Cancer

Princess Margaret Cancer Centre

University Health Network

A preclinical study is revealing new insights into the molecular machinery that drives the aggressiveness of pancreatic cancer.

The ability of pancreatic cancer to invade and spread to other parts of the body is a major factor in its poor prognosis, with an overall five-year survival rate of less than 10 per cent.

“Pancreatic cancer cells are known to be very metastatic and that’s a big problem,” says Leonardo Salmena, an associate professor of pharmacology and toxicology in the University of Toronto’s Temerty Faculty of Medicine.

Salmena is the senior author of a study, published in the Journal of Cell Biology, that investigates the role of a gene called INPP4B in pancreatic cancer’s ability to spread. Led by post-doctoral researcher Golam Saffi and former master’s student Lydia To, the team found that INPP4B exerts its tumour-promoting effects via a cellular organ called the lysosome.

“Classically, the lysosome is a garbage disposal organelle where old and tired proteins and other organelles get degraded to be used for energy and other building blocks for the cell,” says Salmena.

In most cells, lysosomes typically cluster around the nucleus. But in pancreatic cancer cells, the researchers found that INPP4B drove the lysosomes from the cell interior to the periphery, where these organelles fuse with the cell’s outer membrane. In doing so, the enzymes and other lysosomal factors responsible for breaking down cellular waste are dumped into the space surrounding the tumour cells.

This space contains a network of proteins and molecules that provides crucial structural support to cells and tissues while also restricting a cell’s ability to move. The release of the lysosome’s protein-degrading contents into this extracellular space causes the stabilizing network to fall apart, thus making it easier for pancreatic cancer cells to migrate and invade other tissues.

Crucially, Salmena and his team also identified the signalling pathway by which INPP4B drives the movement of lysosomes to the cell edge. INPP4B works with two other proteins – PIKfyve and TRPML-1 – to modify the lysosome’s surface structure and alter local calcium levels so that the organelle is propelled to the cell periphery.

Based on these findings, the researchers are testing two experimental drugs that target TRPML-1 and PIKfyve in a preclinical model of pancreatic cancer. They are also studying how the release of lysosomal contents can change the immunological environment of the cancer cells, and what effects that might have on the immune system’s ability to respond to the tumour.

Salmena first became interested in INPP4B when, during his post-doctoral research, he found that it was involved in breast cancer. Since then, he and his team have shown that the effects of INPP4B vary depending on the context.

For example, in some breast cancer types, INPP4B behaves as a tumour suppressor whereas it has an activating role in other aggressive cancers like pancreatic cancer – which the Canadian Cancer Society expects to be the third leading cause of cancer death in Canada in 2024, with an estimated 6,100 people dying from the disease.

Salmena and his colleagues later showed that among all cancers, INPP4B levels are highest in pancreatic tumours, and that high levels of the protein are associated with decreased overall survival in people with pancreatic cancer.

The study was a collaboration between Salmena’s group, Roberto Botelho, a professor of chemistry and biology at Toronto Metropolitan University, and Steven Gallinger, a hepatobiliary and pancreatic surgical oncologist and clinician-scientist at Princess Margaret Cancer Centre, University Health Network and a professor of surgery and laboratory medicine and pathobiology in Temerty Medicine. He is also director of the PanCuRx Translational Research Initiative at the Ontario Institute for Cancer Research.

The study was supported by the Cancer Research Society and the Canadian Institutes of Health Research.

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 ��TV'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

Molecular Genetics

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.

Study points to improved detection of thyroid cancer

Christopher.Sorensen — Thu, 04 Jul 2024 20:22:19 +0000

Study points to improved detection of thyroid cancer

Christopher.Sorensen Thu, 07/04/2024 - 16:22

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(photo by Basak Gurbuz Derman/Getty Images)

Gabrielle Giroday

Topic

Sinai Health

Subheadline

“(This finding) enhances the preoperative diagnostic accuracy for patients in order to avoid unnecessary surgery for benign thyroid nodules”

Researchers from Sinai Health and the University of Toronto have gleaned new insights into how thyroid cancer could be more effectively treated.

The study, which looked at thyroid tumour tissues and thyroid nodule biopsies from 620 patients at Mount Sinai Hospital from 2016 to 2022, examined whether differences in patients' RAS genomic variants were reflected in the status of their tumours. It also investigated the presence of the variant BRAF V600E and TERT promoter variants in the patient’s samples.

Researchers ultimately concluded that differences in RAS in combination with BRAF V600E and TERT promoter variants could be used to arrive at more accurate cancer diagnoses in patients with indeterminate thyroid nodules.

“The findings help promote understanding of the interpatient differences in genomic variation among patients who carry the same genetic mutation, thereby facilitating individualized treatment based on the extent of the mutation present in the patient,” says Guodong (David) Fu, a researcher at the Lunenfeld-Tanenbaum Research Institute and the Alex and Simona Shnaider Research Laboratory in Molecular Oncology at Mount Sinai Hospital.

Fu adds that researchers developed novel molecular assays for the study using digital polymerase chain reaction, a technique that means they could sensitively quantify the genetic mutation level of the patient materials.

The results were published recently in JAMA Network. Other researchers involved in the study included: Ronald Chazen, also of the Lunenfeld-Tanenbaum Research Institute and the Alex and Simona Shnaider Research Laboratory in Molecular Oncology, and Christina MacMillan, a pathologist at Sinai Health and an assistant professor in the Temerty Faculty of Medicine’s department of laboratory medicine and pathobiology, and Ian Witterick, surgeon-in-chief at Sinai Health and a professor in Temerty Medicine’s department of otolaryngology – head and neck surgery.

The paper notes that there has been a sharp increase in papillary thyroid cancer since the 1980s, and that in 30 per cent of cases where a fine-needle aspiration biopsy of a suspected nodule takes place, there is an indeterminate diagnosis that may lead to a diagnostic surgery.

Fu says research that assists with precision thyroid cancer detection is important for many reasons, including that some patients who seek treatment for thyroid tumours end up finding out their tumours are benign after diagnostic surgery. The findings could help medical practitioners differentiate low-risk tumours from high-risk ones, he says, and help avoid unneeded surgical procedures.

“(This finding) enhances the preoperative diagnostic accuracy for patients, in order to avoid unnecessary surgery for benign thyroid nodules,” says Fu.

Witterick, who is also otolaryngologist-in-chief at Mount Sinai Hospital, says the research is important because identifying differences in genomic variants between patients can enhance precision in cancer detection, especially diagnosing malignancies before surgery and distinguishing low-risk cancers from more aggressive ones.

New cancer treatment slows aggressive neuroendocrine tumours: Study

rahul.kalvapalle — Tue, 02 Jul 2024 13:45:10 +0000

New cancer treatment slows aggressive neuroendocrine tumours: Study

rahul.kalvapalle Tue, 07/02/2024 - 09:45

Cutline

Simron Singh, a medical oncologist at Sunnybrook Health Sciences Centre and associate professor in the Temerty Faculty of Medicine, led a study that found that radioligand therapy reduces the risk of advanced neuroendocrine tumour progression and death (photo by Kevin Van Paassen, Sunnybrook)

Topic

Sunnybrook Health Sciences Centre

Department of Medicine

Subheadline

Research led by scientists at Sunnybrook Health Sciences Centre and ��TV showed radioligand therapy to be an effective first-line treatment for advanced uncurable cancers

A novel approach for early cancer treatment known as radioligand therapy (RLT) has been shown to significantly reduce the risk of advanced neuroendocrine tumour progression and death, according to research led by scientists at Sunnybrook Health Sciences Centre and the University of Toronto.

Results of the multi-centre clinical trial, which were published in The Lancet, provided evidence for the first time that RLT – when applied in the early stages after a patient’s diagnosis – slowed down the progression of aggressive grade 2 and 3 neuroendocrine tumours of the gastrointestinal tract.

The treatment was shown to extend the average time of “progression-free survival” from approximately 8.5 months to 22.8 months.

“This is the first study to show the effectiveness of RLT as the ‘first-line’ treatment with advanced uncurable cancer, or any cancer,” said the study’s global principal investigator Simron Singh, a medical oncologist at Sunnybrook and associate professor in the department of medicine at ��TV’s Temerty Faculty of Medicine. “This trial is groundbreaking not only for patients with neuroendocrine cancers, but for all cancer patients as it has implications for the practice of cancer treatment broadly.”

Singh described RLT as a “game changer” in the treatment of cancer, which has traditionally been carried out by surgery, drugs or radiation. “While it’s technically radiation, it is given via a chemotherapy route through the blood until it reaches the precise location of the tumour,” said Singh, who is also an affiliate scientist at Sunnybrook Research Institute and co-founder of the Susan Leslie Clinic for Neuroendocrine Tumours at Sunnybrook’s Odette Cancer Centre.

RLT involves injecting radioactive isotopes – in this case, the drug Lutathera – through an IV. This method targets specific cancer cell receptors, delivering precise radiation to kill cancer cells while preserving healthy tissue.

The study evaluated the use of RLT earlier as a first-line (or “up front”) treatment for patients newly diagnosed with grade 2 or 3 advanced gastrointestinal neuroendocrine tumours. Although neuroendocrine cancer is uncommon, incidence is rising rapidly, and few treatments exist for patients. This cancer is resistant to most therapies, making it challenging to treat.

The results confirm the clinical benefit of earlier use of RLT for patients diagnosed with aggressive and life-threatening tumours, said Singh. “This is the next step in personalized targeted cancer therapy for patients, focused on more effectively killing cancer cells, while limiting the damage to surrounding healthy tissues.”

Further investigations of RLT as a therapeutic option are ongoing to evaluate overall survival and long-term safety, which will better define next steps for how this therapy will change cancer treatment world-wide.

The multi-site trial included investigators and participants from Canada, the United States, France, Germany, Italy, Netherlands, South Korea, Spain and the UK. An overview of the results was presented at the 2024 American Society of Clinical Oncology (ASCO) Gastrointestinal (GI) Cancers Symposium in January 2024.

Add new author/reporter

Nadia Radovini

Researchers uncover DNA repair mechanism that could yield treatments for cancer, premature aging

Christopher.Sorensen — Wed, 08 May 2024 14:03:08 +0000

Researchers uncover DNA repair mechanism that could yield treatments for cancer, premature aging

Christopher.Sorensen Wed, 05/08/2024 - 10:03

Cutline

From left to right: researchers Mia Stanić, Razqallah Hakem, Mitra Shokrollahi, Karim Mekhail and Anisha Hundal (photo by Erin Howe)

Erin Howe

Topic

Princess Margaret Cancer Centre

Resarch & Innovation

Laboratory Medicine and Pathobiology

University Health Network

Subheadline

“It’s exciting to think about where these findings will lead us next”

Researchers at the University of Toronto and partner hospitals have discovered a DNA repair mechanism that advances understanding of how human cells stay healthy – a finding that could lead to new treatments for cancer and premature aging.

The study, published in the journal Nature Structural and Molecular Biology, also sheds light on the mechanism of action of some existing chemotherapy drugs.

“We think this research solves the mystery of how DNA double-strand breaks and the nuclear envelope connect for repair in human cells,” said Karim Mekhail, co-principal investigator on the study and a professor of laboratory medicine and pathobiology in ��TV’s Temerty Faculty of Medicine.

“It also makes many previously published discoveries in other organisms applicable in the context of human DNA repair, which should help science move even faster.”

DNA double-strand breaks arise when cells are exposed to radiation and chemicals, and through internal processes such as DNA replication. They are one of the most serious types of DNA damage because they can stall cell growth or put it in overdrive, promoting aging and cancer.

The new discovery, made in human cells and in collaboration with Razqallah Hakem – a senior scientist at UHN’s Princess Margaret Cancer Centre, University Health Network, and a professor in Temerty Medicine’s department of medical biophysics and department of laboratory medicine and pathobiology – extends prior research on DNA damage in yeast by Mekhail and other scientists.

In 2015, Mekhail and collaborators showed how motor proteins deep inside the nucleus of yeast cells transport double-strand breaks to “DNA hospital-like” protein complexes embedded in the nuclear envelope at the edge of the nucleus.

Other studies uncovered related mechanisms during DNA repair in flies and other organisms. However, scientists exploring similar mechanisms in human and other mammalian cells reported little to no DNA mobility for most breaks.

“We knew that nuclear envelope proteins were important for DNA repair across most of these organisms, so we wondered how to explain the limited mobility of damaged DNA in mammalian cells,” Mekhail says.

The answer is both surprising and elegant.

When DNA inside the nucleus of a human cell is damaged, a specific network of microtubule filaments forms in the cytoplasm around the nucleus and pushes on the nuclear envelope. This prompts the formation of tiny tubes, or tubules, which reach into the nucleus and catch most double-strand breaks.

“It’s like fingers pushing on a balloon,” says Mekhail. “When you squeeze a balloon, your fingers form tunnels in its structure, which forces some parts of the balloon’s exterior inside itself.”

Further research by the study authors detailed several aspects of this process. Enzymes called DNA damage response kinases and tubulin acetyltransferase are the master regulators of the process, and promote the formation of the tubules.

Enzymes deposit a chemical mark on a specific part of the microtubule filaments, which causes them to recruit tiny motor proteins and push on the nuclear envelope. Consequently, the repair-promoting protein complexes push the envelope deep into the nucleus, creating bridges to the DNA breaks.

“This ensures that the nucleus undergoes a form of reversible metamorphosis, allowing the envelope to temporarily infiltrate DNA throughout the nucleus, capturing and reconnecting broken DNA,” says Mekhail.

The findings have significant implications for some cancer treatments.

Normal cells use the nuclear envelope tubules to repair DNA, but cancer cells appear to need them more. To explore the mechanism's potential impact, the team analyzed data representing over 8,500 patients with various cancers. The need was visible in several cancers, including triple-negative breast cancer, which is highly aggressive.

“There is a huge effort to identify new therapeutic avenues for cancer patients, and this discovery is a big step forward,” says Hakem.

“Until now, scientists were unclear as to the relative impact of the nuclear envelope in the repair of damaged DNA in human cells. Our collaboration revealed that targeting factors that modulate the nuclear envelope for damaged DNA repair effectively restrains breast cancer development,” Hakem says.

In the aggressive triple-negative breast cancer, there are elevated levels of the tubules – likely because they have more DNA damage than normal cells. When the researchers knocked out the genes needed to control the tubules, cancer cells were less able to form tumours.

One medication used to treat triple-negative breast cancer is a class of drugs called PARP inhibitors. PARP is an enzyme that binds to damaged DNA and helps repair it. PARP inhibitors block the enzyme from performing repair, preventing the ends of a DNA double-strand break in cancer cells from reconnecting to one another.

The cancer cells end up joining two broken ends that are not part of the same pair. As more mismatched pairs are created, the resulting DNA structures become impossible for cells to copy and divide.

“Our study shows that the drug’s ability to trigger these mismatches relies on the tubules. When fewer tubules are present, cancer cells are more resistant to PARP inhibitors,” says Hakem.

Mekhail says the work underscores the importance of cross-disciplinary collaboration.

“The brain power behind every project is crucial. Every team member counts. Also, every right collaborator added to the research project is akin to earning another doctorate in a new specialty – it’s powerful,” he says.

Mekhail notes the discovery is also relevant to premature aging conditions like progeria. The rare genetic condition causes rapid aging within the first two decades of life, commonly leading to early death.

Progeria is linked to a gene coding for lamin A. Mutations in this gene reduce the rigidity of the nuclear envelope. The team found that expression of mutant lamin A is sufficient to induce the tubules, which DNA damaging agents further boosted. The team thinks that even weak pressure on the nuclear envelope spurs the creation of tubules in premature aging cells.

The findings suggest that in progeria, DNA repair may be compromised by the presence of too many or poorly regulated tubules. The study results also have implications for many other clinical conditions, Mekhail says.

“It’s exciting to think about where these findings will lead us next,” says Mekhail. “We have excellent colleagues and incredible trainees here at Temerty Medicine and in our partner hospitals. We’re already working toward following this discovery and using our work to create novel therapeutics.”

The research was supported by the Canadian Institutes of Health Research, Royal Society of Canada, ��TV and Princess Margaret Hospital.

Researchers pinpoint issue that could be hampering common chemotherapy drug

Christopher.Sorensen — Mon, 18 Mar 2024 15:00:03 +0000

Researchers pinpoint issue that could be hampering common chemotherapy drug

Christopher.Sorensen Mon, 03/18/2024 - 11:00

Cutline

(photo by Glasshouse Images/Getty Images)

Anika Hazra

Topic

Donnelly Centre for Cellular & Biomolecular Research

Biochemistry

Subheadline

Study finds two enzymes that work against the chemotherapy drug gemcitabine, preventing it from effectively treating pancreatic cancer

Researchers at the University of Toronto’s Donnelly Centre for Cellular and Biomolecular Research have found two enzymes that work against the chemotherapy drug gemcitabine, preventing it from effectively treating pancreatic cancer.

The enzymes – APOBEC3C and APOBEC3D – increase during gemcitabine treatment and promote resistance to DNA replication stress in pancreatic cancer cells.

This, in turn, counteracts the effects of gemcitabine and allows for the growth of cancer cells.

Tajinder Ubhi and Grant Brown (supplied images)

“Pancreatic cancer has proven to be very challenging to treat, as it is usually diagnosed at stage 3 or 4,” said Tajinder Ubhi, first author on the study and a former PhD student in biochemistry in ��TV’s Temerty Faculty of Medicine.

“It is the most lethal type of cancer in Canada, with an average survival time of less than two years. While chemotherapy with gemcitabine has increased survival by a few months in clinical trials, options for treatment of pancreatic cancer remain limited.”

The findings were published in the journal Nature Cancer.

Replication stress is the key process by which gemcitabine stops cancer cells from continuing to multiply. It involves the dysregulation of DNA replication, which occurs when cells divide. Replication stress can transform a healthy cell into a cancerous one, but can also be activated within cancer cells to eliminate them.

Gemcitabine has been used for nearly three decades to treat a wide variety of cancers, including pancreatic, breast and bladder cancer. However, a downside of using gemcitabine to target dividing cells is that it can produce toxic side effects in tissues that aren’t being targeted for treatment.

Ubhi and other members of Professor Grant Brown’s lab at the Donnelly Centre have been trying to understand the possible causes of replication stress and its impacts. One way to do this is by studying the stress response mechanisms in cancer cells treated with gemcitabine.

“We conducted a genome-wide CRISPR screen to find genes that could increase the sensitivity of pancreatic cancer cells to gemcitabine,” said Brown, professor of biochemistry at the Donnelly Centre and in the Temerty Faculty of Medicine who is the principal investigator on the study.

“We were excited to identify APOBEC3C and APOBEC3D because other enzymes in the APOBEC3 family can cause cancers to eventually become resistant to treatment. We discovered a more direct role for the enzymes, where they actually protect pancreatic cancer cells from gemcitabine therapy.”

Neither enzyme is naturally found in high concentrations within healthy or cancerous cells. The catch is that the replication stress the drug causes in pancreatic cancer cells in turn triggers an increase in both enzymes. The research team found that removing either APOBEC3C or APOBEC3D kills pancreatic cells by stymieing DNA repair and destabilizing the cell genome.

“What is most exciting is that the removal of just APOBEC3C or APOBEC3D is enough to stop the replication of gemcitabine-treated pancreatic cancer cells,” said Ubhi. “This indicates that the enzymes could be effective new targets for treating this form of cancer.”

The research received support from the Canada Foundation for Innovation, the Canadian Cancer Society, Canadian Friends of the Hebrew University, the Canadian Institutes of Health Research, Cold Spring Harbor Laboratory, the Government of Ontario, the Lustgarten Foundation, the Ministry for Culture and Innovation of Hungary, the U.S. National Institutes of Health, the Northwell Health Affiliation, the Ontario Institute for Cancer Research, Pancreatic Cancer Canada, the Princess Margaret Cancer Foundation, the Simons Foundation, the Terry Fox Research Institute and the Thompson Foundation.

��TV researchers develop rapid MRI technique for better cancer detection and therapy

Christopher.Sorensen — Fri, 23 Feb 2024 19:30:43 +0000

��TV researchers develop rapid MRI technique for better cancer detection and therapy

Christopher.Sorensen Fri, 02/23/2024 - 14:30

Cutline

(photo by Willie B. Thomas/Getty Images)

Matthew Tierney

Topic

Institute of Biomedical Engineering

Electrical & Computer Engineering

Faculty of Applied Science & Engineering

Subheadline

“We create images every second, and sometimes less, and those images are not going to suffer from low resolution”

Researchers at the University of Toronto’s Faculty of Applied Science & Engineering have developed a rapid magnetic resonance imaging (MRI) technique to help doctors better detect and diagnose tumours.

The new approach – by Hai-Ling Cheng, a professor in the Institute of Biomedical Engineering and the Edward S. Rogers Sr. department of electrical and computer engineering, and PhD candidate Alex Mertens – could provide physicians with guidance during surgery and other therapeutic interventions.

Based on novel analysis of raw patient data collected from imaging sessions with standard MRI equipment, the algorithm Cheng and Mertens developed reduces the duration between each image acquisition from more than 20 seconds to one second without sacrificing image sharpness.

“People in the field have been trying to get high spatial resolution concurrently with temporal resolution for the past 25 years,” says Cheng.

Cheng and Mertens, with the help of the ��TV Innovations and Partnerships Office, have applied for a patent and are partnering with companies to bring their MRI technique to market.

“In practice, doctors always follow up imaging results with a biopsy for definitive confirmation to more accurately determine the grade of cancer and its stage,” Cheng says.

“Our technique is not meant to displace the biopsy. But by better characterizing the underlying pathology at the vascular and cellular level, we can mitigate randomness in the sampling when the doctor goes in with a biopsy needle.”

Professor Hai-Ling Cheng, pictured, and ECE PhD candidate Alex Mertens have developed a novel method to analyze data acquired from magnetic resonance imaging (photo by Matthew Tierney)

MRI is used to scan soft tissues like muscle or fat because it offers the best contrast compared to other modalities such as X-rays and ultrasounds. The contrast allows doctors to discern different cell types and identify small cancerous growths.

“Let’s say you’ve got a liver and a kidney, and you want to image them both in the same area of the body,” says Cheng. “If you were to take an X-ray, you would get one contrast level – one grey scale specific to the liver and one grey scale specific to the kidney.”

With MRI technology, however, there’s different physics at play that allows for refined gradients. An MRI scanner produces a strongly magnetized field inside the patient’s body into which it pulses a radio frequency, or RF, wave. The wave affects the water protons in soft tissues, which react to the pulse and emit signature return signals.

“The data from the return signal doesn’t tell you the shape of an object but the frequency content of the object,” says Cheng. “We structure that return RF signal into a matrix, which we can then convert into a high resolution image.”

Researchers can change the magnetic strength and the frequency of the pulse to obtain different contrasts, much like a music producer can increase and decrease the volume of individual tracks in a song.

To enhance the RF signal further, a contrast agent is intravenously injected into the patient beforehand: usually gadolinium, which is non-radioactive. The dynamics of the gadolinium distribution – that is, the speed of its uptake and washout in cells – give doctors additional information about the malignancy of the tumour.

“Tumours not only have a larger blood volume, but because their blood vessels are very messed up and tortuous, they also tend to be very, very leaky,” says Cheng.

However, the MRI procedure is notoriously slow. The scanner must repeatedly acquire frequency domain data at different coarse and fine-grain resolutions. Typical temporal resolution is 20 seconds and gadolinium washout in a tumour can take as little as 10 seconds.

“Typically, it takes 256 acquisition lines to create one image,” says Cheng. “Rather than reconstructing a full image every 20 seconds or every minute – that’s kind of pointless, because you’re missing the dynamics – our algorithm extrapolates information based on successive sampling of just one acquisition line.

“We create images every second, and sometimes less, and those images are not going to suffer from low resolution.”

“The work that Hai-Ling and her team are doing is a testament to how electrical and computer engineering technologies can impact the health-care sector,” says Professor Deepa Kundur, chair of the electrical and computer engineering department in the Faculty of Applied Science & Engineering. “Hai-Ling and Alex have spent years building on their knowledge of MRI physics and human biology, demonstrating how interdisciplinary perspectives in engineering save lives. Well done.”

Researchers discover lipid nanoparticle that delivers mRNA to muscles, avoids other tissues

Christopher.Sorensen — Fri, 15 Dec 2023 20:01:28 +0000

Researchers discover lipid nanoparticle that delivers mRNA to muscles, avoids other tissues

Christopher.Sorensen Fri, 12/15/2023 - 15:01

Cutline

“The substantial anti-tumor effects observed with iso-A11B5C1 underscore its promise as a viable candidate for cancer vaccine development,” says Jingan Chen, a PhD trainee from the Institute of Biomedical Engineering (photo by Steve Southon)

Kate Richards

Topic

Institute of Biomedical Engineering

Institutional Strategic Initiatives

PRiME

Leslie Dan Faculty of Pharmacy

Graduate Students

Vaccines

Subheadline

Study also showed the mRNA triggered potent cellular-level immune responses, suggesting it could be used to develop a melanoma cancer vaccine

A team of researchers based at the University of Toronto’s Leslie Dan Faculty of Pharmacy have discovered an ionizable lipid nanoparticle that delivers mRNA to muscles while avoiding other tissues.

The study, led by Assistant Professor Bowen Li and published in Proceedings of the National Academy of Sciences, also showed that mRNA delivered using the lipid nanoparticles triggered potent cellular-level immune responses – a proof-of-concept that could lead to a potential melanoma cancer vaccine.

Called iso-A11B5C1, the new lipid nanoparticle demonstrates exceptional mRNA delivery efficiency in muscle tissues while also minimizing unintended mRNA translation in organs such as the liver and spleen. Additionally, study results show that intramuscular administration of mRNA formulated with this nanoparticle caused potent cellular immune responses, even with limited expression observed in lymph nodes.

“Our study showcases for the first time that mRNA lipid nanoparticles can still effectively stimulate a cellular immune response and produce robust anti-tumor effects, even without direct targeting or transfecting lymph nodes,” said Li.

“This finding challenges conventional understandings and suggests that high transfection efficiency in immune cells may not be the only path to developing effective mRNA vaccines for cancer.”

Lipid nanoparticles, also called LNPs, are crucial for delivering mRNA-based therapies including COVID-19 mRNA vaccines that were used worldwide during the recent pandemic. However, many LNP designs can inadvertently result in substantial mRNA expression in off-target tissues and organs like the liver or heart, resulting in often treatable but unwanted side effects. The drive to improve the safety of mRNA therapies that have the potential to treat a broad range of diseases means there is an urgent need for LNPs designed to minimize these off-target effects, explains Li, a recent recipient of the Gairdner Early Career Investigator Award.

From left to right: researchers Jingan Chen, Bowen Li and Yue Xu (photo by Steve Southon)

The new research shows that, compared to the current benchmark LNP developed by the Massachusetts-based biotechnology company Moderna, iso-A11B5C1 demonstrated a high level of muscle-specific mRNA delivery efficiency. It also triggered a different kind of immune response than what is seen in vaccines used to treat infectious diseases.

“Interestingly, iso-A11B5C1 triggered a lower humoral immune response, typically central to current antibody-focused vaccines, but still elicited a comparable cellular immune response. This finding led our team to further explore this as a potential cancer vaccine candidate in a melanoma model, where cellular immunity plays a pivotal role,” Li said.

The interdisciplinary research team that conducted the study includes Jingan Chen, a PhD trainee from the Institute of Biomedical Engineering, and Yue Xu, a postdoctoral researcher in the Li lab and a research fellow associated with PRiME, a ��TV institutional strategic initiative.

“Although iso-A11B5C1 showed limited capacity to trigger humoral immunity, it effectively initiated cellular immune responses through intramuscular injection,” said Chen. “The substantial anti-tumor effects observed with iso-A11B5C1 underscore its promise as a viable candidate for cancer vaccine development.”

New platform allows for faster, more precise lipid design

The research team identified iso-A11B5C1 by using an advanced platform developed to quickly create a range of chemically diverse lipids for further testing. This platform, newly introduced as part of the study, overcomes several challenges by streamlining the process of creating ionizable lipids that have a high potential to be translated into therapies.

By rapidly combining three different functional groups, hundreds to thousands of chemically diverse ionizable lipids can be synthesized within 12 hours.

“Here we report a powerful strategy to synthesize ionizable liquids in a one-step chemical reaction,” said Xu. “This new platform provides new insights that could help guide lipid design and evaluation processes going forward and allows the field to tackle challenges in RNA delivery with a new level of speed, precision and insight.”

Certain cancers can activate 'enhancer' in the genome to drive tumour cell growth: Study

Christopher.Sorensen — Mon, 16 Oct 2023 14:30:36 +0000

Certain cancers can activate 'enhancer' in the genome to drive tumour cell growth: Study

Christopher.Sorensen Mon, 10/16/2023 - 10:30

Cutline

(Photo by Ewa Krawczyk, National Cancer Institute \ Georgetown Lombardi Comprehensive Cancer Center, National Institutes of Health)

Neil Macpherson

Topic

Cell and Systems Biology

Faculty of Arts & Science

Graduate Students

Researchers at the University of Toronto have found that cancer cells can enhance tumour growth by hijacking enhancer DNA normally used when tissues and organs are formed.

The mechanism, called “enhancer reprogramming,” occurs in bladder, uterine, breast and lung cancer – and could cause these types of tumors to grow faster in patients.

Jennifer Mitchell (supplied image)

The research was conducted in the lab of Jennifer Mitchell, a professor in the department of cell and systems biology in the Faculty of Arts & Science, and published recently in the journal Nucleic Acids Research. It pinpoints the role that specific proteins play in regulating the enhancer region which may lead to improved treatments for these cancer types.

Living cells, even cancer cells, follow instructions in the genome to turn genes on and off in different contexts, says first author Luis Abatti, a PhD candidate in Mitchell’s lab.

“The genome is like a recipe book written in DNA that gives instructions on making all the parts of the body,” Abatti says.

“In each organ, only the recipes relevant to that organ should be followed – whether it’s the instructions for lung, breast or some other tissue. Like flipping pages in a recipe book, the DNA containing the instructions for turning genes on in the lung is open and used in the lung, for example, but closed and ignored in other types of cells.

Luis Abatti (supplied image)

“We know that some cancer cells are opening the wrong pages in the recipe book – ones that contain the SOX2 gene, which can cause tumours to grow uncontrollably. We wanted to find out: How does the gene become expressed in cancer cells?”

The researchers analyzed genome data to look for enhancer DNA that could activate SOX2 in cancer cells. The enhancer they found is open in many different types of patient tumours, meaning this could be a cancer enhancer active in bladder, uterus, breast and lung tumours. Unlike many cancer-causing changes, the enhancer reprogramming mechanism does not arise out of mutation due to DNA damage – it is caused by part of the genome opening when it should be staying closed.

The researchers then determined that the enhancer causes increased cancer cell growth because when they removed the enhancer in lab-grown cells, the cancer cells created fewer new tumour colonies.

To figure out why cells have a DNA region that makes cancer worse, the team examined mice without this DNA region and found they do not form a separate passage for air and food in their throat as they develop. Thus, this potentially dangerous cancer-enhancer region is likely in the human genome to regulate airway formation as the human body forms. However, if a developing cancer cell opens this region, it will form a tumour that grows faster and is more dangerous for the patient.

The researchers unravel the mechanism of how developmentally active enhancers become repurposed in a tumour (image: © Abatti et al, 2023, published by Oxford University Press on behalf of Nucleic Acids Research)

“We also found that two proteins known to have a role in the developing airways – FOXA1 and NFIB – are now regulating SOX2 in breast cancer,” says Mitchell, who is associate chair of research in the department of cell and systems biology and is cross-appointed to the department of laboratory medicine and pathobiology in the Temerty Faculty of Medicine.

The enhancer is activated by the FOXA1 protein and suppressed by the NFIB protein. This means that drugs suppressing FOXA1 or activating NFIB may lead to improved treatments for bladder, uterine, breast and lung cancer.

“Now that we know how the SOX2 gene is activated in certain types of cancers, we can look at why this is happening,” Mitchell says.

“Why did the cancer cells end up on the wrong page of the genome recipe book?”

The research received support from the Canadian Institutes of Health Research, the Canada Foundation for Innovation and the Ontario government.

Researchers challenge long-standing theory guiding nanoparticle treatment of tumours

Christopher.Sorensen — Mon, 25 Sep 2023 13:25:30 +0000

Researchers challenge long-standing theory guiding nanoparticle treatment of tumours

Christopher.Sorensen Mon, 09/25/2023 - 09:25

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PhD student Matthew Nguyen and Professor Warren Chan found that about 45 per cent of nanoparticles that accumulate in tumours end up exiting them (supplied photos)

Anika Hazra

Topic

Institute of Biomedical Engineering

Princess Margaret Cancer Centre

Donnelly Centre for Cellular & Biomolecular Research

Faculty of Applied Science & Engineering