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Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma

Author

Listed:
  • Julien Calderaro

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18
    European Reference Network (ERN) RARE-LIVER)

  • Narmin Ghaffari Laleh

    (Technical University Dresden
    University Hospital RWTH Aachen, RWTH Aachen university)

  • Qinghe Zeng

    (Centre d’Histologie, d’Imagerie et de Cytométrie (CHIC), Centre de Recherche des Cordeliers
    Université Paris Cité)

  • Pascale Maille

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18)

  • Loetitia Favre

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18)

  • Anaïs Pujals

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18)

  • Christophe Klein

    (Centre d’Histologie, d’Imagerie et de Cytométrie (CHIC), Centre de Recherche des Cordeliers
    Université Paris Cité)

  • Céline Bazille

    (Caen University Hospital, Department of Pathology)

  • Lara R. Heij

    (University Hospital RWTH Aachen
    Institute of Pathology, University Hospital RWTH Aachen)

  • Arnaud Uguen

    (CHRU Brest, Department of Pathology
    Univ Brest, Inserm, CHU de Brest, LBAI)

  • Tom Luedde

    (University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf)

  • Luca Tommaso

    (Humanitas University, Humanitas Clinical and Research Center, IRCCS, Rozzano)

  • Aurélie Beaufrère

    (Beaujon University Hospital, Department of Pathology
    Université de Paris, Inflammation Research Center, Inserm, U1149, CNRS, ERL8252)

  • Augustin Chatain

    (Inserm, U955, Team 18)

  • Delphine Gastineau

    (Inserm, U955, Team 18)

  • Cong Trung Nguyen

    (Hanoi Medical University)

  • Hiep Nguyen-Canh

    (Pathology Center, Bachmai Hospital
    Kanazawa University Graduate School of Medicine)

  • Khuyen Nguyen Thi

    (Pathology and Molecular biology Center, National Cancer Hospital)

  • Viviane Gnemmi

    (University Lille, UMR9020-U1277, Cancer Heterogeneity Plasticity and Resistance to Therapies
    CHU Lille, Institute of Pathology)

  • Rondell P. Graham

    (Mayo Clinic Rochester)

  • Frédéric Charlotte

    (Pitié-Salpêtrière University Hospital, Department of Pathology)

  • Dominique Wendum

    (Saint-Antoine University Hospital, Department of Pathology)

  • Mukul Vij

    (Bharath Institute of Higher Education and Research)

  • Daniela S. Allende

    (Cleveland Clinic Foundation
    Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic)

  • Federico Aucejo

    (Cleveland Clinic Foundation)

  • Alba Diaz

    (Universitat de Barcelona)

  • Benjamin Rivière

    (Gui-de-Chauliac University Hospital, 80)

  • Astrid Herrero

    (Gui-de-Chauliac University Hospital, 80)

  • Katja Evert

    (University of Regensburg, Franz-Josef-Strauß-Allee 11)

  • Diego Francesco Calvisi

    (University of Regensburg, Franz-Josef-Strauß-Allee 11)

  • Jérémy Augustin

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18)

  • Wei Qiang Leow

    (Singapore General Hospital)

  • Howard Ho Wai Leung

    (The Chinese University of Hong Kong)

  • Emmanuel Boleslawski

    (CHU Lille, Department of Digestive and Hepatobiliary Surgery)

  • Mohamed Rela

    (Dr Rela Institute and Medical Centre, Bharath Institute of Higher Education and Research)

  • Arnaud François

    (Rouen University Hospital, Department of Pathology)

  • Anthony Wing-Hung Cha

    (The Chinese University of Hong Kong)

  • Alejandro Forner

    (Universidad de Barcelona)

  • Maria Reig

    (Universidad de Barcelona)

  • Manon Allaire

    (Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Hepatology)

  • Olivier Scatton

    (Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Denis Chatelain

    (Centre Hospitalier Universitaire d’Amiens, Département de Pathologie)

  • Camille Boulagnon-Rombi

    (Reims University Hospital, Department of Pathology)

  • Nathalie Sturm

    (University Hospital
    Translational Innovation in Medicine and Complexity, Centre National de la Recherche Scientifique UMR5525)

  • Benjamin Menahem

    (Caen University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Eric Frouin

    (Poitiers University Hospital, Department of Pathology
    LITEC, Université de Poitiers)

  • David Tougeron

    (Poitiers University Hospital, Department of Hepatogastroenterology and Oncology)

  • Christophe Tournigand

    (Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Medical Oncology)

  • Emmanuelle Kempf

    (Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Medical Oncology)

  • Haeryoung Kim

    (Seoul National University Hospital, Seoul National University College of Medicine)

  • Massih Ningarhari

    (CHU Lille, Department of Hepatology)

  • Sophie Michalak-Provost

    (Angers University Hospital, Department of Pathology)

  • Purva Gopal

    (Department of Pathology, UT Southwestern Medical Center)

  • Raffaele Brustia

    (Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Eric Vibert

    (Paul Brousse University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Kornelius Schulze

    (University Medical Center Hamburg-Eppendorf)

  • Darius F. Rüther

    (University Medical Center Hamburg-Eppendorf)

  • Sören A. Weidemann

    (University Medical Center Hamburg-Eppendorf)

  • Rami Rhaiem

    (Reims University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Jean-Michel Pawlotsky

    (Université Paris Est Créteil, INSERM, IMRB
    Inserm, U955, Team 18
    Paul Brousse University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Xuchen Zhang

    (Yale University School of Medicine)

  • Alain Luciani

    (Henri Mondor University Hospital, Department of Medical Imaging)

  • Sébastien Mulé

    (Henri Mondor University Hospital, Department of Medical Imaging)

  • Alexis Laurent

    (Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital, Department of Digestive and Hepatobiliary Surgery)

  • Giuliana Amaddeo

    (Henri Mondor University Hospital, Department of Hepatology)

  • Hélène Regnault

    (Henri Mondor University Hospital, Department of Hepatology)

  • Eleonora Martin

    (Paul Brousse University Hospital, Department of Hepatology)

  • Christine Sempoux

    (Lausanne University Hospital (CHUV), University of Lausanne (UNIL))

  • Pooja Navale

    (Washington University in St. Louis)

  • Maria Westerhoff

    (Department of Pathology University of Michigan)

  • Regina Cheuk-Lam Lo

    (The University of Hong Kong, Pok Fu Lam
    State Key Laboratory of Liver Research, (The University of Hong Kong), Pok Fu Lam)

  • Jan Bednarsch

    (University Hospital RWTH Aachen)

  • Annette Gouw

    (University Medical Center Groningen)

  • Catherine Guettier

    (University Hospital RWTH Aachen
    University Medical Center Groningen
    Paul Brousse University Hospital, Department of Pathology)

  • Marie Lequoy

    (Assistance Publique-Hôpitaux de Paris, Saint Antoine University Hospital, Department of Hepatology)

  • Kenichi Harada

    (Kanazawa University Graduate School of Medicine)

  • Pimsiri Sripongpun

    (Prince of Songkla University)

  • Poowadon Wetwittayaklang

    (Prince of Songkla University, Department of Pathology)

  • Nicolas Loménie

    (Université Paris Cité)

  • Jarukit Tantipisit

    (Prince of Songkla University, Department of Pathology)

  • Apichat Kaewdech

    (Prince of Songkla University)

  • Jeanne Shen

    (Stanford University
    Stanford University School of Medicine)

  • Valérie Paradis

    (Beaujon University Hospital, Department of Pathology
    Université de Paris, Inflammation Research Center, Inserm, U1149, CNRS, ERL8252)

  • Stefano Caruso

    (Université Paris Est Créteil, INSERM, IMRB
    Henri Mondor-Albert Chenevier University Hospital, Department of Pathology
    Inserm, U955, Team 18)

  • Jakob Nikolas Kather

    (Technical University Dresden
    University Hospital Heidelberg)

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.

Suggested Citation

  • Julien Calderaro & Narmin Ghaffari Laleh & Qinghe Zeng & Pascale Maille & Loetitia Favre & Anaïs Pujals & Christophe Klein & Céline Bazille & Lara R. Heij & Arnaud Uguen & Tom Luedde & Luca Tommaso & , 2023. "Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43749-3
    DOI: 10.1038/s41467-023-43749-3
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    as
    1. James J. Harding & Sarina A. Piha-Paul & Ronak H. Shah & Jessica J. Murphy & James M. Cleary & Geoffrey I. Shapiro & David I. Quinn & Irene Braña & Victor Moreno & Mitesh Borad & Sherene Loi & Iben Sp, 2023. "Antitumour activity of neratinib in patients with HER2-mutant advanced biliary tract cancers," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
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