Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs

Abstract

The platinum-based drug cisplatin is a widely used first-line therapy for several cancers. Cisplatin interacts with DNA mainly in the form of Pt-d(GpG) di-adduct, which stalls cell proliferation and activates DNA damage response. Although cisplatin shows a broad spectrum of anticancer activity, its utility is limited due to acquired drug resistance and toxicity to non-targeted tissues. Here, by integrating genome-wide high-throughput Damage-seq, XR-seq, and RNA-seq approaches, along with publicly available epigenomic data, we systematically study the genome-wide profiles of cisplatin damage formation and excision repair in mouse kidney, liver, lung and spleen. We find different DNA damage and repair spectra across mouse organs, which are associated with tissue-specific transcriptomic and epigenomic profiles. The framework and the multi-omics data we present here constitute an unbiased foundation for understanding the mechanisms of cellular response to cisplatin. Our approach should be applicable for studying drug resistance and for tailoring cancer chemotherapy regimens.

Fig. 1

Overview of experimental design. a Outline of the experimental design. Cisplatin was administered by intraperitoneal injection in mouse. DNA damage, excision repair, and gene expression were assayed by Damage-seq, XR-seq, and RNA-seq. b PCA reveals tissue-specific damage, repair, and transcription across four mouse organs. All experiments were performed with two biological replicates

Fig. 2

Cisplatin-induced differential gene expression between treated and control groups. Venn diagram shows the numbers of significantly differentially expressed genes across mouse kidney, liver, lung, and spleen four hours after treatment with cisplatin. a Three genes are significantly upregulated. b Twelve genes are significantly downregulated in all mouse organs

Fig. 3

Effect of transcription on cisplatin-induced damage formation and repair. Genes are grouped based on their gene expression quantiles (x-axis) in the cisplatin-treated group. Log normalized read counts for DNA damage and repair (y-axis) are separated by strands and averaged between replicates. Spearman correlation coefficients are included in each panel. TCR increases with gene expression and removes damage in the TS strand; GR also increases with gene expression, but at a lower rate

Fig. 4

Association of DNA damage and repair with gene expression and chromatin states. a A total of 602 genes that are highly expressed in liver show higher transcription-coupled repair (in TS) and global repair (in NTS). Expression levels for these genes are also correlated with ChIP-seq signals for histone modification markers (H3K4me1, H3K4me3, H3K27ac, and H3K36me3). b A total of 414 genes that are lowly expressed in liver have lower repair and are characterized by H3K27me3, a marker for gene inactivation. Chromatin accessibility (DNase I hypersensitivity site) is higher for both groups of genes in a and b, indicating a role of chromatin states in transcriptional regulation. Median fold change (fc) between liver and the other organs across all significant genes is included on the upper right corner within each panel. c Whole-genome analysis results of DNA damage and repair in liver, with different genomic annotations. Analysis of repair (left) and damage (right) levels across nine genomic annotations for mouse liver reveals uniform distribution of damage but higher repair in active promotor, CpG island (enriched at transcription start sites), transcription elongation and transition regions in genome

Fig. 5

DNA damage, repair, gene expression, and epigenomic markers for Per1. Per1 is significantly upregulated after cisplatin treatment across all four organs. Damage-seq and XR-seq data are shown for both strands. Pt-d(GpG) damage (Damage-seq) and repair (XR-seq) distribution on the TS and NTS are shown with − and +, respectively. Epigenetic data from ChIP-seq of H3K4me3 and H3K27me3, as well as DNase-seq, are plotted at the bottom of each organ section. We show that the transcriptional and epigenomic profiles of Per1 and neighboring region across all four organs recapitulate the differences in DNA damage and repair between the TS and NTS