Artificial intelligence predicts immune and inflammatory gene signatures directly from hepatocellular carcinoma histology

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Qinghe Zeng - , Sorbonne Université, Laboratoire d’Informatique Paris Descartes (Author)
  • Christophe Klein - , Sorbonne Université (Author)
  • Stefano Caruso - , Université Paris Cité (Author)
  • Pascale Maille - , Hôpital Henri Mondor, Université Paris-Est Créteil, INSERM - Institut national de la santé et de la recherche médicale (Author)
  • Narmin Ghaffari Laleh - , RWTH Aachen University, Heidelberg University  (Author)
  • Daniele Sommacale - , Hôpital Henri Mondor (Author)
  • Alexis Laurent - , Hôpital Henri Mondor (Author)
  • Giuliana Amaddeo - , Hôpital Henri Mondor (Author)
  • David Gentien - , Université PSL (Author)
  • Audrey Rapinat - , Université PSL (Author)
  • Hélène Regnault - , Hôpital Henri Mondor (Author)
  • Cécile Charpy - , Hôpital Henri Mondor (Author)
  • Cong Trung Nguyen - , Université Paris-Est Créteil, INSERM - Institut national de la santé et de la recherche médicale (Author)
  • Christophe Tournigand - , Hôpital Henri Mondor (Author)
  • Raffaele Brustia - , Hôpital Henri Mondor (Author)
  • Jean Michel Pawlotsky - , Université Paris-Est Créteil, INSERM - Institut national de la santé et de la recherche médicale (Author)
  • Jakob Nikolas Kather - , RWTH Aachen University, Heidelberg University  (Author)
  • Maria Chiara Maiuri - , Sorbonne Université (Author)
  • Nicolas Loménie - , Laboratoire d’Informatique Paris Descartes (Author)
  • Julien Calderaro - , Hôpital Henri Mondor, Université Paris-Est Créteil, INSERM - Institut national de la santé et de la recherche médicale (Author)

Abstract

Background & Aims: Patients with hepatocellular carcinoma (HCC) displaying overexpression of immune gene signatures are likely to be more sensitive to immunotherapy, however, the use of such signatures in clinical settings remains challenging. We thus aimed, using artificial intelligence (AI) on whole-slide digital histological images, to develop models able to predict the activation of 6 immune gene signatures. Methods: AI models were trained and validated in 2 different series of patients with HCC treated by surgical resection. Gene expression was investigated using RNA sequencing or NanoString technology. Three deep learning approaches were investigated: patch-based, classic MIL and CLAM. Pathological reviewing of the most predictive tissue areas was performed for all gene signatures. Results: The CLAM model showed the best overall performance in the discovery series. Its best-fold areas under the receiver operating characteristic curves (AUCs) for the prediction of tumors with upregulation of the immune gene signatures ranged from 0.78 to 0.91. The different models generalized well in the validation dataset with AUCs ranging from 0.81 to 0.92. Pathological analysis of highly predictive tissue areas showed enrichment in lymphocytes, plasma cells, and neutrophils. Conclusion: We have developed and validated AI-based pathology models able to predict the activation of several immune and inflammatory gene signatures. Our approach also provides insights into the morphological features that impact the model predictions. This proof-of-concept study shows that AI-based pathology could represent a novel type of biomarker that will ease the translation of our biological knowledge of HCC into clinical practice. Lay summary: Immune and inflammatory gene signatures may be associated with increased sensitivity to immunotherapy in patients with advanced hepatocellular carcinoma. In the present study, the use of artificial intelligence-based pathology enabled us to predict the activation of these signatures directly from histology.

Details

Original languageEnglish
Pages (from-to)116-127
Number of pages12
JournalJournal of hepatology
Volume77
Issue number1
Publication statusPublished - Jul 2022
Peer-reviewedYes
Externally publishedYes

External IDs

PubMed 35143898

Keywords

ASJC Scopus subject areas

Keywords

  • artificial intelligence, deep learning, immune gene signatures, pathology, whole slide image

Library keywords