Genome-wide single-nucleotide resolution of oxaliplatin–DNA adduct repair in drug-sensitive and -resistant colorectal cancer cell lines

Abstract

Platinum-based chemotherapies, including oxaliplatin, are a mainstay in the management of solid tumors and induce cell death by forming intrastrand dinucleotide DNA adducts. Despite their common use, they are highly toxic, and approximately half of cancer patients have tumors that are either intrinsically resistant or develop resistance. Previous studies suggest that this resistance is mediated by variations in DNA repair levels or net drug influx. Here, we aimed to better define the roles of nucleotide excision repair and DNA damage in platinum chemotherapy resistance by profiling DNA damage and repair efficiency in seven oxaliplatin-sensitive and three oxaliplatin-resistant colorectal cancer cell lines. We assayed DNA repair indirectly as toxicity and directly measured bulky adduct formation and removal from the genome by slot blot and repair capacity in an excision assay, and used excision repair sequencing (XR-seq) to map repair events genome-wide at single-nucleotide resolution. Using this combinatorial approach and proxies for oxaliplatin–DNA damage, we observed no significant differences in repair efficiency that could explain the relative sensitivities and chemotherapy resistances of these cell lines. In contrast, the levels of oxaliplatin-induced DNA damage were significantly lower in the resistant cells, indicating that decreased damage formation, rather than increased damage repair, is a major determinant of oxaliplatin resistance in these cell lines. XR-seq–based analysis of gene expression revealed up-regulation of membrane transport pathways in the resistant cells, and these pathways may contribute to resistance. In conclusion, additional research is needed to characterize the factors mitigating cellular DNA damage formation by platinum compounds.

Genomic Characterization of Cisplatin Response Uncovers Priming of Cisplatin-Induced Genes in a Resistant Cell Line

“…This lower damage accumulation is not due to faster repair, as overall NER efficiency is similar in both resistant and sensitive cells. These results are consistent with recent study of oxaliplatin-sensitive and -resistant colon cancer cell lines [ 28 ]. As in lymphoblast and colorectal cancer cell lines, our genome-wide maps of cisplatin removal showed higher NER in transcribed and accessible regions of the genome [ 11 , 28 , 31 ].…”

“…These results are consistent with recent study of oxaliplatin-sensitive and -resistant colon cancer cell lines [ 28 ]. As in lymphoblast and colorectal cancer cell lines, our genome-wide maps of cisplatin removal showed higher NER in transcribed and accessible regions of the genome [ 11 , 28 , 31 ]. We find that the balance between transcription-coupled and global NER was shifted towards transcription-coupled repair in the resistant cell line.…”

“…Previous studies have shown that cisplatin damage formation is relatively uniform across the genome, dictated primarily by the frequency of target G-G dinucleotides [11,32,33]. Accessible regions in the genome are not associated with overall higher damage formation [11], but this and previous works show that repair is significantly enhanced at these regions [11,28]. Similar findings were reported for UV-induced damage [10,31,34].…”

“…In general, A2780 and Acis cell lines showed very similar repair, transcription, and chromatin accessibility profiles ( Figure 3 A, Supplementary Figure S4 ). Consistent with previous findings [ 11 , 28 ], the cisplatin repair signal positively correlated with both transcription levels at genes and with accessibility level at ATAC-seq peaks ( Figure 3 B,C). Cisplatin treatment did not result in a large shift of accessibility.…”

“…Furthermore, higher transcription-coupled repair could allow transcription to continue, explaining the attenuated transcriptional response to damage in resistant cells. However, we cannot conclude that this is a general mechanism for resistance since a parallel study in colorectal cancer cell lines actually reported an opposite shift, towards global genome repair in resistant cell lines [ 28 ].…”