2. Academic Validation
  3. Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity

Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity

  • Nat Commun. 2025 Mar 25;16(1):2890. doi: 10.1038/s41467-025-58032-w.
Chuannan Fan # 1,  Qian Wang # 2,  Peter H L Krijger 3,  Davy Cats 4,  Miriam Selle 5,  Olga Khorosjutina 5,  Soniya Dhanjal 5,  Bernhard Schmierer 5,  Hailiang Mei 4,  Wouter de Laat 3,  Peter Ten Dijke 6
Affiliations

Affiliations

  • 1 Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
  • 2 Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands. q.wang@lumc.nl.
  • 3 Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.
  • 4 Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands.
  • 5 Department of Medical Biochemistry and Biophysics, SciLifeLab and Karolinska Institute, Solna, Sweden.
  • 6 Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands. p.ten_dijke@lumc.nl.
  • # Contributed equally.
PMID: 40133308 DOI: 10.1038/s41467-025-58032-w
Abstract

Enhancer RNAs (eRNAs) are a pivotal class of enhancer-derived non-coding RNAs that drive gene expression. Here we identify the SNAI1 enhancer RNA (SNAI1e; SCREEM2) as a key activator of SNAI1 expression and a potent enforcer of transforming growth factor-β (TGF-β)/SMAD signaling in Cancer cells. SNAI1e depletion impairs TGF-β-induced epithelial-mesenchymal transition (EMT), migration, in vivo extravasation, stemness, and chemotherapy resistance in breast Cancer cells. SNAI1e functions as an eRNA to cis-regulate SNAI1 enhancer activity by binding to and strengthening the enrichment of the transcriptional co-activator bromodomain containing protein 4 (BRD4) at the local enhancer. SNAI1e selectively promotes the expression of SNAI1, which encodes the EMT transcription factor SNAI1. Furthermore, we reveal that SNAI1 interacts with and anchors the inhibitory SMAD7 in the nucleus, and thereby prevents TGF-β type I receptor (TβRI) polyubiquitination and proteasomal degradation. Our findings establish SNAI1e as a critical driver of SNAI1 expression and TGF-β-induced cell plasticity.

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