Q&A with Alyssa Walker: Studying neurodegenerative diseases in C. elegans

The author of the article “Colonization of the Caenorhabditis elegans gut with human enteric bacterial pathogens leads to proteostasis disruption that is rescued by butyrate”, Alyssa Walker got her bachelor’s degree at The University of Florida where she majored in animal biology. She has extensive research as a veterinary technician on small animals and dairy farms. Currently, she is a graduate student working with Dr. Daniel Czyz’s lab at the Department of Microbiology and Cell Science, University of Florida. Her research includes proteotoxic host-pathogen interactions that can lead to protein conformational neurodegenerative diseases such as Alzheimer’s disease Huntington’s, Parkinson’s, amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease.

Where did the idea of your project come from?

Dr. Czyz worked in the lab that coined the term proteostasis. They used C. elegans as their animal model and looked at stressors and how that affected protein aggregation. There were research linking bacteria to protein conformational neurodegenerative diseases but those correlations had been seen on an organismal level only. What was happening on a mechanistic level was then a knowledge gap which Dr. Czyz aimed to find out in his lab using C. elegans.

Why did you decide to have C. elegans as a model organism and not e.g. cockroaches (don’t they have the most similar gut microbiome to humans)?

C. elegans has a relatively short life span so you can start the experiments with them within a couple of days of their life. They also have a quick regeneration time, they start laying eggs two days post-birth, depending on the temperature that they are kept at. These nematodes are transparent so you can see fluorescently tagged reporters through them to quantify protein aggregates. C. elegans is widely implicated as a good model for enteric, pathogen-related illnesses because the natural diet of these worms is bacteria, and their intestines are easily colonized by those bacteria. 

The article mentions that when comparing the worms to humans some complexities were removed. Can you give us more details about those complexities?

1. The worms do not have inflammasome and inflammatory responses. Even though neurodegenerative diseases are widely associated with inflammation, C. elegans model will help understand if there is another mechanism (independent of inflammation) at work. 2. Another eliminated complexity was the number of cells. C. elegans has 959 somatic nuclei. 3. The complexity of the human microbiome does hinder our ability to understand those interactions. And so, we colonized the intestine of C. elegans with one single bacterium at a time and looked at the effect of a single bacterial strain on protein aggregation and the host.

Does C. elegans have any kind of immune response? 

C. elegans has what is known as surveillance immunity- they can sense DAMPs via G-protein coupled receptors and can remove the foreign material via endocytosis by scavenger cells called coelomocytes. They do not produce any cytokines or even their homologs.

What are the diseases you are looking into and how are they related to aggregates and polyQs?

PolyQs refer to the polyglutamine tracts where the number of glutamines determines the severity of a disease. When these tracts become abnormally long in humans, like in Huntington’s disease, they come closer and aggregate. A link-dependent and age-dependent aggregation have been observed in the worms, like that of Huntington’s disease. In our worm model, we use polyQ as a sensor of the protein folding environment in the host caused by bacteria. We are trying to apply that to other protein-folding diseases that are not necessarily polyQ induced, like Alzheimer’s disease, Parkinson’s disease, and Lou Gehrig’s disease.

How long should the human gut be infiltrated with pathogenic bacteria for it to influence polyQ aggregation?

For protein conformation diseases in general my wild guess would be- long enough to cause enteric infection or colonize the intestine. Additionally, a nerve called the vagus nerve (called the Vegas highway in neurodegenerative disease) was shown to transport bacteria and metabolites from the gut to the brain. That connection can cause protein confirmational disease in mice because aggregates were found to migrate from the gut to the brain via the Vagus nerve. The brain is the site of protein aggregates or plaques in Alzheimer’s disease. So, the bacteria need to be there long enough for the bacterial products to reach that “biggest highway”.

In your research, you reported when looking at the gonads that only the F1 generation inherited the aggregation and not F2. Do you have a hypothesis on why is that?

Proteostasis may be disrupted in the gonad and that extends to the progeny. Also, the bacterial metabolites may be making their way into the gonad if barriers are breached by the infection. We did speculate, that transmission of aggregate prone proteins from bacteria between tissues might underlie how bacterial colonization of parental intestines affects protein aggregation in the progeny. We do plan to follow up with that because those are my favorite results.

How do you think butyrate inhibited aggregation?

Our RNAi results and published data from other models show that the benefits of butyrate are depended on SKN-1 and DAF16 transcription factors, suggesting that butyrate might inhibit bacteria-induced aggregation by activating protective stress responses like oxidative stress response. It has been shown in our article that oxidative stress does contribute to polyQ aggregation. Bacteria are known to trigger oxidative stress, but whether butyrate affects specific bacterial signals that contribute to protein conformational diseases is still under investigation. Our results do suggest that whatever the mechanism is, there’s therapeutic potential there.

Do bacteria in our gut microbiome produce butyrate? Can that production be modified based on different nutrient intake? 

Bacteria like Firmicutes (species like bacillus, lactobacillus, enterococcus, clostridium) produce butyrate. As far as the nutrient intake, the ketogenic diet induces fermentation processes (end products of fermentation in the colon are short-chain, fatty acids, such as butyrate) and was shown to increase the concentration of butyrate in the gut, but there has been no link connecting that to neurodegenerative diseases. 

Could there be a higher possibility for people with inflammatory bowel disease (IBD) to develop a neurodegenerative disease associated with protein aggregates? 

IBD is hallmarked by the leaky gut syndrome where the intestinal permeability is breached, and bacteria and their metabolites can very easily get into the bloodstream which would reduce the time bacteria need to be present in the host to affect protein conformation leading to disease. 

What is the next step of your project?

Our article is the first direct link connecting bacterial protein aggregates to host protein aggregation, so there is a lot to follow up on. Currently, we are screening around 300 islets from the human microbiome project; we will see if we can connect the aggregates from those strains to C. elegans. We are also performing in vitro studies on neuronal cells and cells with inflammatory responses. 

Listen to the full interview to learn more:

Source: Walker AC, Bhargava R, Vaziriyan-Sani AS, Pourciau C, Donahue ET, Dove AS, Gebhardt MJ, Ellward GL, Romeo T, Czyż DM. Colonization of the Caenorhabditis elegans gut with human enteric bacterial pathogens leads to proteostasis disruption that is rescued by butyrate. PLoS Pathog. 2021 May 6;17(5):e1009510. doi: 10.1371/journal.ppat.1009510.

Check out Antibuddies’ blog post “Q&A with Alyssa Walker: Studying neurodegenerative diseases in C. elegans”.