Deciphering serous ovarian carcinoma histopathology and platinum response by convolutional neural networks

• Published in: BMC medicine Vol. 18; no. 1; pp. 236 - 14
• Main Authors: Yu, Kun-Hsing, Hu, Vincent, Wang, Feiran, Matulonis, Ursula A., Mutter, George L., Golden, Jeffrey A., Kohane, Isaac S.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.08.2020; BioMed Central; BMC
• Subjects: Adenocarcinoma; Algorithms; Artificial neural networks; Cancer; Cancer therapies; Carcinoma; Chemotherapy; Classification; Datasets; Development and progression; Digital pathology; Female; Gene expression; Histochemistry; Histopathology; Humans; Immune response; Innate immunity; Machine learning; Medical research; Middle Aged; Morphology; Neural networks; Ovarian cancer; Ovarian carcinoma; Ovarian Neoplasms - drug therapy; Ovarian Neoplasms - pathology; Pathology; Patients; Platinum; Platinum - therapeutic use; Platinum response; Prognosis; Proteins; Proteomics; Quality; Ribonucleic acid; RNA; RNA sequencing; Serous ovarian carcinoma; Tumors; Digital pathology; Platinum response; Gene expression; Serous ovarian carcinoma; Machine learning; Proteomics
• DOI: 10.1186/s12916-020-01684-w
• ISSN: 1741-7015

Ovarian cancer causes 151,900 deaths per year worldwide. Treatment and prognosis are primarily determined by the histopathologic interpretation in combination with molecular diagnosis. However, the relationship between histopathology patterns and molecular alterations is not fully understood, and it is difficult to predict patients' chemotherapy response using the known clinical and histological variables. We analyzed the whole-slide histopathology images, RNA-Seq, and proteomics data from 587 primary serous ovarian adenocarcinoma patients and developed a systematic algorithm to integrate histopathology and functional omics findings and to predict patients' response to platinum-based chemotherapy. Our convolutional neural networks identified the cancerous regions with areas under the receiver operating characteristic curve (AUCs) > 0.95 and classified tumor grade with AUCs > 0.80. Functional omics analysis revealed that expression levels of proteins participated in innate immune responses and catabolic pathways are associated with tumor grade. Quantitative histopathology analysis successfully stratified patients with different response to platinum-based chemotherapy (P = 0.003). These results indicated the potential clinical utility of quantitative histopathology evaluation in tumor cell detection and chemotherapy response prediction. The developed algorithm is easily extensible to other tumor types and treatment modalities.