U of T researchers uncover a network of genes linked to autism

The finding could explain the molecular basis of autism

U of T researchers uncover a network of genes linked to autism

Professor Ben Blencowe and his team at U of T have uncovered a network of around 200 genes that are linked to autism. Blencowe and his team published these findings in a study in Molecular Cell.

Autism spectrum disorder (ASD) comprises a range of conditions that affect social interaction, behaviour, and communication skills.

Because autism is not a single disorder but a spectrum of related conditions, there is no one discernible cause for it. Instead, a combination of biological, environmental, and genetic factors can be attributed to ASD.

There is also evidence of a strong genetic component in individuals with autism. Previous studies have found that in a family with one autistic child, the chance of having another autistic child is higher than the general population. Identical twins are also more likely to both develop autism than fraternal twins.

Most gene variations affect neural development and produce ASD symptoms through interactions with other genetic and environmental factors.

To determine a genetic link to autism, Blencowe and his team used a CRISPR-based method — a powerful gene editing tool — to identify neuronal microexons that are commonly misregulated in individuals with autism.

Microexons are small protein-coding regions in a gene locus, and are often involved in alternative splicing. Alternative splicing codes for different proteins in the same gene through different combinations of exons — protein-coding sequences — and removing different introns — non-coding sequences — from the messenger RNA (mRNA) transcript.

The altered versions of the mRNA transcript are then translated into several different types of proteins.

According to lead researcher Dr. Thomas Gonatopoulos-Pournatzis, the study was based on the team’s previous research which showed “that a network of neuron-specific microexons is frequently disrupted in the brains of autistic individuals.”

In other words, disruptions in alternative splicing affect how proteins communicate with one another, and could explain the molecular basis of autism.

The researchers isolated SRRM4, a protein that regulates splicing in neural cells, and found that mice with lowered SRRM4 expression displayed ASD-like traits.

The study reports that SRRM4 disruption in the brain has been found in one third of individuals with autism and has been identified as a convergent mechanism for the disorder.

“A critical challenge emerging from these findings is to identify the full repertoire of factors and pathways that converge on SRRM4 to control microexon splicing,” wrote Gonatopoulos-Pournatzis in an email to The Varsity.

In particular, SRRM4 is critical during embryonic development. It helps differentiate neural cells and promotes the development and proper functioning of a working adult nervous system.

In this study, the CRISPR-based screening identified and targeted specific DNA regions using a genome-wide approach.

“[It] systematically [inactivated] all protein-coding genes,” and tagged and isolated cells with altered microexon splicing levels. Then, high throughput sequencing identified “genes responsible for controlling micro-exon splicing,” wrote Gonatopoulos-Pournatzis.

“The screen performance exceeded our expectations and we captured over ~200 regulators that affect microexon splicing by direct or indirect mechanisms. Interestingly, these genes are enriched for genetic links to autism,” he added.

Uncovering “a core set of factors that are critical for microexon splicing” has implications beyond autism. Such factors could help inform researchers developing treatments for neurodevelopment disorders, including through the potential restoration of microexon splicing in misregulated cells.

In the future, the researchers hope to determine the association of microexon misregulation to specific behaviours characteristic to autism, and the roles of individual microexons.

SickKids scientists restore muscle function of mice

CRISPR technology treats muscular dystrophy in mice

SickKids scientists restore muscle function of mice

Our genes contain strands of DNA that give us our distinguishing features. Some of these genes may also carry diseases and ailments that can affect our daily lives. But what if there were a way to remove those genes?

Scientists at The Hospital for Sick Children (SickKids) have used a gene editing technology known as CRISPR to snip out a gene that causes muscular dystrophy in mice. The study, recently published in Nature Medicine, was led by Dr. Ronald Cohn, the study’s principal investigator and Senior Scientist at the SickKids Research Institute.

The mouse model they studied had a form of congenital muscular dystrophy called MDC1A. This condition renders the body unable to produce dystrophin, a protein in muscle fibres that acts like a shock absorber. Insufficient function of these proteins will cause muscles to become a fat-like substance.

When infants are diagnosed with the disease, they will lose muscle function over time and eventually become paralyzed. People with this disease have a life expectancy of roughly 20 years.

In the study, the team restored muscle function in the mice by using CRISPR technology to ‘fix’ the disease-causing mutation classified as a “splice site mutation.”

CRISPR, which stands for “Clustered Regularly Interspaced Short Palindromic Repeats,” is a unique sequence of DNA in bacteria and other microorganisms that contributes to their defense against foreign genetic elements. CRISPR is useful for gene editing because it uses RNA to direct an enzyme called Cas9, which acts like molecular scissors to cut strands of DNA.

The research used the CRISPR system to cut DNA associated with skeletal muscles and peripheral nerves to improve the mice’s mobility. Focusing on these targeted areas has helped centralize the treatment.

“This is important because the development of therapeutic strategies for muscular dystrophies have largely focused on improving the muscle conditions,” said Dwi Kemaladewi, a Research Fellow at SickKids, in an interview with The Scientist. “Experts know the peripheral nerves are important, but the skeletal muscles have been perceived as the main culprit in MDC1A and have traditionally been the focus of treatment options.”

Cohn’s team used an efficient technique that allowed them to snip the DNA without having to replace it with a new piece of DNA. Once the CRISPR system cuts out the disease-causing gene, natural cell repair mechanisms can directly reconnect the severed strands of DNA so the sequence can be read normally. In some follow-up tests, it was observed that the mice regained a level of activity that was close to the control group of the non-affected mice.

CRISPR technology can be revolutionary for treating other muscle diseases like Duchenne muscular dystrophy (DMD), which Cohn’s team had worked on in 2015 in an effort to remove a duplicated gene and restore protein function in a patient. It also has the potential to treat other splice site mutations like congenital epilepsy and hereditary vision loss.

However, this technology has a ways to go before it can be used as a therapy for humans. A concern that researchers have raised is the unpredictability of how the body’s immune system would react to the bacteria used to produce proteins that the body cannot generate. Scientists are also unsure if CRISPR could cause other mutations in our DNA.

Using CRISPR to treat humans with muscular dystrophy may end up being ineffective because mature muscle cells in adults cannot divide, and so their DNA repair technology do not have the tools to add or correct genes. However, Cohn’s team is attempting to change this by working with nonreproductive “somatic cells” that have specialized into different cells.

Humans are more complex creatures than mice, and editing human genes may have unknown effects on future generations.

The future of CRISPR is bright, but the scientific community should use this tool with caution because it is still a very new technology. In an article in the Toronto Star, Cohn noted that it was unlikely for long-term patients with muscular dystrophy to recover muscle function. “Having said that, after speaking with so many patients and their families, if we can just keep them where they are and not have them deteriorate… that would already change the world for these patients,” Cohn explained.

Op-ed: Minding our makeup

Considering the pros and cons of DNA editing

Op-ed: Minding our makeup

Not too long ago, ‘designer babies,’ genome editing and gene therapy were futuristic and expensive ideas that were available only to the most affluent elite.

Yet, today, this baffling feat is becoming shockingly affordable. In the last few years you may have been hearing about the new technology known as CRISPR/cas9, more commonly referred to as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). It is a new, precise, and efficient method for editing DNA.

Since its initial debut in 2012, CRISPR’s capabilities have leapt forward every year. Some highlights include modifications of genomes in non-viable human embryos by Chinese scientists, modifications in pig embryos by US scientists in an effort to create pig organs viable for human organ transplants, and more recently, the authorization for UK scientists to begin experimentation in modifying viable human embryos.

CRISPR/Cas9 is not without its drawbacks. Although its precision has improved since its first introduction, the risk of off-target cuts exists and can range from 0.1 per cent to more than 60 per cent, depending on the target cell and sequence used in the experiment. Its power to wipe out entire species in under a year can be disastrous and have widespread effects on entire ecosystems.

For example, scientists have shown that by mutating a single gene in a single mosquito to render it sterile, they could essentially kill off all mosquitos in roughly 12 generations (36 weeks). But what does that mean for bats who rely on mosquitos as a food source? Use in human embryos could lead to ‘designer babies’ with the ability to pick and choose certain traits, consequently reducing genetic variation in populations.

It is a rather inexpensive and simple technique that can be easily accessed, and dangerous if not regulated. There has been such an explosive reaction to this new technique that it has outpaced our ability to create legal and ethical guidelines, and mandates for its use.

CRISPR has opened up new avenues for researching genetic diseases and gene therapy. While there are a number of concerns that accompany this research, the potential advantages are notable. CRISPR is more precise, efficient, and affordable than past methods of gene editing. There is still a lot of work to be done but initial studies have shown promising results.

In Toronto, CRISPR gene editing is currently being tested as a way to prevent and eliminate hereditary diseases like cystic fibrosis or muscular dystrophy, which do not currently have cures. It also has the potential to regulate genes instead of simply editing them. This means that it could activate some genes and silence others (like those which fuel cancer growth). 

CRISPR technology is propelling genetics research forward. There are a number of ethical concerns accompanying this advancement, and regulatory bodies need to catch up. As the leading agency responsible for regulating health products, Health Canada’s responsibility for creating a comprehensive regulatory framework will ultimately determine how CRISPR’s capabilities will affect our society.

The agency has prioritized a sub-program for Biologics and Radiopharmaceuticals for 2015-2016 (which covers gene therapy products) with the goal of generating a regulatory framework to develop, maintain, and implement the program. As the CRISPR technology is moving forward rapidly in Canada and abroad, this regulatory framework is urgently needed.

Health Canada must ensure that the regulatory framework adequately addresses the concerns that are surfacing with the development of CRISPR, both domestically and internationally. Harmonization of CRISPR regulations and requirements will be necessary to ensure equal protection for citizens and reduce medical tourism. Countries are moving forward at different paces — the United Kingdom for example has already approved use of CRISPR for research on human embryos.

In December 2015, the National Academy of Sciences (NAS) held an international summit on Human Gene Editing after the Chinese Academy of Scientists asked for a ban on clinical use of human germ line editing. The meeting concluded that research should continue with proper oversight, and that editing germ line cells should not proceed until safety and efficacy concerns have been resolved. These discussions should continue to form the basis of a comprehensive regulatory framework for the use of CRISPR worldwide.

So why does CRISPR matter to us as students? CRISPR is not elusive technology. It is already being used in many labs at the university because of its broad range of applications and its ability to rapidly create animal models for testing. Students have an obligation to understand the benefits of CRISPR technology and the current debates surrounding its application.

Students have an important voice to advocate for how CRISPR technology can be used in the future because its implications will directly affect our generation. CRISPR offers substantial benefits and holds promise as an inexpensive treatment for a variety of genetic disorders. However, its powers should be used cautiously so as to not let it become a destructive villain.

Anna Foster and Parmida Jafari are on the advocacy sub-committee of IMAGINE at U of T, a student-run community health initiative aimed at promoting and discussing healthcare in Toronto.