Abstract

Colorectal cancer stem cells (CSCs) drive tumor progression through poorly understood metabolic-epigenetic crosstalk. Here, we identify mitochondrial RNA polymerase POLRMT as a key link connecting mitochondrial transcription to CSC maintenance. Clinically, POLRMT is overexpressed in colorectal cancer (CRC) tissues and correlates with poor prognosis. Genetic ablation or pharmacological inhibition of POLRMT suppresses CSC self-renewal and tumorigenicity across cell line-derived CSCs, CRC organoids, and xenograft models. Mechanistically, POLRMT deficiency triggers mitochondrial dysfunction, which unexpectedly elevates the demethylase KDM6B expression, α-ketoglutarate (α-KG) levels, and Dickkopf-1 (DKK1) expression, thereby transcriptionally silencing Wnt/β-catenin signaling and collapsing the CSC niche. Restoration of β-catenin rescues tumorigenicity in POLRMT-knockout (KO) cells, confirming the hierarchy of this signaling cascade. Crucially, POLRMT catalytic activity and mitochondrial localization are indispensable for sustaining this axis. Our work unveils POLRMT as a metabolic gatekeeper that licenses CSC plasticity through KDM6B–α-KG/H3K27me3-mediated chromatin remodeling, proposing the mitochondrial transcription machinery as a therapeutic target for dismantling the CSC hierarchy in CRC.