Newly Found DNA Repair Pathway Exclusive to Neurons

Published
Immunohistochemistry image of an Npas4fl/fl mouse injected with AAV to express Cre-mCherry (shown in red) and collected 2 h post low-dose KA to induce NPAS4 (shown in cyan).
Credit: Nature (2023). DOI: 10.1038/s41586-023-05711-7

While using brain cells may help maintain memory and other cognitive functions throughout life, prior research shows that the associated activity also harms neurons by inviting more breaks in their DNA. This begs the question, how do neurons remain healthy and functional after carrying out their vital work in the brain for a lifetime?

Now, researchers at Harvard Medical School have discovered a novel DNA repair mechanism that only occurs in neurons, the body’s longest-living cells. The study in mice helps to explain why neurons continue to function over time despite intense repetitive work.

The findings show that a protein complex known as NPAS4-NuA4 initiates a pathway to repair DNA breaks caused by neuronal activity.

“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. If the findings are confirmed in additional animal studies and then in humans, they could aid scientists in understanding the precise process by which neurons in the brain degrade during aging or in neurodegenerative diseases.

The Cost of Active Transcription

npas4-fh generation
Top, schematic of generation of the Npas4–FH mouse model. Bottom, representative immunohistochemistry (performed in triplicate) for NPAS4 and HA in hippocampus samples from Npas4–FH mice following 2 h of KA stimulation. Credit: Nature (2023). DOI: 10.1038/s41586-023-05711-7

Neurons stand out in the vast landscape of cell types in the body because, unlike most other cells, they do not regenerate or replicate. They work tirelessly day after day, year after year, to remodel themselves in response to environmental cues, ensuring that the brain can adapt and operate over a lifetime.

This remodelling process is aided partly by activating new gene transcription programs in the brain. These programs are used by neurons to convert DNA into instructions for protein assembly.

But active transcription in neurons comes at a high cost: it weakens the DNA, causing damage to the genetic instructions required to make proteins that are critical for cellular function.

“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,”

said co-first author Daniel Gilliam.

NPAS4 Damage Control

The way that the brain balances the advantages and disadvantages of neuronal activity piqued the interest of the researchers.

“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,”

said Pollina, who carried out the work as a research fellow at Harvard Medical School, and is now an assistant professor of developmental biology at the Washington University School of Medicine.

The group focused on NPAS4, a transcription factor whose purpose was identified by Michael Greenberg’s group in 2008. In order to control inhibition in excitatory neurons as they react to external stimuli, NPAS4, a protein with a high degree of specificity for neurons, regulates the expression of activity-dependent genes.

“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, the senior author on the new paper.

“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.

Preventing Transcription Breaks

NPAS4–NuA4 function model
A model for the dual function of NPAS4–NuA4 in stimulating transcription and DNA repair in active neurons. Credit: Nature (2023). DOI: 10.1038/s41586-023-05711-7

In the latest study, the scientists ran several biochemical and genomic tests on mice.

First, they discovered that NPAS4 is a component of the NPAS4-NuA4 complex, which consists of 21 different proteins. They mapped the locations of those sites after determining that the complex binds to areas of the neuronal DNA that have sustained significant damage.

More DNA breaks happened, and fewer repair factors were called upon when parts of the complex were inactivated. Furthermore, sites with the complex accumulated mutations more gradually than sites without it. Finally, mice lacking the NPAS4-NuA4 complex in their neurons lived much shorter lives.

“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.

This extra layer of DNA maintenance is part of how neurons respond to activity, and it could help solve the problem that neurons need a certain amount of activity to stay healthy and live longer, but the activity itself is bad for them.

Next Steps

The researchers see many future directions for their work now that they have identified the NPAS4-NuA4 complex and laid out the basics of what it does.

Pollina is interested in taking a broader view and investigating how the mechanism differs between long-lived and short-lived species. She also wants to look into whether there are other DNA repair mechanisms in neurons and other cells, as well as how those mechanisms work and in what contexts they are 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. There are likely many mechanisms of activity-dependent genome protection that we have yet to discover,”

Pollina said.

Greenberg is eager to delve deeper into the mechanism’s details to better understand what each protein in the complex is doing, what other molecules are involved, and how the repair process is carried out. The next step, he says, is to replicate the results in human neurons, which is already being done 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,” he 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 the findings are confirmed in humans, they could shed light on how and why neurons break down as we age and when we develop neurodegenerative diseases like Alzheimer’s. It may also aid scientists in developing strategies to protect other areas of the neuronal genome vulnerable to damage or treat disorders where DNA repair in neurons fails.

Reference:
  1. Pollina, E.A., Gilliam, D.T., Landau, A.T. et al. A NPAS4–NuA4 complex couples synaptic activity to DNA repair. Nature (2023). DOI: 10.1038/s41586-023-05711-7