Laying the foundation for neuronal development

If you want to build a house correctly, you must follow a standard sequence of events. You cannot put up walls before laying the foundation. The same logic applies to a developing brain. The blueprint of the human brain is written in our genes, but how and when those genes are accessed plays a critical role in neuronal development. Any discrepancy in following the plan may lead to catastrophic neurodevelopmental disorders.

Jamy Peng, PhD, St. Jude Department of Developmental Neurobiology, is keenly interested in understanding the genetic architecture of neuronal development and the sequence of events that define it — a pursuit that surprises as often as it informs.

Organoid model system helps answer big questions

Peng’s model system of choice is cortical organoids – lab-grown replicas of the brain’s outermost layer (the cortex) that mimic its structure and function. “Since my lab started, we've been making cortical organoids, quality controlling them, and then building a complete system we can use to figure out brain development,” she said.

In a 2019 paper published in Nature Neuroscience, Peng and her team identified a curious pairing of proteins at work during neuronal development. Peng wasn’t surprised to see UTX, a chromatin modifier she knew played a role in brain growth, but an apparent partnership between UTX and the DNA-damage response protein 53BP1 did surprise her.

“53BP1 is a well-studied protein, but it's strictly focused on DNA damage repair,” Peng said. “So, we were intrigued to come across a non-canonical role of DNA damage repair response in developmental gene regulation.”

Peng’s curiosity toward 53BP1 was piqued again a few years later when it appeared in another cortical organoid investigation. This time, it was linked to the protein ataxia telangiectasia mutated (ATM). The clues left behind by 53BP1 put Peng on the path to understanding foundational events in neuronal development.

ATM kicks 53BP1 into gear

ATM is a kinase, a protein that triggers activity in other proteins by plugging in a “phosphate battery” in a process called phosphorylation. As the name suggests, the gene causes ataxia telangiectasia, a devastating rare neurodegenerative disorder that affects the nervous system, among a slew of other systems. It is also frequently mutated in cancer due to its primary role in DNA damage repair.

In a 2024 publication in PLOS Biology, Peng further investigated the connection between ATM and 53BP1. “We did a deep dive using our cortical organoids to characterize the ATM-dependent phosphorylation of neurodevelopmental regulators,” Peng said. “We found that 53BP1 is very heavily phosphorylated in that system.” In fact, they noted that phosphorylation was increased when human pluripotent stem cells were maturing into neural progenitor cells. It appeared that ATM was responsible for activating 53BP1 during neuronal development.

This theory was confirmed by removing the protein’s ability to be phosphorylated. “It had a pretty drastic effect – the organoids were smaller and much more disorganized, which implies premature maturation,” Peng explained. “Essentially, the tissue can’t grow as fast because the cells just immediately turn into neurons.”

From what Peng’s team observed in the lab, it appeared the walls were being installed before the foundation. Some key steps in neuronal development were being disrupted, so the team dug deeper.

Phosphorylation to prevent prematuration

Further investigation into ATM function showed that the protein acted as a foreman on a construction site, only activating the needed systems to ensure proper neuronal construction. It does this by phosphorylating proteins, such as 53BP1, which activate genes vital to neurogenesis, differentiation and morphogenesis. This collectively suppresses neuronal function and encourages stem cell differentiation, i.e., well-timed growth.

“During the protracted process of neuronal cell differentiation and maturation, 53BP1 binds to key developmental genes to prepare them for future expression when the neuronal mature stage kicks in,” Peng said. “The failure to phosphorylate 53BP1 led to increased expression of genes early on in cortical organoid development, leading to premature neuronal maturation and smaller cortical organoids.”

Laying the groundwork for addressing disease

To build off this work, Peng hopes to add an extra factor into her studies: time. “Human neuronal maturation takes months and years,” she said. “I’m excited to track this phenomenon at different neuronal stages to understand the temporal control of genetic programs better.”

As Peng’s work shows, fully appreciating brain development requires more than knowing the pieces that need to be assembled. It requires in-depth knowledge on how and when these pieces fit together. By carefully teasing out the complex sequence of events that need to occur during neuronal development, researchers, such as those in Peng’s team, are laying a solid foundation to better understand diseases like ataxia telangiectasia and ultimately support disease treatment and prevention.