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Study details RNA editing in virus-infected cancer cells

Apr. 20, 2023, 11:05 AM

From left, Xiang Ye, PhD, Suba Rajendren, PhD, Antiana Richardson, and John Karijolich, PhD, are studying how the cancer-causing virus KSHV commandeers host gene expression and regulatory machinery.
From left, Xiang Ye, PhD, Suba Rajendren, PhD, Antiana Richardson, and John Karijolich, PhD, are studying how the cancer-causing virus KSHV commandeers host gene expression and regulatory machinery. (photo by Susan Urmy)

by Leigh MacMillan

Vanderbilt University Medical Center researchers have published the first comprehensive analysis of RNA editing — a form of RNA modification — for the oncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV).

KSHV causes Kaposi’s sarcoma, a cancer that develops from cells that line blood vessels and often appears on the skin, and it also causes primary effusion lymphoma, an aggressive cancer of B cells.

The study in Nature Communications details the landscape of RNA editing in primary effusion lymphoma cells during both latent (dormant) and lytic (active) KSHV infection and identifies an edited viral microRNA that is critical for infection. The findings could suggest new therapeutic strategies to prevent KSHV infection and tumorigenesis.

“For KSHV in particular, the lytic cycle is required for transformation — to cause cancer, the virus has to be replicating and spreading,” said John Karijolich, PhD, associate professor of Pathology, Microbiology and Immunology. “Now that we’ve been able to identify the microRNA miR K12-4 as being required for efficient viral infection, we are trying to develop strategies to deplete this microRNA and test if targeted disruption prevents viral infection and transformation.”

RNA editing, as its name suggests, is a process that changes the bases in RNA (the “letters” that define an RNA molecule) to regulate gene expression and protein function. In humans, editing of certain neurotransmitter receptor RNAs is essential for normal brain function, and mutations in an RNA editing enzyme can lead to autoimmune disease.

“Oncogenic herpesviruses, and all DNA viruses, have to infect cells, set up shop, and then persist for a very long time, so they’re exquisitely fine-tuned to commandeer host gene expression and regulatory machinery, including RNA editing,” Karijolich said.

In the current study, led by postdoctoral fellow Suba Rajendren, PhD, the researchers characterized “adenosine-to-inosine” (A-to-I) editing of both cellular RNA and viral RNA in primary effusion lymphoma cells, during the latent and lytic stages of the viral life cycle.

“This is the first characterization of A-to-I editing in a global manner — in the host and viral transcripts — and of how editing sites change from the latent to the lytic stage,” Rajendren said. “We saw a huge variation in the RNA modification landscape and found that host and viral transcripts are differentially edited during latent and lytic stages.”

Only one A-to-I editing site was previously known in KSHV viral RNA. The investigators found and validated about 30 more sites and characterized editing in the microRNA miR K12-4. They found that if they deleted miR K12-4, viral particles (virions) were still produced by the cells, but they were much less infectious. Adding back the edited version of miR K12-4 restored infectivity.

“This is a really interesting phenomenon where the virus has hijacked this RNA modification of a noncoding microRNA to allow it to infect other cells, which is pretty remarkable,” Karijolich said. “We’re excited to try to understand how that microRNA is regulating virion production to allow it to be infectious, and to develop strategies to reduce its expression and impair the ability of the virus to replicate.”

While the miR K12-4 microRNA is unique to KSHV, RNA editing is “almost certainly an important process for all viruses,” Karijolich said.

In particular, it’s likely to be important for Epstein-Barr Virus (EBV), another oncogenic herpesvirus that causes mononucleosis and can cause B cell lymphomas and gastric cancers.

“We think RNA editing will also impact EBV biology; those are certainly areas that need to be further explored,” Karijolich said. “It’s biochemically and bioinformatically intensive to do these types of analyses, so not a lot of global RNA editing studies have been done.”

Other authors of the Nature Communications paper include Xiang Ye, PhD, William Dunker and Antiana Richardson. The research was supported by startup funds from Vanderbilt University Medical Center, grants from the National Institutes of Health (AI141448, CA250051), and an American Cancer Society Research Scholar Award. Karijolich is a Pew Biomedical Scholar.

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