How Proteomics Could Solve Puzzling Neuromuscular Diagnoses

For people living with rare diseases, finding a diagnosis can sometimes feel like solving a puzzle with missing pieces. Over the past two decades, advances in genetic testing have transformed that puzzle for hundreds of people living with inherited conditions. Genomics — the study of our genetic code — has reduced uncertainty and opened doors to clinical trials, proactive care, and emerging gene therapies.

But genes don’t always tell the whole story. Some people with symptoms of neuromuscular conditions, like amyotrophic lateral sclerosis (ALS), have no known disease-causing genetic changes. Others may have variants of unknown significance — genetic variants whose meaning is still unclear. Researchers are now looking to another promising field that could fill these gaps: proteomics.

Proteomics is the study of proteins, the molecules that carry out nearly all the body’s work. If genes are like blueprints, proteins are the builders that put those plans into action.

Because proteins change as cells become healthy or diseased, they can signal what is happening inside the body. Scientists hope these protein signals, called biomarkers, could make it easier to diagnose diseases earlier, distinguish between conditions with similar symptoms, and even predict how a disease may progress or respond to treatment.

Just as genomics revolutionized genetic testing, proteomics has the potential to usher in a new generation of diagnostic tools — bringing researchers one step closer to faster, more accurate answers for people living with difficult-to-diagnose diseases.

Changing the ALS journey

Today’s ALS diagnostic landscape is imprecise and time-consuming. No objective, reliable method exists for making an ALS diagnosis, and the initial symptoms, which include cramping, twitching, and muscle weakness, among others, can often mimic other diseases.

Brian Lin, PhD

“Usually, people come in to their primary care physician already experiencing certain symptoms,” says Brian Lin, PhD, Research Portfolio Director at MDA. “But primary care physicians don’t necessarily know the signs of ALS, or it’s very similar to other neuromuscular or neurological diseases.”

Depending on how quickly a referral is made, months can pass before a patient sees an ALS specialist. From there, a battery of tests follows — clinical exams, respiratory testing, electromyography (EMG) tests — that track neurological deficits and weakness over time. But even then, a diagnosis can be elusive.

“Only about 10% of cases are familial or linked to the most common ALS gene mutations,” Dr. Lin says. And, currently, there are no widely accepted blood-based biomarkers specific to ALS. “That’s what makes diagnosing ALS so difficult, because outside of some of those genetic familial markers, there isn’t necessarily a way to say definitively that it’s ALS.”

This makes a timely diagnosis challenging; by the time ALS is formally diagnosed, significant time has elapsed. “That’s partly why so many ALS clinical trials fail. People have progressed too far with their disease to respond to treatments,” Dr. Lin says.

But now, thanks to advances in proteomics, this diagnostic journey may be changing.

A research team led by Bryan Traynor, MD, PhD, Senior Investigator in the Laboratory of Neurogenetics at the National Institutes of Health (NIH), has identified a set of plasma proteins in blood that may signal ALS up to 10 years before symptoms appear. If confirmed by future clinical studies, a test for these proteins could someday allow doctors to begin ALS treatment before a significant number of motor neurons have died, potentially leading to better long-term outcomes.

A groundbreaking discovery in proteomics

After a 2004 MDA Development Grant helped Dr. Traynor launch his career in the neuromuscular field, he made significant discoveries about the genetic causes of familial ALS. Then, in 2019, a company called Olink launched a new technology for advanced protein analysis.

Bryan Traynor, MD, PhD

Similar to next-generation gene sequencing, Olink technology is innovative because it allows scientists to rapidly analyze many proteins at once.

“We’d always wanted to do biomarker discovery,” Dr. Traynor says. Olink finally made proteomics study feasible for his lab, allowing his team to detect proteins using the same tools they used to analyze genetic data.

In 2024, Dr. Traynor and his team conducted a study using about 200 blood samples from ALS patients and about 400 from people who were healthy or had other neurological diseases. The team used Olink to analyze almost 3,000 different proteins in the samples.

Dr. Traynor’s team identified 33 proteins that existed in the ALS blood samples but not in the other samples. That was notable enough, but what the pilot study showed — results later published in the journal Nature Medicine — was something even more remarkable.

Using machine learning to assist with analyzing and identifying patterns in the data, Dr. Traynor’s team narrowed the list to 17 proteins that could identify ALS with 98.3% accuracy.

To further test his team’s discovery, Dr. Traynor turned to the UK Biobank, a massive public database of blood samples taken from volunteers in the United Kingdom. Looking at the blood of 109 people who had developed ALS years after their blood sample was taken, Dr. Traynor’s team found the same 17-protein signature, meaning that, years before they were diagnosed, warning signs of the disease were already detectable in their blood.

“We’ve always thought of ALS as a disease that only starts inside the body 12 to 18 months before symptoms start,” Dr. Traynor says. “But our plasma protein panel was showing that this could be starting at least 10 years beforehand. That was a game changer.”

Another surprise to Dr. Traynor was that the protein signature was primarily driven by muscle, not motor neurons, as he had originally expected. “It was muscle degeneration and regeneration that was the pattern we were picking up, with a little bit of energy metabolism on top of it,” he says. “What we think is happening is there’s a mechanism that kicks in where the muscles try to compensate for the loss of those motor neurons. But then ultimately, when that compensation mechanism dwindles away, that’s when you get the symptoms.”

The result of this discovery is a test he calls the ALS Plasma Proteomics Panel — plasma proteomics being the field that analyzes proteins in blood plasma, the liquid part of blood left after blood cells are removed.

The implications are profound: Having biomarkers that are reliable across all types of ALS — both familial (inherited through a gene mutation) and sporadic (no known family history) — could fundamentally change how the disease is diagnosed and ultimately treated.

“Having a molecular signature that can possibly identify ALS years earlier is pretty significant because, as we know with neuromuscular diseases, if you can get treatments into patients earlier, it leads to significantly better outcomes,” Dr. Lin says. In other words, if more motor neurons are available to target, more muscle function could be preserved, or the rate of loss slowed.

A dose of reality

Despite all the optimism surrounding the test, it still has a way to go before it can become a standard diagnostic tool.

There are several reasons:

1. Cost. The ALS Plasma Proteomics Panel measures 3,000 proteins and costs about $1,000 per blood sample. To bring the cost down, Dr. Traynor’s team is developing a smaller, faster version of the test that measures only the 17 targeted proteins.
2. Time. It will take a few years to validate the test’s accuracy across more groups of people and determine how it can best be utilized in diagnostics and clinical trials.
3. Infrastructure. Unlike with a newly discovered disease-causing gene — where gene testing companies are prepared to quickly build and sell a test — no such pipeline exists yet for protein-based testing.

“We’re really at a very beginning, rudimentary stage when it comes to proteomics,” Dr. Traynor says. In fact, he explains, the 17 proteins currently in the ALS panel represent a “candidate panel,” requiring further analysis and refinement. “I am sure that as plasma proteomics advances — and already we’ve gone from testing 3,000 proteins to 5,000 — other proteins will emerge that are even more helpful in diagnosing ALS,” he says.

Proteomics benefits beyond ALS

Innovations in the proteomics field hold promise for many diseases.

“Not to sound too grandiose, but I think all neurological diseases could be impacted,” Dr. Traynor says.

Dr. Lin is equally hopeful. Because the proteins in the ALS panel reflect broad biological processes — including muscle regeneration and energy metabolism — similar proteins may appear in other diseases.

“Having similar biological processes makes it likely they’re also involved in other motor neuron diseases, like spinal muscular atrophy or spinal bulbar muscular atrophy, and they could potentially be useful early indicators in primary muscle wasting diseases, such as muscular dystrophies and inflammatory myopathies,” he says.

Looking to the future

Dr. Traynor looks at proteomics the way genomics was viewed 10 to 15 years ago — on the cusp of becoming mainstream. To illustrate the potential that proteomics holds, Dr. Traynor quotes his wife, fellow NIH researcher Sonja Scholz, MD, PhD: “Genetics shows us the causes of disease. Proteomics shows us biology in action.”

Even though the field is still in its relative infancy, proteomics is already promising to change our understanding of ALS and what may be possible in diagnosing and treating it. Other hard-to-diagnose diseases are sure to follow.

“The potential here is huge,” Dr. Traynor says. “I think that 10 years from now, when you and I are going to our physicians for our annual checkup, just like you get your lipids tested to look for cardiovascular disease risk factors, they’ll also be taking a sample of your plasma and measuring your proteomics across the gamut of neurological diseases. And they will have worked out what plasma proteins actually mean for which diseases.”

Proteomics may be the missing piece to the diagnostic puzzle that we’ve been looking for all along.

Chris Anselmo is an author who lives in Connecticut with limb-girdle muscular dystrophy type 2B (LGMD2B).