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Investigational Cancer Drug Deemed Highly Mutagenic in Cell Line Sequencing Study

NEW YORK – New research on cultured human cells suggests a compound under investigation as a potential cancer drug can cause extensive genetic mutations in non-cancer cells, prompting investigators behind the study to urge more extensive analyses of the drug and its mutagenic activity.

"We did not know anything about the potential mutagenic effects of the compound in humans in the past," senior and corresponding author Serena Nik-Zainal, a research professor at the UK's National Institute for Health and Care Research and genomic medicine and bioinformatics researcher at the University of Cambridge's Early Cancer Institute, said in an email.

"I don't believe that this was something that could have been predicted," she noted, adding that "[w]e still don't fully understand the impact of this level of mutation, but it is very, very high and does require further investigation."

For a study appearing in Nature Genetics on Thursday, Nik-Zainal and colleagues from the University of Cambridge and Pennsylvania State University College of Medicine used whole-genome sequencing to profile two- to four-subclones apiece in several human cell lines repeatedly exposed to "pharmacologically relevant" doses of CX-5461 — being developed by Taiwanese company Senhwa Biosciences under the brand name Pidnarulex — or to two other cancer treatment-related compounds, etoposide or pyridostatin.

Along with immortalized retinal pigment epithelial 1 cells missing both TP53 and either BRCA1 or BRCA2, the team assessed drug effects on an induced pluripotent stem cell line as well as cells that had not been exposed to the compounds.

CX-5461 is a small molecule that acts as a selective RNA polymerase I-dependent RNA synthesis inhibitor, the authors explained. Because the drug appears to prompt synthetic lethal interactions in cells containing defects to DNA repair genes such as BRCA1 or BRCA2, the drug has been fast-tracked by the US Food and Drug Administration for early-stage clinical trials for ovarian or breast cancer cases involving germline alterations in genes such as BRCA1, BRCA2, or PALB2.

Unexpectedly, though, the new whole-genome sequence profiles suggested that the investigational compound not only impacts cells that are missing BRCA1 or BRCA2 but also appears to cause pronounced DNA damage in non-cancerous cells.

Established cancer treatments ranging from radiation to platinum-based chemotherapy can cause mutations in exposed tissues as an indirect consequence of their activities against cancer. However, the cell line experiments suggested that the extent of the new mutations introduced by CX-5461 eclipsed such treatments, leading to DNA damage exceeding that found after exposure to carcinogens such as polycyclic aromatic hydrocarbon in tobacco smoke, the authors reported.

"Here, we find that, although CX-5461 exhibits synthetic lethality in BRCA1-/BRCA2-deficient cells, it also causes extensive, nonselective, collateral mutagenesis in all three cell lines tested, to magnitudes that exceed known environmental carcinogens," they wrote.

In particular, the team linked the drug to a rise in mutations associated with single base substitution (SBS), double base substitution (DBS), and small insertion and deletion (indel) mutational signatures.

When they compared mutation patterns across all three cell lines and drug exposures, meanwhile, the authors found that CX-5461 substitution burdens were some 10 times to 13 times greater than the other treatments considered, regardless of a cell line's genotype. They saw between 22,000 and 31,000 new mutations per cell line, noting that these mutational burdens were on par with those previously found in human cancers.

In contrast, the investigators explained, the PARP inhibitor olaparib, which also has synthetic lethal interactions with BRCA1-/BRCA1-deficient cells, has not been linked to such mutational signatures.

And while SBS, DBS, and indel mutational signatures have been described in cells exposed to the platinum chemotherapy drug cisplatin, a mutagenicity index established in the study suggests CX-5461 "is nearly over 10 times more mutagenic for SBS and around two times more mutagenic for indels" than the platinum chemotherapy drug.

"For any chemical agent that causes this level of mutational damage, one has to be concerned regarding the risk of inducing or promoting secondary cancers," Nik-Zainal explained.

"It may not. It may simply be highly mutagenic but not have any secondary cancer risk, but it needs to be investigated," she explained. "There could be other sources of the mutagenesis as well — perhaps there are impurities in the way that the compound is prepared. All of these things need to be investigated."

More broadly, Nik-Zainal noted that the current findings may prompt the use of whole-genome sequencing on drug-exposed human cells in future drug development efforts, where mutational damage is typically tested more indirectly.

"At the end of the day, we need to balance benefits of a new drug to their associated risks," Nik-Zainal said, adding that "[p]erhaps the day has come in drug development, where we need to explore the direct impact of any new drug on human DNA by whole-genome sequencing of treated human cells."