Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity

Chuannan Fan, Qian Wang (), Peter H. L. Krijger, Davy Cats, Miriam Selle, Olga Khorosjutina, Soniya Dhanjal, Bernhard Schmierer, Hailiang Mei, Wouter de Laat and Peter ten Dijke ()
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Chuannan Fan: Leiden University Medical Center
Qian Wang: Leiden University Medical Center
Peter H. L. Krijger: Hubrecht Institute-KNAW and University Medical Center Utrecht
Davy Cats: Sequencing Analysis Support Core, Leiden University Medical Center
Miriam Selle: SciLifeLab and Karolinska Institute
Olga Khorosjutina: SciLifeLab and Karolinska Institute
Soniya Dhanjal: SciLifeLab and Karolinska Institute
Bernhard Schmierer: SciLifeLab and Karolinska Institute
Hailiang Mei: Sequencing Analysis Support Core, Leiden University Medical Center
Wouter de Laat: Hubrecht Institute-KNAW and University Medical Center Utrecht
Peter ten Dijke: Leiden University Medical Center

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-58032-w

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