Molecular Genetics

Convocation 2024

Trinity College

Subheadline

Abidur Rahman, who earned an honours bachelor of science in molecular genetics, says it's important to stay focused on your own journey

Abidur Rahman, a recent honours graduate in molecular genetics at the University of Toronto, has already made impressive strides.

He earned a prestigious fellowship at the Max Planck Institute for Multidisciplinary Sciences in Germany, interned at the International Centre for Genetic Engineering and Biotechnology in Italy, collaborated with biotech startups and mentored several students – all while volunteering as a community advisor at Trinity College.

Rahman credits his success to the boundless opportunities offered by U of T’s Faculty of Arts & Science. “The amount of research opportunities, internships and collaborations you have access to is unparalleled,” says Rahman, who also found time to volunteer as a community advisor at Trinity College.

“You don’t get the same magnitude of possibilities at other universities.”

Now pursuing a master of science in genetic counselling at U of T, Rahman reflected on his ��οjourney thus far and shared some of his insights and tips for current and future students:

What drew you to molecular genetics?

When I came to U of T, I was planning to major in neuroscience and psychology. It wasn’t until my second year when I took a course with Naomi Levy-Strumpf, an assistant professor, teaching stream in the human biology program, that I became fascinated with the complexity of genetics and how it can be used to tell the stories of entire generations.

What motivated you to volunteer with Trinity College?

My family moved from Bangladesh when I was a teenager, and being a first-generation immigrant, I felt lost when I started university. That’s why I wanted to give back. As a community advisor, I connected students with resources and clubs, like the Trinity College Multicultural Society, and created social programming that addressed mental health.

��οhas so many opportunities; it can also be like a maze. My goal was to help students find their way, just like my mentors helped me.

Can you tell us about your research fellowship at the Max Planck Institute?

I spent this past summer in Göttingen, Germany, working on bio-engineered heart muscle cells. My project focused on observing them in low-oxygen conditions, simulating what happens during a stroke. This research has the potential for real-world applications, like developing treatments for heart disease. The work makes you feel as though you’re on the cusp of something that could help thousands of patients, and that’s what excited me the most.

What are your plans after graduation?

I’m currently pursuing my master of science in genetic counselling, which is a clinical and professional program focusing on patient counselling and calculating genetic risks. My research project will examine how racialized families perceive the clinical utility of genetic testing. Most studies are based on individuals of European ancestry and that affects how well genetic testing works for people from other backgrounds.

I’m still exploring my future career path, but I can envision myself working in healthcare. During my undergraduate studies, I also had the opportunity to collaborate with several biotech startups, which I thoroughly enjoyed. Additionally, Toronto offers a wealth of opportunities in both fields, making it an exciting place to build a career.

What advice would you give to your first-year self?

Don’t be in a rush to figure everything out. In my first semester, I was so focused on the future, but university isn’t just an academic endeavor, it’s also about personal growth and professional development. Take the time to enjoy your courses and build relationships with your professors.

My other critical piece of advice is to never compare yourself to others because, as the saying goes, comparison is the thief of joy. I remember feeling behind because I was still relatively new to Canada, and I didn’t have the same high school experience as some of my peers. Stay focused on your journey and don’t stress about what other people are doing.

New study identifies two critical genes in pancreatic tumours

rahul.kalvapalle — Thu, 25 Jul 2024 14:46:33 +0000

New study identifies two critical genes in pancreatic tumours

rahul.kalvapalle Thu, 07/25/2024 - 10:46

Cutline

A team led by Daniel Schramek, a researcher at the Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health and U of T's Temerty Faculty of Medicine, identified two genes that are associated with fast-growing tumours in the pancreas (photo courtesy of Mount Sinai)

Jovana Drinjakovic

Topic

Sinai Health

Lunenfeld-Tanenbaum Research Institute

Cancer

Subheadline

The findings mark a significant step forward in research on pancreatic cancer, a disease that has seen little progress in treatment options

University of Toronto researchers have identified two genes that play a critical role in tumour growth in the pancreas – findings that have significant implications for understanding and treating pancreatic cancer.

The tumour suppressor genes USP15 and SCAF1 were discovered by a research team led by Daniel Schramek, a senior investigator at the Lunenfeld-Tanenbaum Research Institute (LTRI) and deputy director of discovery research and Tony Pawson Chair in Cancer Research at Sinai Health.

The team found that people who have mutations in these genes are more likely to develop fast-growing tumours – but these tumours are also more susceptible to chemotherapy. The findings, described in a study published in Nature Communications, mark a significant step forward in research on pancreatic cancer, a disease that has seen little progress in treatment options.

“While mutations in USP15 and SCAF1 make tumours more aggressive, they also sensitize tumours towards standard chemotherapy,” says Schramek, who is also an associate professor in the department of molecular genetics and Canada Research Chair in functional cancer genomics at the Temerty Faculty of Medicine.

“And that means that you could stratify patients and they should have a better response to treatment.”

The project was spearheaded by Sebastien Martinez, a former postdoctoral fellow at LTRI who is now a senior scientist at Centre de Recherche en Cancérologie de Lyon (CRCL) in France.

Pancreatic cancer continues to have few treatment options with devastatingly low survival rates, under five years post-diagnosis. According to one estimate, pancreatic cancer could be the second leading cause of cancer deaths in the United States by 2040.

Schramek's team achieved their breakthrough by leveraging advances in genomic medicine, specifically tumour DNA sequencing, to identify mutations and genome editing technologies.

“Sequencing tumours allows you to find the genes that are affected and use that knowledge to develop treatments. But the problem is that every cancer has a plethora of mutations, and not all of them are disease-causing,” says Schramek.

Cancers often feature common mutated genes in many patients, along with hundreds of less frequent mutations that appear in a smaller subset. While mutations in USP15 and SCAF1 were found in less than five per cent of patients, their effects on cancer remained unclear.

Traditionally, tumour suppressor genes have been pinpointed by sequentially deleting genes in cancer cell lines and noting which deletions increase cell growth. However, these cell-based studies don't replicate the tumour's natural environment and interactions with the immune system, which are crucial for cancer progression. This likely explains why previous screens overlooked USP15 and SCAF1.

A few years ago, Schramek's team developed a genome editing approach enabling them to remove hundreds of genes simultaneously from individual cells. This method helps identify genes that, when absent, trigger cancer in the natural body environment.

Utilizing this technology, the Schramek lab targeted 125 genes recurrently mutated in patient pancreatic tumours and pinpointed USP15 and SCAF1 as crucial tumor suppressors and potentially prognostic factors for chemotherapy response.

It just so happens that these genes are also absent in about 30 per cent of patients due to common genomic rearrangements in cancer.

This finding indicates that as many as a third of pancreatic patients who lack these genes might benefit from chemotherapy and have better outcomes.

“Historically, mutations in USP15 and SCAF1 would have been considered less important because they are not found in many patients,” Schramek says. “Our work shows that it is critical that we understand the functional consequences of these rare mutations as they can reveal new biology and therapeutic opportunities”

Anne-Claude Gingras, director of the Lunenfeld-Tanenbaum Research Institute and vice-president of research at Sinai Health, says the study “represents an important step forward in our understanding of the genes involved in pancreatic cancer.

“It also shows how a cutting-edge technology developed at Sinai Health is enabling new discoveries with the potential to create benefits to patients.”

This research was supported by funding from the Ontario Institute of Cancer Research, Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Foundation, Terry Fox Research Institute, Canadian Cancer Society Research Institute, Pancreatic Cancer Canada and the Canadian Institute of Health.

��οresearchers lead discovery of natural compounds that selectively kill parasites

rahul.kalvapalle — Tue, 21 May 2024 17:46:46 +0000

��οresearchers lead discovery of natural compounds that selectively kill parasites

rahul.kalvapalle Tue, 05/21/2024 - 13:46

Cutline

An international study led by PhD student Taylor Davie (L) and Professor Andrew Fraser (R) of the Donnelly Centre for Cellular and Biomolecular Research could have important implications for treatment of lethal parasitic worms (supplied images)

Anika Hazra

Topic

Donnelly Centre for Cellular & Biomolecular Research

Subheadline

The compounds stall a unique metabolic process that parasitic worms use to survive in the human gut

An international team led by researchers at the University of Toronto has found a family of natural compounds that could potentially be harnessed as treatments for parasitic worms, which wreak havoc in developing countries in the tropics.

Infection by these parasites, which are transmitted through soil, leads to malaise, weakness, malnutrition and other debilitating symptoms, and can cause developmental defects and growth impairments in children.

The newly discovered compounds stall the unique metabolic process that the worms use to survive in the human gut, according to the study, which was published in Nature Communications.

“Soil-transmitted parasitic worms infect over one billion people around the world, typically in low-income communities of developing countries without comprehensive health care and infrastructure for sanitation,” said Taylor Davie, first author on the study and a PhD student at U of T’s Donnelly Centre for Cellular and Biomolecular Research. “Parasites are becoming less susceptible to the few anthelmintic drugs available, so there’s an urgent need to find new compounds.”

Many parasitic worm species spend a large portion of their life cycle inside a human host. To adapt to the environmental conditions of the gut, particularly a lack of oxygen, the parasite switches to a type of metabolism that depends on a molecule called rhodoquinone (RQ).

The parasite can survive inside its human host for many months using RQ-dependent metabolism.

The research team chose to target the adaptive metabolic process of the parasitic worm because RQ is only present in the parasite’s system – humans do not produce or use RQ. Therefore, compounds that can regulate the molecule’s production or activity would selectively kill the parasite, with no harm done to the human host.

The researchers conducted a screen of natural compounds isolated from plants, fungi and bacteria on the model organism C. elegans. Although C. elegans is not a parasite, this worm also depends on RQ for metabolism when oxygen is not available.

“This is the first time that we have been able to screen for drugs that specifically target the unusual metabolism of these parasites,” said Andrew Fraser, principal investigator on the study and professor of molecular genetics at the Donnelly Centre and the Temerty Faculty of Medicine.

“The screen was only possible because of recent progress made by our group and others in using C. elegans to study RQ-dependent metabolism, and our collaboration with RIKEN, one of Japan’s biggest research agencies.

“We screened their world-class collection of 25,000 natural compounds, resulting in our discovery of a family of benzimidazole compounds that kills worms relying on this type of metabolism.”

The researchers suggest a multi-dose regimen using the newly discovered family of compounds to treat parasitic worms. While a single-dose treatment is easier to facilitate in mass drug administration programs, a longer treatment program would eliminate the parasite more effectively.

“We are very pleased with the results of the study, which made use of our library,” said Hiroyuki Osada, professor of pharmacy at the University of Shizuoka and group director of the Chemical Biology Research Group at the RIKEN Center for Sustainable Resource Science.

“The study shows the power of the screening approach, allowing researchers in this case to search through a very large number of molecules within a focused collection of natural products. Screens are very efficient, which is key for addressing urgent research questions of global relevance like this one.”

Next steps for the research team are to refine the new class of inhibitors through additional in-vivo testing with parasitic worms, which will be performed by the Keiser lab at the University of Basel in Switzerland, and to continue screening for compounds that inhibit RQ.

“This study is just the beginning,” said Fraser. “We have found several other very powerful compounds that affect this metabolism including, for the first time, a compound that blocks the ability of the worms to make RQ.

“We hope our screens will deliver drugs to treat major pathogens around the world.”

This research was supported by the Canadian Institutes of Health Research and the European Molecular Biology Organization.

A master neuron controls movement in worms, with implications for human disease: Study

Christopher.Sorensen — Thu, 16 May 2024 15:01:59 +0000

A master neuron controls movement in worms, with implications for human disease: Study

Christopher.Sorensen Thu, 05/16/2024 - 11:01

Cutline

Researchers at the Lunenfeld-Tanenbaum Research Institute have revealed the crucial role of a neuron called AVA in controlling the worm C. elegans’s ability to shift between forward and backward motion ( photo by ZEISS Microscopy from Germany)

Jovana Drinjakovic

Topic

Sinai Health

Cell and Systems Biology

Subheadline

The discovery offers a major new insight into a neural circuit that scientists have studied since the inception of modern genetics.

Researchers at Sinai Health and the University of Toronto have uncovered a mechanism in the nervous system of the tiny roundworm C. elegans that could have significant implications for treating human diseases and advancing robotics.

The study, led by Mei Zhen and colleagues at the Lunenfeld-Tanenbaum Research Institute, was published in the journal Science Advances and reveals the crucial role of a specific neuron called AVA in controlling the worm’s ability to shift between forward and backward motion.

Crawling towards food sources and swiftly reversing from danger is a matter of life and death for the worms. This type of behaviour, where two actions are mutually exclusive, is common in many animals including humans – we cannot sit and run at the same time, for example.

Scientists long believed that control of movements in worms was due to straightforward reciprocal actions between two neurons: AVA and AVB. The former was thought to promote backward motion while AVB facilitated forward motion, with each neuron inhibiting the other to control movement direction.

However, the new data from Zhen’s team challenge this notion, uncovering a more complex interaction where the AVA neuron plays a dual role. It not only instantly stops forward motion by inhibiting AVB, but also maintains a longer-term stimulation of AVB to ensure a smooth transition back to forward movement.

The discovery highlights the AVA neuron’s ability to finely control movement through distinct mechanisms, depending on different signals and across different time scales.

“In terms of engineering, this is a very economical design,” said Zhen, who is also a professor of molecular genetics in U of T’s Temerty Faculty of Medicine. “The strong, robust inhibition of the backward circuit allows the animals to respond to bad environments and escape. At the same time, the controller neuron continues to put in constitutive gas into the forward circuit to generate movement towards safer places.”

Jun Meng, a former PhD student in the Zhen lab who led the research, said understanding how animals transition between such opposing motor states is crucial for insights into how animals move as well as neurological disorder research – and that the worms provide a unique window into basic neural wiring that's to their simple, see-through bodies.

The discovery that the AVA neuron plays such a dominant role offers a major new insight into the neural circuit that scientists have studied since the inception of modern genetics over half a century ago. The Zhen lab successfully leveraged cutting-edge technology to precisely modulate the activity of individual neurons and record data from living worms in motion.

Zhen, who is also a professor of cell and systems biology at U of T’s Faculty of Arts & Science, emphasizes the importance of interdisciplinary collaboration in this research. Meng performed key experiments, while neuronal electrical recordings were conducted by Bin Yu, a PhD student in Shangbang Gao’s lab at Huazhong University of Science and Technology in China.

Tosif Ahamed, a former post-doctoral researcher in the Zhen lab and now a Theory Fellow at the HHMI Janelia Research Campus in the United States, led mathematical modelling efforts that were crucial for testing hypotheses and gaining the new insights.

The findings provide a simplified model to study how neurons can manage multiple roles in movement control – a concept that might extend to human neurological conditions.

For example, AVA’s dual role depends on its electric potential, which is regulated by ion channels on its surface. Zhen is already exploring how similar mechanisms could be involved in a rare condition known as CLIFAHDD syndrome, caused by mutations in similar ion channels. Additionally, the new findings could inform the development of more adaptable and efficient robotic systems capable of complex movements.

“From the origin of modern science to the forefront of today’s research, model organisms like C. elegans have been instrumental in peeling back the layers of complexity in our biological systems," said Anne-Claude Gingras, director of the Lunenfeld-Tanenbaum Research Institute, vice-president of research at Sinai Health and a professor of molecular genetics in U of T’s Temerity Faculty of Medicine.

“This research is a great example of how much we can learn from simple animals, to then think about applying this new knowledge to advancing medicine and technology.”

The research was supported by the Canadian Institute of Health Research, the Natural Sciences and Engineering Research Council of Canada, the National Natural Science Foundation of China and the European Research Council.

Researchers discover one million new components of the human genome

Christopher.Sorensen — Thu, 08 Feb 2024 19:16:32 +0000

Researchers discover one million new components of the human genome

Christopher.Sorensen Thu, 02/08/2024 - 14:16

Cutline

Timothy Hughes, professor and chair of U of T’s department of molecular genetics in the Temerty Faculty of Medicine, is the principal researcher on a study that found nearly one million new exons, or stretches of DNA that are expressed in mature RNA (photo courtesy of the Donnelly Centre)

Anika Hazra

Topic

Donnelly Centre for Cellular & Biomolecular Research

Genome

Subheadline

“We’ve started to chip away at the dark genome by finding nearly one million previously unknown exons through a method called exon trapping”

Researchers at the University of Toronto’s Donnelly Centre for Cellular and Biomolecular Research have found nearly one million new exons – stretches of DNA that are expressed in mature RNA – in the human genome.

There are around 20,000 protein-coding genes in humans that contain approximately 180,000 known internal exons. These protein-coding regions account for only one per cent of the entire human genome. The vast majority of what remains is a mystery – aptly referred to as the “dark genome.“

“We’ve started to chip away at the dark genome by finding nearly one million previously unknown exons through a method called exon trapping,” said Timothy Hughes, principal investigator on the study and professor and chair of the department of molecular genetics in U of T’s Temerty Faculty of Medicine.

“The technique involves an assay with plasmids to find exons in DNA fragments of unknown composition,” said Hughes, who holds the Canada Research Chair in decoding gene regulation and the John W. Billes Chair of Medical Research at U of T. “While exon trapping is not widely used anymore, it proved to be effective when used in combination with high-throughput sequencing to scan the entire human genome.”

The findings were published recently in the journal Genome Research.

Exons are segments of the genome that can encode proteins to direct tissue development and biological processes within the body. They are considered to be autonomous if they don’t require external assistance to splice into a mature RNA transcript, which is then translated into a protein.

The team behind the study was driven to test the exon definition model that guides research in molecular genetics after questioning one of its assumptions – that the accurate removal of non-protein-coding intron regions of the genome is aided by clear and consistent indicators of where exons begin and end. This assumption does not seem to hold in all cases as the splicing of exons does not always go smoothly, sometimes resulting in mature RNA transcripts that contain non-functional components.

“Almost none of the newly discovered exons are found consistently across genomes of different species,” said Hughes. “They seem to appear in the human genome mainly due to random mutation and are unlikely to play a significant role in our biology. This is evidence that evolution in humans involves a lot of trial and error – most likely enabled by the vast size of our genome.”

It is helpful to document randomly mutated exons within the human genome as their translation could potentially be harmful. Long non-coding RNA exons, which are autonomous but often have no known function, have been connected to the development of cancer. Of the roughly 1.25 million known and unknown exons the team found through exon trapping, almost four per cent were long non-coding RNA exons.

In addition, the exons residing within non-coding introns, called pseudoexons, can mutate to make a weak splice site stronger. This results in the exon being included in a mature RNA transcript, potentially leading to disease.

“This is an interesting study that broadens our knowledge of sequences across the human genome that have the potential to be recognized as exons in transcribed RNA,” said Benjamin Blencowe, professor of molecular genetics in U of T’s Temerty Faculty of Medicine, who was not involved in the study. “While the significance of the majority of the newly detected exons is unclear, some of them may be activated in certain contexts – for example, by disease mutations – and therefore cataloguing them is important. This study will further serve as a valuable resource facilitating ongoing efforts directed at deciphering the splicing code.”

A stronger understanding of the factors impacting exon inclusion in mature RNA can help improve programs like SpliceAI, a widely used tool for predicting splice sites and aberrant splicing. SpliceAI can be trained on new data such as that produced through this study to refine its prediction capabilities.

“SpliceAI often doesn’t provide details on the characteristics of exons and has a poor ability to predict splicing in exons that aren’t already catalogued,” said Hughes. “Our exon trapping data contains biologically meaningful information that can be fed into SpliceAI and other splicing predictors to open up new paths for exploring the dark genome.”

The research was supported by the Canadian Institutes of Health Research and the U.S. National Institutes of Health.

��οresearchers find vulnerability in COVID-19 variants that reduces transmissibility

Christopher.Sorensen — Mon, 12 Jun 2023 20:45:36 +0000

��οresearchers find vulnerability in COVID-19 variants that reduces transmissibility

Christopher.Sorensen Mon, 06/12/2023 - 16:45

Cutline

(illustration by NIAID)

Anika Hazra

Topic

COVID-19

Donnelly Centre for Cellular & Biomolecular Research

Biochemistry

Medical Research

Researchers at the University of Toronto have found that Omicron variants of the COVID-19-causing virus can be hindered in their ability to infect people by mutations in the spike protein that prevent the virus from binding to and entering cells.

The spike protein is a distinctive feature of viruses, found on their outside surface. The researchers found that mutations in this protein influence the sensitivity of Omicron variants to chemical reduction – a process that can prevent Omicron variants from spreading and could potentially be delivered to patients through aerosol therapy.

“While infection by the Omicron variant usually leads to milder symptoms, this variant is unique in how easily it can spread,” said Zhong Yao, lead author on the study and senior research associate in the lab of Igor Stagljar, a professor at U of T’s Donnelly Centre for Cellular and Biomolecular Research.

“Our study clearly demonstrates a significant vulnerability of Omicron to chemical reduction – one that is either not found or is much less potent in previous variants of coronavirus.”

The team's findings were published in the Journal of Molecular Biology.

The researchers found that Omicron-specific mutations in the virus’s spike protein reduce its ability to bind to a key receptor in host cells, called ACE2. The spike protein’s receptor-binding domain, the surface of which comes into contact with the ACE2 receptor, consists of multiple disulfide bonds. Two of these bonds, involving the C480-C488 and C379-C432 disulfides, are highly susceptible to cleavage through chemical reduction, the team showed.

Researchers Zhong Yao, left, and Igor Stagljar (supplied images)

The internal environment of a cell is in a naturally reduced state compared to the surface, and does not usually support disulfides bonds. In contrast, extracellular proteins and protein domains contain disulfide bonds that are oxidized, creating a structural conformation that helps them bind to receptors.

Breaking disulfide bonds changes the conformation of the proteins, so they can no longer fit into their receptors. Treating the Omicron spike protein with a reducing agent breaks the disulfide bonds at the surface, inhibiting the spike protein from binding to the ACE2 receptor.

“While mutations, in general, have increased the transmissibility of Omicron subvariants, as well as their ability to evade the immune system, this vulnerability to disulfide cleavage presents potential target areas for treating Omicron infections,” said Stagljar, who is also a professor of biochemistry and molecular genetics at U of T’s Temerty Faculty of Medicine.

One potential treatment method that takes advantage of Omicron’s structural vulnerability is aerosol therapy. Reducing agents can be toxic to the body at higher levels and can potentially harm non-target proteins. Aerosol therapy overcomes this obstacle by delivering the reducing agent directly to the lungs, which can tolerate a higher concentration level of the reducing agent than the rest of the body.

The researchers found that Omicron variants were particularly sensitive to an antioxidant called bucillamine, which is in a Phase 3 clinical trial by Revive Therapeutics to evaluate its safety and efficacy.

“While Omicron is less deadly overall, it still poses a threat to older, immunocompromised and unvaccinated groups,” Yao said.

“It’s helpful to understand the mechanism through which Omicron variants are transmitted between people, so that we can harness it for therapeutic treatments and be more prepared.”

The research was supported by the PRiME COVID-19 Task Force, COVID Relief, the Toronto COVID-19 Action Fund and the Temerty Knowledge Translation grant.

Researchers use generative AI to design novel proteins

Christopher.Sorensen — Fri, 05 May 2023 16:40:22 +0000

Researchers use generative AI to design novel proteins

Christopher.Sorensen Fri, 05/05/2023 - 12:40

Cutline

Professor Philip Kim and PhD student Jin Sub (Michael) Lee have developed a generative AI system that can create proteins not found in nature, promising to speed drug development (supplied images)

Jim Oldfield

Topic

Donnelly Centre for Cellular & Biomolecular Research

Artificial Intelligence

Computer Science

Proteins

Researchers at the University of Toronto have developed an artificial intelligence system that can create proteins not found in nature using generative diffusion – the same technology behind popular AI image-creation platforms such as Midjourney and OpenAI’s DALL-E.

The system will help advance the field of generative biology, which promises to speed up drug development by making the design and testing of entirely new therapeutic proteins more efficient and flexible.

“Our model learns from image representations to generate fully new proteins at a very high rate,” says Philip M. Kim, a professor in the Donnelly Centre for Cellular and Biomolecular Research at U of T’s Temerty Faculty of Medicine. “All our proteins appear to be biophysically real, meaning they fold into configurations that enable them to carry out specific functions within cells.”

The findings were published in the journal Nature Computational Science and are the first of their kind in a peer-reviewed journal. Kim’s lab also published a pre-print on the model last summer through the open-access server bioRxiv ahead of two similar pre-prints from last December – RF Diffusion by the University of Washington and Chroma by Generate Biomedicines.

Proteins are made from chains of amino acids that fold into three-dimensional shapes, which in turn dictate protein function. Those shapes evolved over billions of years and are varied, complex and limited in number.

Now, with a better understanding of how existing proteins fold, researchers have begun to design folding patterns not produced in nature.

A major challenge, says Kim, has been to imagine folds that are both possible and functional.

“It’s been very hard to predict which folds will be real and work in a protein structure,” says Kim, who is also a professor in the departments of molecular genetics in the Temerty Faculty of Medicine and computer science in the Faculty of Arts & Science. “By combining biophysics-based representations of protein structure with diffusion methods from the image generation space, we can begin to address this problem.”

The new system, which the researchers call ProteinSGM, draws from a large set of image-like representations of existing proteins that encode their structure accurately. The researchers feed these images into a generative diffusion model that gradually adds noise until each image becomes all noise. The model tracks how the images become noisier and then runs the process in reverse, learning how to transform random pixels into clear images that correspond to fully novel proteins.

Jin Sub (Michael) Lee, a doctoral student in the Kim lab and first author on the paper, says that optimizing the early stage of this image generation process was one of the biggest challenges in creating ProteinSGM.

“A key idea was the proper image-like representation of protein structure, such that the diffusion model can learn how to generate novel proteins accurately,” says Lee, who is from Vancouver but did his undergraduate degree in South Korea and master’s degree in Switzerland before choosing ��οfor his doctorate.

Also difficult was validation of the proteins produced by ProteinSGM. The system generates many structures – often unlike anything found in nature. Almost all of them look real according to standard metrics, says Lee, but the researchers needed further proof.

To test their new proteins, Lee and his colleagues first turned to OmegaFold, an improved version of DeepMind’s software AlphaFold 2. Both platforms use AI to predict the structure of proteins based on amino acid sequences.

With OmegaFold, the team confirmed that almost all their novel sequences fold into the desired protein structures. They then chose a smaller number to create physically in test tubes, to confirm the structures were proteins and not just stray strings of chemical compounds.

“With matches in OmegaFold and experimental testing in the lab, we could be confident these were properly folded proteins. It was amazing to see validation of these fully new protein folds that don’t exist anywhere in nature,” Lee says.

Next steps based on this work include further development of ProteinSGM for antibodies and other proteins with the most therapeutic potential, Kim says. “This will be a very exciting area for research and entrepreneurship.”

Lee says he would like to see generative biology move toward joint design of protein sequences and structures, including protein side-chain conformations. Most research to date has focused on generation of backbones, the primary chemical structures that hold proteins together.

“Side-chain configurations ultimately determine protein function, and although designing them means an exponential increase in complexity, it may be possible with proper engineering,” Lee says. “We hope to find out.”

This research was funded by the Canadian Institutes of Health Research.

Zombies aren’t real – but fungal health threats are: U of T’s Leah Cowen on CBC Radio

siddiq22 — Fri, 10 Mar 2023 21:16:31 +0000

Zombies aren’t real – but fungal health threats are: U of T’s Leah Cowen on CBC Radio

siddiq22 Fri, 03/10/2023 - 16:16

Cutline

(photo by Liane Hentscher/HBO)

Tabassum Siddiqui

Topic

Leah Cowen

Vice-president of Research and Innovation and Strategic Initiatives

CIFAR

Fans following every twist and turn of the HBO series The Last of Us have found themselves intrigued by its premise – based on a 2013 video game, the series is set 20 years into a pandemic caused by a mass fungal infection, which causes its hosts to transform into zombie-type creatures.

Leah Cowen

With the season finale on March 12 approaching, Leah Cowen, co-director of the fungal kingdom program at the Canadian Institute for Advanced Research and U of T’s vice-president, research and innovation, and strategic initiatives, spoke with CBC Radio’s The Current about the staggering impact of fungi on our world – from benefits to threats.

“They're the only organisms that are causing extinctions in real time. There are millions of different kinds of fungal species out there, and they cause different kinds of infections,” Cowen, a professor in the department of molecular genetics in the Temerty Faculty of Medicine, told host Matt Galloway.

“Some of them you can acquire by inhaling spores that are widespread in the environment. Some of them are already inside your body and living there as sort of natural members of your microbiota. And so there are different kinds of infection … all the way through to invasive disease, which would be disseminated through the bloodstream – and those are the ones that are really deadly.”

While fungi may not turn people into zombie-like creatures like on The Last of Us, they do kill an estimated 1.5 million people each year and can threaten the health of immunocompromised people, Cowen said, noting that despite such serious implications, research into fungi remains underfunded.

The fungal world does have its benefits, Cowen pointed out – including helping plants to “colonize the planet,” their ability to break down plastics and help with carbon capture – but more study of both the positives and negatives would further reveal the full complexity of these organisms.

Cowen, who admits she hasn’t yet seen The Last of Us, said that understanding fungi could help us better understand ourselves.

“Fungi are actually closely related to humans. It may not look like it – but in fact, it's true,” she said. “Which means that fungi serve as fantastic model organisms – so we can study the function of genes or biological processes in a simpler system and be able to learn what might be relevant in the context of more complex organisms and human biology and disease.”

Listen to Leah Cowen on The Current

New research tool tackles deadly mosquito-borne diseases

Christopher.Sorensen — Tue, 07 Feb 2023 21:07:35 +0000

New research tool tackles deadly mosquito-borne diseases

Christopher.Sorensen Tue, 02/07/2023 - 16:07

Cutline

Kathryn Rozen-Gagnon, an assistant professor of molecular genetics who is a member of the Emerging and Pandemic Infections Consortium, is studying the relationship between mosquito-borne viruses and their mosquito and human hosts (photo by Betty Zou)

Betty Zou

Topic

Emerging and Pandemic Infections Consortium

Institutional Strategic Initiatives

Disease

For most people living in Canada, mosquitoes are nothing more than a summertime nuisance, intruding on nights at the cottage and evenings around the campfire. But for millions of people around the world, particularly in the Global South, they are a serious and potentially fatal threat.

According to a 2017 report from the World Health Organization, mosquito-transmitted diseases such as malaria, dengue and Chikungunya affect an estimated 347.8 million people annually and are responsible for nearly 450,000 deaths each year, making the insects one of the most dangerous animals in the world.

Yet, despite a devastating impact that’s predicted to get worse as climate change drives global temperatures higher, research on the mosquito has lagged behind that of other model organisms such as the fruit fly – in part due to the lack of appropriate tools and resources.

Kathryn Rozen-Gagnon is trying to change that.

She recently joined the department of molecular genetics in the Temerty Faculty of Medicine as an assistant professor. Her lab will study the relationship between mosquito-borne viruses and their mosquito and human hosts. Specifically, she is focusing on viruses such as Zika, dengue and Chikungunya, which have RNA as their genetic material.

“It fascinates me that you have a virus with this very small piece of single-stranded RNA that encodes about 10 genes and yet, with this minimal system, it can navigate very, very different host species,” says Rozen-Gagnon, who is also a member of the Emerging and Pandemic Infections Consortium (EPIC), one of several Institutional Strategic Initiatives at the university.

Rozen-Gagnon’s approach integrates diverse fields like computational biology, insect immunology, RNA biology and virology to dissect how these viruses succeed by interacting with their hosts’ RNA and immune systems. As a post-doctoral fellow and research associate in Nobel Laureate Charles Rice’s lab at the Rockefeller University, she developed cutting-edge methods to better understand how the mosquito immune system responds to viral infection.

One of the tools she created is a universal software package called CLIPflexR that can help researchers uncover a protein’s RNA targets. It improves upon existing software by providing a more reproducible and streamlined approach for data analysis. More importantly, CLIPflexR has the flexibility to work with genome datasets from any organism, including ones like the mosquito where genomes are not as complete or well characterized as the genomes of more commonly studied species.

Using this new software package, Rozen-Gagnon mapped out the RNA targets for a family of RNA-binding proteins called Argonaute proteins, which play a crucial role in mosquitoes’ antiviral defence. Mosquitoes rely on a system called RNA interference to protect themselves from viral infection. A specific Argonaute protein facilitates this by targeting and destroying viral RNA, which reduces virus replication.

“It’s important that the virus can maintain a high level in the mosquito without damaging the mosquito too much because it needs that mosquito to go on to bite people,” says Rozen-Gagnon. “Some scientists have argued that this RNA-based immune response enables viral persistence by keeping the virus at a level where it’s not going to have negative effects on the mosquito, but there is still enough virus to transmit to humans,”

By providing snapshots of which RNAs are targeted by Argonaute proteins, her work is providing new insights into how the mosquito’s immune system maintains this delicate balance.

To further expand the toolbox for mosquito research, Rozen-Gagnon developed the first-of-its-kind CRISPR gene editing system optimized for mosquito cells. The new tool allows scientists to conduct large genetic studies using mosquito cells grown in a lab to understand the function of different genes. In a proof-of-principle study published in Scientific Reports, she and her colleagues showed that the mosquito-optimized CRISPR system was efficient and versatile. Further, because the system uses DNA components known as plasmids, which are cheap to buy and easy to make and modify, it is more cost-effective than versions that rely on expensive purified proteins.

“This is a really great tool that will allow us to ask, what mosquito genes are important for virus replication?” says Rozen-Gagnon. “We haven’t been able to do that using updated gene editing technologies like CRISPR in an unbiased way.

“It also democratizes who can do these kinds of studies. Providing cheap methods like this one allows labs from many different parts of the world to contribute to the field in a meaningful way, which I think is very important.”

Both tools will play a central role in her lab’s work as she continues to delve into the inner workings of mosquito immunity and the interplay between viral infection and a particular type of RNA called microRNA in human and mosquito cells.

Rozen-Gagnon’s research will be further enabled by access to an insectary in the revitalized Toronto High Containment Facility, which recently received a $35 million federal investment to support its modernization. The specially designed space will allow her to infect mosquitoes with viruses like dengue and Chikungunya in a safe and secure way and conduct complementary studies in lab-grown mosquito cells and live insects.

A new model for innovation? How Elizabeth and Aled Edwards are driving an open science revolution

rahul.kalvapalle — Mon, 07 Nov 2022 15:38:12 +0000

A new model for innovation? How Elizabeth and Aled Edwards are driving an open science revolution

rahul.kalvapalle Mon, 11/07/2022 - 10:38

Cutline

Elizabeth and Aled Edwards say an open science approach promises to accelerate key discoveries that will help address everything from the next pandemic to climate change (photo by Johnny Guatto)

Rahul Kalvapalle

Topic

Open Science

Structural Genomic Consortium

Cell and Systems Biology

Faculty of Applied Science & Engineering