An Integrated Genome Wide CRISPRa Approach to Functionalize IncRNAs in Drug Resistance

• Published in: Cell 2018-04, Vol.173 (3), p.649-664.e20
• Main Authors: Bester, Assaf C., Lee, Jonathan D., Chavez, Alejandro, Lee, Yu-Ru, Nachmani, Daphna, Vora, Su, Victor, Joshua, Sauvageau, Martin, Rinn, John L., Provero, Paolo, Church, George M., Clohessy, John G., Pandolfi, Pier Paolo
• Format: Article
• Language: English
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2018.03.052

Resistance to chemotherapy plays a significant role in cancer mortality. To identify genetic units affecting sensitivity to cytarabine, the mainstay of treatment for AML, we developed a comprehensive and integrated genome wide platform based on a Dual protein-coding and noncoding Integrated CRISPRa Screening (DICaS). Putative resistance genes were initially identified using pharmacogenetic data from 517 human pan-cancer cell lines. Subsequently, genome scale functional characterization of both coding and lncRNA genes by CRISPR activation was performed. For lncRNA functional assessment we developed a CRISPR activation of lncRNA (CaLR) strategy, targeting 14,701 lncRNA genes. Computational and functional analysis identified novel cell cycle regulation, survival/apoptosis, and cancer signaling genes. Furthermore, transcriptional activation of the GAS6-AS2 lncRNA, identified in our analysis, leads to hyperactivation of the GAS6/TAM pathway, a resistance mechanism in multiple cancers, including AML. Thus, DICaS represents a novel and powerful approach to identify integrated coding and non-coding pathways of therapeutic relevance. A CRISPR activation screen identifies both coding and noncoding pathways involved in resistance to chemotherapy