Long-term, genome-wide kinetic analysis of the effect of the circadian clock and transcription on the repair of cisplatin-DNA adducts in the mouse liver

Abstract

Edited by Patrick Sung Cisplatin is the most commonly used chemotherapeutic drug for managing solid tumors. However, toxicity and the innate or acquired resistance of cancer cells to the drug limit its usefulness. Cisplatin kills cells by forming cisplatin-DNA adducts, most commonly the Pt-d(GpG) diadduct. We recently showed that, in mice, repair of this adduct 2 h following injection is controlled by two circadian programs. 1) The circadian clock controls transcription of 2000 genes in liver and, via transcription-directed repair, controls repair of the transcribed strand (TS) of these genes in a rhythmic fashion unique to each gene's phase of transcription. 2) The excision repair activity itself is controlled by the circadian clock with a single phase at which the repair of the nontranscribed strand (NTS) and the rest of the genome takes place. Here, we followed the repair kinetic for long periods genome-wide both globally and at single nucleotide resolution by the Excision Repair-sequencing (XR-seq) method to better understand cisplatin DNA damage and repair. We find that transcription-driven repair is nearly complete after 2 days, whereas weeks are required for repair of the NTS and the rest of the genome. TS repair oscillates in rhythmically expressed genes up to 2 days post injection, and in all expressed genes, we see a trend in TS repair with time from the 5 to 3 end. These findings help to understand the circadian-and transcription-dependent and-independent control of repair in response to cisplatin, and should aid in designing cisplatin chemotherapy regimens with improved therapeutic indexes. Circadian rhythmicity of metabolic processes significantly impacts physiology and behavior (1). As a notable example, in mice, excision repair of DNA damage is rhythmic, and daily variations in repair activity are associated with daily variations in sensitivity to UV-induced skin cancer (2, 3). The molecular basis for the circadian clock is a transcription-translation feedback loop in which transcription of clock-controlled genes is activated by BMAL1-CLOCK heterodimers binding to E-box

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

“…Next, repair across the sensitive and resistant cell lines were averaged. The average unit gene repair profiles in Figure 4C are similar to profiles seen in other human cell types, and in cells of other species, which show elevated TS repair which peaks near the TSS, and largely depressed non-transcribed strand (NTS) repair which peaks immediately upstream of the TSS and results from antisense transcription at the promoter (28)(29)(30)(31)(32). Figure 4C shows that overall, there is no difference in amount or pattern of genespecific repair between oxaliplatinsensitive and oxaliplatin-resistant cell lines.…”

“…Repair patterns were visualized using the Integrated Genome Viewer from the Broad Institute. Average repair patterns for a unit gene was determined and plotted as described (31,32). Repair read counts from the transcribed strands of genes were analyzed with the DESeq2 package in R to determine genes with significant differential repair.…”

Molecular connections between circadian rhythm and genome maintenance pathways

“…Secondly, the global repair activity is clock controlled, exhibiting the repair of circadian timing of ~8 h (Yang et al 2018). To better understand DNA repair outcome, from clinical perspective, recently, using mouse liver extracts, long-term genomewide kinetic analyses of the effect of circadian rhythm and transcription on cisplatin repair were studied at singlenucleotide resolution (Yang et al 2019). After injecting cisplatin to mouse, transcribed strand (TS) showed rhythmic repair activity of cisplatin adducts within 2 days.…”

Cisplatin's dual-effect on the circadian clock triggers proliferation and apoptosis

“…Their quantitative analyses determined which strand of which gene is repaired at a given time of the day for the entire mouse genome and revealed that for many genes the transcribed strand and non-transcribed strand are repaired out of phase ( Yang et al, 2018 ). Similar experiments in mice showed that transcription-driven repair is nearly complete after 2 days post-DNA damage, whereas after several weeks for repair of the non-transcribed strand and the rest of the genome ( Yang et al, 2019 ). Transcribed strand repair oscillates in rhythmically expressed genes up to 2 days post-DNA damage, and in all expressed genes, there was an increase in transcribed strand repair with time from the 5′ to 3′ end ( Yang et al, 2019 ).…”

“…Similar experiments in mice showed that transcription-driven repair is nearly complete after 2 days post-DNA damage, whereas after several weeks for repair of the non-transcribed strand and the rest of the genome ( Yang et al, 2019 ). Transcribed strand repair oscillates in rhythmically expressed genes up to 2 days post-DNA damage, and in all expressed genes, there was an increase in transcribed strand repair with time from the 5′ to 3′ end ( Yang et al, 2019 ).…”