Snapshot: What are mitochondria?

Every organ in our body requires a constant supply of energy to function. Our brain and muscles, for instance, need energy to perform tasks such as thinking, walking, and running. The major energy generators in our cells are compartmentalized machines known as “mitochondria.” Mitochondria rely on a series of biochemical steps (collectively referred to as “cellular respiration”) to create ATP (adenosine triphosphate), which is used throughout the cell as a common currency for energy-dependent processes. Almost all cellular processes require ATP, making it a critical part of cellular health and survival.

When we eat, our food gets broken down into nutrients such as proteins, fats, and sugars. In the mitochondria, these nutrients are processed further to generate molecules of ATP. You may have heard mitochondria referred to “the powerhouses of the cell” for their role in producing ATP – because the cell uses energy nearly exclusively in the form of ATP, mitochondria are the major fuel source for our bodies. Some cells, like brain and muscle cells, require much more energy, and therefore contain many more mitochondria than cells that are less active. Additionally, the need for mitochondria can change in different parts of the body depending on energy demands. For example, a new exercise regime can change the number and activity of mitochondria in muscle cells.

 

cartoon of a mitochondria
Cartoon of mitochondria with its different features labeled. Image courtesy of Wikimedia

Mitochondria are classically represented as oval-shaped, but that’s not always the case: they can have a shape anywhere from a long tube to a small sphere. Mitochondrial contents are held in by two separate layers or “membranes”. The inner membrane is dotted with several proteins that perform complex chemical reactions (known collectively as “oxidative phosphorylation”) to turn the broken-down nutrients of our food into ATP. An important feature of the inner membrane is that it folds into “cristae.” These cristae allow more membrane to be packed into less space. With a larger surface area, more reactions can occur simultaneously, thus increasing the efficiency of ATP production.

Why is mitochondrial function important?

 When mitochondria do not function properly, energy production becomes faulty, and cells become starved for energy. Mitochondria are also involved in processes that regulate cell survival; sickly mitochondria, for instance, can send out a biological signal that promotes cell death. Because of the need for energy in every one of our cells, mitochondria are critical for many different functions throughout the body. As such, there are multiple types of conditions that can result from mitochondrial dysfunction. Symptoms between mitochondrial diseases vary, but can include muscle weakness, heart problems, liver problems, vision problems, and learning disabilities. Mitochondrial dysfunction is also involved in brain disorders such as Parkinson’s disease, Alzheimer’s disease, Huntington’s disease, and spinocerebellar ataxias (SCAs). Effective treatments for mitochondrial diseases still need further research; currently, physicians focus on using exercise and dietary supplements to promote ATP production and the formation of new mitochondria in patients with mitochondrial dysfunction.

If you would like to learn more about mitochondria, take a look at these resources by the Mitochondrial Biology Unit and London Health Science Centre.

Snapshot written by Dr. Claudia Hung and edited by Dr. Judit Perez Ortiz.

Snapshot: What are single nucleotide polymorphisms (SNPs)?

It’s in our DNA

If you were to unravel the tightly wound packages of our genome known as chromosomes, you would find long strings of DNA. The strings are made up of only four different building blocks, compounds abbreviated as adenine (A), thymine (T), guanine (G) and cytosine (C). Picture a ridiculously long hospital baby bracelet made only of beads bearing the letters A, T, C, and G.

handmade bead bracelet. Each bead has either "A", "T", "C", or "G" on it. It represents the genetic code that is DNA.
Bead bracelet of A, T, G, and C bead. Image courtesy of Tamara Maiuri.

Our genes are simply stretches along the string of DNA–regions where the order of the compound “beads” is especially important. Genes are the blueprints that code for all the materials needed by our cells. Changes in the order of the building blocks (or, in the case of many spinocerebellar ataxias (SCAs), the addition of too many C-A-Gs), can result in faulty gene products, which can cause disease.

But we can’t all be walking around with identical DNA sequences, like an army of clones! What makes us different? One difference is the small, less consequential changes in the order of the building blocks: variations that usually occur in regions of the DNA between genes, which aren’t critical to gene function.

One such type of variation is called a single nucleotide polymorphism (SNP, pronounced “snip”). Nucleotide is the scientific name for the A, T, C, and G compounds. Polymorphism derives from poly (many) and morph (forms). So a SNP is a change at a single position in the DNA, for example from an A to a C.

Why are SNPs important?

SNPs have been hugely beneficial in helping scientists figure out which genes are linked to disease by acting as biological markers that track with disease genes within families. They may also play a role in therapeutic strategies to lower disease-causing proteins such as the Ataxin proteins that cause some SCAs. SCAsource has previously covered ASO therapy and the clinical trials happening for Huntington’s disease. How can SNPs help with ASO therapies?

ASO therapies are based on the idea of blocking toxic protein production from the inherited disease gene, or “shooting the messenger”. The trouble with this strategy is that everyone actually has two copies of each gene in the genome: one from Mom and one from Dad. Sometimes we don’t necessarily want to block both copies because these genes, when functioning normally, have essential jobs to do in the cell. The ideal situation would then be to block the production of the toxic copy and leave the good copy alone.

For most SCAs, the toxicity comes from the expanded CAG region of the gene. So why not target the extra CAGs? The main problem is that a handful of other genes also have stretches of CAGs. So the drug would have off-target effects. But SNPs lying close to a disease gene are usually inherited along with it. These SNP sites can be targeted by ASO drugs, allowing the drugs to hone in on the toxic copy. The drawback is that these drugs wouldn’t work for people who don’t have the right SNP attached to their disease gene (or who have the same SNP on both copies of the gene).

In summary, just as SNPs tracking with a disease gene helped identify the causes of many genetic diseases, they may also help in their treatment. Vive la difference!

If you would like to learn more about Single Nucleotide Polymorphisms (SNPs), take a look at these resources by the Encyclopedia Brittanica and National Human Genome Research Institute.

Snapshot written by Dr. Tamara Maiuri and edited by Dr. Hayley McLoughlin.

Snapshot: What are stem cells?

Embryonic and adult stem cells

Stem cells are cells that provide new cells during growth, and replace cells that are damaged or lost during life. They have the following two important properties that enable them to do this:

  1. The ability to develop (differentiate) into many other, different cell types, for example brain cells, heart cells or liver cells.
  2. The capacity to replicate (self-renewal) and generate more of these important cells.

Mammals have two types of stem cells; embryonic stem cells (ESCs) and adult stem cells. ESCs are derived from an early-stage embryo, while adult stem cells are found throughout the body after development. The main difference between these cells is their ability in the number and type of different cell types they can become. Embryonic stem cells are pluripotent, meaning that they can become all cell types. Adult stem cells are multipotent and can only develop into a limited set of cell types.

magnified image of stem cells with a blue tint
Human embryonic stem cells, image courtesy of WikiMedia.

Induced pluripotent stem cells

In 2006, the lab of Shinya Yamanaka showed that mouse skin cells could be converted into stem cells by using four specific factors, the Yamanaka factors (1). These cells were named “induced pluripotent stem cells (iPSC). For this important finding Yamanaka was awarded the 2012 Nobel Prize together with Sir John Gurdon. One year later a similar strategy was used to successfully reprogram human skin cells into human iPSCs (2). Nowadays, these iPSCs are an important tool in biomedical research and used for disease modelling, to study disease mechanisms, for drug development and cell replacement studies. To model a disease, a skin biopsy or a urine sample from a patient can be used to generate patient-specific iPSCs. Another option is to modify iPSCs using CRISPR/Cas9. Using defined protocols, these iPSCs can be converted into, for example, brain cells or even mini brains (organoids), which can be used to study a disease. Furthermore, when differences (phenotypes) are found in these cultures, this can be used to screen for drugs that reverse this particular aspect of the disease.

Stem cell-based therapies for SCA

A last aspect is that these iPSCs can be used to replace damaged or lost cells. Since the first stem cell-based clinical trials to replace brain cells that are lost in Parkinson Disease, stem cell replacement therapy has evolved and numerous clinical trials were initiated. In the spinocerebellar ataxia (SCA) field, the first preclinical experiment of embryonic transplants into a mouse model of SCA1 showed a positive effect on animal behaviour and brain pathology (4). Although these first preclinical experiments in SCA disease models are positive, an iPSC-based therapy for SCAs is far from a clinical application.

If you would like to learn more about stem cells, take a look at these resources by the National Ataxia Foundation and National Institutes of Health.

Snapshot written by Dr. Ronald A.M. Buijsen and edited by Frida Niss.

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Snapshot: What is drug repurposing?

To repurpose drugs is to find new ways that they can be applied to treat other conditions and illnesses. Although our knowledge of diseases is greater than ever before, the development of novel therapies has yet to catch up. Drug development is slow, expensive and risky. These challenges have made drug repurposing a more attractive option in recent years. Drug repurposing can be quicker, more cost-effective, and less risky than traditional drug development strategies since the bulk of the work is already done. There are many ways to find new uses for old drugs. The process starts with finding evidence that a drug has useful effects, or new targets, outside of its current clinical use. Then the new mechanism is studied and tested. The process ends within traditional drug development, in some cases skipping the already completed safety phases, and instead focuses on how well the drug works for its new purpose.

pink medication tablets in a bubble packet
Photo by Pixabay on Pexels.com

The barriers to drug repurposing

Despite clear advantages of drug repurposing, there are numerous challenges to this process. The pharmaceutical industry and scientific community tend to focus on new and innovative therapies. While new drugs are certainly needed, an unintended consequence is overlooking many valuable drugs that already exist. Unfortunately, drug repurposing is not as lucrative as new drug development which particularly hurts rare disorders like SCA. With old drugs, patent protection and legal hurdles are also barriers hindering alternative use. And while drug repurposing is financially less risky, there always exists the possibility that a drug will fail somewhere in development. Finally, it is also important to keep in mind that not all drugs can be repurposed. Even if two disorders are similar, this does not mean that similar drugs can be used to treat them both.

Drug repurposing in practice

It is noteworthy that in addition to old drugs, drugs that have previously failed in treating one condition can be considered when developing treatments for other disorders. A notable example is the drug thalidomide, which infamously led to birth defects but has now been repurposed to treat certain blood cancers (Singhal et al., 1999) and leprosy (Teo et al., 2002). There are also several notable recent examples of drug repurposing in SCA. One example is the proposed repurposing of the drug 4-aminopyridine, or 4-AP. This drug, which is also used to treat multiple sclerosis, has been shown to aid with motor symptoms in a mouse model of SCA6. Hopefully, we will see more drugs repurposed to treat SCA and other rare disorders in the near future.

If you would like to learn more about drug repurposing, take a look at our past SCAsource article on drug repurposing in SCA6 or this resource by Findacure.

Snapshot written by Carlos Barba and edited by Dr. David Bushart.

Continue reading “Snapshot: What is drug repurposing?”

Snapshot: The next-generation of CRISPR is prime editing – what you need to know

The CRISPR gene-editing toolbox expanded with the addition of prime editing. Prime editing has astounding potential for both basic biology research and for treating genetic diseases by theoretically correcting ~89% of known disease-causing mutations.

What is prime editing?

Prime editing is coined as a “search-and-replace” editing technique that builds on the “search-and-cut” CRISPR technology. Like CRISPR, prime editing utilizes the Cas9 enzyme targeted to a specific location in the genome by a guide RNA (gRNA). With a few ingenious modifications, including an enzyme called a reverse transcriptase (RT) fused to Cas9, prime editors can be targeted to nearly anywhere in the genome where the RT writes in new DNA letters provided by a template on the gRNA.

graphic drawing of red handled scissors
New gene-editing techniques offer more opportunities for therapy development. Each new discovery makes the techniques more and more accurate. Image courtesy of yourgenome.

 How is prime editing different from CRISPR?

Scientists are excited about prime editing because it has several advantages and overcomes many of the limitations of previous CRISPR systems. CRISPR Cas9, an endonuclease, cuts—like scissors—both DNA strands to inactivate a gene or to insert a new sequence of donor DNA. Unlike CRISPR edits, the prime editing Cas9, a nickase, cuts a single DNA strand and does not rely on the cell’s error-prone repair machinery, thereby minimizing any resulting deleterious scars left on the DNA. It has a broader range of targets because it is not limited by the location of short DNA sequences required for Cas9 binding to DNA. The versatility and flexibility of the system allows for more control to inactivate genes as well as to insert, remove, and change DNA letters, and, combine different edits simultaneously—analogous to a typewriter. Importantly, the edits are precise with relatively infrequent unwanted edits. Initial indications showed fewer off-target edits in the genome, possibly because more steps are required for a successful edit to occur. In some cases, it may be more efficient than CRISPR, depending on the targeted cell type, such as in a non-dividing cell like a neuron in the brain. However, with all these advantages, CRISPR still remains the tool of choice for making large DNA deletions and insertions because the prime editing system is limited by the RT and template RNA length.

How could prime editing help ataxia patients?

Prime editing offers enormous possibility for correcting heritable ataxia mutations accurately and safely. In dominantly inherited SCAs, like SCA1 or SCA2, prime editing could shorten the pathogenic repeat expansion allele to the normal length, or inactivate the pathogenic allele without creating unwanted, deleterious mutations. It also provides researchers with a powerful tool to study disease-causing genes in cells and animal models in new ways to advance our knowledge about the underlying mechanisms in ataxia.

What barriers are there to using prime editing as a treatment?

Prime editing will require rigorous testing in cells and animals before moving into humans in a clinical trial. Optimizing delivery and efficiency in target cells and tissues, and minimizing side-effects will be the key barriers to overcome.

To read the original Nature article describing prime editing, it can be found from the Liu lab here.

If you would like to learn more about Prime Editing, take a look at these news stories by The Broad Institute and Singularity Hub.

Snapshot written by Bryan Simpson and edited by Dr. Hayley McLoughlin.