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.

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.

Snapshot: What is RNA?

RNA is an important molecule that helps with regulating the function of cells. To fully understand how RNA fits in here, we must first look at the bigger picture: genetics. The central dogma of molecular biology, depicted below, states that DNA is copied (transcribed) into RNA, which is later decoded (translated) into proteins, which perform many vital functions in the cell. So, when the cell needs a specific protein, it locates the stretch of DNA that contains the code for this protein and starts to write a copy of that stretch of DNA. This copy is made using RNA, or ribonucleic acid, as a backbone. RNA is very similar to DNA, but contains one extra oxygen atom in the basic building block. Only one strand of the DNA is copied, so RNA ends up looking like half a DNA molecule. The RNA molecule can be seen as the messenger between the archive of your genes (DNA) and the protein production site. However, RNA is very versatile and is also involved in protein regulation, transport of molecules and as a structural component of large complexes in the cell.

The "central dogma" of molecular biology: DNA makes RNA, then RNA makes protein.
The “central dogma” of molecular biology: DNA makes RNA, then RNA makes protein. Adapted from Wikimedia.

The shifting stream of RNA

Apart from small random mutations during the course of a lifetime, the DNA contained in every cell remains the same from birth to death. However, since different cells need different proteins at different stages of growth, there needs to be a selection of which genes are copied and translated into proteins. This means that the process of making RNA has to be very flexible. This flexibility is achieved through a large network of signals that tell the cell which regions of DNA should be transcribed into RNA, and at what rate. To keep up with the demands of the cell, there are millions of RNAs being made at all times, to send out instructions to makes proteins.

How can RNA cause disease?

In some spinocerebellar ataxias, such as e.g. SCA8, the messenger RNA molecules contain long repetitive sequences that become sticky to other copies of the same RNA or to proteins, forming both small and large clumps in the cell. There is still controversy surrounding which steps in the process that ultimately causes cell death in large brain areas, but it seems that unsolicited binding of these sticky RNAs to proteins and other RNAs causes disruption to several functions in the cell simultaneously. Therefore, many researchers are hopeful that reducing the amount of these RNAs in the cell using Antisense Oligonucleotides or RNA interference can help treat spinocerebellar ataxias and other similar diseases.

If you would like to learn more about RNA, take a look at these resources by the Encyclopedia Britannica and Khan Academy.

Snapshot written by Frida Niss and edited by Dr. Hayley McLoughlin.

Snapshot: What is Gene Therapy?

Gene therapy is using nucleic acids to treat a genetic disorder.  These nucleic acids can be designed in a variety of ways to achieve the same therapeutic outcome. Gene therapy tools can be used to correct a mutant gene by one of three ways:

  1. Expressing a healthy copy of a gene
  2. Silencing or inactivating the mutant gene transcript
  3. Using genome editing tools to repair or turn-off the mutated gene.
computer desk laptop stethoscope
Photo of a stethoscope by Negative Space on Pexels.com

How is gene therapy used?

Monogenic disorders, like some spinocerebellar ataxias (SCAs), are excellent targets for gene therapy approaches. Gene therapies are currently being used throughout ataxia research for studying disease mechanisms and for preclinical therapeutic application.

Overview of how gene therapy works. First, Package the healthy gene, RNAi, or gene editing tools into the AAV (can also deliver as naked DNA or in a nanoparticle). Second, Inject the packaged AAV into the tissue of interest. Third, AAV will enter the cell and release the genetic material. The cell will become healthy by either 1) expressing the normal gene, 2) repressing the mutant RNA, or by 3) correcting the mutant gene.
Overview of gene therapy, designed by Stephanie Coffin using Biorender.

One gene therapy approach for rescuing SCA1 phenotypes involves overexpressing a healthy gene, ataxin-1-like, which competes with the mutant ATXN1 protein for complex formation. This work, conducted by Keiser and colleagues in 2016, showed phenotypic rescue in a mouse model of SCA1.

There are two common technologies for silencing or inactivating disease genes: RNA interference (RNAi) or antisense oligonucleotides (ASOs). RNAi strategies utilize small RNA molecules to knock down the expression of target mutant RNA transcripts, while ASOs are DNA molecules used to knock down or correct mutant RNA transcripts. Both therapeutic approaches are being pursued in SCAs. For example, Carmo and colleagues in 2013 showed that using RNAi against the SCA3 disease gene, ATXN3, could longitudinally decrease mutant ATXN3 levels. See the SCAsource snapshot on ASOs for further information about their use in SCAs.

The most common genome editing tool is the CRISPR/Cas9 system, which uses an RNA guide to direct the Cas9 nuclease to the region of the genome to be edited. One can then knockout that gene or correct the mutant gene. It is early days for this technology as a potential therapeutic option due to the challenges of delivery and the risk of off-target editing.

How is gene therapy delivered?

One of the most difficult aspects of gene therapy is how to deliver these various molecules to the cells of interest. One of the most common delivery methods is through viral delivery.  The “drug” nucleic acid is transferred into the disease cells by a vector, which is a virus that has been modified to remove viral components. The most common viral vectors for gene therapies currently are adeno-associated viruses (AAVs). Other delivery methods include non-viral vectors such as naked DNA and nanoparticles.

How long-lasting is gene therapy?

Viral delivery of gene therapy products provides a longitudinal expression of the nucleic acid, while naked DNA and nanoparticles express the nucleic acid drug transiently, thus typically requiring ongoing treatment.

If you would like to learn more about gene therapy, take a look at these resources by the National Institutes of Health and KidsHealth.

Snapshot written by Stephanie Coffin and edited by Dr.Hayley McLoughlin.

Snapshot: What is a biomarker?

A biomarker is any biological-based measurement that provides useful information regarding a person’s health. For example, blood test results showing increased glucose levels can be used as a biomarker for diabetes. A blood test showing an increased white blood cell count is a biomarker for infection. There are many sources of biomarkers beyond blood biomarkers. MRI, CT, and x-ray scans are all examples of imaging biomarkers. Scored motor assessments can also be used as biomarkers. For example, police use the field sobriety test as a biomarker for alcohol consumption.

Biomarkers can be used to:

  • Diagnose an existing disease or predict a patient’s prognosis.
  • Track disease progression.
  • Determine whether experimental drugs prevent, improve, or slow progression of disease within clinical trials.
close up photo of a measuring tape on a white background, with the end fading off into the distance.
Biomarkers act like a measure tape for diseases. Photo by Pixabay on Pexels.com

What are current biomarkers for spinocerebellar ataxias (SCAs)?

There are multiple biomarkers that are commonly used for patients with ataxia. DNA sequencing from saliva or blood samples of undiagnosed patients with ataxia symptoms can be used to diagnose or rule out SCAs caused by known genetic mutations. The Scale for the Assessment and Rating of Ataxia (SARA) scoring is a common motor assessment used to measure and track severity of ataxia-related balance and coordination issues in patients. MRI scans and other brain imaging techniques can be used to examine brain abnormalities or loss of brain cells.

Why do we need better biomarkers for SCAs?

In an ideal clinical trial, a patient would receive the potential treatment and then undergo a simple assessment (i.e. give a blood sample) shortly after that could conclusively determine whether the drug is working. Thankfully, many potential ataxia treatments are currently in development or are already being tested in clinical trials for patients with SCAs. Unfortunately, we currently do not have an easy, cheap, and sensitive way to measure whether ataxia symptoms are worsening or improving in a relatively short amount of time.

How can we identify better biomarkers for the SCAs?

Researchers are actively seeking better biomarkers for SCAs in animal and cell models of ataxia. There are also multiple ongoing “Natural History” and biomarker clinical trials that focus on different types of SCA diseases. These clinical studies aim to improve our understanding of the SCAs and identify new biomarkers to improve ataxia diagnosis and drug development. These studies may track patients over months or years, and can involve multiple tests, including blood or cerebrospinal fluid samples, brain imaging, or SARA scoring.

If you would like to learn more about biomarkers, take a look at these resources by the ALS Association and News Medical.

Snapshot written by Dr. Lauren Moore and edited by Dr. Gulin Oz.