NF1 deficiency correlates with estrogen receptor signaling and diminished survival in breast cancer

The key negative regulatory gene of the RAS pathway, NF1, is mutated or deleted in numerous cancer types and is associated with increased cancer risk and drug resistance. Even though women with neurofibromatosis (germline NF1 mutations) have a substantially increased breast cancer risk at a young age and NF1 is commonly mutated in sporadic breast cancers, we have a limited understanding of the role of NF1 in breast cancer. Much of our understanding of the mechanisms underlying the functional loss of NF1 comes from mouse models that do not completely recapitulate the phenotypes of human NF1. We utilized CRISPR-Cas9 gene editing to create Nf1 rat models to evaluate the effect of Nf1 deficiency on tumorigenesis. The resulting Nf1 indels induced highly penetrant, aggressive mammary adenocarcinomas that express estrogen receptor and progesterone receptor. We identified distinct Nf1 isoforms that were altered during tumorigenesis.\n\nTo evaluate NF1 in human breast cancer, we analyzed genomic changes in a breast cancer dataset of 2,000 clinically annotated breast cancers. We found NF1 shallow deletions in 25% of sporadic breast cancers, which correlated with poor clinical outcome. To identify biological networks impacted by NF1 deficiency, we constructed gene co-expression networks using weighted gene correlation network analysis (WGCNA) and identified a network connected to ESR1 (estrogen receptor). Moreover, NF1-deficient cancers correlated with established RAS activation signatures. Estrogen-dependence was verified by estrogen-ablation in Nf1 rats where rapid tumor regression was observed. These results demonstrated the significant role NF1 plays in both NF1-related breast cancer and sporadic breast cancer.