BioCentury
ARTICLE | Distillery Techniques

Techniques: Combining genetic and small molecule screens to identify therapeutic targets for rare cancers

July 14, 2016 7:00 AM UTC

A protocol that combines the results of gene editing, RNAi and small molecule screens in patient-derived cancer cell lines could help identify therapeutic targets for rare cancers lacking known driver mutations. The protocol involved conducting proliferation assays in patient-derived cancer cells against 429 targets using two types of genetic screens - CRISPR-Cas9 gene editing with single-guide RNA (sgRNA) libraries and knockdown with shRNA libraries - and a third screen with a library of 440 small molecule inhibitors, then identifying targets that were hits in all three screens. In a cancer cell line derived from a pediatric patient with a rare, undifferentiated metastatic sarcoma, the protocol yielded 32 hits in the CRISPR-Cas9 screen, 21 hits in the shRNA screen and 31 hits in the small molecule screen, but only two targets - cyclin dependent kinase 4 (CDK4) and exportin 1 (XPO1; CRM1) - that were hits in all three screens. In a patient-derived xenograft mouse model of the sarcoma, the CDK4 inhibitor Ibrance palbociclib or the XPO1 inhibitor selinexor decreased tumor growth compared with a compound that inhibited a target not identified in any of the screens. Also in the model, Ibrance plus selinexor decreased tumor growth compared with either agent alone. Next steps could include testing the combination of screening methods in other rare cancers.

Pfizer Inc. and Amgen Inc. market Ibrance, an oral CDK4/CDK6 inhibitor, to treat breast cancer and have the compound in Phase II testing for sarcoma, head and neck, and brain cancers...