Validation of transcriptome signature reversion for drug repurposing in oncology. Issue 1 (29th November 2022)

• Record Type: Journal Article
• Authors: Koudijs, Karel K M; Böhringer, Stefan; Guchelaar, Henk-Jan
• Is Part Of: Briefings in bioinformatics. Volume 24:Issue 1(2023)
• Publication Date: 2022-11-29
• Subjects: Drug repositioning -- Systematic validation -- Gene expression -- Bioinformatics -- Oncology; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac490
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Transcriptome signature reversion (TSR) has been extensively proposed and used to discover new indications for existing drugs (i.e. drug repositioning, drug repurposing) for various cancer types. TSR relies on the assumption that a drug that can revert gene expression changes induced by a disease back to original, i.e. healthy, levels is likely to be therapeutically active in treating the disease. Here, we aimed to validate the concept of TSR using the PRISM repurposing data set, which is—as of writing—the largest pharmacogenomic data set. The predictive utility of the TSR approach as it has currently been used appears to be much lower than previously reported and is completely nullified after the drug gene expression signatures are adjusted for the general anti-proliferative downstream effects of drug-induced decreased cell viability. Therefore, TSR mainly relies on generic anti-proliferative drug effects rather than on targeting cancer pathways specifically upregulated in tumor types.