New Protein Aggregation Tool Opens Door to Better Understanding of Neurodegenerative Diseases

A common thread ties seemingly unlinked disorders like Alzheimer’s disease and type II diabetes together. This thread is known as protein aggregation and happens when proteins clump together. These complexes are a hallmark of many diseases, but have recently been linked to beneficial functions as well.

Scientists from Boston University (BU), MIT, and the Whitehead Institute for Biomedical Research, and others, say they have made a synthetic genetic tool named yTRAP (yeast transcriptional reporting of aggregating proteins) to quantitatively sense, measure, and manipulate protein aggregation in live cells. Their study (“A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance”), published in Cell, used yTRAP to research protein aggregates, including disease-relevant proteins, RNA-binding proteins, and prions.

“Protein aggregation is a hallmark of many diseases but also underlies a wide range of positive cellular functions. This phenomenon has been difficult to study because of a lack of quantitative and high-throughput cellular tools,” write the investigators.

“Here, we develop a synthetic genetic tool to sense and control protein aggregation. We apply the technology to yeast prions, developing sensors to track their aggregation states and employing prion fusions to encode synthetic memories in yeast cells. Utilizing high-throughput screens, we identify prion-curing mutants and engineer “anti-prion drives” that reverse the non-Mendelian inheritance pattern of prions and eliminate them from yeast populations. We extend our technology to yeast RNA-binding proteins (RBPs) by tracking their propensity to aggregate, searching for co-occurring aggregates, and uncovering a group of coalescing RBPs through screens enabled by our platform. Our work establishes a quantitative, high-throughput, and generalizable technology to study and control diverse protein aggregation processes in cells.”

Prions are best known for transmitting neurodegenerative diseases in mammals. However, some organisms also use them to carry out a number of beneficial functions that are just starting to be identified. Using the novel tool, Ahmad S. Khalil, Ph.D., an assistant professor in biomedical engineering at BU, and colleagues also identified genes that can cure cells of prions and enable high-throughput studies to learn what can influence protein aggregation and its consequences. Although developed and tested in yeast, yTRAP could allow scientists to test and develop treatments for currently incurable diseases like Alzheimer’s and potentially turn on new, beneficial functions in other types of cells, according to the researchers.

One part of yTRAP couples to the protein of interest and a second part produces a fluorescent signal to measure the amount of aggregation in a cell. Each piece can be customized to study different proteins or express different genes and signals, notes Dr. Khalil. For example, the team was able to measure how one prion influenced another by developing a dual sensor that produced either a red or green fluorescent signal, depending on how abundant each prion was.

In addition to tracking prion states, yTRAP can also be used to control those states. Because prions are heritable, once they are triggered in a cell, all of the cells in later generations will inherit the same prion state. “Prions are a biological equivalent of a toggle light switch—you don’t have to keep your finger on the switch to keep the light on,” says Dr. Khalil.

They used this light switch–like heritable property of prions to build a synthetic memory device. Heat activated the prion to aggregate in a batch of cells, and the hotter it got, the more aggregates formed. Then, 10 generations later, cells that were never exposed to heat maintained the same level of aggregation their predecessors did. Additionally, the scientists used yTRAP as part of a method to identify genes that could be used to essentially turn prions off, handing researchers the ability to toggle that light switch in the other direction.

Dr. Khalil and his team also demonstrated how the tool can be used to study other proteins, including RNA-binding proteins. Many of these proteins in yeast and humans have similarities to prions, and mutations of those similarities have been linked to neurodegenerative diseases like amyotrophic lateral sclerosis (ALS). With the help of the tool, they uncovered aggregation-prone RNA-binding proteins, monitored the consequences of their aggregation, and performed screens to see how the aggregation of one protein influences another.

“Protein aggregates can cause a cell to gain or lose a function,” says Dr. Khalil. “This could be beneficial or harmful. For example, they could allow a cell to survive stressful conditions or change its metabolic function to digest a different type of sugar. And the discovery of these beneficial functions has often been serendipitous.”

With yTRAP, Dr. Khalil hopes to change that. All of these functions that yTRAP provides will allow researchers to discover new protein aggregates, track their complicated behaviors, and look for factors and drugs that alter protein aggregation as potential treatments for currently incurable neurodegenerative diseases, or, on the flip side, figure out how to turn on a beneficial function of an aggregate, explains Dr. Khalil.