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By leveraging an artificial intelligence approach solely based on transcriptomics data, this study scored a large library of small molecules based on their predicted ability to induce differentiation in stem-like cells. In particular, a deep neural network model was trained using publicly available single-cell RNA-Seq data obtained from untreated human-induced pluripotent stem cells at various differentiation stages and subsequently utilized to screen drug-induced gene expression profiles from the Library of Integrated Network-based Cellular Signatures (LINCS) database. The challenge of adapting such different data domains was tackled by devising an adversarial learning approach that was able to effectively identify and remove domain-specific bias during the training phase. Experimental validation in MDA-MB-231 and MCF7 cells demonstrated the efficacy of five out of six tested molecules among those scored highest by the model. In particular, the efficacy of triptolide, OTS-167, quinacrine, granisetron and A-443654 offer a potential avenue for targeted therapies against breast CSCs.<\/jats:p>","DOI":"10.1093\/bib\/bbae207","type":"journal-article","created":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T20:42:48Z","timestamp":1713300168000},"source":"Crossref","is-referenced-by-count":6,"title":["AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data"],"prefix":"10.1093","volume":"25","author":[{"given":"Zhongxiao","family":"Li","sequence":"first","affiliation":[{"name":"Computer Science Program , Computer, Electrical and Mathematical Sciences and Engineering Division, , Thuwal, 23955 , Saudi Arabia"},{"name":"King Abdullah University of Science and Technology (KAUST) , Computer, Electrical and Mathematical Sciences and Engineering Division, , Thuwal, 23955 , Saudi Arabia"},{"name":"Computational Bioscience Research Center, King Abdullah University of Science and Technology , Thuwal, 23955 , Saudi Arabia"}]},{"given":"Antonella","family":"Napolitano","sequence":"additional","affiliation":[{"name":"Institute of Experimental Endocrinology and Oncology \u201cG. Salvatore\u201d (IEOS), National Research Council (CNR) , Via De Amicis, 95 - 80131 Napoli , Italy"}]},{"given":"Monica","family":"Fedele","sequence":"additional","affiliation":[{"name":"Institute of Experimental Endocrinology and Oncology \u201cG. Salvatore\u201d (IEOS), National Research Council (CNR) , Via De Amicis, 95 - 80131 Napoli , Italy"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Computer Science Program , Computer, Electrical and Mathematical Sciences and Engineering Division, , Thuwal, 23955 , Saudi Arabia"},{"name":"King Abdullah University of Science and Technology (KAUST) , Computer, Electrical and Mathematical Sciences and Engineering Division, , Thuwal, 23955 , Saudi Arabia"},{"name":"Computational Bioscience Research Center, King Abdullah University of Science and Technology , Thuwal, 23955 , Saudi Arabia"}]},{"given":"Francesco","family":"Napolitano","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center, King Abdullah University of Science and Technology , Thuwal, 23955 , Saudi Arabia"},{"name":"Department of Science and Technology, University of Sannio , Via dei Mulini 74, 82100 Benevento , 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