During her time as a postdoc at the University of Basel in Switzerland, Sarah Shahmoradian decided to study the abnormal aggregates of protein that develop inside nerve cells and contribute to Parkinson’s disease. The protein clumps develop over time in the brains of Parkinson’s patients, leading some scientists to think they wreak havoc on nerve cells, causing severe damage and hastening their death. A fresh look at the clumps, called Lewy bodies, with cutting-edge microscopy tools could reveal insights that might lead to new treatments for Parkinson’s, Shahmoradian recalls thinking. “The original goal was to really find out what the building blocks of Lewy bodies are, what they are made of, and what they actually look like.” 

The clumps were first identified in the early 1900s, appearing as abnormal material in nerve cells viewed under a microscope. Additional studies using antibodies that bound to...

“We were originally looking for fibrils,” Shahmoradian says, “but unexpectedly, we found an abundance of . . . mitochondria, other organelles, and lipid membranes [in the Lewy bodies].” The researchers also found evidence of lysosomes, organelles that facilitate cellular waste removal. They did see α-synuclein in the Lewy bodies, as well, but the cores of the structures weren’t composed of twisted and tangled fibrils as researchers had thought. Instead, the protein was intermingled with other cellular material.  

The study is one of many that raise questions about the prevailing idea that α-synuclein accumulation is the underlying cause of the neurodegeneration in Parkinson’s disease. Rather, α-synuclein buildup may be just one symptom of a more fundamental problem: the cells’ inability to break down excess lipids and proteins, including α-synuclein. Some Parkinson’s patients carry mutations in genes associated with lysosomal function, and studies in mice have revealed that natural aging leads to the build-up of lipids associated with Parkinson’s disease. These findings have led a small but growing set of scientists to propose that for a vast majority of Parkinson’s patients, the disease is fundamentally a cellular machinery problem, not a protein problem.

“In this new story, α-synuclein is actually a reaction to the root cause of Parkinson’s,” Ole Isacson, a neuro-scientist at Harvard Medical School, tells The Scientist.

Parkinson’s in the gut

In 1912, Fritz Heinrich Lewy, a doctor working in Berlin, studied the brains of patients who had died from Parkinson’s disease (then known as shaking palsy) and found odd clumps of proteins in their nerve cells. Several years later, Spanish neurologist Gonzalo Rodríguez Lafora, who had identified the protein inclusions in the brain of another patient who had died of shaking palsy, dubbed them Lewy bodies. 

Based on additional probes into diseased patients’ brains, neurologists found Lewy bodies to be particularly common in the substantia nigra, a brain region that sits in the center of the head directly behind the eyes. It’s where many of the neurons that produce dopamine, a neurotransmitter involved in movement and learning and in regulating mood, originate. These neurons send signals to another brain region called the striatum, forming a neural pathway that facilitates muscle motion; in Parkinson’s disease, it’s the dopamine neurons in the substantia nigra that are damaged or destroyed. People with Parkinson’s typically have trouble with balance and walking, and they often suffer from tremors in the hands or fingers and other involuntary movements. 

In this new story, α-synuclein is actually a reaction to the root cause of Parkinson’s.

 —Ole Isacson, Harvard Medical School

Laboratory investigations in the 1990s suggested that Lewy bodies were composed of α-synuclein, while early explorations of the genetics of Parkinson’s published around the same time revealed that patients with an inherited form of the disease often carried mutations in the SNCA gene, which encodes α-synuclein.  Together, the pathology and genetic findings suggested that α-synuclein might be the pathologic protein underlying Parkinson’s disease, pathologist Kelvin Luk of the Perelman School of Medicine at the University of Pennsylvania tells The Scientist.

In the early 2000s, Goethe University Frankfurt neuroanatomist Heiko Braak built on that work, observing that α-synuclein accumulation didn’t just occur in the brain. Postmortem analyses showed that it had accumulated in the nasal cavity, in nerves in the throat, and in the gut of deceased Parkinson’s patients. Braak’s postmortem observations also showed that aggregations of the protein appeared in the vagus nerve—a superhighway of nerve-fiber bundles running between the brain and various organs of the body, including the heart, lungs, and gut. He concluded that some type of pathogen causing the neuronal cell damage seen in Parkinson’s could invade through the nose or gut and then travel up to the brain via the vagus nerve.

Researchers then started to wonder if aggregates of α-synuclein might move through the body in a similar way—and studies have shown that it can. In 2014, Staffan Holmqvist, then at Lund University in Sweden, and colleagues showed that if they injected α-synuclein into the guts of rats, the protein could travel up the vagus nerve to their brains. And this June, Johns Hopkins University neuroscientist Ted Dawson and an international team of researchers showed that the fibrillar, pathological form of the protein can travel in a similar way in mice and lead to Parkinson’s-like symptoms in the rodents. “Not only do the mice have the motor features of Parkinson’s disease, they also have the nonmotor features,” Dawson told The Scientist at the time. “They’ve got cognitive dysfunction, anxiety, depression, problems with smell”—all symptoms seen in human patients with Parkinson’s.

These studies led researchers to propose that Parkinson’s might start in the gut years before the disease manifested as neurodegeneration in the brain. Despite the growing popularity of this hypothesis, however, new work is challenging the idea. For example, according to one study, there is no change in the risk of the disease among patients who have had their vagal nerves cut to stop the development of gastric ulcers. Moreover, in a recent study of more than 2,000 Parkinson’s patients, only 0.05 percent had mutations in the SNCA gene, leaving scientists questioning how α-synuclein accumulates in the other 99.95 percent of cases, and therefore if the protein is, in fact, at the root of Parkinson’s disease.

That result sent a signal to the community that we need to be looking at [the lysosome] critically to try and understand what the mechanism is . . . [that] makes dopaminergic neurons so dependent on normal lysosomal function.  

—Frances Platt, University of Oxford

Hints that something other than α-synuclein might be to blame started to circulate in the late 1990s and early 2000s. In 2004, for example, Enza Maria Valente, then at the Mendel Institute in Rome, and colleagues found that early-onset Parkinson’s disease appeared to be caused by mutations in the gene PINK1, which plays a role in mitochondrial function. (See “Malfunctioning Mitochondria” below.) In 2009, Ellen Sidransky, a neurogeneticist at the National Human Genome Research Institute, and colleagues reported results suggesting that Parkinson’s might stem more from a fundamental cellular problem than from the accumulation of a particular protein. In an analysis of a genetic panel taken from more than 5,600 Parkinson’s patients and more than 4,800 healthy individuals from around the world, the team found genes associated with Parkinson’s disease that encoded lysosomal components. For example, 15 percent of Ashkenazi Jewish patients with the disease and 3 percent of non–Ashkenazi Jewish patients had a mutation in a gene called GBA, which encodes a protein active in lysosomes that helps clear cellular waste. The faulty protein made by the mutated GBA gene prevents the breakdown of an intermediary compound in the metabolism of carbohydrate-containing lipids, or glycolipids. Other mutations in the same gene can cause the metabolic disorder known as Gaucher disease, which can lead to brain damage, among numerous other outcomes, strengthening the suspicion that lysosomes play a role in Parkinson’s.

Intrigued by the results, Baylor College of Medicine geneticist Joshua Shulman looked into the genomes of Parkinson’s patients for mutations in lysosomal genes other than GBA. In 2017, he and colleagues reported that more than 50 percent of Parkinson’s disease patients carry a putatively damaging mutation in one or more genes that are known to cause lysosomal storage diseases, inherited metabolic disorders caused by enzyme deficiencies that allow the buildup of toxic materials inside cells. That result “sent a signal to the community that we need to be looking at [the lysosome] critically to try and understand what the mechanism is . . . [that] makes dopaminergic neurons so dependent on normal lysosomal function,” Frances Platt, an expert in lysosomal storage diseases at the University of Oxford, tells The Scientist

As it turned out, Isacson was already at work on the question, and in 2015 his team found that the enzymatic activity of GBA decreased in mice and in human dopamine neurons (examined postmortem) with increasing age. This resulted in the accumulation of glycolipids that could disrupt neuronal function, suggesting that natural aging alone was enough to reduce GBA activity, leading to lipid buildup. That same year, Isacson’s group also showed that blocking the activity of the GBA enzyme—a proxy for lysosomal dysfunction—caused a dramatic accumulation of α-synuclein in neurons, spurring neuroinflammation, which is characteristic of Parkinson’s.

“The genetics, the biochemistry, and the cell biology tell us that the lysosome plays a major role in disease pathogenesis” of Parkinson’s, cell and molecular biologist Andres Klein of Universidad del Desarrollo in Santiago, Chile, tells The Scientist

Malfunctioning Mitochondria


While some researchers are studying lysosomal dysfunction as a potential cause of Parkinson’s disease, others have been probing the connections turned up by genetic studies, such as the link between mitochondrial dysfunction and α-synuclein accumulation. For example, immature human neurons carrying knockout mutations in the PINK1 gene, which encodes a protein involved in mitochondrial function and has been linked to Parkinson’s, died sooner than cells without the mutation.

Recently, researchers found that the PINK1 protein is vital to stabilizing another protein, MIC60, which is essential for mitochondria to generate energy. Young fruit flies that didn’t produce PINK1, and therefore didn’t have healthy mitochondria, didn’t crawl well and died relatively early in adulthood. But when researchers overexpressed the protein MIC60 in the brains of flies lacking PINK1, the animals’ neuronal mitochondria started generating more energy—enough to prevent dopamine-producing nerve cells from dying . The study suggests that mitochondrial problems might spark a cascade of cellular issues that cause Parkinson’s disease. 

Other new research indicates that Parkinson’s could stem from a combination of lysosomal and mitochondrial problems. Using dopaminergic neurons derived in culture from samples of Parkinson’s patients’ skin cells, Northwestern University Feinberg School of Medicine neurogeneticist Dimitri Krainc and colleagues found that reactive oxygen species in the cells damaged mitochondria and that oxidized dopamine began to build up. This caused a drop in GBA enzyme activity, lysosomal dysfunction, and eventually α-synuclein accumulation.

“Lipid regulation, lipid function, and lysosomal function are tightly regulated normally,” says the University of Oxford’s Frances Platt, who studies lysosomal storage diseases. “If you cause an imbalance . . . you end up causing collateral problems for other organelles, and ultimately you trigger cell death pathways” and neurodegeneration.

Imaging living cells, Krainc’s group has found that lysosomes and mitochondria come into direct contact in a cell, providing a mechanism by which damaged mitochondria might interact with and disrupt the function of lysosomal enzymes. The work, says Universidad del Desarrollo’s Andres Klein, suggests that problems with the mitochondria and lysosomes may create a problematic loop that lies at the heart of Parkinson’s disease.

Parkinson’s as a waste problem

In an August 2018 review published in Brain, Klein and neuroscientist Joseph Mazzulli of Northwestern’s Feinberg School of Medicine laid out all of the evidence for Parkinson’s disease as a lysosomal disorder. In animal models of the disease and in neurons cultured from induced pluripotent stem cells (iPSCs) of Parkinson’s patients, when researchers treat the lysosome to correct for the cell clearance problems, the toxic buildup of lipids and proteins, including α-synuclein, is halted, and memory improves in mice. There are now even a few clinical trials for Parkinson’s disease drugs that target faulty lysosome function instead of α-synuclein aggregation, Klein says. Considering all the evidence together, “we really had . . . the guts to [say] that Parkinson’s is a lysosomal disease.”

Failure to Clear

Many patients with Parkinson’s disease carry gene variants that lie at the root of problems with cellular waste-clearing processes, mediated by the lysosome. One of the proteins that must be cleared from cells is α-synuclein—the protein that scientists have long-fingered as a prime pathogenic suspect in Parkinson’s. When α-synuclein isn’t cleared from neurons, it can become misfolded and clump together in Lewy bodies that prevent these cells from functioning and ultimately cause them to die, leading to telltale symptoms of the disease. But α-synuclein is not the only material accumulating in the neuron when the lysosomes aren’t functioning properly; Lewy bodies are composed of a mix of cellular material.

Further evidence that Parkinson’s disease might be driven by problems with cellular waste-clearing processes comes from genes that are related to mitochondrial dysfunction. Certain gene variants related to Parkinson’s can cause the mitochondria to form reactive oxygen species and other compounds that can damage the lysosome, leading to problems with waste removal. 

Healthy Cells

Unneeded proteins, lipids, and other cellular materials are typically gathered into vacuoles, which fuse with lysosomes to clear the cells of the waste.


Diseased Cells

In the neurons of Parkinson’s patients, something appears to have gone wrong with the cellular waste-clearing process. Reactive oxygen species (ROS) released from mitochondria may play a role, damaging lysosomes. If the lysosomes don’t function properly, then cellular waste products are left in the cell to accumulate. 

© Lisa clark
See full infographic: WEB | PDF

Even as Klein and Mazzulli were collating the findings for their review, researchers were publishing more data to support their argument. Isacson and Platt reported in 2018, for example, that in healthy mice, aging alone causes an accumulation of glycolipids also involved in Parkinson’s disease. Later that same year, Isacson and another group of colleagues published data showing that aging causes α-synuclein and lipids to stick to each other and then to the membranes of dopamine-containing vesicles in neurons. These results reveal how natural aging changes lipids and lysosomes, accelerating neuronal degeneration—a direct challenge to the hypothesis that Parkinson’s is primarily a protein problem, as changes to the lipids and lysosomes would precede or provoke α-synuclein aggregation.  

Last December, Isacson and colleagues found more evidence to challenge the proteinopathy view of Parkinson’s. In the substantia nigra of deceased patients, levels of a glycoprotein called GPNMB were elevated compared with age-matched controls. Transgenic mice modeling Parkinson’s with excess α-synuclein did not show higher levels of GPNMB, but when wild-type mice were given lipid-based drugs to simulate lysosomal dysfunction, their levels of GPNMB skyrocketed, mirroring relative levels of the glycoprotein in the Parkinson’s patients’ brains. An accumulation of stray lipids in nerve cells might be enough to spur inflammation and cause neuronal damage and death, Isacson says. 

If Parkinson’s is in fact a lysosomal disorder, it raises the question of whether “some of the treatments that are being developed for lysosomal diseases may unexpectedly turn out to be useful in Parkinson’s,” Platt notes. Several clinical trials have begun or are being planned to test whether drugs already used to treat well-characterized lysosomal storage disorders might also work as Parkinson’s therapeutics. One sponsored by University College London is testing ambroxol, a drug that reduces mucus production in the respiratory tract, for its ability to increase activity of the lysosomal enzyme GBA and, as a result, reduce the buildup of excess lipids and proteins, such as α-synuclein. Another, sponsored by Sanofi Genzyme, is recruiting Parkinson’s patients with GBA mutations and treating them with GZ/SAR402671, a drug designed to lower glucosylceramide, a compound that accumulates as a result of lysosomal damage and can cause the aggregation of α-synuclein.

By and large, however, the field seems to be sticking with the idea of α-synuclein as the underlying pathological driver of Parkinson’s disease, Isacson says. Luk concedes the field’s focus on the protein is probably not going to shift any time soon, mainly because an overwhelming majority of Parkinson’s patients have Lewy bodies. “It’s very hard to find Parkinson’s cases that don’t have Lewy pathology,” Luk says, and notes most scientists still think α-synuclein is their major constituent. “It’s hard to ignore synuclein,” Dawson agrees. But he adds that more researchers are starting to integrate the data on mitochondrial and lysosomal dysfunction into their ideas on the disease. They are realizing “it’s all intertwined.” 

Ashley Yeager is an associate editor at The Scientist. Email her at ayeager@the-scientist.com.

Interested in reading more?

Magaizne Cover

Become a Member of

Receive full access to digital editions of The Scientist, as well as TS Digest, feature stories, more than 35 years of archives, and much more!
Already a member?