Simultaneous analysis of multiple samples made possible with new shRNA screening method
A collaborative research group including RIKEN CSRS and Waseda University has streamlined a short-hairpin RNA (shRNA) library screening method and applied it to the natural marine product aurilide B, identifying new genes related to the mechanisms that aurilide B uses to induce apoptosis. shRNA libraries are used to screen the mechanisms of action for potential chemotherapy compounds.
The group developed a method for concurrently analyzing multiple samples with a next-generation sequencer as part of genome-wide shRNA library screening, confirming reproducibility and quantitativeness with improved processing efficiency at reduced cost (several times lower). The method was then used to identify genes involved in the mechanisms of action for aurilide B, which induces apoptosis in cells, and led to the identification of ATP1A1 as a gene involved in aurilide B susceptibility. ATP1A1 is an alpha subunit gene of Na＋/K＋ATPase (a sodium pump). Additionally, when the ATP1A1 protein inhibitor ouabain (a cardiac glycoside) was combined with aurilide B, the researchers found the combination was able to suppress cell proliferation at a lower concentration than did aurilide B alone.
This newly established method is expected to help clarify the genes involved in the mechanisms of action for many compounds.
Scientific Reports doi:10.1038/s41598-017-02016-4
S. Takase, R. Kurokawa, D. Arai, K. K. Kanto, T. Okino, Y. Nakao, T. Kushiro, M. Yoshida, K. Matsumoto,
"A quantitative shRNA screen identifies ATP1A1 as a gene that regulates cytotoxicity by aurilide B".
Shohei Takase; Student Trainee
Minoru Yoshida; Group Director
Ken Matsumoto; Senior Research Scientist
Chemical Genomics Research Group