Downregulation of the splicing regulator NSRP1 confers resistance to CDK4/6 inhibitors via activation of interferon signaling in breast cancer

Abstract

The combination of CDK4/6 inhibitors (CDK4/6i) and endocrine therapy is the first-line therapy for ER+/Her2-breast cancer; however, the development of drug resistance limited the efficacy of the agents. Although activation of the IFN signaling pathway has been identified as a critical driver of intrinsic and acquired CDK4/6i resistance, it remains unknown how the IFN signaling pathway was activated in resistant cells. Here, we report that NSRP1, a regulator of alternative mRNA splicing is downregulated in CDK4/6i resistant breast cancer cells and contributes to CDK4/6i resistance by mediating alternative splicing of NSD2 mRNA and activation of the IFN signaling pathway. Knockdown of NSRP1 reduces CDK4/6i (palbociclib) sensitivity of MCF7 cells while overexpression of NSRP1 sensitizes MCF7-PalR cells towards palbociclib treatment. Mechanistically, RNA sequencing suggests that NSRP1 knockdown strongly activates the IFN signaling pathway in MCF7 cells and elevates the expression of most of the "IFN-related palbociclib-resistance Signature" (IRPS) genes. NSRP1 also regulates numerous alternative splicing (AS) events in breast cancer cells, several of which are key regulators of the IFN signaling pathway. Among them, the inclusion of NSD2 exon 2 is elevated upon NSRP1 knockdown. Our data further show that the inclusion of NSD2 exon 2 is increased in breast cancer and associated with the poor prognosis of patients. In addition, including NSD2 exon 2 elevates NSD2 protein expression to activate the IFN signaling pathway. This study unveils the critical role of NSRP1 in regulating the IFN signaling pathway and the CDK4/6i resistance, which could be a promising biomarker for predicting therapy response.

Keywords: CDK4/6 inhibitor; NSRP1; breast cancer; cell cycle; immunosuppression; interferon; spliceosome.