NF1 splicing reprograms ERα signaling to promote luminal breast cancer progression

Alternative splicing is an emerging driver of cancer progression, yet its role in modulating tumor suppressor function remains incompletely understood. Here, we identify an alternatively spliced NF1 isoform lacking the nuclear localization sequence (NLS; NLS SE) as a clinically and functionally relevant regulator of breast cancer progression. Analysis of TCGA and AURORA cohorts revealed that NF1 NLS SE is enriched in metastatic tumors, preferentially occurs in luminal subtypes, and is associated with decreased overall survival independent of NF1 genomic alterations.

Using a CRISPR-engineered MCF7 model, we show that NLS SE expression abolishes nuclear localization of neurofibromin, enhances ERK signaling, and promotes proliferation and resistance to endocrine and MAPK-targeted therapies. Despite increased ERα protein levels, transcriptomic analysis revealed suppression of canonical estrogen response programs and activation of KRAS, EMT, and inflammatory pathways. Mechanistically, NLS SE expression increased RNA-bound ERα and reprogrammed RNA binding protein networks, including CELF, ESRP1, and SRSF family members, leading to widespread alternative splicing.

Together, these findings define NF1 NLS exon skipping as a luminal breast cancer-associated, isoform-level mechanism that disrupts nuclear neurofibromin function, rewires ERα signaling towards post-transcriptional regulation, and promotes endocrine-resistant disease. Targeting splicing regulatory networks may represent a therapeutic strategy in NF1- dysregulated breast cancer.