A1 Refereed original research article in a scientific journal
Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets
Authors: Gautam P, Jaiswal A, Aittokallio T, Al-Ali H, Wennerberg K
Publisher: CELL PRESS
Publication year: 2019
Journal: Cell Chemical Biology
Journal name in source: CELL CHEMICAL BIOLOGY
Journal acronym: CELL CHEM BIOL
Volume: 26
Issue: 7
First page : 970
Last page: 979
Number of pages: 14
ISSN: 2451-9448
eISSN: 2451-9448
DOI: https://doi.org/10.1016/j.chembiol.2019.03.011
Abstract
The lack of functional understanding of most mutations in cancer, combined with the non-druggability of most proteins, challenge genomics-based identification of oncology drug targets. We implemented a machine-learning-based approach (idTRAX), which relates cell-based screening of small-molecule compounds to their kinase inhibition data, to directly identify effective and readily druggable targets. We applied idTRAX to triple-negative breast cancer cell lines and efficiently identified cancer-selective targets. For example, we found that inhibiting AKT selectively kills MFM-223 and CAL148 cells, while inhibiting FGFR2 only kills MFM-223. Since the effects of catalytically inhibiting a protein can diverge from those of reducing its levels, targets identified by idTRAX frequently differ from those identified through gene knockout/knockdown methods. This is critical if the purpose is to identify targets specifically for small-molecule drug development, whereby idTRAX may produce fewer false-positives. The rapid nature of the approach suggests that it may be applicable in personalizing therapy.
The lack of functional understanding of most mutations in cancer, combined with the non-druggability of most proteins, challenge genomics-based identification of oncology drug targets. We implemented a machine-learning-based approach (idTRAX), which relates cell-based screening of small-molecule compounds to their kinase inhibition data, to directly identify effective and readily druggable targets. We applied idTRAX to triple-negative breast cancer cell lines and efficiently identified cancer-selective targets. For example, we found that inhibiting AKT selectively kills MFM-223 and CAL148 cells, while inhibiting FGFR2 only kills MFM-223. Since the effects of catalytically inhibiting a protein can diverge from those of reducing its levels, targets identified by idTRAX frequently differ from those identified through gene knockout/knockdown methods. This is critical if the purpose is to identify targets specifically for small-molecule drug development, whereby idTRAX may produce fewer false-positives. The rapid nature of the approach suggests that it may be applicable in personalizing therapy.
UTU Research Portal