Curiosity, connection and C. elegans

The long path from curiosity to cure in disease research often branches in many unpredictable directions.

The path that led molecular biologist Nicolas Lehrbach, PhD, to publication in PLOS Biology of a genetic study that sheds light on an extremely rare genetic disorder — the first for his lab at Fred Hutch Cancer Center — took an unexpected turn about a decade ago.

Lehrbach was a postdoctoral researcher in Boston studying how cells in a tiny worm dispose of damaged proteins when he found an unexpected connection to an extremely rare genetic disorder in humans called NGLY1 deficiency.

The disorder emerges in early childhood and causes a bewildering range of problems including developmental delays in walking and talking and life-threatening impairment of liver function.

His discovery caught the attention of Grace Science Foundation, which gave him funding to pursue the connection and included him in a community of patients’ families and fellow scientists recruited to better understand and eventually cure the disease.

Lehrbach’s study brings his work with the foundation to fruition, laying the groundwork for potential dietary and drug therapies to treat the disorder.

Taking out the trash

The path for Lehrbach began when he was a postdoctoral researcher working with Gary Ruvkun, PhD, at Massachusetts General Hospital from 2013 to 2021, studying the genetics of a microscopic worm called C. elegans that shares much of its fundamental biology with humans.

He was curious about the genes that regulate how cells destroy damaged and malformed proteins, an essential function for survival. He focused on a complex assemblage of molecular machinery called a proteasome, which basically acts like the cell’s garbage disposal.

A proteasome resembles a barrel with a lid on one end covering a tiny funnel. The lid opens, and malformed or damaged proteins unravel into single long noodles that get sucked into the funnel and chopped inside the barrel into pieces that can be recycled to form new proteins.

Cells contain tens of thousands of proteasomes that take out the trash. If they fall behind, as they often do in aging, the trash builds up, which is associated with neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases.

Lehrbach wanted to know which genes regulate how many proteasomes get made in the cell.

“I was asking a basic science question,” Lehrbach said. “If it’s important to have the right number of proteasomes per cell, what is the genetic system that regulates that?”

He discovered that a key gene that indirectly affects whether the cell makes enough proteasomes is the worm’s version of NGLY1.

And that’s when Lehrbach crossed paths with a girl in California named Grace, who was born in 2009 with defective copies of the NGLY1 gene inherited from both of her parents — an extraordinarily rare occurrence that changed the life of their family.

Investing in basic science

In 2013, the year that Lehrbach began his postdoc in Boston, Grace Wilsey became one of the first six known patients in the world diagnosed with NGLY1 deficiency.

The next year, Grace’s parents — Matt Wilsey, an angel investor in Silicon Valley startups and Kristen Wilsey, a marriage and family therapist — started the Grace Science Foundation to fund research into the disorder, which was too rare to attract investment from drug companies.

As of early this year, 130 patients are confirmed to have NGLY1 deficiency, according to the foundation.

“It was very farsighted of this family,” Lehrbach said. “They connected with good scientists and got good advice. They have funded research that has been very basic science-oriented. They appreciated that the beginnings of these therapeutic discoveries actually come from basic science.”

Lehrbach’s discovery that the NGLY1 gene also plays an important role in the production of proteasomes landed him on the foundation’s radar.

When neuroscientist Kevin J. Lee, PhD, became Grace Science Foundation’s chief science officer in 2015, only a few patients had been identified and researchers were just beginning to characterize the disease.

“We knew the gene responsible, NGLY1, and we knew that it produced an enzyme found in all cells of the body that is responsible for removing the sugar side chains from proteins as part of a process of cellular recycling,” Lee said.

What they didn’t know was how the loss of this enzyme could cause such a wide range of symptoms. 

Carolyn Bertozzi, PhD, an expert in glycobiology and a Nobel laureate at Stanford University, had a hunch that the NGLY1 enzyme might serve another function beyond waste removal in the cell, which led her to consider whether NGLY1 could activate a protein that regulates the level of proteasomes.

Lee knew the same protein was being studied in research about aging, which led him to Ruvkun in Boston, who told him about Lehrbach’s discovery of the worm version of NGLY1.

“It immediately confirmed Carolyn Bertozzi's hunch and it gave us our first real insights into why NGLY1 is essential,” Lee said. “It plays a key function in regulation and fine tuning of the cell's capacity to degrade and recycle proteins and handle changes in metabolism and cellular stress.”

Since connecting with the Grace Science Foundation, Lehrbach has met at annual meetings with patients’ families who are eager to hear about his progress.

“We’ve met lots of families. It’s very motivating for the work,” Lehrbach said. “These people really are very excited about what we’re doing, even though we’re doing things in worms.”

Their experiences with NGLY1 deficiency differ greatly from child to child, raising questions about how the loss of a single gene could cause such a wide range of problems.

“There are children who never learn to walk and talk,” Lehrbach said. “There are children who do learn to walk and talk and who go to school with some assistance.”

The foundation has also recruited scientists in other fields who compare notes in monthly virtual meetings.

“There are fly geneticists and mouse geneticists and cell biologists,” Lehrbach said. “It’s also a fantastic meeting, scientifically — all these brilliant people tackling the problem from different angles.”

From Boston to Seattle

In 2021, Lehrbach joined the Fred Hutch Basic Sciences Division, where he carried on the research he began as a postdoc while also exploring more broadly how proteasome dysfunction contributes to aging, cancer and neurodegenerative diseases.

Lehrbach figured that many of the symptoms of NGLY1 deficiency result from cells failing to make enough proteasomes, but it wasn’t obvious where to target a drug when NGLY1 is missing.

He and Katherine Yanagi, PhD, a postdoctoral researcher in his new lab at Fred Hutch, discovered that when the worm version of that gene is deleted, the performance of its proteasomes is somehow connected to the availability of nutrients called nucleotides, which provide the basic building blocks of DNA.

Humans make their own nucleotides and extract them from many food sources including meat, mushrooms and legumes. Lehrbach’s worms get them from eating bacteria.

Worms with healthy proteasome production do well regardless of how many nucleotides they get fed, but worms without the NGLY1 equivalent gene do better when they eat fewer nucleotides.

“The reason for that, we do not know,” Lehrbach said.

It will take more research to explain why in these cases, less is more.

 “It should be good to have nucleotides there,” Lehrbach said. “There’s no cellular function without them.”

Dietary differences might help explain why NGLY1 deficiency varies so much in severity from child to child.

“It certainly tells us that it is complicated,” he said. “If we understood why one child can be relatively so healthy compared to another child who has the same disorder, then we might learn something about how we should help.”

Lehrbach’s study doesn’t provide an easy answer like “eat fewer mushrooms,” but it sheds light on where drugs or dietary changes could make a difference.

“We’ve laid out great places to look,” Lehrbach said.

Curiosity will also drive the Lehrbach Lab in new directions.

The next three papers in the pipeline explore other dimensions of the proteasome.

“I now have 20 better hypotheses about experiments we should do to test new ideas to help NGLY1 deficiency patients," Lehrbach said. 

This work is supported by Grace Science Foundation and grants from the National Institutes of Health.