Prediction of cancer treatment response from histopathology images through imputed transcriptomics.

Authors

null

Danh-Tai Hoang

The Biological Data Science Institute, College of Science, The Australian National University, Canberra, Australia

Danh-Tai Hoang , Gal Dinstag , Leandro C. Hermida , Doreen Ben-Zvi , Chani Stossel , Tejas Patil , Stephen-John Sammut , Wiem Lassoued , Clint Allen , Tuvik Beker , Peng Jiang , Talia Golan , Adam G. Sowalsky , Sharon R Pine , Carlos Caldas , James L. Gulley , Kenneth D. Aldape , Ranit Aharonov , Eric Stone , Eytan Ruppin

Organizations

The Biological Data Science Institute, College of Science, The Australian National University, Canberra, Australia, Pangea Biomed, Tel Aviv, Israel, University of Pittsburgh, Pittsburgh, PA, Sheba Medical Center at Tel-Hashomer, Tel Aviv, Israel, University of Colorado School of Medicine, Aurora, CO, Department of Oncology and Cancer Research UK Cambridge Institute, Cambridge, United Kingdom, National Cancer Institute, Bethesda, MD, National Institutes of Health, Bethesda, MD, Sheba Medical Center, Ra'anana, Israel, University of Colorado Anschutz Medical Campus, Aurora, CO, University of Cambridge, Cambridge, United Kingdom, The Australian National University, Canberra, Australia, Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD

Research Funding

U.S. National Institutes of Health
U.S. National Institutes of Health, Australian National University

Background: In recent years, the use of tumour molecular profiling within the clinic has allowed for more accurate cancer diagnostics, as well as the delivery of precision oncology. Rapid advances in digital histopathology have allowed the extraction of clinically relevant information embedded in tumor slides by applying machine learning methods, capitalizing on recent advancements in image analysis via deep learning. However, as in many supervised learning approaches, predicting response to therapy using whole slide images (WSI) of tissue stained with hematoxylin and eosin (H&E) requires large datasets comprising matched imaging and response data, severely restricting the applicability of this approach. Methods: To overcome this critical challenge, we introduce here for the first time a generic methodology for generating WSI-based predictors of patients’ response for a broad range of cancer types and therapies, which does not require matched WSI and response data for training. The approach, termed ENLIGHT-DeepPT, consists of: (1) DeepPT, a new deep-learning framework that predicts exome-wide tumor mRNA expression from slides, and (2) ENLIGHT, a recently published response prediction algorithm, applied here to predict response based on the DeepPT predicted expression values, instead of measured values. Results: First, we study the ability to predict tumor expression, showing that DeepPT successfully predicts transcriptomics in all 16 TCGA cohorts tested and generalizes well to two independent datasets. Second, aligned with our key aim, we analyze six independent clinical trial datasets of patients with different cancer types that were treated with various targeted and immune therapies, on which DeepPT was never trained. We show that ENLIGHT, without any adaptation, can successfully predict the true responders from the expression values imputed by DeepPT, using only H&E images: ENLIGHT-DeepPT successfully predicts true responders in these cohorts with an overall odds ratio of 2.19, increasing the baseline response rate by 38.8% on average among predicted responders. Conclusions: ENLIGHT-DeepPT is the first approach to successfully predict response to multiple targeted and immune cancer therapies directly from H&E slides, without requiring any drug-specific training data. ENLIGHT-DeepPT can provide rapid treatment recommendations without requiring tumor sequencing, bringing precision oncology to low-income countries and other situations where NGS is prohibitive.

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Abstract Details

Meeting

2023 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Care Delivery and Regulatory Policy

Track

Care Delivery and Quality Care

Sub Track

Clinical Informatics/Advanced Algorithms/Machine Learning

Citation

J Clin Oncol 41, 2023 (suppl 16; abstr 1551)

DOI

10.1200/JCO.2023.41.16_suppl.1551

Abstract #

1551

Poster Bd #

145

Abstract Disclosures

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