Camille Mojica Rey Contributing Editor Clinical OMICs

Can Transcriptomics Help Find the Right Time to Administer Chemotherapy?

For the first time, scientists have tracked the repair of DNA damage induced by the popular chemotherapy drug, cisplatin, at the whole-genome level in a mammal around the clock. Using single-nucleotide sequencing, the team of scientists lead by Nobel laureate Aziz Sancar, M.D., Ph.D., found that DNA repair of transcribed genes is controlled by two circadian programs in mouse tissue. The findings are a significant step toward a goal Sancar has been working toward for 15 years: developing mechanism-based cisplatin chronochemotherapy protocols that will reduce toxicity and tumor resistance in cancer patients.

“This was the first time the repair of DNA damage caused in an animal was analyzed at the whole-genome level at single-nucleotide resolution,” says Sancar, a professor of biochemistry and biophysics at the University of North Carolina School of Medicine. Sancar is the senior author of the current study, which appeared in the May 7 issue of the Proceedings of the National Academy of Sciences.

Sancar is hoping to reduce the negative impact cisplatin can have on cancer patients by taking advantage of the body’s natural DNA repair clock, something scientists have been trying to do for 30 years. These scientists, argues Sancar, just didn’t have the right tools. “The development of next-generation sequencing has revolutionized the field, and that is really what enabled us to do this study,” he says.

In the current study, Sancar and his team injected mice with cisplatin over a 24-hour period. After each injection, they took tissues and analyzed the repair pathways. “We generated a circadian repair map of mouse kidney and liver,” Sancar says. (Damage to these organs in humans treated with cisplatin is common.) In 2015, another team led by Sancar developed a method for isolating DNA fragments that are removed by repair enzymes and, using RNA sequencing, generated repair maps for DNA damage in human cell lines, plant cells, and E. coli. The current study describes the first time those methods have been applied to the whole animal, Sancar notes.

The Penicillin of Chemotherapy

For more than 30 years, scientists have been working to optimize the efficacy and reduce the toxicity of cisplatin, through chronochemotherapy—the practice of giving the drug at different times of day. Researchers call cisplatin, which kills cancers by damaging their DNA, the penicillin of chemotherapy. It is a frontline treatment for testicular, ovarian, colorectal, breast, and head and neck cancers. It is also used to prevent recurrence of those and other cancer types. Its use is limited, however, by the damage it can cause to the kidney, liver, and nervous system, as well as by tumor resistance. “The goal of chronochemotherapy is to deliver the drug at a time of day that is optimal for killing cancer cells while sparing normal tissue and avoiding development of resistance,” the study authors write.

The premise behind the current study is that mechanism-based chronochemotherapy would be a better way to develop drug-delivery protocols as opposed to ad hoc, arbitrary, or empirical approaches that have been tried to date. According to Sancar, previous chronochemotherapy studies had no mechanistic rationales for when to administer the drug. Scientists would just pick time points and see if they got better or worse results. Sancar and his team reasoned that cisplatin kills cancer cells by damaging their DNA. So, they wanted to determine when cancer cells repair their DNA. These would be the times that cancer cells are least efficient at repairing their DNA. Then, patients could be given cisplatin at those time points. “To do that, we needed to determine what genes are repaired at what times of the day.”

And that meant looking at all 21,000 or so mouse genes. “We generated the repair map for these 21,000 genes and it turns out that about 2,000 of them have a circadian pathway that [is] expressed at certain times of day and not expressed at other times of day,” Sancar says. He and his team found that genome repair in cisplatin-exposed mice occurred in the transcribed strand of active, circadian-controlled genes across the circadian cycle with prominent peaks at dawn and dusk. Repair of non-transcribed strands of all genes, repair of intergenic DNA, and global repair overall peaks at 8 a.m. Therefore, repair of genes happens out of phase. “As most cancers are thought to have defective circadian rhythms, these results suggest that future research on timed dosage of cisplatin could potentially reduce damage to healthy tissue and improve its therapeutic index,” the authors write.

Source: NCI

Mechanism-Based Protocols

Sancar admits that these findings are but one small step in the direction of his ultimate goal of designing mechanism-based chronochemotherapy protocols. “Whether having this knowledge allows us to design better treatment regimens remains to be seen,” he said. Currently, he and his colleagues are looking at using mechanism-based chronochemotherapy to treat various human cancers using mouse xenograft models. “Once we find a way to overcome resistance or reduce the toxicity in normal tissue and inflict maximum damage to the tumor tissues in xenografts, then we will start, with our oncologist colleagues, clinical trials,” Sancar explains. “We are not at that stage yet.”

Sancar does maintain, however, that the current study provides a rationale for why other studies have either failed or failed to be replicated. “They just didn’t have mechanistic data,” he points out. He also said that the scientific community, including the popular science media, was too quick to call chronochemotherapy a success. Two large chronochemotherapy trials were conducted: in the United States in 2003, and in Europe in 2006. The U.S. study showed no benefit to a combination therapy of doxorubicin plus cisplatin to patients with endometrial cancer. The European study showed that the risk of death was reduced 25% in men with metastatic colorectal cancer, but increased the risk of death in women by 38%.

Chronochemotherapy using cisplatin is already used in France to treat metastatic colorectal, breast, pancreatic, and gastrointestinal cancer, according to Francis Lévi, M.D., Ph.D., a medical oncologist and professor of biomedicine at the Warwick Medical School in England. Lévi directed the 2006 study for the European Organisation for Research and Treatment of Cancer Chronotherapy Group.

“I think it is interesting to report the mechanisms of DNA repair following cisplatin treatment, but this is one mechanism that has to be integrated within a global picture of cisplatin chronopharmacology,” Lévi said. Previous studies have detailed the cisplatin pathway throughout the body and into the nucleus of cells. While the new study adds information, Lévi says, “I don’t see how this mechanism alone will change the chronotherapy of cisplatin.” He also says that what is needed is a systems approach that considers all the different steps in the metabolism of the drug. He points out that, in humans, molecular markers of circadian rhythm exist that will allow for the personalization of chronochemotherapy treatments.

“I think it is wrong to continue with the idea that we should move from mouse studies to clinical trials in the domain of chronotherapy as we have done before. We need to integrate all in a systems approach…We have to have proof from clinical studies,” Lévi says. He expresses frustration that, 30 years after the discovery of cisplatin, basic studies continue. “Identifying DNA repair will not change the picture. What will change the picture is clinical work.”

For his part, Sancar says, via email, that the path he and his colleagues are following is the conventional one. “First, you figure out the mechanism in cell lines, which we did in 2016. Second, you analyze the drug response in mice and develop a mechanistic view. In this case, high-resolution damage formation and repair. Third, you analyze the response of human tumor xenografts in mice. We are currently doing this. Finally, if all these steps reveal a logical approach to do a trial on patients, then you proceed with clinical trials. All of the previous attempts on chronochemotherapy skipped steps one through three and used ad hoc (or arbitrary) drug delivery regimens and failed. When all is said and done, we may fail also, but at least we will know that there’s no benefit in cisplatin chronochemotherapy for solid scientific reasons.”

This article was originally published in the July/August 2018 issue of Clinical OMICs. For more content like this and details on how to get a free subscription, go to

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