NSUN7 Suppression Reduces Metastatic Potential and Restores Sensitivity to 4-OH Tamoxifen in Resistant MCF-7 Cells

Tamoxifen remains a first-line treatment for estrogen receptor-positive breast cancer. Emerging evidence indicates that aberrant 5-methylcytosine (m⁵C) modification of RNAs contributes to chemotherapeutic resistance in various types of cancer, however their role in determining tamoxifen resistance in breast cancer remains elusive.

We measured global m⁵C RNA methylation and expression of its regulating enzymes in tamoxifen-sensitive (MCF-7) versus tamoxifen-resistant cells (MCF-7 Tam1). Expression of the most significantly dysregulated enzyme NOP2/Sun RNA methyltransferase family member 7 (NSUN7), the key m⁵C writer methyltransferase, was depleted using siRNA-mediated knockdown. Functional assays were performed to measure sensitivity to tamoxifen, cell migration, and colony-forming potential. RNA sequencing followed by enrichment and network analysis identified NSUN7-regulated pathways and hub genes. Finally, the prognostic relevance of hub genes was assessed using the Gene Expression Profiling Interactive Analysis platform.

Tamoxifen-resistant cells exhibited a significant elevation in global m⁵C levels and expression of NSUN7. siRNA-mediated reduction of NSUN7 significantly restored sensitivity to tamoxifen, reducing the half-maximal inhibitory concentration by ~50%, and significantly inhibited cell migration and colony-forming potential. Transcriptomic profiling and enrichment analysis identified that NSUN7 targets were enriched in crucial pathways, including mitogen-activated protein kinase pathway, phosphatidylinositol signaling, cell cycle, and focal adhesion. Notably, NSUN7 depletion caused dysregulation in the expression of genes implicated in tamoxifen resistance, such as brain acid-soluble protein 1 (BASP1), tissue inhibitor of metalloproteinase 3 (TIMP3), ajuba LIM protein (AJUBA), S-phase kinase-associated protein 2 (SKP2) and yes-associated protein 1 (YAP1). Network analysis further identified NSUN7-regulated hub genes significantly associated with disease prognosis.

Our study identified that NSUN7 regulates key oncogenic pathways associated with tamoxifen resistance and metastasis. Its suppression enhanced tamoxifen sensitivity and reduced metastatic potential, collectively highlighting NSUN7 as a novel driver of tamoxifen resistance and a potent therapeutic target in estrogen receptor-positive breast cancer.