In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors

Background and aims Cisplatin reacts with DNA, and thereby likely generates a characteristic pattern of somatic mutations, called a mutational signature. Despite the widespread use of cisplatin in cancer treatment and its role in contributing to secondary malignancies, its mutational signature has not been delineated. Delineation of the mutational signature of cisplatin would enable identification of cisplatin-induced secondary malignancies, and consequently potentially improve screening for secondary malignancies after cisplatin chemotherapy. Methods We sequenced the whole genomes of 6 10 independent clones of cisplatin-exposed MCF 10A and HepG2 cells, and delineated the patterns of single- and di-nucleotide mutations in each clone in terms of flanking sequence context, transcription strand bias, and other characteristics. We used statistical tests the mSigAct signature presence test and non-negative matrix factorization to search for these signaturescisplatin mutagenesis in hepatocellular carcinomas and esophageal adenocarcinomas. Results All clones showed highly consistent patterns of single- and di-nucleotide substitutions in the contexts of immediately flanking bases. The proportion of dinucleotide substitutions was high: 7.38.1% of single nucleotide substitutions were part of dinucleotide substitutions, presumably due to cisplatin's propensity to form intra strand and inter-strand crosslinks between purine bases in DNA. Statistical and non-negative-factorization-based analyses identified likely cisplatin exposure in 8 9 hepatocellular carcinomas and 2 3 esophageal adenocarcinomas. All hepatocellular carcinomas for which clinical data were available and both esophageal cancers indeed had histories of prior cisplatin treatment. Conclusions We experimentally delineated the mutational signature of cisplatin based on the patterns of the single nucleotide and dinucleotide substitutions. This signature enabled us to detect previous cisplatin exposure in human hepatocellular carcinomas and esophageal adenocarcinomas with high confidence. Background and aims Cisplatin reacts with DNA, and thereby likely generates a characteristic pattern of somatic mutations, called a mutational signature. Despite the widespread use of cisplatin in cancer treatment and its role in contributing to secondary malignancies, its mutational signature has not been delineated. Delineation of the mutational signature of cisplatin would enable identification of cisplatin-induced secondary malignancies, and potentially improve screening for secondary malignancies after cisplatin chemotherapy. Methods We sequenced the whole genomes of 10 independent clones of cisplatin-exposed MCF 10A and HepG2 cells, and delineated the patterns of single- and di-nucleotide mutations in each clone in terms of flanking sequence context, transcription strand bias, and other characteristics. We used the mSigAct signature presence test and non-negative matrix factorization to search for cisplatin mutagenesis in hepatocellular carcinomas and esophageal adenocarcinomas. Results All clones showed highly consistent patterns of single- and di-nucleotide substitutions in the contexts of immediately flanking bases. The proportion of dinucleotide substitutions was high: 8.1% of single nucleotide substitutions were part of dinucleotide substitutions, presumably due to cisplatin's propensity to form intra strand and inter-strand crosslinks between purine bases in DNA. Statistical and non-negative-factorization-based analyses identified likely cisplatin exposure in 9 hepatocellular carcinomas and 3 esophageal adenocarcinomas. All hepatocellular carcinomas for which clinical data were available and both esophageal cancers indeed had histories of prior cisplatin treatment. Conclusions We experimentally delineated the mutational signature of cisplatin based on the patterns of the single nucleotide and dinucleotide substitutions. This signature enabled us to detect previous cisplatin exposure in human hepatocellular carcinomas and esophageal adenocarcinomas with high confidence.