A Deep Learning Framework for Predicting Response to Therapy in Cancer.

Journal: Cell reports
Published Date: Dec 10, 2019

Abstract

A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed their performance on multiple clinical cohorts. We demonstrate that deep neural networks outperform the current state in machine learning frameworks. We provide a proof of concept for the use of deep neural network-based frameworks to aid precision oncology strategies.

Authors

  • Theodore Sakellaropoulos
    Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
  • Konstantinos Vougas
    Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens GR-11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str, Athens GR-11527, Greece.
  • Sonali Narang
    Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
  • Filippos Koinis
    Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str, Athens GR-11527, Greece.
  • Athanassios Kotsinas
    Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str, Athens GR-11527, Greece.
  • Alexander Polyzos
    Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
  • Tyler J Moss
    Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.
  • Sarina Piha-Paul
    Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.
  • Hua Zhou
    Department of Biostatistics, UCLA.
  • Eleni Kardala
    Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece.
  • Eleni Damianidou
    Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece.
  • Leonidas G Alexopoulos
    School of Mechanical Engineering, National Technical University of Athens, Zografou 15780, Greece.
  • Iannis Aifantis
    Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
  • Paul A Townsend
    Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK.
  • Mihalis I Panayiotidis
    Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Department of Electron Microscopy & Molecular Pathology, Cyprus Institute of Neurology & Genetics, Nicosia, 2371, Cyprus.
  • Petros Sfikakis
    Rheumatology Unit, Laikon University Hospital, Athens, Greece.
  • Jiri Bartek
    Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, Copenhagen DK-2100, Denmark; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Hněvotínská, Olomouc 1333/5 779 00, Czech Republic; Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-171 77, Sweden.
  • Rebecca C Fitzgerald
    MRC Cancer Unit, University of Cambridge, Cambridge, United Kingdom.
  • Dimitris Thanos
    Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens GR-11527, Greece.
  • Kenna R Mills Shaw
    Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.
  • Russell Petty
    Division of Molecular and Clinical Medicine, Ninewells Hospital and School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland.
  • Aristotelis Tsirigos
    Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA. Electronic address: aristotelis.tsirigos@nyulangone.org.
  • Vassilis G Gorgoulis
    Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens GR-11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str, Athens GR-11527, Greece; Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Str, Athens GR-11527, Greece. Electronic address: vgorg@med.uoa.gr.

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