The enzyme poly [ADP-ribose] polymerase 1 (PARP1) is well known for its role in DNA damage repair, and multiple FDA-approved PARP inhibitors are used to treat BRCA-mutated tumors.

Now, researchers at the Wistar Institute have described a role for PARP in regulating the genome of Epstein-Barr virus (EBV).

"PARP has always been looked at... as a protein that has a role in DNA damage," Italo Tempera told BioWorld Science. But there have been "lots of hints that it also regulates chromatin and gene expression."

In the January 17, 2022, issue of Nature Communications, Tempera and his co-authors reported new insights into the nature of this second role for PARP1.

They found that "by using an FDA-approved PARP inhibitor, we were able to reprogram the 3D structure of the virus, which has consequences for EBV gene expression," Tempera said.

Maintaining order in the chromosome structure is important for mammalian genome, and also relevant for those viruses that replicate in the nucleus, he explained.

Depending on its size, a chromosome's worth of DNA can be several meters long. Meanwhile, the size of the nucleus where it resides is measured in micrometers.

"It's like packing into your pocket a string that is as tall as the Empire State building," Tempera said. "You have to fold no matter what... but it has to still be accessible to keep the DNA functional."

The specifics of that folding can bring regions together that are distant from each other in the DNA sequence, for example, enhancers and promoters. Or it can keep them separate.

"That has deep consequences for the way a gene can be expressed, or not," said Tempera, who is an associate professor in the Gene Expression & Regulation Program at The Wistar Institute.

"The viral genome of EBV inside the nucleus of B cells is folded in a very precise way, and this has consequences for function."

The work began as an attempt to understand the details of how EBV uses the machinery of its host's cells to replicate its own genome. The EBV genome does not integrate into the genome of host cells, staying as a separate circular chromosome called an episome instead. That episome has different latency states that allow it to have its genome replicated along with cellular DNA during host cell division, and remain quiet otherwise.

They found that two cellular proteins, PARP and the chromatin-binding protein CTCF, played important roles in EBV replication and latency, and that they did so via their effects on genome folding.

Latency

Tempera said he was surprised by how much the genome structure differed between latency states.

"We never suspected that the folding of the genome could be so different if you looked at different stages of infection," he said. Although EBV infection is all but universal in adults, and mostly harmless, infection does raise the risk of several diseases, and the exact disease depends in part on the viral latency state.

Tempera and his colleagues plan to investigate whether PARP1 also plays a role in the folding in the human genome. "We don't have enough data yet to establish how this could be relevant..., but we think it could be," he said.

In a more translational vein, the team plans to look at the translational potential of PARP targeting in B-cell cancers. EBV infection raises the risk of certain B-cell lymphomas, although its strongest link is to nasopharyngeal carcinoma.

Co-author Paul Lieberman, director of the Wistar Institute's Center for Chemical Biology & Translational Medicine, and his colleagues are the developers of VK-2019, which is being tested in a phase II trial in nasopharyngeal carcinoma patients. VK-2019 inhibits EBNA-1, which regulates EBV gene expression.

In addition to cancer, EBV has long been linked to the development of multiple sclerosis (MS). Using a database of more than 10 million active-duty military personnel, a recent paper in Science magazine demonstrated a causal link between EBV infection and MS. Given that 95% of the general population are infected with EBV, and most of them do not develop MS (or EBV-related cancer, for that matter), whether the findings by Tempera and his team will have a translational impact of MS remains to be seen.

"Right now, it's very hard to predict," Tempera said. "Our work suggests that targeting PARP1 is something that affects expression of a group of EBV genes. What we don't know is whether that group of genes has any role in MS."

"There is potential if we are able to establish a link," he added. But for now, "we have a few pieces missing in the puzzle."