[HTML][HTML] Deep learning integrates histopathology and proteogenomics at a pan-cancer level

JM Wang, R Hong, EG Demicco, J Tan, R Lazcano… - Cell Reports …, 2023 - cell.com
JM Wang, R Hong, EG Demicco, J Tan, R Lazcano, AL Moreira, Y Li, A Calinawan…
Cell Reports Medicine, 2023cell.com
We introduce a pioneering approach that integrates pathology imaging with transcriptomics
and proteomics to identify predictive histology features associated with critical clinical
outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients
across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily
made by human pathologists: tumor vs. normal (AUROC= 0.995) and tissue-of-origin
(AUROC= 0.979). We further investigate predictive power on tasks not normally performed …
Summary
We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.
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