Using your loaf to fight brain disease

Experts analyse baker’s yeast to discover potential for combatting neurological conditions like Parkinson’s and even cancer

A humble ingredient of bread – baker’s yeast – has provided scientists with remarkable new insights into understanding basic processes likely involved in diseases such as Parkinson’s and cancer.

In a new study published in the prestigious journal PNAS (Proceedings of the National Academy of Science), the team from Germany, Leicester, and Portugal detail a new advance – describing for the first time a key feature in cellular development linked to the onset of these devastating diseases.

The research team is from the University Medical Center Goettingen, University of Leicester, and Instituto de Medicina Molecular, Lisbon, directed by long-time collaborators and senior authors Professor Tiago Outeiro and Dr Flaviano Giorgini.

Professor Outeiro, of the University Medical Center Goettingen, Goettingen and Instituto de Medicina Molecular, Lisbon, said: “This work shows how taking advantage of simple model organisms might help us speed up the discovery of more complex biological processes. Yeast cells are really excellent living test tubes, with a powerful toolbox that enabled us to learn about the underpinnings of complex human disorders.”

Dr Giorgini, of the world-renowned Department of Genetics, at the University of Leicester, added: “We are tremendously excited by our results. The family of proteins under investigation have always been a bit of a “black box”, and a true understanding of what these proteins do at a cellular level - and why they are important - has remained elusive. This work provides a step into this darkness.”

The current research takes advantage of the simplicity and genetic power of the baker’s yeast Saccharomyces cerevisiae to understand basic cellular processes underlying Parkinson’s disease. The team studied a family of proteins in yeast (Hsp31, Hsp32, Hsp33, and Hsp34) which are related to a human protein known as DJ-1. Mutations in the human DJ-1 protein cause early-onset inherited forms of Parkinson’s disease, and alterations in the human protein have been associated with more common forms of Parkinson’s disease as well. In addition, changes in DJ-1 function are also associated with certain forms of cancer.

Claire Bale, Research Communications Manager at Parkinson’s UK, commented: “This important research sheds new light on the root causes of Parkinson’s.

“Although mutations in the DJ-1 gene cause rare inherited forms of the condition, we believe that understanding the role of this crucial protein and how it helps keep nerve cells healthy could be important for developing treatments that can help all people with Parkinson’s. We look forward to hearing the results of future investigations in this emerging new area.”

Professor Outeiro continued: “We reasoned that, by studying the yeast cousins of the human protein we would gain important insight into the function these proteins play, and understand why they may cause disease.

Dr Giorgini added: “Though the human protein DJ-1 has been linked to Parkinson’s disease, its central cellular role is not well understood, and thus it is not clear why mutations in this protein cause this devastating disease. Our study sheds new light on what DJ-1 and related proteins are doing at a cellular level, and may thus ultimately have importance for better understanding Parkinson’s.”

The scientists discovered that the yeast versions of the human protein are important for maintenance of normal lifespan of the yeast cell and are involved in regulation of autophagy – a process which the cell employs to breakdown and recycle damaged cellular components. Lifespan and autophagy are central processes in the context of both Parkinson’s disease and cancer. This work is critical because it provides a precise cellular role for DJ-1 family proteins, which links to some of the molecular functions previously ascribed to these proteins. This work could ultimately provide new insight into the mechanisms that contribute to Parkinson’s and cancer.

Leonor Miller-Fleming, of the Instituto de Medicina Molecular, Lisbon and University of Leicester, said: “Our work is important because it suggests that human DJ-1 may function in a similar manner to the yeast version of this protein. We feel that similar studies should be performed with human DJ-1 in nerve cells, to clarify its function and to see if this contributes to the formation of Parkinson’s disease. Ultimately, the detailed understanding of how these proteins function may enable us to come up with novel strategies to treat Parkinson’s disease, cancer, and other related disorders.”

The collaborators believe the next steps in the research are to better understand the details of how the DJ-1 family of proteins regulates autophagy, and if this applies in human neurons, particularly dopaminergic neurons, which are the nerve cells most sensitive to loss in the Parkinson’s brain. Once the researchers build up on the findings they have now described, they will be in a better position to design novel strategies for therapeutic intervention.

Professor Outeiro explained: “This study highlights the importance of international collaborations and networks, in which different strengths are combined to yield novel insights into science. Importantly, this scientific collaboration is also based upon personal friendship between the two senior authors, which makes science ever more exciting and fun.”

Dr Giorgini added: “In addition, this work was primarily spearheaded by a single PhD student – Leonor Miller-Fleming – who drove the project forward with passion and creativity, showing the importance of promoting, supporting and funding doctoral research.”

Professor Outeiro said: “We were pioneers in the development of the first model of Parkinson’s disease in yeast cells. With this work, we explored the powerful toolbox of yeast cells to learn about DJ-1 proteins, also intimately linked to Parkinson’s disease. We are basically adding pieces to this complicated puzzle, and getting one step closer to understanding the origin of this disorder.”

(Image: © Wikipedia)

Yeast, human stem cells drive discovery of new Parkinson’s disease drug targets

Using a discovery platform whose components range from yeast cells to human stem cells, Whitehead Institute scientists have identified a novel Parkinson’s disease drug target and a compound capable of repairing neurons derived from Parkinson’s patients.

The platform—whose effectiveness is described in dual papers published online this week in the journal Science—could accelerate the discovery of drug candidates that address the underlying pathology of Parkinson’s and other neurodegenerative diseases. Today, no such drugs exist.

Parkinson’s disease (PD) and such neurodegenerative diseases as Huntington’s and Alzheimer’s are characterized by protein misfolding, resulting in toxic accumulations of proteins in the cells of the central nervous system. Cellular buildup of the protein alpha-synuclein, for example, has long been associated with PD, making this protein a seemingly appropriate target for therapeutic intervention.

In the search for compounds that might alter a protein’s behavior or function—such as that of alpha-synuclein—drug companies often rely on so-called target-based screens that test the effect large numbers of compounds have on the protein in question in rapid, automated fashion. Though efficient, such an approach is limited by the fact that it essentially occurs in a test tube. Seemingly promising compounds emerging from a target-based screen may act quite differently when they’re moved from the in vitro environment into a living setting.

To overcome this limitation, the lab of Whitehead Member Susan Lindquist has turned to phenotypic screens in which candidate compounds are studied within a living system. In Lindquist’s lab, yeast cells—which share the core cell biology of human cells —serve as living test tubes in which to study the problem of protein misfolding and to identify possible solutions. Yeast cells genetically modified to overproduce alpha-synuclein serve as robust models for the toxicity of this protein that underlies PD.

“Phenotypic screens are probably underutilized for identifying drug targets and potential compounds,” says Daniel Tardiff, a scientist in the Lindquist lab and lead author of one of the Science papers. “Here, we let the yeast tell us what is a good target. We let a living cell tell us what’s critical for reversing alpha-synuclein toxicity.”

In a screen of nearly 200,000 compounds, Tardiff and collaborators identified one chemical entity that not only reversed alpha-synuclein toxicity in yeast cells, but also partially rescued neurons in the model nematode C. elegans and in rat neurons. Significantly, cellular pathologies including impaired cellular trafficking and an increase in oxidative stress, were reduced by treatment with the identified compound. Enabled by the chemistry provided by Nate Jui in the Buchwald lab at MIT, Tardiff found that the compound was working by restoring functions mediated by a cellular protein critical for trafficking that was previously thought to be “undruggable.”

But would these findings apply in human cells? To answer that question, husband-and-wife team Chee-Yeun Chung and Vikram Khurana led the second study published in Science to examine neurons derived from induced pluripotent stem (iPS) cells generated from Parkinson’s patients. The cells and differentiated neurons (of a type damaged by the disease) were derived from patients that carried alpha-synuclein mutations and develop aggressive forms of the disease. To ensure that any pathology developed in the cultured neurons could be attributed solely to the genetic defect, the researchers also derived control neurons from iPS cells in which the mutation had been corrected.

Chung and Khurana used the wealth of data from the yeast alpha-synuclein toxicity model to clue them in on key cellular processes that became perturbed as patient neurons aged in the dish. Strikingly, exposure to the compound identified via yeast screens in Tardiff’s study reversed the damage in these neurons.

“It was remarkable that the compound rescued yeast cells and patient neurons in similar ways and through the same target—a target we would not have identified without yeast genetics to guide us,” says Khurana, a postdoctoral scientist in the Lindquist lab and a neurologist at Massachusetts General Hospital who recruited patients for participation in this research. Khurana believes that the abnormalities discovered occur in the early stages of disease. If so, successful manipulation of the targets identified here might help slow or even prevent disease progression.

For the researchers involved, these findings are a bit of surprise. Because neurodegenerative disorders like PD are largely diseases of aging, modeling them in a culture dish using neurons grown from iPS cells has been thought to be exceedingly difficult, if not impossible.

“Many, ourselves included, were skeptical that we could find any important pathologies for a neurodegenerative disorder by reprogramming patient cells,” says Chung, a Senior Research Scientist in the Lindquist lab. “Critically, we also validated these pathologies in post-mortem brains, so we’re quite confident these are relevant for the disease.”

Next steps for these scientists include chemically optimizing the compound identified and testing it in animal models. Moreover, they are convinced that this yeast-human stem cell discovery platform could be applied to other neurodegenerative diseases for which yeast models have been developed.

“Using yeast genetics to identify a compound and its mechanism of action against the fundamental pathology of a disease illustrates the power of the system we’ve built,” says Lindquist, who is also professor of biology at MIT and a Howard Hughes Medical Institute investigator. “It’s critical that we continue to leverage this power because as we reduce the rate at which people are dying from cancer and heart disease, the burden of these dreaded neurodegenerative diseases is going to rise. It’s inevitable.”

The green spots above are clumps of protein inside yeast cells that are deficient in both zinc and a protein that prevents clumping. Research by Colin MacDiarmid and David Eide is exploring how a shortage of zinc can contribute to diseases. Photo: Colin MacDiarmid and David Eide/Journal of Biological Chemistry

Zinc discovery may shed light on Parkinson’s, Alzheimer’s

Scientists at UW-Madison have made a discovery that, if replicated in humans, suggests a shortage of zinc may contribute to diseases like Alzheimer’s and Parkinson’s, which have been linked to defective proteins clumping together in the brain.

With proteins, shape is everything. The correct shape allows some proteins to ferry atoms or molecules about a cell, others to provide essential cellular scaffolding or identify invading bacteria for attack. When proteins lose their shape due to high temperature or chemical damage, they stop working and can clump together — a hallmark of Parkinson’s and Alzheimer’s.

The UW researchers have discovered another stress that decreases protein stability and causes clumping: a shortage of zinc, an essential metal nutrient.

Zinc ions play a key role in creating and holding proteins in the correct shape. In a study just published in the online Journal of Biological Chemistry, Colin MacDiarmid and David Eide show that the gene Tsa1 creates “protein chaperones” that prevent clumping of proteins in cells with a zinc shortage. By holding proteins in solution, Tsa1 prevents damage that can otherwise lead to cell death.

For simplicity, the researchers studied the system in yeast — a single-celled fungus. Yeast can adapt to both shortages and excesses of zinc, says MacDiarmid, an associate scientist. “Zinc is an essential nutrient but if there’s too much, it’s toxic. The issue for the cell is to find enough zinc to grow and support all its functions, while at the same time not accumulating so much that it kills the cell.”

Cells that are low in zinc also produce proteins that counter the resulting stress, including one called Tsa1.

The researchers already knew that Tsa1 could reduce the level of harmful oxidants in cells that are short of zinc. Tsa1, MacDiarmid says, “is really a two-part protein. It can get rid of dangerous reactive oxygen species that damage proteins, but it also has this totally distinct chaperone function that protects proteins from aggregating. We found that the chaperone function was the more important of the two.”

"In yeast, if a cell is deficient in zinc, the proteins can mis-fold, and Tsa1 is needed to keep the proteins intact so they can function," says Eide, a professor of nutritional science. "If you don’t have zinc, and you don’t have Tsa1, the proteins will glom together into big aggregations that are either toxic by themselves, or toxic because the proteins are not doing what they are supposed to do. Either way, you end up killing the cell."

While the medical implications remain to be explored, there are clear similarities between yeast and human cells. “Zinc is needed by all cells, all organisms, it’s not just for steel roofs, nails and trashcans,” Eide says. “The global extent of zinc deficiency is debated, but diets that are high in whole grains and low in meat could lead to deficiency.”

If low zinc supply has the same effect on human cells as on yeast, zinc deficiency might contribute to human diseases that are associated with a build-up of “junked” proteins, such as Parkinson’s and Alzheimer’s. Eide says a similar protective system to Tsa1 also exists in animals, and the research group plans to move ahead by studying that system in human cell culture.

Yeast Protein Breaks up Amyloid Fibrils and Disordered Protein Clumps In Different Ways

Several fatal brain disorders, including Parkinson’s disease, are connected by the misfolding of specific proteins into disordered clumps and stable, insoluble fibrils called amyloid. Amyloid fibrils are hard to break up due to their stable, ordered structure. For example, a-synuclein forms amyloid fibrils that accumulate in Lewy Bodies in Parkinson’s disease. By contrast, protein clumps that accumulate in response to environmental stress, such as heat shock, possess a less stable, disordered architecture.

Hsp104, an enzyme from yeast, breaks up both amyloid fibrils and disordered clumps. In the most recent issue of Cell, James Shorter, PhD, assistant professor of Biochemistry and Biophysics, and colleagues from the Perelman School of Medicine, University of Pennsylvania, show that Hsp104 switches mechanism to break up amyloid versus disordered clumps. For stable amyloid-type structures, Hsp104 needs all six of its subunits, which together make a hexamer, to pull the clumps apart. By contrast, for the more amorphous, non-amyloid clumps, Hsp104 required only one of its six subunits.

Yeast experiment offers fresh insights on the nature of natural selection

An experiment involving yeast has revealed a method that allows organizations to avoid the “tragedy of the commons,” the situation in which individuals take advantage of shared resources — such as common grazing land for animals — without paying for their use or maintenance.

By performing the experiment on small organisms, researchers have shown a way to avert a prediction of evolution theory: that natural selection necessarily favors “cheaters” — individual organisms determined to game the system — over “cooperators” who obey the rules.

The experiment, reported in Proceedings of the National Academy of Sciences, reveals a way in which evolutionary adaptation via mutations can benefit cooperators over cheaters.

"It gives a larger role to adaptation," said Adam Waite, a graduate student in molecular and cellular biology at the University of Washington, who performed the research with his supervisor, Wenying Shou, at the Fred Hutchinson Cancer Research Center in Seattle. "While natural selection should help cheaters, it can also help cooperators defeat cheaters."