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

Abstract

Cisplatin reacts with DNA and thereby likely generates a characteristic pattern of somatic mutations, called a mutational signature. Despite widespread use of cisplatin in cancer treatment and its role in contributing to secondary malignancies, its mutational signature has not been delineated. We hypothesize that cisplatin's mutational signature can serve as a biomarker to identify cisplatin mutagenesis in suspected secondary malignancies. Knowledge of which tissues are at risk of developing cisplatin-induced secondary malignancies could lead to guidelines for noninvasive monitoring for secondary malignancies after cisplatin chemotherapy. We performed whole genome sequencing of 10 independent clones of cisplatin-exposed MCF-10A and HepG2 cells and delineated the patterns of single and dinucleotide mutations in terms of flanking sequence, transcription strand bias, and other characteristics. We used the mSigAct signature presence test and nonnegative matrix factorization to search for cisplatin mutagenesis in hepatocellular carcinomas and esophageal adenocarcinomas. All clones showed highly consistent patterns of single and dinucleotide substitutions. 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- and interstrand crosslinks between purine bases in DNA. We identified likely cisplatin exposure in nine hepatocellular carcinomas and three esophageal adenocarcinomas. All hepatocellular carcinomas for which clinical data were available and all esophageal cancers indeed had histories of cisplatin treatment. We experimentally delineated the single and dinucleotide mutational signature of cisplatin. This signature enabled us to detect previous cisplatin exposure in human hepatocellular carcinomas and esophageal adenocarcinomas with high confidence.

The genomic imprint of cancer therapies helps timing the formation of metastases

“…However, we showed earlier that cisplatin induces specific types of dinucleotide mutations at sites of intrastrand crosslinks 9 and the cisplatin treatment of human cell lines led to a closely related pattern of DNV mutations to what we found in chicken DT40 cells. 10 Remarkably, we found very similar types of DNVs in the sequenced samples to those induced by cisplatin in cell lines ( Figs. 3c and 3d).…”

“…In a DT40 cell culture model we previously estimated the mutagenicity of cisplatin treatment at IC 50 concentration as 200 base substitutions per gigabase per treatment cycle, 9 and not entirely comparable weekly treatments of MCF10A and HepG2 cells caused 150-450 base substitutions per gigabase per treatment. 10 To find the mutagenicity of cisplatin per tumour cell, we must consider only clonal mutations in the sequenced samples. Eight percent of the 476 SNVs common to the liver and lymph node samples belong to the cisplatin signature, and these mutations are clonal in the liver metastasis, suggesting that at least 13 SNVs per gigabase were induced by cisplatin in its single ancestral cell.…”

“…The resulting triplet SNV spectra, were analysed for contributions of known mutational signatures in the COSMIC cancer mutation database. 21 The deconstructSigs R package 22 was applied using a restricted set of COSMIC signatures that included ageing and tissue-specific cancer signatures 1,2,[4][5][6]12,13,[15][16][17]23 supplemented with the signature drawn from cisplatin-treated human cell lines, 10 and with a minimum signature contribution of 6%.…”

“…To further explore whether the single cycle of cisplatin treatment administered to the patient was mutagenic, we defined a cisplatin-induced triplet SNV signature based on the mutation spectrum of cisplatin-treated human cell lines 10 and looked for its contribution to the detected SNV pools. A decomposition into all triplet signatures implicated in cancers of the lung and the sampled metastatic sites in COSMIC, 21 plus the cisplatin signature, revealed a contribution of the cisplatin SNV signature to unique mutations in the lung primary tumour sample as well as in the bone and lymph node metastases ( Fig.…”

“…We have recently demonstrated the mutagenicity of the cytotoxic agents cisplatin and cyclophosphamide in cell linebased studies, 9 and an experimentally derived cisplatin mutation spectrum was subsequently found in cisplatin-treated esophageal and liver tumours. 10 If certain somatic mutations in tumour samples can be assigned to a treatment agent that the patient received, then the branching time of two samples can be determined relative to the time of the treatment based on whether the treatment-derived mutations in two samples are unique or shared. Accurate mutation detection is critical for such analyses, confounded by varying tumour content and the varying allele frequency (AF) of subclonal mutations, necessitating a careful bioinformatics approach.…”