Identifying a cancer therapeutic target: Cell-SELEX identifies a membrane protein for aptamer-mediated growth suppression

The identification of functional ligand-membrane protein interactions under native conditions remains a major challenge in cancer biology. Using cell-systematic evolution of ligands by exponential enrichment, we identified a high-affinity DNA aptamer, CW06, against breast cancer cells. To precisely identify its native membrane target, we developed Aptamer-mediated Metabolic Glycan-labeling Proximity Hybridization (Apt-MGPH), which revealed the mitochondrial solute carrier SLC25A24 as the specific target. Unexpectedly, CW06 treatment upregulated SLC25A24 expression, disrupting methionine metabolism, depleting cytosolic SAM, and inducing G1 cell cycle arrest and senescence via the p21-HMGA1 axis. In mouse xenograft models, CW06 significantly inhibited tumor growth without affecting healthy tissues. Targeted degradation of SLC25A24 reverses these effects, confirming its regulatory role in the metabolism-senescence axis. Our study establishes Apt-MGPH as a robust tool for membrane target identification and highlights aptamer-induced target overexpression as a strategy for cancer therapy.