Regulation of chemoresistance by a novel p53-regulated long noncoding RNA

Authors

• XL Li
• M Jones
• M Subramanian
• Y Zhu
• S Sindiri
• B Gryder
• H Chou
• M Min
• M Dasso
• Y Yang
• LM Wakefield
• P Perez-Pinera
• B Moriarity
• KV Prasanth
• A Lal

Abstract

Resistance to chemotherapy is a major challenge in cancer. Here, we show that a novel p53-regulated long non-coding RNA (lncRNA) which we named PINCR (p53-induced non-coding RNA), is induced >100-fold after DNA damage and plays a critical role in chemoresistance in colorectal cancer (CRC), both in vitro and in vivo. Targeted deletion of PINCR using CRISPR/Cas9 significantly reduced G1 arrest and induced hypersensitivity to multiple chemotherapeutic drugs. Importantly, this reduced G1 arrest was significantly rescued by re-introduction of PINCR in PINCR-/- cells. We found that PINCR is necessary for the upregulation of select p53 targets and G1 regulators, including BTG2 and RRM2B. This upregulation was mediated by the binding of PINCR to Matrin 3, a RNA-binding protein that we identified by in vitro RNA pulldowns followed by mass spectrometry. We found that PINCR binds to Matrin 3 and is necessary for the efficient binding of a Matrin 3-p53 complex to the p53-response element of BTG2 and RRM2B. To determine if endogenous PINCR is associated with the p53-response element of BTG2 and RRM2B, we used CRISPR/Cas9 to knock-in in the PINCR genomic locus, a S1-tag which is an RNA aptamer that binds to streptavidin with high affinity. Pulldowns from the S1-tagged PINCR cells showed that endogenous PINCR binds to Matrin 3 and also to the p53-response elements of BTG2 and RRM2B. These findings demonstrate a critical role of a PINCR/Matrin 3/p53 axis in chemoresistance in CRC and suggest that targeting PINCR may be utilized for future translational studies.

Scientific Focus Area: Cancer Biology

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