Snapshot: What is Magnetic Resonance Imaging (MRI)?

What is it?

Magnetic resonance imaging (MRI) is a type of technology used to take detailed pictures of the body. It is commonly used to detect abnormalities in the body, diagnose diseases, and to regularly monitor patients who are undergoing treatments. It can generate three-dimensional images of non-bony tissues, such as the brain. MRI procedures are non-invasive, require minimal preparation, and are not associated with health risks, as it does not use harmful types of radiation such as X-rays.

How does it work?

Human tissues contain water, which contain very small particles known as protons that behave like tiny magnets. An MRI machine uses large, powerful magnets to generate a magnetic field that can change how these particles rotate in your body, making them align with the magnetic field. Non-harmful radio waves are then pulsed through the patient, changing the direction of these particles, such that they are no longer aligned with the magnetic field. The radio waves are then turned off, and the particles can then re-align with the magnetic field. Different types of tissue and structures in the body will have particles that re-align differently, which can be detected by the machine to generate a detailed black and white image of the scanned area of the body. In addition to such structural information, MRI scans can provide information about how the brain is wired, levels of important chemicals, blood flow, metabolism, and brain function by acquiring information differently with the same machine.

3D view of an entire human brain taken by MRI, shown from two angles.
3D view of an entire human brain taken by 7 Tesla MRI. Photo courtesy of  B.L. Edlow et al, bioRxiv, 2019.

How do you prepare for an MRI scan?

Since an MRI scan uses a large magnet, electronic devices and metal objects, such as glasses and jewelry, must be removed. There is usually no other preparation required for the scan. Patients must lie very still to generate a clear image. Patients do not need to be sedated, unless they have trouble lying still for the procedure. MRI scans that are obtained for research do not use anaesthesia to avoid unnecessary risk to research participants.

What happens during an MRI scan?

The patient lies down on a table that will move into the tunnel-shaped chamber. The patient is usually awake and will remain in the chamber as several scans are taken during the procedure (about 30-60 minutes). As the scan proceeds, there are often loud mechanical sounds, so earplugs are provided for protection. Some patients may experience claustrophobia, or are bothered by the noises. Becoming more familiar with the procedure, or listening to music or closing your eyes can help alleviate discomfort during the scan.

What do doctors look for in patients with SCAs?

MRI scans are often used to image the brain to detect signs of spinocerebellar ataxia (SCA), especially in a region of the brain known as the cerebellum. SCA is associated with brain cell loss, and appears as reduced volume of brain tissue in the MRI image.

If you would like to learn more about Magnetic Resonance Imaging (MRI), take a look at these resources by the National Institutes of Health and the Mayo Clinic.

Snapshot written by Dr. Claudia Hung and edited by Dr. Gülin Öz.

Mitochondrially Stressed

Written by Dr. Judit M. Pérez Ortiz Edited by Dr. Brenda Toscano Márquez

Scientists describe how SCA2 oxidative stress can affect mitochondrial function, and potentially how to fix it

Mitochondrial Stress

We all have experienced stress. When cramming for an exam last minute, or getting ready for a job interview, our bodies feel stress-related energetic drive and hyperfocus. Small bursts of stress can help us get through specific demands, but too much constant stress takes a toll and makes it difficult for us to function. It turns out that the cells in our bodies experience stress too! While the stress response that we experience in our hectic lives is associated with stress hormones, the stress cells experience is from another source altogether – mitochondria. Scientists at the University of Copenhagen in Denmark identified a novel link between mitochondrial oxidative stress and spinocerebellar ataxia type 2 (SCA2).

Classically, we learn that mitochondria are the powerhouse of the cell responsible for making the bulk of the energy currency that cells need to work and survive, ATP. To do this, mitochondria rely on a cooperative group of protein complexes called the Electron Transport Chain (ETC). Albeit via a more sophisticated procedure than a hot-potato game, the complexes mediate chemical reactions (called redox reactions) by which “hot” electrons are passed from high energy molecules to lower-energy molecules, and so on. The final electron recipient (“acceptor”) is a stable oxygen molecule and their encounter is used to make water. The activity of the ETC helps harness energy that is ultimately used to make ATP in what is called oxidative phosphorylation.

Sometimes not all the electrons make it through; the hot potato “drops”. Electrons leak out and react directly with molecular oxygen (chemical formula O2), turning unstable superoxide (chemical formula O2) which in turn, can create other reactive oxygen species (ROS). The extra electron in superoxide gives it a negative charge and makes it highly reactive and toxic. Just like the small amount of stress primes your body for a challenge to come, low levels of ROS hints the cell that it needs to make some changes to optimize the system. As the superoxide levels go up, cells make more antioxidant enzymes available to keep ROS in check. Antioxidant enzymes convert the highly reactive superoxide to a less reactive hydrogen peroxide (like the one in your bathroom cabinet). This, in turn, can be converted to water and ordinary oxygen molecules. In a word, the antioxidants “detox” the cells from ROS insult.

The cell becomes “stressed out” when there’s too much ROS that can’t be compensated for. This stress caused by oxygen or “oxidative stress” can damage DNA, fats, and proteins that affect the cell and organism as a whole. For example, oxidative stress can contribute to heart disease, diabetes, cancer, and neurodegenerative diseases.

cartoon drawing of human cells that are blue
An artist’s drawing of human cells under a microscope.

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Snapshot: What is RNAi?

RNA interference, or RNAi, is a natural biological process that inhibits the expression of a specific gene. In medicine, targeted RNAi therapies can be used to silence the expression of a disease-causing gene. To understand RNAi, you first have to understand RNA.

DNA is transcribed to make mRNA, which is tranlated by the ribosome to make protein.

An overview of  RNA is the messager between the DNA (the instructions) and the protein (the product). RNA is transcribed from the DNA. The ribosome translates the mRNA into protein. Graphic designed by Colleen Stoyas and illustrated by Celeste Suart.

Genes encode the instruction manual of our biology, but this material cannot leave the nucleus of your cells. Think of genes as a lecturer that provides instruction for your homework, which you must copy and take home to use later. The equivalent of copying this message in the cell is RNA, which transcribes the gene instructions and leaves the nucleus to be read and translated into protein. This protein then performs functions within the cell (see above image).

How can RNAi be used in ataxia?

In specific forms of ataxia, a gene mutation may provide the instructions for a protein that acts improperly and leads to disease. RNAi is a method of silencing RNA that interferes with the reading of this message, keeping a protein from being made. It works by generating a small interfering RNA in the laboratory that matches the gene of interest. When this small interfering RNA enters the cell, it binds the matching messenger RNA copied from a gene. When these two RNAs bind, the cell is triggered to cut up the message and destroy it. This means the disease-causing protein is never made. (see below image)

RNAi works by binding the mRNA, preventing it from being transcribed by the ribosome. This stops protein from being made.
How does RNAi work? It binds matching messenger RNA. This stops it from being translated by the ribosome into protein. Graphic designed by Colleen Stoyas and illustrated by Celeste Suart.

While RNAi is straightforward in the lab, getting it to work in humans can be tricky. The small interfering RNA cannot be taken in a pill, because it will not survive digestion. Additionally, the small interfering RNA is degraded along with the target messenger RNA, and so it must be continually administered. Using a viral payload, or encapsulating the interfering RNA in the coat proteins of a virus, has successfully delivered RNAi therapies in mouse models of SCA1, SCA3, and SCA7. In this method the virus integrates into your cells, which can then continue to produce the small interfering RNA. This means a single dose could potentially be all that is needed. Viral delivery to the brain is complicated, but not impossible. More work remains to be done clinically in order to determine if RNAi therapy is viable in a viral payload to treat multiple forms of spinocerebellar ataxia.

If you would like to learn more about RNAi, take a look at this video by TED-ED or entry in the Encyclopedia Britannica.

Snapshot written by Dr. Colleen Stoyas and edited by Frida Niss.

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Zapping the brain to help ataxia

Written by Dr. Judit M. Perez Ortiz Edited by Dr. Sriram Jayabal

In a new study, scientists have found that “zapping” the brain with an electromagnetic wand may someday help patients with spinocerebellar ataxia.

In an era of ever-evolving technological advances used for personal entertainment and space travel, medical scientists are harnessing the power of electromagnetism to safely penetrate the skull and manipulate brain cells by mimicking their favorite language – electric current.

Clinicians currently have access to powerful and effective tools designed to stimulate brain cells (known as neurons) for various neurological and psychiatric conditions. Spinocerebellar ataxias (SCAs), however, are not yet in the mix. Though several techniques exist, the methods used to stimulate neurons in the brain can be broadly classified into invasive and non-invasive approaches. For instance, Vagus Nerve Stimulation is used for drug-resistant epileptic seizures, while Deep Brain Stimulation is used for Parkinson’s disease and severe depression. In both instances, a surgical procedure is required because the implanted electrodes have to come in direct contact with the target nerve or brain structure. Disadvantages associated with these surgical methods include the risk of infection, bleeding, and hardware malfunction. Non-invasive approaches to stimulate the brain include electroconvulsive (“shock”) therapy, in which electrodes are placed on the scalp surface to provoke a controlled seizure that yields a therapeutic effect. However, shock therapy requires anesthesia, and patients run the risk of memory issues as a side effect. A second non-invasive brain stimulation tool is also available, called repetitive Transcranial Magnetic Stimulation (rTMS). There are many factors that make rTMS clinically appealing: it does not require surgery, it is already FDA-approved (for severe depression), it is painless, and it has been found to be safe. Further, unlike the broad brain stimulation achieved by electroshock therapy, rTMS delivers a more precise stimulation in a defined brain region, which leaves untargeted brain regions untouched.

cartoon of neuronal brain cells and electricity flowing between them
Artist’s depiction of electrical signals in the brain. Image courtesy of flickr.

Besides its circular or figure-eight attachment, the rTMS device looks quite a bit like a magic wand. Though this is no wizard’s tool, you could say that it does cast a powerful spell: the attachments on the end of the rTMS device are electromagnetic coils, which have the power to “zap” specific brain regions. In a remarkably simple procedure, the wand is gently placed over the patient’s scalp, where it delivers electromagnetic pulses that create just enough electric current to stimulate underlying brain cells without adversely affecting them.

A new pilot study conducted at the Beth Israel Deaconess Medical Center found that using rTMS to stimulate the cerebellum of SCA patients is safe and may improve some aspects of ataxia. First, the investigators recorded the study participants’ baseline movement performance using a battery of tests designed to evaluate different features of ataxia, including balance, gait, and posture. Then, half of the study participants were randomly assigned to receive rTMS, while the other half were assigned to the control, or “sham” group.

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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.

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.