Abstract Breast cancer is the most commonly diagnosed type of cancer worldwide in women. Estrogen receptor alpha (ERα), a well-studied transcription factor, is the major oncogene in over 70% of breast cancer cases. The majority of earlier studies have primarily focused on ERα transcriptional activity that promotes tumor progression. We discovered that ERα is a non-canonical RNA-binding protein that associates with over 1,000 mRNAs, mainly through their 3’-untranslated regions (UTRs), in breast cancer cells. Interestingly, recent studies have shown that a broad spectrum of transcription factors (TFs), including ERα, directly bind RNA; yet, how this association directly orchestrates gene expression remains largely unexplored. This led us to ask an outstanding question about the functional role of oncogenic ERα on RNA metabolism in breast cancer. Since the 3’-UTR is a molecular hub where cis and trans-regulatory elements converge to determine mRNA fate, we hypothesized that oncogenic ERα regulates the stability of a set of mRNAs by binding to its 3’-UTR, which in turn affects the downstream gene expression program that promotes breast cancer progression. To address this question, we performed SLAM-seq, a genome-wide approach for characterizing mRNA stability in MCF7 WT cells and MCF7 cells harboring an ER⍺ RNA binding domain mutation (ER⍺ RBDM). We found that the stability of a subset of ERα mRNA targets is decreased upon loss of ERα RNA-binding activity. We then focused on a critical oncogenic mRNA, NSUN2, an enzyme that catalyzes the 5-methylcytosine (m5C) modification on mRNA, which is an ERα target. NSUN2 is a m5C writer protein, a well-studied RNA methyltransferase enzyme, and is significantly upregulated in breast cancer. Interestingly, survival analysis shows that high NSUN2 correlates with poor prognosis in ER-positive breast cancer patients, but not in ER-negative patients. We show that ER⍺ WT strongly binds to the 3’UTR of NSUN2 mRNA, whereas the ER⍺ RNA binding mutant (ER⍺ RBDM) doesn’t bind to NSUN2 3’UTR. Strikingly, we observed that the loss of ERα RNA binding destabilizes NSUN2 mRNA and protein levels. Furthermore, we found that global RNA m5C methylation is significantly downregulated in breast cancer cells expressing the ERα RBD. Notably, ERα RBDM cells are impaired in forming tumors in vivo, and this phenotype is rescued by overexpressing NSUN2. This suggests the existence of ERα-mediated epitranscriptomic marks via NSUN2 in breast cancer progression. Citation Format: N. Mohan, A. Dabrowska, V. Subramanyam, I. Liu, D. Kuzuoglu-Öztürk, D. Ruggero. Oncogenic er alpha as an rna-binding protein controls mrna stability and epitranscriptome of breast cancer abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-11-26.
Mohan et al. (Tue,) studied this question.