Hoang Danh-Tai, Dinstag Gal, Hermida Leandro C, Ben-Zvi Doreen S, Elis Efrat, Caley Katherine, Sammut Stephen-John, Sinha Sanju, Sinha Neelam, Dampier Christopher H, Stossel Chani, Patil Tejas, Rajan Arun, Lassoued Wiem, Strauss Julius, Bailey Shania, Allen Clint, Redman Jason, Beker Tuvik, Jiang Peng, Golan Talia, Wilkinson Scott, Sowalsky Adam G, Pine Sharon R, Caldas Carlos, Gulley James L, Aldape Kenneth, Aharonov Ranit, Stone Eric A, Ruppin Eytan
Biological Data Science Institute, College of Science, Australian National University, Canberra, ACT, Australia.
Pangea Biomed Ltd., Tel Aviv, Israel.
Res Sq. 2023 Sep 15:rs.3.rs-3193270. doi: 10.21203/rs.3.rs-3193270/v1.
Advances in artificial intelligence have paved the way for leveraging hematoxylin and eosin (H&E)-stained tumor slides for precision oncology. We present ENLIGHT-DeepPT, an approach for predicting response to multiple targeted and immunotherapies from H&E-slides. In difference from existing approaches that aim to predict treatment response directly from the slides, ENLIGHT-DeepPT is an indirect two-step approach consisting of (1) DeepPT, a new deep-learning framework that predicts genome-wide tumor mRNA expression from slides, and (2) ENLIGHT, which predicts response based on the DeepPT inferred expression values. DeepPT successfully predicts transcriptomics in all 16 TCGA cohorts tested and generalizes well to two independent datasets. Our key contribution is showing that ENLIGHT-DeepPT successfully predicts true responders in five independent patients' cohorts involving four different treatments spanning six cancer types with an overall odds ratio of 2.44, increasing the baseline response rate by 43.47% among predicted responders, without the need for any treatment data for training. Furthermore, its prediction accuracy on these datasets is comparable to a supervised approach predicting the response directly from the images, which needs to be trained and tested on the same cohort. ENLIGHT-DeepPT future application could provide clinicians with rapid treatment recommendations to an array of different therapies and importantly, may contribute to advancing precision oncology in developing countries.
人工智能的进展为利用苏木精和伊红(H&E)染色的肿瘤切片用于精准肿瘤学铺平了道路。我们提出了ENLIGHT-DeepPT,一种从H&E切片预测对多种靶向治疗和免疫治疗反应的方法。与旨在直接从切片预测治疗反应的现有方法不同,ENLIGHT-DeepPT是一种间接的两步法,包括:(1)DeepPT,一种从切片预测全基因组肿瘤mRNA表达的新深度学习框架;(2)ENLIGHT,它基于DeepPT推断的表达值预测反应。DeepPT在所有测试的16个TCGA队列中成功预测了转录组学,并能很好地推广到两个独立数据集。我们的关键贡献在于表明,ENLIGHT-DeepPT在涉及六种癌症类型的四种不同治疗的五个独立患者队列中成功预测了真正的反应者,总体优势比为2.44,在预测的反应者中基线反应率提高了43.47%,且无需任何治疗数据进行训练。此外,它在这些数据集上的预测准确性与直接从图像预测反应的监督方法相当,而后者需要在同一队列上进行训练和测试。ENLIGHT-DeepPT未来的应用可以为临床医生提供针对一系列不同疗法的快速治疗建议,重要的是,可能有助于在发展中国家推进精准肿瘤学。
EBioMedicine. 2022-6
World J Gastroenterol. 2020-10-28