DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration

	DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration
	Wang, Yongcui; Yang, Yingxi; Chen, Shilong; Wang, Jiguang
刊名	BRIEFINGS IN BIOINFORMATICS
	2021
卷号	22 期号:5
关键词	drug repurposing multi-omics data sources kernel-based data integration machine learning cancer precision medicine
英文摘要	Recent pharmacogenomic studies that generate sequencing data coupled with pharmacological characteristics for patient-derived cancer cell lines led to large amounts of multi-omics data for precision cancer medicine. Among various obstacles hindering clinical translation, lacking effective methods for multimodal and multisource data integration is becoming a bottleneck. Here we proposed DeepDRK, a machine learning framework for deciphering drug response through kernel-based data integration. To transfer information among different drugs and cancer types, we trained deep neural networks on more than 20 000 pan-cancer cell line-anticancer drug pairs. These pairs were characterized by kernel-based similarity matrices integrating multisource and multi-omics data including genomics, transcriptomics, epigenomics, chemical properties of compounds and known drug-target interactions. Applied to benchmark cancer cell line datasets, our model surpassed previous approaches with higher accuracy and better robustness. Then we applied our model on newly established patient-derived cancer cell lines and achieved satisfactory performance with AUC of 0.84 and AUPRC of 0.77. Moreover, DeepDRK was used to predict clinical response of cancer patients. Notably, the prediction of DeepDRK correlated well with clinical outcome of patients and revealed multiple drug repurposing candidates. In sum, DeepDRK provided a computational method to predict drug response of cancer cells from integrating pharmacogenomic datasets, offering an alternative way to prioritize repurposing drugs in precision cancer treatment. The DeepDRK is freely available via https://github.com/wangyc82/DeepDRK.
内容类型	期刊论文
源URL	[http://210.75.249.4/handle/363003/60724]
专题	西北高原生物研究所_中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Wang, Yongcui,Yang, Yingxi,Chen, Shilong,et al. DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration[J]. BRIEFINGS IN BIOINFORMATICS,2021,22(5).
APA	Wang, Yongcui,Yang, Yingxi,Chen, Shilong,&Wang, Jiguang.(2021).DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration.BRIEFINGS IN BIOINFORMATICS,22(5).
MLA	Wang, Yongcui,et al."DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration".BRIEFINGS IN BIOINFORMATICS 22.5(2021).