Journal
ELIFE
Volume 11, Issue -, Pages -Publisher
eLIFE SCIENCES PUBL LTD
DOI: 10.7554/eLife.78012
Keywords
drug candidate; sensitivity ML prediction; mechanism of action; multi-omics; transcriptome; chromatin accessibility; Human
Categories
Funding
- Helmholtz Association HGF Helmholtz AI grant Pro-Gene-Gen [ZT-IPF5-23]
- Deutsche Forschungsgemeinschaft German Research Foundation (DFG) Excellence Strategy [EXC2151-390873048]
- Deutsche Forschungsgemeinschaft German Research Foundation (DFG) [SCHU 950/8-1, GRK 2168, TP11, SFB704]
- Bundesministerium fur Bildung und Forschung BMBF
- Horizon 2020 Framework Programme EU project SYSCID [733100]
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This study demonstrates the use of multi-omics to support the development of a new class of candidate anticancer agents. Combined analysis of transcriptome and chromatin accessibility identified mechanisms underlying sensitivity to test agents. A versatile strategy for integrating RNA- and ATAC-seq data was implemented to accelerate and extend standalone analyses. This approach offers a scalable pipeline for early drug discovery and understanding of mechanisms.
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines' sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.
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