AI-powered omics-based drug pair discovery for pyroptosis therapy targeting triple-negative breast cancer

Affiliations
  • 1Department of Pharmaceutics, School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, Fudan University, Shanghai, 201203, P. R. China.
  • 2Department of Integrative Medicine, Huashan Hospital, Institutes of Integrative Medicine, Fudan University, Shanghai, 200040, P. R. China.
  • 3Microsoft Research Asia, Shanghai, 200232, P. R. China.
  • 4Pharmacy Department & Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, P. R. China.
  • 5State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438, P. R. China.
  • 6School of Computer Science, Fudan University, Shanghai, 200438, P. R. China.
  • 7State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, P. R. China.
  • 8Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University); Zhuhai, Guangdong, 519000, P. R. China. shaojunpeng@ext.jnu.edu.cn.
  • 9Department of Radiology, Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China. zhj81828@163.com.
  • 10Department of Pharmaceutics, School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, Fudan University, Shanghai, 201203, P. R. China. jxwang@fudan.edu.cn.
  • 11Microsoft Research Asia, Shanghai, 200232, P. R. China. dongsheng.li@microsoft.com.
  • 12Department of Pharmaceutics, School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, Fudan University, Shanghai, 201203, P. R. China. zqpang@fudan.edu.cn.

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Abstract

Due to low success rates and long cycles of traditional drug development, the clinical tendency is to apply omics techniques to reveal patient-level disease characteristics and individualized responses to treatment. However, the heterogeneous form of data and uneven distribution of targets make drug discovery and precision medicine a non-trivial task. This study takes pyroptosis therapy for triple-negative breast cancer (TNBC) as a paradigm and uses data mining of a large TNBC cohort and drug databases to establish a biofactor-regulated neural network for rapidly screening and optimizing compound pyroptosis drug pairs. Subsequently, biomimetic nanococrystals are prepared using the preferred combination of mitoxantrone and gambogic acid for rational drug delivery. The unique mechanism of obtained nanococrystals regulating pyroptosis genes through ribosomal stress and triggering pyroptosis cascade immune effects are revealed in TNBC models. In this work, a target omics-based intelligent compound drug discovery framework explores an innovative drug development paradigm, which repurposes existing drugs and enables precise treatment of refractory diseases.