Targeting cancer-associated cell surface RNAs with oligonucleotide-drug conjugates enables broad antitumor activity

Abstract Recent studies have revealed the presence of RNAs on mammalian cell surfaces, yet the linkage of cell surface RNAs (csRNAs) to cellular states and their potential as extracellular accessible drug targets remains unexplored. Here we develop Cell-surface and Intracellular RNAs Co-mapping (CIRCmap), a highly multiplexed in situ profiling approach that simultaneously detects thousands of cell-surface and intracellular RNAs at single-cell resolution. Using CIRCmap, we uncover that csRNA distributions are correlated with cellular states and identified cancer-associated csRNAs. Integrative analysis of cell-surface and intracellular RNAs within the same cells implies that the csRNAs undergo endocytosis and endolysosomal trafficking, which is further supported by perturbation experiments and co-localization visualization. We design oligonucleotide-drug conjugates (ODCs) that target cancer-associated csRNAs for endocytic delivery of cytotoxic payloads selectively to cancer cells. ODCs exhibit broad antitumor activity in cell lines and an in vivo mouse tumor model, opening a promising new avenue for targeted cancer therapy. Competing Interest Statement H.Z., C.L., X.Z., and Q.M. have filed patent applications related to this work. The other authors declare no competing financial interests.