Pt-seq unveils the genomic binding pattern of platinum-based drugs.

Abstract

Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide binding patterns remain incompletely understood. Here, we present Pt sequencing (Pt-seq), an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By using exo- and endonucleases to remove background, Pt-seq enables robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified tens to hundreds of binding clusters that are 10 to 20 kilobases in median length and highly consistent among different drugs, predominantly localizing to centromeric and ribosomal DNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions. Moreover, we found that mutations in cancer cells can generate previously unidentified binding sites. On this basis, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA binding and sensitizes cells to cisplatin. Collectively, Pt-seq sensitively profiles Pt-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.