When DNA breaks inside the cell, it can spell disaster, especially if the damage occurs in areas of the genome that are difficult to repair. Now, scientists Irene Chiolo and Chiara Merigliano at the USC Dornsife College of Letters, Arts and Sciences have discovered that a protein called Nup98, long known for helping traffic molecules in and out of the cell's nucleus, plays another surprising role: guiding the cell's most delicate repairs and reducing the risk of genetic mistakes that can lead to cancer. Their findings were published in Molecular Cell.
With support from the National Institutes of Health, the National Science Foundation, and the American Cancer Society, the researchers revealed that Nup98 forms droplet-like structures deep inside the nucleus. These "condensates" act as protective bubbles around broken strands of DNA in areas called heterochromatin - zones where the genetic material is so tightly packed that making accurate repairs is especially challenging.
Heterochromatin - a major focus of Chiolo's research - is filled with repeated DNA sequences, making it easy for the cell to confuse one stretch for another. Nup98's droplets help lift the damaged section out of that dense zone and create a safer space where it can be repaired accurately, reducing the chance of genetic mix-ups that could lead to cancer.
The researchers also found that Nup98 helps mobilize the damaged site in tightly packed heterochromatin, so it can reach a different part of the nucleus where repair is safer.
Coordinating the repair crew
Timing is everything when it comes to DNA repair, and one of Nup98's most important roles is knowing when to say, "Not yet."
The protein's droplet-like condensates act as a temporary shield around damaged DNA, keeping out certain repair proteins that can cause trouble if they arrive too soon. One of those proteins, called Rad51, can accidentally stitch together the wrong pieces of DNA if it gets involved too early in the process.
"The Nup98 droplets keep Rad51 away until other mechanisms have done their work to line up the correct pieces," Chiolo said. "Only once the damaged heterochromatin moves into a different nuclear space, Rad51 can safely finish the repair."
By coordinating this carefully staged process, Nup98 helps cells avoid dangerous genetic rearrangements - a key part of maintaining genome stability and slowing processes responsible for cancer and aging.
Implications for cancer and therapy
Although the researchers studied cells of fruit flies, the insights gained can help explain how similar DNA repair mechanisms work in humans. Many DNA repair mechanisms in fruit flies are shared across species, making them a powerful model for understanding genome stability.
The Nup98 discovery could have real-world impact, especially for diseases like acute myeloid leukemia, where mutations in Nup98 are known to play a role. By elucidating how Nup98 guides DNA repair, scientists hope to uncover why its mutations are so dangerous - and how to harness the mutations to disrupt cancer cells in targeted treatments.
"Eventually, we may also be able to turn Nup98 mutations that lead to cancer, especially acute myeloid leukemia, into treatment targets - either by specifically disrupting the cells carrying the mutation or by inactivating the harmful functions of the mutated proteins," Merigliano said.
The team also sees long-term potential for therapies that could enhance or mimic Nup98's protective functions, reducing the risk of genome instability, which is a major factor not only in cancer, but also in aging and other genome instability disorders.
About the study
The study, which is available for free download through July 9, was an international effort with 17 scientists from seven institutions collaborating.
In addition to Chiolo and Merigliano, study authors include Chetan Rawal, Colby See, Anik Mitra, Trevor Reynolds, Nadejda Butova and Christopher Caridi of USC Dornsife; Taehyun Ryu of USC Dornsife and Harvard University; Xiao Li of USC Dornsife and the University of Calgary, Alberta; Jeff Wang and Patrick Sung of the University of Texas Health Science Center; Changfeng Deng and David Chenoweth of the University of Pennsylvania; Maya Capelson of San Diego State University; and Lumír Krejčí and Jakub Cibulka of Masaryk University in the Czech Republic.
The research was supported by the following National Institutes of Health grants: F31ES036878; T32GM118289; P01CA265794; R01AR077094; R01GM124143; T32GM145432; CA148724; R35CA241801; and R01GM117376.
National Science Foundation grants DMR-2309043 and 1751197, American Cancer Society grant ACS RSG-24-1325787-01-DMC, an AAUW International Fellowship, USC Research Enhancement Fellowships, a Rose Hills Foundation Fellowship, and grants from the Czech Science Foundation also supported the research.
