Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [scRNA-seq]

Sustained proliferation and aberrant cellular plasticity are the hallmarks of breast premalignancy, yet the mechanisms driving this process remain unclear. Using CRISPR knockout screens, we systematically characterized the regulators of cellular fitness in the normal mammary epithelium. We found that loss of RNA methyltransferase METTL3 initiates mammary epithelial proliferation and reprograms gene expression, which depends on its catalytic activity. Single-cell analysis in normal breast organoids revealed that METTL3 ablation causes disruption of the mammary cellular hierarchy through increased aberrant luminal differentiation. Mechanically, METTL3 loss reduces the RNA m6A modification of transcribed transposable elements leading to their increased expression and upregulating interferon-STAT signaling. This inflammatory response leads to the crosstalk between STAT and GATA3 transcription factors, resulting in transcriptional activation of luminal genes in the mammary epithelium. These findings identify a cell-intrinsic epigenetic loop contributing to mammary epithelial plasticity and highlight a potential role of METTL3-dependent m6A modification during neoplastic transformation. Overall design: To systematically understand the cellular and molecular changes that associated with aberrant mammary epithelial differentiation upon METTL3 loss, we performed single-cell RNA sequencing in the normal breast organoids with or without METTL3 sgRNA-mediated depletion