NF1-depleted ER⁺ breast cancers are differentially sensitive to CDK4/6 inhibitors

Neurofibromin/NF1 is a RAS (rat sarcoma virus) GTPase-activating protein and estrogen receptor (ER) transcriptional corepressor. NF1^low status, identified by copy number loss or low mRNA/protein expression, is associated with endocrine therapy resistance in ~20% of ER⁺/HER2^- (human epidermal growth factor receptor 2) early-stage breast cancers. The identification of targeted treatments for NF1^low ER⁺/HER2^- breast cancer is therefore a priority. In this study, proteogenomic analysis of ER⁺/HER2^- breast cancer demonstrated that NF1^low tumors exhibited elevated cyclin-dependent kinase 4/6 (CDK4/6) activity. In cell lines, NF1 deletion had a dual effect on CDK4 activity: first, by promoting ER recruitment to CCND1 (cyclin D1), thereby increasing CDK4-cyclin D1 complex formation, and second, by activating C-RAF (rapidly accelerated fibrosarcoma), which drove phosphorylation of the CDK4 activation loop. Preclinical modeling demonstrated that NF1^low ER⁺ cancer cells were more sensitive to fulvestrant combined with a CDK4/6 inhibitor versus fulvestrant alone, with the induction of cell death in vitro and durable tumor regressions in ER⁺ NF1^low patient-derived xenograft models in vivo. Furthermore, NF1^low ER⁺/HER2^- tumors were more sensitive to neoadjuvant aromatase inhibitor (AI) plus palbociclib than to neoadjuvant AI alone, as indicated by suppression of mRNA-based proliferation scores. These data are consistent with a model whereby ER and RAS coactivation upon NF1 loss can drive CDK4/6 activity and endocrine therapy resistance but renders NF1^low ER⁺ tumors susceptible to CDK4/6 inhibition. Development of clinical-grade NF1 diagnostics should be prioritized to determine whether NF1^low ER⁺ breast cancers should receive adjusted adjuvant treatment recommendations that reflect increased responsiveness to CDK4/6 inhibition.