Biochemistry

COVID-19

Donnelly Centre for Cellular & Biomolecular Research

Medical Research

Researchers at the ��Ƶ 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 rapid antibody test to gauge immune response to SARS-CoV-2 variants

Christopher.Sorensen — Wed, 06 Jul 2022 13:17:59 +0000

Researchers use rapid antibody test to gauge immune response to SARS-CoV-2 variants

Christopher.Sorensen Wed, 07/06/2022 - 09:17

Cutline

A U of T study found the antibodies generated by people who were vaccinated and/or recovered from COVID-19 prior to 2022 failed to neutralize today's variants (photo by Shawn Goldberg/SOPA Images/LightRocket via Getty Images)

Jovana Drinjakovic

Topic

COVID-19

Donnelly Centre for Cellular & Biomolecular Research

COVID-19 infections are once again on the rise as our immune systems struggle to combat new variants.

That’s according to a ��Ƶ study that found the antibodies generated by people who were vaccinated and/or recovered from COVID-19 prior to 2022 failed to neutralize the variants circulating today.

Furthermore, the researchers expect that the antibody test they developed to measure immunity in the study’s participants will become a valuable tool for deciding who needs a booster and when, helping to save lives and avoid future lockdowns.

“The truth is we don’t yet know how frequent our shots should be to prevent infection,” said Igor Stagljar, a professor of biochemistry and molecular genetics at the Donnelly Centre for Cellular and Biomolecular Research and at the Temerty Faculty of Medicine. “To answer these questions, we need rapid, inexpensive and quantitative tests that specifically measure Sars-CoV-2 neutralizing antibodies, which are the ones that prevent infection.”

The study was led by Stagljar and Shawn Owen, an associate professor of pharmaceutics and pharmaceutical chemistry, at the University of Utah.

The journal Nature Communications recently published their findings.

Many antibody tests have been developed over the past two years. But only a few of the authorized ones are designed to monitor neutralizing antibodies, which coat the viral spike protein so that it can no longer bind its receptor and enter cells.

It's an important distinction, as only a fraction of all Sars-CoV-2 antibodies generated during infection are neutralizing. And while most vaccines were specifically designed to produce neutralizing antibodies, it’s not clear how much protection they give against variants.

“Our method, which we named Neu-SATiN, is as accurate as – but faster and cheaper than – the gold standard, and it can be quickly adapted for new variants as they emerge,” Stagljar said.

Neu-SATiN stands for Neutralization Serological Assay based on split Tri-part Nanoluciferase, and it is a newer version of SATiN, which monitors the complete IgG pool they developed last year.

The development of Neu-SATiN was spearheaded by Zhong Yao, a senior research associate in Stagljar’s lab, and Sun Jin Kim, a post-doctoral researcher in Owen’s lab, who are the co-first authors on the paper.

The pinprick test is powered by the fluorescent luciferase protein from a deepwater shrimp. It measures the binding between the viral spike protein and its human ACE2 receptor, each of which is attached to a luciferase fragment. The engagement of the spike protein with ACE2 pulls the fragments close, catalyzing reconstitution of the full length luciferase with a concomitant glow of light captured by the luminometer instrument. When a patient’s blood sample is added into the mixture, the neutralizing antibodies bind to – and mop up – all spike protein, while ACE2 remains in unengaged state. Consequentially, the luciferase remains in pieces and the light signal drops. The researchers say the plug-and-play design of the test means it can be adapted to emerging variants by engineering mutations in the spike protein.

The researchers applied Neu-SATiN to blood samples collected from 63 patients with different histories of COVID-19 and vaccination up to November 2021. Patient neutralizing capacity was assessed against the original Wuhan strain and the following variants: Alpha, Beta, Gamma, Delta and Omicron.

“We thought it would be important to monitor people that have been vaccinated to see if they still have protection and how long it lasts,” said Owen, who did his post-doctoral training in the Donnelly Centre with distinguished bioengineer and University Professor Molly Shoichet of the Faculty of Applied Science & Engineering. “But we also wanted to see if you were vaccinated against one variant, does it protect you against another variant?”

The neutralizing antibodies were found to last about three to four months before their levels would drop by about 70 per cent irrespective of infection or vaccination status. Hybrid immunity, acquired through both infection and vaccination, produced higher antibody levels at first, but these too dropped significantly four months later.

Most worryingly, infection and/or vaccination provided good protection against the previous variants, but not Omicron or its sub-variants BA.4 and BA.5.

The data match those from a recent U.K. study that showed that both neutralizing antibodies and cellular immunity – a type of immunity provided by memory T cells – from either infection, vaccination, or both, offered no protection from catching Omicron. In a surprising twist, the U.K. group also found that infections with Omicron boosted immunity against earlier strains, but not against Omicron itself for reasons that remain unclear.

“It's important to stress that vaccines still confer significant protection from severe disease and death,” said Stagljar. Still, he added that the findings from his team and others call for vigilance in the coming period given that the more transmissible BA.4 and BA.5 sub-variants can escape immunity acquired from earlier infections with Omicron, as attested by rising reinfections.

“There will be new variants in the near future for sure,” Stagljar said. “Monitoring and boosting immunity with respect to circulating variants will become increasingly important and our method could play a key role in this since it is fast, accurate, quantitative and cheap.”

He is already collaborating with the Canadian vaccine maker Medicago to help determine the efficacy of their candidates against Omicron and its sub-variants. Meanwhile, U of T is negotiating to license Neu-SATiN to a company which will scale it up for real world uses such as population immunosurveillance and vaccine development.

The research was supported with funding from the Toronto COVID-19 Action Fund, Division of the Vice-President, Research & Innovation and the 3i Initiative at the University of Utah.

New drug shows promise slowing tumour growth in some hard-to-treat cancers

Christopher.Sorensen — Thu, 28 Apr 2022 15:40:28 +0000

New drug shows promise slowing tumour growth in some hard-to-treat cancers

Christopher.Sorensen Thu, 04/28/2022 - 11:40

Cutline

Daniel Durocher's lab designed a new drug with CRISPR-Cas9 gene-editing technology that blocks an enzyme essential for the survival of certain cancer cells (photo courtesy of Sinai Health)

Amanda Ferguson

Topic

Sinai Health

Alumni

Scientists at Sinai Health and the ��Ƶ say a new drug designed to block an enzyme essential for the survival of certain cancer cells shows promise in curbing tumour growth.

The preclinical findings, published this month in the journal Nature, describe a new drug designed with CRISPR-Cas9 gene-editing technology in the lab of Daniel Durocher, a senior investigator at Sinai Health’s Lunenfeld-Tanenbaum Research Institute (LTRI) and a professor of molecular genetics in U of T’s Temerty Faculty of Medicine.

The researchers identified genes that are essential for the viability of CCNE1 amplified cancer cells, which are characteristic of some hard-to-treat ovarian, endometrial and bladder cancers. They found the enzyme PKMYT1 is essential in CCNE1 amplified cells, but not in otherwise healthy cells. In collaboration with precision oncology company Repare Therapeutics, the team developed a drug called RP-6306, which blocks PKMYT1 activity and effectively kills the cancer cell.

“These cancer cells depend on the PKMYT1 enzyme to survive,” said Durocher. “Our preclinical data show enormous promise in the drug RP-6306’s ability to target these types of tumours and profoundly inhibit tumour growth.”

Currently, tumors with CCNE1 amplification have very few therapeutic options. David Gallo, a senior scientist at Repare Therapeutics, said they’ve been able to demonstrate that RP-6306 is both potent and selective for oral use in humans.

“Gynecological and other solid tumours with amplifications of CCNE1 are notoriously resistant to current standard-of-care treatments,” said Gallo, co-first author on the Nature paper. “There is a dire need to find new options for these patients.”

The work was a close collaboration between the Durocher lab and Repare Therapeutics. Durocher founded Repare Therapeutics in 2016 alongside Frank Sicheri, also a Lunenfeld-Tanenbaum Research Institute senior investigator who is a professor of molecular genetics and biochemistry at U of T.

The company is built on the concept of synthetic lethality, a process that incorporates functional genomics to discover genetic vulnerabilities to specific cancer mutations.

“This close collaboration between our group and Repare highlights how industry and academia can work together to discover new treatment options for cancer patients,” said Durocher. “It’s rare that a new target is published alongside a launched clinical trial. This speaks volumes about the innovative capacity of the LTRI and its collaborators.”

Repare Therapeutics has initiated Phase I clinical trials in patients with CCNE1 amplified solid tumours, with initial results expected in late 2022.

The research was funded by Repare Therapeutics and the Canadian Institutes of Health Research.

This story was originally published at Sinai Health.

Startup spun out of Igor Stagljar's U of T lab to develop precision cancer therapies

Christopher.Sorensen — Tue, 15 Feb 2022 20:55:17 +0000

Startup spun out of Igor Stagljar's U of T lab to develop precision cancer therapies

Christopher.Sorensen Tue, 02/15/2022 - 15:55

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Professor Igor Stagljar, left, has partnered with drug discovery firm Cyclica, co-founded by CEO Naheed Kurji, right, to launch the biotech startup Perturba, which is focused on difficult-to-treat cancers (photos courtesy of Tonko Buterin and Cyclica)

Jovana Drinjakovic

Topic

Donnelly Centre for Cellular & Biomolecular Research

Innovation & Entrepreneurship

Entrepreneurship

Startups

The ��Ƶ and the AI drug discovery company Cyclica have launched a biotech startup that will develop targeted therapies for difficult-to-treat cancers.

In partnership with Cyclica, Igor Stagljar, a professor in the Donnelly Centre for Cellular and Biomolecular Research in U of T’s Temerty Faculty of Medicine, founded Perturba to bring together Cyclica’s AI drug design technology with two live cell-based assays from the Stagljar lab, called MaMTH and SIMPL, for validation of selected compounds.

“I am very excited about our collaboration with Cyclica, thanks to their powerful AI platform that has transformed research in my laboratory over the past few years,” said Stagljar, who is also a professor of biochemistry and molecular genetics at Temerty Medicine. “Our combined approach allows us to go after some of the most intractable cancers by selecting in silico drug molecules that specifically target oncogenic proteins.

“It will also accelerate drug development by cutting the time to preclinical testing from several years to months.”

The company builds on an earlier collaboration between Stagljar’s lab and Cyclica, which produced two inhibitors of the osimertinib-resistant triple mutant EGF receptor for the treatment of non-small cell lung cancer, the most common type of lung cancer, which Perturba will initially focus on advancing. Osimertinib is currently the drug of last resort for this type of cancer.

Perturba will also launch four programs targeting small GTPases – enzymes that are mutated in many cancers, but which have been difficult to target with conventional methods.

“What others view as ‘undruggable,’ we see as potential,” said Naheed Kurji, co-founder, CEO and president of Cyclica.

The Stagljar lab is renowned for its study of protein-protein interactions (PPIs). MaMTH and SIMPL were initially developed for mapping human protein networks on a global scale. Understanding how proteins talk to each is important, because when those interactions go awry, it can lead to disease.

Stagljar’s team previously mapped interactions between disease-causing proteins and their partners, revealing potential “weak spots” that can be targeted by small molecule drugs for potential treatments of diseases ranging from cancer to cystic fibrosis.

Perturba’s compounds work by specifically perturbing oncogenic PPIs in cancer cells, thereby sparing the surrounding healthy tissue from harmful effects. But the hunt for such drugs has been slow using traditional approaches, which often resulting in compounds with off-target effects. In other words, they act on unintended proteins as well as their targets, which can have wide side-effects in the body.

Advances in AI have transformed drug discovery thanks to machine learning algorithms that can pick the best candidates from vast chemical libraries containing billions of molecules, which selectively inhibit disease-causing PPIs. That has opened the door to targeting previously “undruggable” proteins, which make up the majority of the human proteome.

“Lots of proteins have smooth surfaces with no pockets for drugs to bind to. But using Cyclica’s approach we can screen protein surfaces for wild type and oncogenic versions, and we can then test our molecules very quickly in our live cell-based assays,” said Stagljar.

“Cyclica’s AI-augmented polypharmacology based drug design platform technology, complemented with Professor Stagljar’s empirical live cell assays, allows us to approach targets we could not before,” said Kurji. “We’re so excited to partner with the world-class Stagljar lab in driving forward our shared vision.”

U of T research may help explain children's immune response to COVID-19

Christopher.Sorensen — Tue, 05 Oct 2021 19:58:39 +0000

U of T research may help explain children's immune response to COVID-19

Christopher.Sorensen Tue, 10/05/2021 - 15:58

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(Photo by Steve Russell via Getty Images)

Jim Oldfield

Topic

Coronavirus

Cell and Systems Biology

Ecology & Evolutionary Biology

Computer Science

Faculty of Arts & Science

Hospital for Sick Children

Immunology

Researchers at the ��Ƶ have found that immune cells from the upper respiratory tracts of children, taken years before the pandemic began, react with the virus that causes COVID-19.

The findings hint at a possible reason why children with COVID-19 are often asymptomatic or have mild symptoms, while many adults experience severe disease and even death.

“We isolated B cells from tonsil tissues collected from children over five years ago, and found that some are reactive to the SARS-CoV-2 spike protein,” said Goetz Ehrhardt, principal investigator on the study and an associate professor of immunology at U of T’s Temerty Faculty of Medicine.

“We found that antibodies generated from these B cells have neutralizing potential against the virus in lab experiments, reducing the ability of the spike protein to bind to its target protein on the cell surface.”

The study, published in the Journal of Immunology, is one of just a few to examine the role of the mucosal immune system in COVID-19. Other studies have looked at immune components in the blood – often after infection has taken hold or during recovery.

Mucosal surfaces comprise one of the largest components of the immune system and include the gut, urogenital tract and respiratory system – all of which teem with microbiota including bacteria, viruses and fungi.

The researchers at first assumed the B cells reacted to SARS-CoV-2 because they had encountered similar coronaviruses in the past, perhaps through common colds and other infections.

But the antibodies did not react to those coronaviruses in further testing, although they did share genetic sequence characteristics linked to other triggers.

Taken together, Ehrhardt said, the results suggest cross-reactivity in the B-cell antibodies. “The immune system makes these antibodies toward certain agents or pathogens and as a by-product the antibodies react to SARS-CoV-2,” he said. “It will be interesting to find out what causes that reaction.”

A better understanding of the antibody reaction could shed light on the mystery of COVID-19 susceptibility in children and adults and inform clinical and public health decisions as well as therapeutic approaches.

Whatever the cause of the reaction, it is likely due to a common element in the childhood environment: all samples tested had the SARS-CoV-2-reactive B cells, many of which the researchers observed among the immune systems' ‘naïve’ or newly generated B cells that had not encountered any pathogen.

“One explanation is that some of these B cells react to triggers in the microbiome,” said Yanling Liu, lead author on the paper and a senior research associate in Ehrhardt’s lab.

“Or it could still be that antibodies are reacting to endemic coronaviruses and we just didn’t see that,” Liu said. “We don’t really know, but one implication of our work is that it suggests children should respond to vaccines very well since they have those naive B cells ready to recognize vaccine in their lymphoid tissue.”

Several other researchers were key to the study, Liu and Ehrhardt said, including James Rini, a professor of biochemistry and molecular genetics at U of T who provided purified spike proteins from viral samples.

Amin Zia used computational biology to scan large databases and predict which antibodies would react to the virus. Zia was a post-doctoral researcher in the lab of Alan Moses, a professor in U of T’s departments of cell and systems biology, ecology and evolutionary biology and computer science in the Faculty of Arts & Science.

“About half the antibodies we generated were based on computer-generated predictions,” said Ehrhardt. “That was first for us, and it won’t be a last.”

Researchers at the Hospital for Sick Children, with whom Ehrhardt’s lab has collaborated for years, supplied the tonsil tissue samples.

“Mucosae are no doubt a very important interface for the immune system’s response to a great variety of pathogens, but availability of samples has been a major impediment,” said Ehrhardt. “Research in this area is gathering steam, and it will be interesting to see where that takes us.”

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

From detecting earthquakes to preventing disease: 27 U of T research projects receive CFI funding

Christopher.Sorensen — Thu, 12 Aug 2021 19:35:43 +0000

From detecting earthquakes to preventing disease: 27 U of T research projects receive CFI funding

Christopher.Sorensen Thu, 08/12/2021 - 15:35

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In a U of T Engineering lab, rock samples are subjected to the stress, fluid pressure and temperature conditions they experience in nature (photo courtesy of Sebastian Goodfellow)

Tyler Irving

Topic

Institute of Biomedical Engineering

Princess Margaret Cancer Centre

Donnelly Centre for Cellular & Biomolecular Research

Resarch & Innovation

Cell and Systems Biology

Dalla Lana School of Public Health

Chemistry

Earth Sciences

Faculty of Applied Science & Engineering

Faculty of Arts & Science

Laboratory Medicine and Pathobiology

Mount Sinai Hospital

Nutritional Sciences

Psychology

St. Michael's Hospital

U of T Mississauga

U of T Scarborough

University Health Network

UTIAS

Sebastian Goodfellow, a researcher at the ��Ƶ, listens for hidden signals that the ground is about to move beneath our feet.

That includes so-called “induced” earthquakes that stem from human activities such as hydraulic fracturing (‘fracking’) and enhanced geothermal systems.

“Think of the cracking sounds a cube of ice makes when you drop it in a cup of warm water, or the sound a wooden stick makes when you bend it until it breaks,” says Goodfellow, an assistant professor in the department of civil and mineral engineering in the Faculty of Applied Science & Engineering.

“This occurs as a consequence of sudden localized changes in stress, and we study these microfracture sounds in the lab to understand how rock responds to changes in stress, fluid pressure and temperature.”

While the frequency of these sonic clues is beyond the range of human hearing, they can be picked up with acoustic emission sensors. The challenge, however, is that scientists must listen continuously for hours in the absence of a method to predict when they will occur.

“We’re talking about more than a terabyte of data per hour,” says Goodfellow. “We use a form of artificial intelligence called machine learning to extract patterns from these large waveform datasets.”

Goodfellow’s study of induced seismicity project is one of 27 at U of T – and nine from U of T Engineering – to share more than $8.2 million in funding from the Canada Foundation for Innovation’s John R. Evans Leaders Fund (Read the full list of researchers and their projects).

Named for the late U of T President Emeritus John R. Evans, the fund equips university researchers with the technology and infrastructure they need to remain at the forefront of innovation in Canada and globally. It also helps Canadian universities attract top researchers from around the world.

“From sustainable electric transportation and engineering of novel materials to non-invasive neuro-imaging and applications of AI in public health, U of T researchers across our three campuses are advancing some of the most important discoveries of our time,” said Leah Cowen, U of T’s associate vice-president, research.

“Addressing such complex challenges often requires cutting-edge technology, equipment and facilities. The support provided by the Canada Foundation for Innovation will go a long way towards enabling our researchers’ important work.”

Goodfellow’s team will use the funding to buy a triaxial geophysical imaging cell fitted with acoustic emissions sensors as well as hardware for high-frequency acquisition of acoustic emissions data. The equipment will enable them to carry out controlled experiments in the lab, test better algorithms and develop new techniques to turn the data into insights – all to better understand processes that lead to induced earthquakes.

By learning more about how these tiny cracks and pops are related to larger seismic events such as earthquakes, the team hopes to help professionals in a wide range of sectors make better decisions. That includes industries that employ underground injection technologies – geothermal power, hydraulic fracturing and carbon sequestration, among others – along with the bodies charged with regulating them.

“Up until now, our poor understanding of the causal links between fluid injection and large, induced earthquakes limited the economic development of these industries,” says Goodfellow.

“Our research will help mitigate the human and environmental impacts, leading to new economic growth opportunities for Canada.”

Here is the full list of 27 U of T researchers who received support for their projects:

Cristina Amon, department of mechanical & industrial engineering in the Faculty of Applied Science & Engineering: Enabling sustainable e-mobility through intelligent thermal management systems for EVs and charging infrastructure

Jacqueline Beaudry, department of nutritional sciences in the Temerty Faculty of Medicine and Lunenfeld-Tannenbaum Research Institute at Sinai Health: Role of pancreatic and gut hormones in energy metabolism

Swetaprovo Chaudhuri, U of T Institute for Aerospace Studies in the Faculty of Applied Science & Engineering: Kinetics-transport interaction towards deposition of carbon particulates in meso-channel supercritical fuel flows

Mark Currie, department of cell and systems biology in Faculty of Arts & Science: Structural Biology Laboratory

Marcus Dillon, department of biology at U of T Mississauga: The evolutionary genomics of infectious phytopathogen emergence

Landon Edgar, department of pharmacology and toxicology in the Temerty Faculty of Medicine: Technologies to interrogate and control carbohydrate-mediated immunity

Gregory Fairn, department of biochemistry in the Temerty Faculty of Medicine and St. Michael’s Hospital: Advanced live cell imaging and isothermal calorimetry for the study immune cell dysfunction and inflammation

Kevin Golovin, department of mechanical and industrial engineering in the Faculty of Applied Science & Engineering: Durable Low Ice Adhesion Coatings Laboratory

Sebastian Goodfellow, department of civil and mineral engineering in the Faculty of Applied Science & Engineering: A study of induced seismicity through novel triaxial experiments and data analysis methodologies

Giovanni Grasselli, department of civil and mineral engineering in the Faculty of Applied Science & Engineering: Towards the sustainable development of energy resources - fundamentals and implications of hydraulic fracturing technology

Kristin Hope, department of medical biophysics in the Temerty Faculty of Medicine and Princess Margaret Cancer Centre, University Health Network: Characterizing and unlocking the therapeutic potential of stem cells and the leukemic microenvironment

Elizabeth Johnson, department of psychology at U of T Mississauga: Baby Brain and Behaviour Lab (BaBBL) – electrophysiological measures of infant speech and language development

Omar Khan, Institute of Biomedical Engineering in the Faculty of Applied Science & Engineering and department of immunology in the Temerty Faculty of Medicine: Combination ribonucleic acid treatment technology lab

Marianne Koritzinsky, department of radiation oncology in the Temerty Faculty of Medicine and Princess Margaret Cancer Centre, University Health Network: Targeted therapeutics to enhance radiotherapy efficacy and safety in the era of image-guided conformal treatment

Christopher Lawson, department of chemical engineering & applied chemistry in the Faculty of Applied Science & Engineering: The Microbiome Engineering Laboratory for Resource Recovery

Fa-Hsuan Lin, department of medical biophysics in the Temerty Faculty of Medicine and Sunnybrook Research Institute: Integrated non-invasive human neuroimaging and neuromodulation platform

Vasanti Malik, department of nutritional sciences in the Temerty Faculty of Medicine: Child obesity and metabolic health in pregnancy – a novel approach to chronic disease prevention and planetary health

Rafael Montenegro-Burke, Donnelly Centre for Cellular and Biomolecular Research and department of molecular genetics in the Temerty Faculty of Medicine: Mapping the dark metabolome using click chemistry tools

Robert Rozeske, department of psychology at U of T Scarborough: Neuronal mechanisms of dynamic emotional behavior

Karun Singh, department of laboratory medicine and pathobiology in the Temerty Faculty of Medicine and Toronto Western Hospital, University Health Network: Stem cell models to investigate brain function in development and disease

Corliss Kin I Sio, department of Earth sciences in the Faculty of Arts & Science: Constraining source compositions and timescales of mass transport using femtosecond LA-MC-ICPMS

Helen Tran, department of chemistry in the Faculty of Arts & Science: Macromolecular bioelectronics encoded for self-assembly, degradability and electron transport

Andrea Tricco, Dalla Lana School of Public Health: Expediting knowledge synthesis using artificial intelligence – CAL®-Synthesi.SR Dashboard

Jay Werber, department of chemical engineering and applied chemistry in the Faculty of Applied Science & Engineering: The Advanced Membranes (AM) Laboratory for Sustainable Water Management and Resource Recovery

Haibo Zhang, department of physiology in the Temerty Faculty of Medicine and St. Michael’s Hospital: Real time high-resolution imaging and cell sorting for studying multi-organ repair and regeneration after lung injury

Gang Zheng, department of medical biophysics in the Temerty Faculty of Medicine and Princess Margaret Cancer Centre, University Health Network: Preclinical magnetic resonance imaging for targeted brain tumour therapies

Shurui Zhou, department of electrical and computer engineering in the Faculty of Applied Science & Engineering: Improving collaboration efficiency for fork-based software development

U of T researchers grow mini-organs to study brain development and disease

Christopher.Sorensen — Wed, 19 May 2021 14:14:39 +0000

U of T researchers grow mini-organs to study brain development and disease

Christopher.Sorensen Wed, 05/19/2021 - 10:14

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Jeff Wrana, a professor in U of T's Temerty Faculty of Medicine, uses "organoids," or mini-organs grown using stem cells, to better understand diseases including cancer (photo courtesy of Sinai Health Foundation)

Paul Fraumeni

Topic

Insulin 100

Donnelly Centre for Cellular & Biomolecular Research

Faculty of Arts & Science

“Organoids.”

It’s a word that has a science-fiction sound to it, but, in fact, organoids are at the core of what scientist Jeff Wrana calls “revolutionizing biology.”

That’s because organoids offer the promise of new treatments for a host of diseases and conditions, from inflammatory bowel disease to autism spectrum disorder.

“An organoid is a little organ that we can create using human and mouse embryonic stem cells,” says Wrana, a professor in the department of molecular genetics in the ��Ƶ’s Temerty Faculty of Medicine and a senior investigator at Mount Sinai Hospital’s Lunenfeld-Tanenbaum Research Institute. “They provide an opportunity to make tiny models of the intestines, liver and kidneys. Our team’s focus now is making cerebral organoids, which are models of parts of the brain.”

The organoids are not “mini-brains,” however, because they are only tiny pieces of tissue that don’t have anywhere near the complexity of even a mouse brain. These are not brains that can think or have consciousness. But these models are offering powerful ways to study disease.

Doing this sophisticated work requires a top-flight team with a wide range of expertise: Like Wrana, Laurence Pelletier is also a senior investigator at the Lunenfeld-Tanenbaum Research Institute and a U of T professor of molecular genetics; Liliana Attisano is a professor in U of T’s department of biochemistry and Canada Research Chair in Signalling Networks in Cancer; Ben Blencowe is a U of T molecular genetics professor and the Banbury Chair in Medical Research; and Sidhartha Goyal is a professor in U of T’s department of physics in the Faculty of Arts & Science. Attisano and Blencowe are also scientists at U of T’s Donnelly Centre for Cellular and Biomolecular Research.

The team is one of 11 sharing nearly $21 million in funding from Medicine by Design over three years. Funded by a $114-million grant from the Canada First Research Excellence Fund, Medicine by Design is a strategic research initiative that is working at the convergence of engineering, medicine and science to catalyze transformative discoveries in regenerative medicine and accelerate them toward clinical impact.

Wrana and his colleagues have already done important work using organoids to study how cancer starts and how the intestines can regenerate after injury.

Now focusing on the brain, the team will use organoids to examine how the tissue in the brain develops. A key part of this process is a complex phenomenon called splicing that starts with the genes. It’s an essential part of development. It is responsible for ensuring that segments of genes, referred to as exons, are precisely joined to make RNA transcripts that can direct the production of proteins, the key building blocks of all cells. Importantly, the process of alternative splicing, whereby exons are joined in different combinations to generate multiple protein products from a single gene, is critical for the development of complex organs such as the brain.

Blencowe and his collaborators showed previously that there is a link between autism and abnormal alternative splicing of very short exons, called microexons, which are found primarily in the brain. These microexons are either spliced in or left out of the final gene transcript before it directs protein synthesis. Microexons can have a dramatic effect on a protein’s ability to bind its partners, which is required during brain development. This was an important finding, but researchers didn’t understand the role of individual microexons until recently.

In January 2020, Blencowe and his team published a paper in the journal Molecular Cell that characterized the function of a single microexon that is frequently skipped in transcripts in the brains of people with autism.

The researchers showed that mice engineered to lack the microexon displayed behaviours related to those seen in autism, such as avoidance of social interactions. The mice also performed poorly in a learning and memory test.

Now Blencowe, working with Wrana’s Medicine by Design-funded research team, will be able to investigate this process further using the human brain model provided through the organoids the team is creating.

“We will be able to model how neural tissues develop with the organoid,” says Wrana. “And, remember, since we are using human stem cells, we will be creating human models of disease and conditions like autism. Using mice is certainly helpful, but a mouse model can’t recapitulate all the aspects of a human disease. We think that using human models will bring us unique insight because there are human-specific aspects to many of these signaling networks.”

Blencowe says this investigation could ultimately lead to important new therapeutic approaches for people with autism. One possibility is increasing the activity of a regulator of microexon splicing using small molecules. An organoid model under development by Wrana’s group will provide a valuable initial test of the efficacy of this approach.

But to do a more complete range of brain research, Wrana’s team ran up against a big problem: they couldn’t get the organoids to grow blood vessels.

“If we’re going to do our work to the full extent, we need these models to include other types of cells typically found in the brain. And blood vessels are essential.”

Fortunately, they discovered a way to get something very much like blood vessels into the models by using microfluidic devices.

“It’s like a little pump where we can implant organoids in these devices. The device pumps nutrient solutions around the organoid. The solution isn’t true blood, but it mimics blood. And that will stimulate the formulation of blood vessels in the device. Those blood vessels will actually support organoid growth.”

Wrana says the development of this device is a major step forward because it will enable the team to examine conditions like stroke. The project will also develop tools to help the development of safer and more efficient drugs and improved strategies to treat stroke.

“You can take the microfluidic device and put in little beads. The beads will get taken up into the blood vessels. As they move towards the organoid brain model, the blood vessels get smaller and smaller. And at some point, these beads will actually clog the blood vessel. So we think this can be a model for stroke. We can induce a stroke-like event and look for the earliest changes that occur in a human system when a stroke happens and that will help in the development of drugs to prevent and treat stroke.”

The vascularized brain model will also enable the researchers to examine the inner workings of the blood-brain barrier that protects the brain from pathogens and toxins.

“This is a big question in drug development,” says Wrana. “You want some drugs to penetrate this barrier to treat diseases that affect the brain, such as multiple sclerosis. But there are other drugs that you don’t want to get into the neural tissue because they could damage the brain. So, this organoid model could potentially allow us to measure if drugs can penetrate the human blood-brain barrier, because the human blood-brain barrier isn’t exactly the same as those in animals like mice.”

Wrana says this kind of adventurous research wouldn’t be possible without the support of Medicine by Design.

“Our work would never be funded through traditional grant funding mechanisms, which tend to be more conservative. Medicine by Design allows you to think about possibilities and then actually try to do the pie-in-the-sky experiment. For example, developing our microfluidic device is not something you could propose to do in a standard grant platform, which would have required preliminary data. We probably wouldn’t get the funding until we had actually produced the device. But Medicine by Design has supported us in these more speculative ideas. That’s really been transformative for our research program. “

With files from Jovana Drinjakovic

U of T researchers to help form national Coronavirus Variants Rapid Response Network

Christopher.Sorensen — Mon, 29 Mar 2021 19:13:41 +0000

U of T researchers to help form national Coronavirus Variants Rapid Response Network

Christopher.Sorensen Mon, 03/29/2021 - 15:13

Cutline

Anne-Claude Gingras, a professor in the Temerty Faculty of Medicine and senior investigator at Sinai Health, is among several Canadian researchers participating in a national network to track and test COVID-19 variants (photo by Colin Dewar/Sinai Health)

Amanda Ferguson

Topic

Coronavirus

Donnelly Centre for Cellular & Biomolecular Research

University Health Network

Canadian scientists at the forefront of the fight against COVID-19 – including several at the ��Ƶ – have received funding from the federal government to track and test viral variants that are now spreading rapidly across the country.

The federal government said it will establish the Coronavirus Variants Rapid Response Network through a $9 million grant from the Canadian Institutes of Health Research, part of $14.3 million in new funding for research on COVID-19 variants.

More than 30 scientists are part of the effort, which is led by Marc-André Langlois at the University of Ottawa.

“Viral variants are emerging that have multiple combinations of mutations that may have different effects on the virus’s ability to infect cells or to hide from the immune system,” said Anne-Claude Gingras, a professor of molecular genetics at U of T’s Temerty Faculty of Medicine and a senior investigator in the Lunenfeld-Tanenbaum Research Institute (LTRI) at Sinai Health who is among eight co-principal applicants on the project.

“While many of the research groups involved, including ours, were already working on characterizing variants, this new funding will enable them to do so in a more efficient manner through collaborations across the country.”

Gingras is a cancer researcher who specializes in proteomics. She pivoted her lab in the early stages of the pandemic to develop blood tests that can look for antibodies to viral proteins. She said laboratories with specialized expertise will be able to join the network and contribute to variant characterization and rapidly share the results back with the rest of the team.

The scientists hope the network will allow them to rapidly act on the emergence of new variants of concern by quickly learning the virus’s features, including the potential for re-infection.

Jennifer Gommerman, a professor of immunology at the Temerty Faculty of Medicine and co-applicant on the grant, said the goal of the network is to communicate the new information in real time to Canadian public health officials and decision-makers, as well to the broader international scientific community.

“The data generated will directly alert us to the potential threats of re-infection, increased transmissibility and pathogenicity, and vaccine resistance,” Gommerman said. “This network was designed on one critical principle: to provide scientifically-based rapid-response to the variants of concern.”

Other Temerty Faculty of Medicine scientists involved in the project include James Rini, a professor in the departments of molecular genetics and biochemistry; Jason Moffat, a professor of molecular genetics and in the Donnelly Centre for Cellular and Biomolecular Research; and Andrew Morris, a professor in the department of medicine who is also medical director of the Sinai Health-University Health Network antimicrobial stewardship program.

Jeff Wrana is also part of the new network. He is professor of molecular genetics in the Temerty Faculty of Medicine and a senior investigator at LTRI who recently used his robotics lab to create an automated, next-generation sequencing platform that can accurately screen thousands for COVID-19.

Wrana and colleagues are now using that system, called SPAR-Seq, to screen all positive samples identified in the shared clinical diagnostics lab at Sinai Health and University Health Network. The goal is to identify known and novel variants that emerge in the population and are resistant to vaccination.

The grant will allow the network to operate for one year and to create a Biobank for rapid sharing of samples and data with other biobanks across Canada in order to have a harmonized approach to fight against COVID-19.

'The future Bantings and Bests': How insulin's discovery at U of T is fuelling research 100 years later

Christopher.Sorensen — Fri, 19 Mar 2021 15:44:14 +0000

'The future Bantings and Bests': How insulin's discovery at U of T is fuelling research 100 years later

Christopher.Sorensen Fri, 03/19/2021 - 11:44

Cutline

U of T's Janet Rossant, pictured here in her SickKids lab, says a $25,000 grant from the Banting Research Foundation was a key moment early in her career (photo by Richard Lautens/Toronto Star via Getty Images)

Paul Fraumeni

Topic

Insulin 100

Donnelly Centre for Cellular & Biomolecular Research

Banting & Best

Hospital for Sick Children

Insulin