Research

• As cells age, they increasingly export nucleic acid structures called R-loops from the nucleus, triggering an immune response that causes harmful inflammation

• This study identified a two-protein complex involved in exporting R-loops and tested an approved drug to block this process

• Results in preclinical models showed decreases in age-associated inflammation, liver damage, fat gain and muscle loss, as well as a significant increase in lifespan

• The drug, called KPT-330 (selinexor), already is FDA-approved to treat multiple myeloma

A new study led by researchers at The University of Texas MD Anderson Cancer Center has uncovered a previously unknown connection between nucleic acid structures called R-loops and age-related inflammation – or inflammaging – that could herald new intervention options for chronic inflammation and the subsequent health conditions.

The study, published in Nature Aging, was led by Rugang Zhang, Ph.D., professor and chair of Experimental Therapeutics. The researchers identified two specific proteins involved in the export of R-loops, a process that leads to inflammaging and related health issues. In preclinical models, the administration of KPT-330 (selinexor) prevented the R-loops from being exported and led to significant improvement in inflammation, liver damage, fat gain, muscle loss and overall lifespan. 

“Chronic, widespread inflammation is a driving factor in many age-related diseases, including cancer, and our research has discovered one reason why this happens,” Zhang said. “Understanding the cause is the first step toward developing treatments. We saw encouraging results using a drug that has already been tested in humans, paving the way for potential clinical use to alleviate age-related conditions.”

What are R-loops and how do they impact inflammation?

As cells age, they stop dividing and enter a “retired” state called senescence, when they begin releasing inflammatory signals that contribute to chronic inflammation. Previously, limited knowledge existed about why these inflammatory signals are released, but researchers have now pinpointed R-loops as a key component. 

An R-loop is a temporary cellular structure created during the transcription process, when a double strand of RNA and DNA becomes tangled with a third displaced single strand of DNA. Normally, R-loops are confined to the cell nucleus. This study found that cells in senescence increasingly export R-loops into the cytoplasm, or the fluid between the cell membrane and the nucleus. 

The exported R-loops attach to fragments of DNA debris in the cytoplasm, alerting the immune system, which mistakes the R-loops for a threat and triggers inflammation. This process creates widespread, chronic inflammation, similar to an alarm that won’t turn off. 

This study identified the two proteins involved in exporting R-loops, DDX1 and XPO1. DDX1 attaches to the R-loop inside the nucleus and carries it outside. XPO1 acts as an “exit gate” from the nucleus, allowing the R-loops to be transported into the cytoplasm by forming a complex with DDX1. 

How does a drug approved for cancer treatment help alleviate inflammation?

R-loop export and DNA debris forming in the cytoplasm happen independently. An immune response is only activated when the two connect, meaning it may be possible to block one without affecting the other. 

Researchers tested this theory by administering KPT-330, a Food and Drug Administration-approved drug for treating multiple myeloma by blocking nuclear export. With no exit, the R-loops remain trapped inside the nucleus and can’t trigger an inflammatory response.

In this study, shutting down nuclear export by blocking XPO1 in preclinical models suppressed inflammaging, reduced liver fibrosis, lowered systemic inflammatory markers, reversed age-related body composition changes, and significantly extended lifespan. 

What’s next for this research?

Since KPT-330 already has been tested and proven safe for humans, these findings show translational promise for treating age-related conditions. 

In a separate experiment, researchers found that the same inflammatory alarm helps the immune system find and eliminate precancerous cells, indicating a need to refine the alarm rather than silence it altogether. With DDX1 identified as the delivery mechanism transporting R-loops outside the nucleus, future studies could explore blocking that protein instead of shutting down all nuclear export, potentially causing fewer side effects. 

Further investigation is still needed regarding why cells export more R-loops as they age. Understanding these mechanisms could lead to more refined strategies for overcoming the effects associated with senescent cells.

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This work was supported by the National Institutes of Health, the National Cancer Institute, the Department of Defense, and the Cancer Prevention and Research Institute of Texas (CPRIT). For a full list of collaborating authors, disclosures and funding sources, see the full paper in Nature Aging.

• Ovarian clear cell carcinoma is difficult to treat, and treatment options are limited

• Patients with specific PPP2R1A mutations in their tumors survived significantly longer after immunotherapy treatment

• Targeting PPP2R1A may improve responses even further according to laboratory studies 

• PPP2R1A is an important predictive biomarker and possible treatment target for multiple cancer types, study found

Patients with ovarian clear cell carcinoma (OCCC) whose tumors have specific mutations in the PPP2R1A gene were found to have improved survival following immunotherapy compared to patients without these mutations, according to researchers from The University of Texas MD Anderson Cancer Center. 

The findings, published today in Nature, suggest PPP2R1A mutations could be a valuable biomarker to help guide treatment for this difficult-to-treat ovarian cancer subtype and may offer a new therapeutic target to further improve outcomes in multiple cancer types.

Results of the study found that patients with PPP2R1A-mutant OCCC had a median overall survival (OS) of more than five years (66.9 months) after immunotherapy treatment, compared to just 9.2 months for patients without this mutation. 

“Developing effective immunotherapies for ovarian cancer, including rare subtypes like ovarian clear cell carcinoma, remains a significant unmet clinical need,” said co-senior author Amir Jazaeri, M.D., professor of Gynecologic Oncology and Reproductive Medicine. “Our study is the first to demonstrate the clinical importance of PPP2R1A mutations, and it opens the door to new strategies that could benefit many more patients.”

In a Phase II trial, researchers investigated outcomes in a cohort of 34 patients with treatment-resistant OCCC who had been treated with a combination of immune checkpoint inhibitors – durvalumab and tremelimumab. Based on their findings in OCCC, experts also looked at two additional independent cohorts, one consisting of patients with endometrial cancer and the other including more than 9,000 patients with multiple cancer types who received immunotherapy treatment. Analyses confirmed the improved OS following immunotherapy in those with tumor PPP2R1A mutations. 

In parallel, laboratory research showed that targeting PPP2R1A both in vitro and in vivo was also associated with improved response to immunotherapy, suggesting a causal link. This too indicates that therapies targeting PPP2R1A and the associated protein phosphatase 2A (PP2A) molecular pathway could be added to immunotherapy to further boost outcomes. 

“Not only did we identify a new biomarker in ovarian cancer, but we also confirmed survival benefits in other cancer types,” Jazaeri said. “Since PPP2R1A mutations are relatively uncommon, we believe the same benefits may be possible by targeting the PPP2A pathway --using drugs, and we currently are evaluating this in a clinical trial at MD Anderson.”

The study represents an ongoing collaboration across multiple disciplines, led by co-senior authors Jazaeri; Linghua Wang, M.D., Ph.D., associate professor of Genomic Medicine and associate member of the James P. Allison Institute and focus area co-lead with the Institute for Data Science in Oncology; and Rugang Zhang, Ph.D., chair of Experimental Therapeutics.

This research was co-lead by first authors Yibo Dai and Minghao Dang, Ph.D., of the Wang laboratory; Anne Knisely, M.D., fellow in Gynecologic Oncology and Reproductive Medicine; and Mitsutake Yano, M.D., Ph.D., postdoctoral fellow in the Zhang laboratory. A full list of collaborating authors and their disclosures can be found in the paper. 

This study was supported through grants from the National Institutes of Health/National Cancer Institute (T32 CA101642, R01CA202919, R01CA239128, R01CA243142, R01CA260661, R01CA276569, P50CA281701 and P50CA272218, K07CA201013), Dunwoody-Reese Philanthropic, MD Anderson’s Ovarian Cancer Moon Shot, the U.S. Department of Defense (OC190181, OC210124, OC180193), the Cancer Prevention and Research Institute of Texas, Pennsylvania Department of Health CURE Funds, the Robert I. Jacobs Fund of The Philadelphia Foundation, the American Cancer Society (CA281701), and Frank McGraw Memorial Chair in Cancer Research.