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 ER 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 ER 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 ER signaling towards post-transcriptional regulation, and promotes endocrine-resistant disease. Targeting splicing regulatory networks may represent a therapeutic strategy in NF1-dysregulated breast cancer. O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/726647v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@d507dborg.highwire.dtl.DTLVardef@1f6f6c9org.highwire.dtl.DTLVardef@c42e1corg.highwire.dtl.DTLVardef@1af38dd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO NF1 NLS exon skipping drives cytoplasmic retention of neurofibromin and reprograms ER toward post-transcriptional regulatory functions. (A) In cells expressing NLS-containing NF1 isoforms, neurofibromin localizes to the nucleus and constrains ER activity. (B-C) Alternative splicing of the NF1 NLS exon generates the NLS SE isoform, resulting in cytoplasmic retention of neurofibromin. This shift disrupts canonical ER signaling and is associated with increased ER phosphorylation and enhanced RNA-binding activity. ER engages RNA and cooperates with splicing machinery, including phosphorylated SF3B1, to promote transcriptomic remodeling. These changes support a therapy-resistant state characteristic of aggressive, endocrine-resistant breast cancer. C_FIG