Snapshot: What is RAN translation?

In many diseases caused by repeat expansion mutations in the DNA, harmful proteins containing repetitive stretches are found to build up in the brain. The repeat expansion mutation, when translated into a protein, results in an abnormally expanded repeat tract that can affect the function of the protein and have harmful consequences for the cells. Following a study published in 2011, we know that repeat expansion mutations can make additional harmful repeat-containing proteins by a process called Repeat Associated Non-AUG translation or RAN translation.

How are proteins made?

To get from DNA to protein, there are two main steps. The first step involves the conversion of a gene in the DNA into an instructional file called messenger RNA (mRNA). The second step is translation, this is where the cellular machinery responsible for making proteins uses mRNA as a template to make the protein encoded by the gene.

During translation mRNA is “read” in sets of three bases. Each set of three bases is called a codon and each codon codes for one amino acid. There is a specific codon that signals where to start making the protein, this codon is AUG. From the point where the cellular machinery “reads” the start codon, the mRNA is “read” one codon at a time and the matching amino acid is added onto the growing protein.

What happens when there is a repeat expansion mutation?

As the name suggests, Repeat Associated Non-AUG (RAN) translation is a protein translation mechanism that happens without a start codon. RAN translation occurs when the mRNA contains a repeat expansion that causes the mRNA to fold into RAN-promoting secondary structures. Because RAN translation starts without an AUG start codon, the mRNA can be “read” in different ways.

Let’s consider a CAG repeat expansion to illustrate this process. In the CAG “reading frame” a polyglutamine containing protein would be made because the codon CAG leads to incorporation of the amino acid glutamine. But a CAG repeat expansion could also be “read” as an AGC or a GCA repeat expansion if you don’t know where in the sequence to start “reading”. When “read” as AGC, the cellular machinery would incorporate the amino acid serine, making a polyserine repeat protein. In the GCA frame a polyalanine repeat protein would be made. This has been shown to happen in Huntington’s disease (HD). In HD, RAN-translated polyserine and polyalanine proteins accumulate in HD patients’ brains, along with the AUG-initiated mutant huntingtin protein containing a polyglutamine expansion.

Diagram show how different DNA sequences can be "read" and translated as different proteins
Overview of repeat proteins that can be produced by RAN-translation from a CAG expansion transcript. Designed by Mónica Bañez-Coronel.

To complicate matters more, RAN translation can happen from different repeat expansions, including those in regions of the DNA that aren’t normally made into proteins at all. Through the process of RAN translation, repeat expansion mutations in the DNA can give rise to multiple different proteins that aren’t made in healthy individuals. RAN proteins have now been identified in several neurodegenerative diseases where they have been shown to be toxic to cells, including in HD, spinocerebellar ataxia type 8, myotonic dystrophy type 1 and 2, and C9orf72 amyotrophic lateral sclerosis (ALS).

To learn more about the implications of RAN proteins for repeat expansion diseases see this article by Stanford Medicine News Center.

To learn more about the process of translation see this article by Nature.

https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/

For the original article describing RAN translation see this article by PNAS, and this article by Neuron about RAN translated proteins in Huntington’s disease.

Snapshot written by Dr. Hannah Shorrock and edited by Dr. Mónica Bañez-Coronel.

Recovering Purkinje cell health could improve quality of life in SCA3

Written by Jorge Diogo Da Silva Edited by Dr. David Bushart

Normalizing neuronal dysfunction in SCA3/MJD by activating a receptor inside cells

Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is an inherited neurodegenerative disease that typically begins in mid-adulthood. This disease causes loss of coordination and balance (a group of symptoms known as ataxia), abnormal eye movements, and other motor symptoms, all of which limit a patient’s daily life activities. Treating SCA3 patients is currently very challenging, since there are no drugs or other treatments that slow or stop the progression of this disease. While several therapeutic options have been tested in clinical trials, none have shown considerable and consistent effects in improving disease symptoms. Therefore, it is imperative that other treatments are investigated and tested in the clinical setting, in the hopes that we might find a way to improve the lives of SCA3 patients.

The cause of this disease is very well-characterized: patients with SCA3 have an abnormal form of a protein called ataxin-3. All proteins are made up of a sequence of several smaller building blocks known as amino acids. In ataxin-3’s sequence, there is a region where one type of amino acid, glutamine, is repeated consecutively. SCA3 arises when the number of these repeated amino acids is very high (an abnormality known as a polyglutamine expansion), which is toxic for cells.

One of the regions of the brain that is most responsible for regulating balance and movement coordination is the cerebellum, which is located just behind the brainstem (the region connecting the spinal cord to the rest of the brain). As expected, the cerebellum is one of the most affected brain regions in SCA3, since it helps control gait and coordination. Purkinje cells, which are some of the largest neurons in the brain, make up a substantial portion of the cerebellum. These cells receive information from other neurons that detect our surroundings, then emit a signal to the brain regions that control muscles and regulate our movement. This allows us to make movements that are coherent and fluid.

cross section of the cerebellum with purkinje cells stained blue
Cerebellum Cross Section with Purkinje Cells. Image courtesy of Berkshire Community College Bioscience Image Library

Since Purkinje cells are dysfunctional in SCA3, it is reasonable to think that improving the well-being of these cells could also reduce symptoms. In a recent publication, Watanave and colleagues described how they explored a strategy to improve Purkinje cell function using drugs in a mouse model of SCA3, with findings that could be relevant for future studies in patients.

Continue reading “Recovering Purkinje cell health could improve quality of life in SCA3”

Snapshot: What is CRISPR?

A common nuisance for bacteria is the bacteriophage: a virus that uses the internal machinery of a bacteria to replicate its own genetic material. Bacteriophages do this by latching onto bacteria and injecting their DNA into the cell. As the cell grows and divides, the bacteriophage’s hope is that their genetic material is replicated alongside the bacteria’s own genome. Unfortunately for bacteriophages, many bacteria have evolved a method to fight off their attacks. After recognizing a viral infection, the bacteria integrate portions of the injected viral DNA into their own genome. The area where these viral DNA segments end up is known as the CRISPR sequence (short for clustered regularly interspaced short palindromic repeat). The viral DNA segments that were integrated into the CRISPR sequence are then replicated and attached to a bacterial protein called Cas9 (CRISPR-associated protein 9). These CRISPR-Cas9 pairs patrol the cell, acting as the bacteria’s antiviral immune system. If the same viral infection happens again, the DNA in one of the CRISP-Cas9 pairs will match part of the injected viral DNA and bind to it. Once bound, Cas9 cuts the viral DNA, which is then destroyed.

a DNA molelcule that has a fragment cut out of it. Scientific drawing and scribble are faint in the background
Artist’s cartoon of DNA that has been cut by CRISPR. Image courtesy of the NIH.

Recently, scientists have found a way to harness this system for manipulating genes (a process broadly called genetic engineering). By making an artificial CRISPR sequence, attaching that sequence to Cas9, then introducing the man-made CRISPR-Cas9 into a cell, it becomes possible to make a targeted cut in any gene. Making a CRISPR-Cas9 pair that targets one specific gene is as simple as making a CRISPR sequence that matches that gene.

Unlike in bacteria, most organisms repair rather than simply destroy cut DNA. This leaves the targeted genetic sequence available for further manipulation, including the introduction of a short mutation or even the insertion of a whole new DNA sequence. In essence, using the CRISPR-Cas9 system, scientists are now able to edit genes in a simple, targeted way.

CRISPR-Cas9 has become quite popular as a genetic tool in research settings: as of now, the genomes of anything from worms and fruit flies to mice and monkeys have been altered using this technique. While its use in humans is still in its early stages – the first patient treated using CRISPR began therapy earlier this year – is plausible that CRISPR-Cas9 could prove useful in altering the genomes of patients with genetic disorders (like, for instance, the SCAs). For patients, this might sound like a miracle cure. However, it is important to note that several concerns remain as to the ethics of human genetic engineering – the concept of “designer babies” being one of them.

If you’re interested in reading more about the conversation around CRISPR and bioethics, check out the articles by NPR and the National Human Genome Research Institute.

Snapshot written by Logan Morrison and edited by Dr. Maxime W. Rousseaux.

1 Year Anniversary of SCAsource!

SCAsource launched one year ago today on September 27, 2018. In that time we’ve had over 18,000 views and published over 40 articles. Now we are launching a survey about the website to make sure we are meeting our goals.

SCAsource is turning a year old! A huge thank you to all our volunteer writers, editors, and proofreaders who help make the content that gets posted every week. We couldn’t do this without them. Also a big thank you to all who read and share SCAsource content. You all are the reason we made SCAsource in the first place.

Here at SCAsource, we are so excited with how we have grown in these first twelve months, and can’t wait to see where we go from here. To get a better idea of if we are meeting our goals and how we can improve, we are launching a survey about SCAsource.

SCAsource reader survey logo, which is a clipboard that has a box with the checkmark in it
Introducing the SCAsource reader survey!

What is the SCAsource Reader Survey?

This study will look at the impact of SCAsource on its readers and their knowledge of research being conducted on spinocerebellar ataxias. For this study, you are invited to complete a brief online survey that will take about 20 minutes to complete.

Why are you doing a survey?

We want to check if SCAsource is achieving its goal of making ataxia research more accessible and understandable to readers. We will use this survey data to help improve future SCAsource content. Also, we hope by studying SCAsource, that we can provide a framework that other rare disease groups can use to launch their own websites.

Additionally, we want to use this data to show the impact SCAsource to potential sponsors and funders. We want to secure funding to cover the costs of keeping the SCAsource website online.

Are there any risks? Can I withdraw part of the way through the survey?

The risks involved in participating in this study are minimal. You do not need to answer questions that make you uncomfortable. If you decide to be part of the study, you can stop (withdraw) from the study at any point before submitting your survey responses. Once you have submitted your responses for this anonymous survey, your answers will be put into a database and will not be identifiable to you. This means that once you have submitted your survey, your responses cannot be withdrawn from the study because we will not be able to identify which responses are yours.

Where can I get more information about the SCAsource Reader Survey?

You can read the Study Letter of Information, which gives you the full details about the survey. This study has been reviewed and cleared by the Hamilton Integrated Research Ethics Board (HiREB).  If you have any concerns or questions about your rights as a participant or about the way the study is being conducted, call the Office of the Chair, HiREB, at 905.521.2100 x 42013.

Where can I fill out the survey?

Thank you in advance for your time and consideration with the SCAsource Reader Survey! You can access the survey online at this link. With your feedback, we look forward to making SCAsource even better!

International Ataxia Awareness Day 2019

Today marks International Ataxia Awareness Day (IAAD), which is celebrated every year on September 25th. IAAD brings people together from around the world to raise awareness about this group of rare diseases and to raise money for continuing research efforts. For more information on how you can participate in IAAD this year, take a look at the National Ataxia Foundation’s event page.

group of people, including some wheelchair users, stand in a circle holding their hands up. They are happy. Overtop is the IAAD2019 logo and website. www.ataxia.org
Image courtesy of the NAF.

Here at SCAsource, we are celebrating IAAD 2019 by highlighting our top ten most-read articles from this year. We hope you enjoy reading these throwbacks!

10. Decreasing ATXN3 levels can alleviate some symptoms in an SCA3 mouse model

Antisense oligonucleotides: a potential treatment for SCA3 that partially rescues SCA3 disease mouse models.

9. The Discovery of SCA8

How one team uncovered the first SCA known to be caused by a CTG repeat expansion mutation.

8. Approaching the age of clinical therapy for spinocerebellar ataxia type 1

New research (published Nov. 2018) reveals promising potential genetic therapy for SCA1.

7. Protein kinase C to the Rescue in Spinocerebellar Ataxias

Protein kinase C: one protein that may help to protect against cerebellar neuronal dysfunction & death in spinocerebellar ataxias.

6. Early Cerebellum Development Abnormality in Adult-Onset Spinocerebellar Ataxia Type 1

Researchers for the first time identified that spinocerebellar ataxia type 1 (SCA1) may have roots in early cerebellar circuit malfunction.

5. Snapshot: What are Clinical Trials?

Ever wonder what clinical trial “phases” mean? Why do trials need so many phases? How does this help test how safe a new treatment is? Here’s a quick overview of how drugs get from an idea in a research lab to market.

4. Dynamic duo strikes again – Orr and Zoghbi discover the primary driver of SCA1 pathology in the cerebellum

Research group uncovers the key molecular interaction that causes spinocerebellar ataxia type 1 (SCA1).

3. ASOs clear toxic protein from cells, reducing ataxia in SCA2 mice

Scientists uncover a promising therapeutic avenue to treat spinocerebellar ataxia type 2 (SCA2).

2. A novel therapeutic approach for the treatment of SCA3 

Researchers in the Netherlands uncover a new way to treat SCA3.

And last, but certainly not least:

1. Accidental discovery reveals possible link between cerebellar function and motivation

Stanford researchers accidentally discover a new role (reward prediction) for the cerebellum, the primary brain region affected by spinocerebellar ataxias.

logo of IAAD2019: a globe with multiple people from around the world marked on it