine · Stanford University
Affiliation as printed
Center for Artificial Intelligence in Medicine and Imaging, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, USA
Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
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Centre National de la Recherche Scientifique · Inserm · Université Paris Cité · Hôpital Beaujon · Assistance Publique – Hôpitaux de Paris · Centre de Recherche sur l'Inflammation
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Beaujon University Hospital, Department of Pathology, F-92110, Clichy, France
Université de Paris, Inflammation Research Center, Inserm, U1149, CNRS, ERL8252, F-75018, Paris, France
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Inserm · Université Paris-Est Créteil · Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor · Hôpital Albert-Chenevier · Institut Mondor de Recherche Biomédicale
Affiliation as printed
Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
Inserm, U955, Team 18, Créteil, France
Université Paris Est Créteil, INSERM, IMRB, F-94010, Créteil, France
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Jakob Nikolas Kather corresponding
Heidelberg University · University Hospital Heidelberg · National Center for Tumor Diseases · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany. jakob_nikolas.kather@tu-dresden.de
Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany. jakob_nikolas.kather@tu-dresden.de
Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
Cited by 85 stored of 85
Cited by patents worldwide 1 (Lens.org)
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