A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response
Aberrant cell cycle regulation is one of central hallmarks for cancer, and cyclin-dependent kinase inhibitors (CDKi) have showed promising clinical outcome in treating ER+/HER2- breast cancer patients. There are also increasing pre-clinical and clinical studies trying to expand the usage of CDKi to more cancer types. However, the underlying mechanism of high individual variability in clinical response remains unclear. LncRNAs are a group of long non-coding RNAs, which have emerged as regulators and biomarkers for cancer therapeutic outcome. In this study, we first performed a CRISPR activation screen of 9744 lncRNAs in breast cancer cells treated with Palbociclib. We identified 144 and 152 lncRNAs that lead to Palbociclib sensitivity and resistance (FDR<0.05), respectively. Further pharmacogenomic analysis from 41 breast cancer cell lines suggested 34 lncRNAs as potential regulators for Palbociclib response (p<0.05). Targeted screen of overlapped lncRNAs and positive control protein-coding genes was performed to further narrow down the hits. Interestingly, we observed a significant association between cancer cell proliferation and Palbociclib response from both screens. Experimental validation of the screen demonstrated that activation of lncRNA CSS1, CSS2 and CSS3 lead to Palbociclib sensitivity. Mechanically, RNA-seq analysis suggested that they may promote cell cycle progression and downregulate cancer stemness. Collectively, our study characterized novel lncRNAs involved in CDK4/6i response which can act as biomarkers for CDK4/6i treatment in cancer patients. Overall design: CRISPR activation sgRNA library targeting lncRNAs was transduced in MCF-7 cells and treated with Palbociclib before sequencing to determine sgRNA distribution