Non-enzymatic SETD1A activity drives breast cancer cell proliferation via cyclin K.

Abstract

Background: Breast cancer is the most common cancer in women worldwide. SETD1A, a histone H3 lysine-4 methyltransferase, is associated with poor prognosis in breast cancer. While both its enzymatic and non-enzymatic functions are implicated in cancer progression, the specific role of SETD1A in breast cancer remains unclear. This study aimed to elucidate the molecular mechanisms underlying SETD1A dependency in breast cancer.

Methods: SETD1A-high breast cancer cell lines were identified using TCGA and DepMap databases, along with SETD1A knockdown experiments. A CRISPR knockout of SETD1A was performed in a doxycycline-inducible Cas9-expressing KPL-1 breast cancer cell line. RNA-seq, ChIP-seq, CRISPR-tiling screening, and rescue experiments with exogenous SETD1A mutants were performed to investigate the roles of SETD1A in breast cancer.

Results: SETD1A is highly expressed in estrogen receptor-positive / human epidermal growth factor receptor 2-negative (ER⁺HER2^-) breast cancer and is associated with shorter overall survival in luminal-type breast cancer patients. We found that SETD1A is required for cell cycle progression from G1 to S phase in KPL-1 breast cancer cells, but its catalytic domain is dispensable. SETD1A disruption reduces the expression of DNA repair-associated genes, including RPA3 and PRIM1. Exogenous expression of both genes restores defective cell proliferation following SETD1A knockout. The non-catalytic function of SETD1A in breast cancer cells depends on its cyclin K-associated FLOS domain. SETD1A disruption also leads to defective transcriptional elongation in downregulated genes. Treatment with the cyclin K degrader CR8 recapitulates the phenotypes observed in SETD1A knockout cells. Both SETD1A knockout and CR8 were also effective in triple negative breast cancer (TNBC) cells.

Conclusions: SETD1A promotes breast cancer cell replication through its non-enzymatic role via cyclin K, suggesting that the SETD1A-cyclin K axis could be a potential therapeutic target in breast cancer.