A team at Harvard Medical School has identified a novel mechanism of DNA repair that occurs exclusively in neurons, which are some of the longest-lived cells in the body. The research, conducted in mice, showed that a protein complex called NPAS4–NuA4 initiates a pathway to repair DNA breaks induced by activity in neurons. The findings could help to explain why neurons continue to function over time, despite their intense repetitive work.
If the findings are confirmed in further animal studies and in humans, they could also help scientists understand the precise process by which neurons in the brain break down during aging or in neurodegenerative diseases. “More research is needed, but we think this is a really promising mechanism to explain how neurons maintain their longevity over time,” said co-first author Elizabeth Pollina, PhD, who carried out the work as a research fellow at HMS, and is now an assistant professor of developmental biology at the Washington University School of Medicine.
Pollina and colleagues reported on their findings in Nature, in a paper titled “A NPAS4-NuA4 complex couples synaptic activity to DNA repair.” In their paper they wrote “Our findings suggest that neurons have evolved a specific chromatin regulatory mechanism that couples synaptic activity to genome preservation.”
“Use it or lose it,” is an adage that is commonly applied to everything from our muscles to our minds, especially as we age. Yet when it comes to the brain, such usage is not entirely a good thing: While using brain cells may indeed help maintain memory and other cognitive functions throughout life, scientists have found that the associated activity also damages neurons by inviting more breaks into their DNA. “ … neuronal activity also threatens the genomic integrity of postmitotic neurons that must survive the lifetime of an organism,” the authors wrote.
Which raises the question: How do neurons remain healthy and functional over a lifetime of carrying out their vital work in the brain? “Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown,” the team continued.
Unlike most other cell types in the body, neurons do not regenerate, or replicate. Day after day, year after year, they work tirelessly to remodel themselves in response to environmental cues, ensuring that the brain can adapt and operate over a lifetime. This remodeling process is in part accomplished by activating new programs for gene transcription in the brain. Neurons use these programs to turn DNA into instructions for assembling proteins. However, this active transcription in neurons comes with a serious cost, as it makes the DNA vulnerable to breaks, damaging the very genetic instructions needed to make proteins that are so essential for cellular functioning.
Moreover, the researchers pointed out, while the coupling of transcription to DNA breaks is observed across cell types, “this process poses a specific challenge to long-lived neurons, which cannot use replication-dependent DNA repair pathways and possess limited regenerative mechanisms to replace damaged cells.”
Co-first author Daniel Gilliam, a graduate student in the Program in Neuroscience at HMS, added, “There’s this contradiction there on a biological level—neuronal activity is critical to neuron performance and survival, yet inherently damaging to the DNA of the cells.”
The researchers were interested in finding out how the brain balances the costs and benefits of neuronal activity. “We wondered whether there were specific mechanisms that neurons employ to mitigate this damage in order to allow us to think and learn and remember throughout decades of life,” Pollina said. As the team commented in their paper, “So far, there are no examples of neuronal-specific repair machinery that mitigate the risks of genome instability during heightened activity.”
For their newly reported work the researchers turned their attention to NPAS4, a transcription factor whose function was discovered by senior author Michael Greenberg, PhD, and researchers in the Greenberg lab in 2008. A protein known to be highly specific to neurons, NPAS4 regulates the expression of activity-dependent genes to control inhibition in excitatory neurons as they respond to external stimuli. “The thing that’s been a mystery to us is why neurons have this extra transcription factor that doesn’t exist in other cell types,” said Greenberg, who is the Nathan Marsh Pusey Professor of Neurobiology in the Blavatnik Institute at HMS.
“NPAS4 is primarily turned on in neurons in response to elevated neuronal activity that’s driven by changes in sensory experience, and so we wanted to understand the functions of this factor,” Pollina added.
In the study published in Nature, the researchers conducted a series of biochemical and genomic experiments in mice. First, they determined that NPAS4 exists as part of a complex made of 21 different proteins, known as NPAS4–NuA4. They then established that the complex binds to sites on neuronal DNA that have a lot of damage, and mapped the locations of those sites. “By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4–NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair,” the scientists stated. “Gene regulatory elements bound by NPAS4–NuA4 are partially protected against age-dependent accumulation of somatic mutations.”
They in addition found that when components of the complex were inactivated, more DNA breaks occurred, and fewer repair factors were recruited. Additionally, sites where the complex was present accumulated mutations more slowly than sites without the complex. Finally, mice lacking the NPAS4–NuA4 complex in their neurons had significantly shortened life spans. “Impaired NPAS4–NuA4 signaling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan,” they wrote.”
“What we found is that this factor plays a critical role in initiating a novel DNA repair pathway that can prevent the breaks that occur alongside transcription in activated neurons,” Pollina said. Gilliam added, “It’s this extra layer of DNA maintenance that’s embedded within the neuronal response to activity, and it provides a potential solution to the problem that you need a certain amount of activity to sustain neuronal health and longevity, but the activity itself is damaging.”
Now that the researchers have identified the NPAS4–NuA4 complex and laid out the basics of what it does, they see many future directions for their work. Pollina is interested in taking a broader view, by exploring how the mechanism varies across longer- and shorter-lived species. She also wants to investigate whether there are other mechanisms of DNA repair—in neurons and in other cells—and how those mechanisms work and in what contexts they’re used.
“I think it opens up the idea that all cell types in the body probably specialize their repair mechanisms depending on their life span, the kinds of stimuli they see, and their transcriptional activity,” Pollina said. “There are likely many mechanisms of activity-dependent genome protection that we have yet to discover.”
Greenberg is eager to delve deeper into the details of the mechanism to understand what each protein in the complex is doing, what other molecules are involved, and how exactly the repair process is carried out. A next step, he suggested, is replicating their murine results in human neurons. This work that is already underway in his lab. “I think there’s tantalizing evidence that this is relevant to humans, but we haven’t yet looked in human brains for sites and damage.” Greenberg said. “It may turn out that this mechanism is even more prevalent in the human brain, where you have so much more time for these breaks to occur and for DNA to be repaired.”
If reaffirmed in humans, the findings could provide insight into how and why neurons break down as we age and when we develop neurodegenerative diseases such as Alzheimer’s. “Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and aging,” they wrote. Interestingly, they further noted, “… mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders.”
The reported discoveries could in addition help scientists develop strategies to protect other regions of the neuronal genome that are prone to damage or to treat disorders in which DNA repair in neurons goes awry.