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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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Centre Hospitalier Universitaire de Caen Normandie

    Affiliation as printed

    Caen University Hospital, Department of Pathology, Caen, France

  9. 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

  10. 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

  11. 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

  12. Humanitas University

    Affiliation as printed

    Department of Pathology, Humanitas University, Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy

  13. 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

  14. Inserm

    Affiliation as printed

    Inserm, U955, Team 18, Créteil, France

  15. Inserm

    Affiliation as printed

    Inserm, U955, Team 18, Créteil, France

  16. Hanoi Medical University

    Affiliation as printed

    Department of Pathology, E Hospital, Hanoi Medical University, Hanoi, Vietnam

  17. 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

  18. Affiliation as printed

    Pathology and Molecular biology Center, National Cancer Hospital, Hanoi, Vietnam

  19. 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

  20. Mayo Clinic

    Affiliation as printed

    Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA

  21. Assistance Publique – Hôpitaux de Paris · Pitié-Salpêtrière Hospital

    Affiliation as printed

    Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Pathology, Paris, France

  22. 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

  23. Bharath University

    Affiliation as printed

    Department of Pathology, Dr Rela Institute and Medical Centre, Bharath Institute of Higher Education and Research, Chennai, India

  24. Cleveland Clinic

    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

  25. Cleveland Clinic

    Affiliation as printed

    Department of Gastrointestinal and Hepatobiliary Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA

  26. 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

  27. Hôpital Gui de Chauliac

    Affiliation as printed

    Department of Pathology, Gui-de-Chauliac University Hospital, 80, avenue Augustin-Fliche, 34295, Montpellier, France

  28. Hôpital Gui de Chauliac

    Affiliation as printed

    Department of Digestive and Hepatobiliary Surgery, Gui-de-Chauliac University Hospital, 80, avenue Augustin-Fliche, 34295, Montpellier, France

  29. University of Regensburg

    Affiliation as printed

    Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany

  30. University of Regensburg

    Affiliation as printed

    Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany

  31. 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

  32. Singapore General Hospital

    Affiliation as printed

    Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore

  33. Chinese University of Hong Kong

    Affiliation as printed

    Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong

  34. Centre Hospitalier Universitaire de Lille

    Affiliation as printed

    CHU Lille, Department of Digestive and Hepatobiliary Surgery, Lille, France

  35. Bharath University

    Affiliation as printed

    Dr Rela Institute and Medical Centre, Bharath Institute of Higher Education and Research, Chennai, India

  36. Affiliation as printed

    Rouen University Hospital, Department of Pathology, Rouen, France

  37. Chinese University of Hong Kong

    Affiliation as printed

    Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong

  38. 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

  39. 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

  40. 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

  41. 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

  42. Centre Hospitalier Universitaire Amiens-Picardie

    Affiliation as printed

    Centre Hospitalier Universitaire d'Amiens, Département de Pathologie, Amiens, France

  43. Centre Hospitalier Universitaire de Reims

    Affiliation as printed

    Reims University Hospital, Department of Pathology, Reims, France

  44. Centre National de la Recherche Scientifique · Centre Hospitalier Universitaire de Grenoble · Translational Innovation in Medicine and Complexity

    Affiliation as printed

    Department of Pathology, University Hospital, Grenoble, France

    Translational Innovation in Medicine and Complexity, Centre National de la Recherche Scientifique UMR5525, La Tronche, France

  45. Centre Hospitalier Universitaire de Caen Normandie

    Affiliation as printed

    Caen University Hospital, Department of Digestive and Hepatobiliary Surgery, Caen, France

  46. 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

  47. Centre Hospitalier Universitaire de Poitiers

    Affiliation as printed

    Poitiers University Hospital, Department of Hepatogastroenterology and Oncology, Poitiers, France

  48. 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

  49. 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

  50. 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

  51. Centre Hospitalier Universitaire de Lille

    Affiliation as printed

    CHU Lille, Department of Hepatology, Lille, France

  52. Centre Hospitalier Universitaire d'Angers

    Affiliation as printed

    Angers University Hospital, Department of Pathology, Angers, France

  53. The University of Texas Southwestern Medical Center

    Affiliation as printed

    Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA

  54. 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

  55. 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

  56. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

  57. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

  58. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

  59. Centre Hospitalier Universitaire de Reims

    Affiliation as printed

    Reims University Hospital, Department of Digestive and Hepatobiliary Surgery, Reims, France

  60. 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

  61. Yale University

    Affiliation as printed

    Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. Assistance Publique – Hôpitaux de Paris

    Affiliation as printed

    Assistance Publique-Hôpitaux de Paris, Paul Brousse University Hospital, Department of Hepatology, Paris, France

  68. Centre Hospitalier Universitaire Vaudois · University of Lausanne

    Affiliation as printed

    Institute of Pathology, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland

  69. Washington University in St. Louis

    Affiliation as printed

    Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, 63110, USA

  70. University of Michigan

    Affiliation as printed

    Department of Pathology University of Michigan, Ann Arbor, MI, USA

  71. University of Hong Kong

    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

  72. Universitätsklinikum Aachen · RWTH Aachen University

    Affiliation as printed

    Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany

  73. University Medical Center Groningen

    Affiliation as printed

    Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands

  74. 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

  75. 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

  76. Kanazawa University

    Affiliation as printed

    Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan

  77. Prince of Songkla University

    Affiliation as printed

    Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand

  78. Prince of Songkla University

    Affiliation as printed

    Prince of Songkla University, Department of Pathology, Hat Yai, Thailand

  79. Université Paris Cité · Laboratoire Informatique Paris Descartes

    Affiliation as printed

    Laboratoire d'Informatique Paris Descartes (LIPADE), Université Paris Cité, Paris, France

  80. Prince of Songkla University

    Affiliation as printed

    Prince of Songkla University, Department of Pathology, Hat Yai, Thailand

  81. Prince of Songkla University

    Affiliation as printed

    Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand

  82. 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

  83. 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

  84. 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

  85. 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)

References 23