Abstract
The roles of long non-coding RNAs (lncRNAs) in tumorigenesis and therapeutic response remain largely unknown. Here we perform genome-wide and focused CRISPR activation screens to identify lncRNAs regulating palbociclib response in breast cancer cells. A synchronized two-stage proliferation screen not only characterizes tumor growth-regulating lncRNAs, but also reveals a strong negative correlation between lncRNA-mediated regulation of tumor proliferation and CDK4/6 inhibitor sensitivity. By integrating CRISPRa screen results with drug response data from 815 cancer cell lines, we identify and functionally validate that TENM3-AS1, LINC01117, and ENSG00000226706 can increase breast cancer sensitivity to CDK4/6i while promoting tumor proliferation. In breast cancer patients, all three lncRNA signatures are associated with CDK4/6 inhibitor response. Mechanistically, we have shown that lncRNA TENM3-AS1 is a potential ERα-interacting lncRNA, and its regulation of CDK4/6 inhibitor sensitivity is dependent on ERα expression. Our integrated strategy characterizes oncogenic lncRNAs as potential therapeutic biomarkers for CDK4/6 inhibitor treatment in cancer.
Code availability
The code used for CRISPRa screen hit analysis, RNA-seq pathway analysis, and snRNA-seq integration in this study is available from GitHub (https://github.com/dyanglab/CRISPRa_CDKi)82.
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Acknowledgements
This study was supported by the Shear Family Foundation (to D.Y.) and National Cancer Institute (R01CA255196, R01CA272866, and R01CA282704 to D.Y.). This research was partly supported by the University of Pittsburgh Center for Research Computing, RRID: SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, supported by NIH award number S10OD028483.
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Conceptualization: D.Y., Yifei W., Yueshan Z. Methodology: Yifei W., Yueshan Z., Z.W., S.L., M.Z., and D.Y. Validation: Yifei W., J.H., Z.W., D.P., Yu Z., and X.W. Formal analysis: Yueshan Z. and M.Z. Resources: S.L., Yue W., and W.X. Visualization: Yifei W., Yueshan Z., M.Z., and D.Y. Supervision: D.Y. and M.Z. Writing (original draft): Yifei W., Yueshan Z., D.Y., and M.Z. Writing (review and editing): Yifei W., Yueshan Z., J.H., D.Y., and M.Z.
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Wang, Y., Zhao, Y., Hu, J. et al. CRISPR activation screens identify oncogenic lncRNAs that are susceptible to CDK4/6 inhibitor treatment. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70816-2
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DOI: https://doi.org/10.1038/s41467-026-70816-2
