Artificial intelligence for predictive biomarker discovery in immuno-oncology: a systematic review

Research output: Contribution to journalReview articleContributedpeer-review

Contributors

  • A. Prelaj - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano, Polytechnic University of Milan, European Society for Medical Oncology (Author)
  • V. Miskovic - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano, Polytechnic University of Milan (Author)
  • M. Zanitti - , Aalborg University (Author)
  • F. Trovo - , Polytechnic University of Milan (Author)
  • C. Genova - , University of Genoa (Author)
  • G. Viscardi - , University of Campania Luigi Vanvitelli (Author)
  • S. E. Rebuzzi - , University of Genoa, University of Milan (Author)
  • L. Mazzeo - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano, Polytechnic University of Milan (Author)
  • L. Provenzano - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • S. Kosta - , Aalborg University (Author)
  • M. Favali - , Polytechnic University of Milan (Author)
  • A. Spagnoletti - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • L. Castelo-Branco - , European Society for Medical Oncology, NOVA University Lisbon (Author)
  • J. Dolezal - , The University of Chicago (Author)
  • A. T. Pearson - , The University of Chicago (Author)
  • G. Lo Russo - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • C. Proto - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • M. Ganzinelli - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • C. Giani - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • E. Ambrosini - , Polytechnic University of Milan (Author)
  • S. Turajlic - , The Francis Crick Institute (Author)
  • L. Au - , Royal Marsden NHS Foundation Trust, Peter Maccallum Cancer Centre, University of Melbourne (Author)
  • M. Koopman - , European Society for Medical Oncology, Netherlands Comprehensive Cancer Organisation (Author)
  • S. Delaloge - , European Society for Medical Oncology, Institut Gustave Roussy (Author)
  • J. N. Kather - , Else Kröner Fresenius Center for Digital Health (Author)
  • F. de Braud - , IRCCS Fondazione Istituto Nazionale per lo studio e la cura dei tumori - Milano (Author)
  • M. C. Garassino - , The University of Chicago (Author)
  • G. Pentheroudakis - , European Society for Medical Oncology (Author)
  • C. Spencer - , The Francis Crick Institute (Author)
  • A. L.G. Pedrocchi - , Polytechnic University of Milan (Author)

Abstract

Background: The widespread use of immune checkpoint inhibitors (ICIs) has revolutionised treatment of multiple cancer types. However, selecting patients who may benefit from ICI remains challenging. Artificial intelligence (AI) approaches allow exploitation of high-dimension oncological data in research and development of precision immuno-oncology. Materials and methods: We conducted a systematic literature review of peer-reviewed original articles studying the ICI efficacy prediction in cancer patients across five data modalities: genomics (including genomics, transcriptomics, and epigenomics), radiomics, digital pathology (pathomics), and real-world and multimodality data. Results: A total of 90 studies were included in this systematic review, with 80% published in 2021-2022. Among them, 37 studies included genomic, 20 radiomic, 8 pathomic, 20 real-world, and 5 multimodal data. Standard machine learning (ML) methods were used in 72% of studies, deep learning (DL) methods in 22%, and both in 6%. The most frequently studied cancer type was non-small-cell lung cancer (36%), followed by melanoma (16%), while 25% included pan-cancer studies. No prospective study design incorporated AI-based methodologies from the outset; rather, all implemented AI as a post hoc analysis. Novel biomarkers for ICI in radiomics and pathomics were identified using AI approaches, and molecular biomarkers have expanded past genomics into transcriptomics and epigenomics. Finally, complex algorithms and new types of AI-based markers, such as meta-biomarkers, are emerging by integrating multimodal/multi-omics data. Conclusion: AI-based methods have expanded the horizon for biomarker discovery, demonstrating the power of integrating multimodal data from existing datasets to discover new meta-biomarkers. While most of the included studies showed promise for AI-based prediction of benefit from immunotherapy, none provided high-level evidence for immediate practice change. A priori planned prospective trial designs are needed to cover all lifecycle steps of these software biomarkers, from development and validation to integration into clinical practice.

Details

Original languageEnglish
Pages (from-to)29-65
Number of pages37
JournalAnnals of oncology
Volume35
Issue number1
Publication statusPublished - Oct 2023
Peer-reviewedYes

External IDs

PubMed 37879443
Mendeley bc7f9969-9473-3682-b16f-7df20a97494d

Keywords

Sustainable Development Goals

ASJC Scopus subject areas

Keywords

  • artificial intelligence, immunotherapy, multimodal, multiomics, real-world