Archives for April 2023

Diversifying Ontario’s Forestry Sector with New High-Value Materials

Canada’s forestry sector contributes significantly to jobs and GDP, but the industry is being challenged by the digitization of print and global market pressures.

A key opportunity identified by the sector and the Ontario Government’s recently published forestry sector strategy is to develop new and innovative wood-based products. By diversifying production away from low-value commodity products like paper, there is an opportunity to transform pulp and paper mills into biomanufacturing plants that produce high-value materials.

To help accomplish this, Ontario Genomics is supporting Fortress Advanced Bioproducts, a company valorizing pulp and paper mill side streams into xylitol, a low-calorie sweetener. Fortress is partnering with the University of Toronto to optimize a key step in the xylitol production process that reduces operational costs and improves competitiveness in the market.


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Environmental DNA Toolkit to Detect and Identify Canadian Freshwater Fish

Freshwater fish contribute to Canada’s economy both directly and indirectly and are critical for the preservation of freshwater resources and food security. Thriving freshwater fish resources are the lifeblood of many rural, northern, and Indigenous communities and are central to the social and cultural lives of millions of Canadians. Yet over 25% of Canadian freshwater fish stocks are under threat.

The logistical difficulties of monitoring fish in Canada’s 2+ million lakes and countless rivers are compounded by the limitations of conventional sampling methods, which provide only a snapshot. This project will use genomic approaches to develop a Fish Survey Toolkit based on environmental DNA from water samples and a Fish Health Toolkit that will provide quantitative assessments of the health of fish and the stressors they face.

Collectively, these toolkits will enable a complete and accurate assessment of the status of Canada’s freshwater fish resources, save millions of dollars in fish survey costs, and result in additional indirect savings through more effective and directed management actions. Furthermore, and most importantly, the project will ensure the sustainability of Canada’s freshwater fish resources for future generations.

“The GEN-FISH network consists of 24 committed and dedicated scientists who care passionately about the freshwater fishes of Canada and around the world. The GEN-FISH funding will ensure the development of novel, ground-breaking genomic technology to help conserve freshwater fish for generations to come.”

— Dr. Daniel Heath, Professor, University of Windsor


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Manufacturing Petroleum-Free, High Purity Sustainable Ingredients

Products made from natural ingredients are the fastest-growing segment in the cosmetics and food industry. However, these industries are dominated by petrochemical-derived ingredients as opposed to natural ingredients. This is because the supply chain of natural ingredients is highly unreliable. Natural ingredients are extracted from botanical raw materials, making their supply unpredictable, high-priced, and with undesirable attributes such as seasonal variation.

Ardra is an engineering biology company producing natural ingredients using fermentation. Ardra’s platform uses designer biochemical pathways to produce a portfolio of high-value natural ingredients using renewable raw materials such as sugars. Ardra’s ingredients have lower production cost, consistent quality, and are free of harmful residues that may be found in petroleum-derived synthetic ingredients.

The investment from Ontario Genomics has helped Ardra advance its lead product – Natural Leaf Aldehyde: apple flavour ingredient used in the beverage industry. The investment enabled Ardra to scale up its process from bench to pilot, thereby producing samples sold to and validated by potential customers. Ardra is currently engaged in the scale-up of the process to demonstration trial and is in discussion for co-development partnerships to commercialize the process.

“At Ardra, we are harnessing the power of engineering biology to solve pressing problems in sustainable supply of natural ingredients.”

— Pratish Gawand, CEO & Co-founder, Ardra Bio, Inc.


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A Thriving and Resilient Dairy Cattle Industry

Canada is the world’s fifth largest exporter of agricultural products. Canadian farmers are poised to play a decisive role in meeting the 70% increase in world food demand expected by 2050. Dairy cow growth, milk production, and reproduction, as well as their overall health and welfare, can be strongly influenced by changes in air temperature, humidity, and other environmental factors, including climate change.

Genetic selection plays an essential role in breeding livestock to better cope with rapidly changing climate and environmental factors. In collaboration, Semex Alliance and the University of Guelph will provide innovative methods to select the right genetic traits to breed robust dairy cows that are resilient to environmental stressors, such as extreme hot or cold temperatures while maintaining health, production, and reproductive efficiency.

This proof-of-concept project integrates phenotypic data collected using automated sensor technologies with high-throughput genotypes of dairy cows. By applying genomics-derived processes for identifying healthy, fertile, resilient animals for use in genomic selection programs, this project strengthens Ontario’s dairy sector leadership and provides opportunities for large-scale application in Canada and around the world.

“Breeding animals resilient to heat stress and other environmental challenges exacerbated through climate change is a very important goal that will ensure a safe and sustainable food supply in a changing environment.”

— Dr. Christine Baes, Assistant Professor at the University of Guelph & Canada Research Chair at Livestock Genomics


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Improving Pediatric Cancers Diagnoses and Treatment with Precision Medicine

The past decade has seen many high-impact, genomics-driven discoveries that have ushered precision medicine as an emerging treatment for pediatric cancer. Pediatric tumours have a different genetic make-up and fewer actionable molecular targets than adult tumours, therefore, precision oncology designed for children promises to greatly improve survival.

There is currently a disconnect, with diagnostic analysis at the DNA level and oncology drugs targeting specific molecular targets at the protein level, leading to response rates of 15-20%. Therefore, there is a pressing need for novel diagnostic tests that examine all levels of cellular information – protein, RNA, and DNA — to accurately guide therapeutic decisions.

The Hospital for Sick Children and US-based NanoString Technologies have collaborated to develop next-generation molecular tools for characterizing children’s cancer. This technology interrogates DNA, RNA, and protein simultaneously, providing better analysis of the patient’s cancer and the information needed to determine the personalized care and accurate assignment of the best class of drugs for each patient. By delivering essential information in a targeted, cost-effective, and timely manner, this diagnostics solution for pediatric cancers will benefit patients, the regional economy, and the healthcare system.

This technology also has the potential in the future as a diagnostic tool for adult cancers. In a previous, successful GAPP project involving the same partners, their commercialized pediatric low-grade glioma (pLGG) and sarcoma tests were recently licensed by the Ontario Ministry of Health and the intellectual property (IP) has been licensed to Singapore and Hong Kong, with interest from Brazil as well. The work performed has created an evidence base for these tests and has resulted in over $1M in instrument and consumable sales for NanoString.

“Our lab is dedicated to improving outcomes for children with cancer. This project will enable us to better predict which drugs will work best for each child’s cancer.”

— Dr. Cynthia Hawkins, Senior Scientist & Principal Investigator, The Hospital for Sick Children


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Upcycling Plastics with Genomics for a Zero-Waste Future

Over 29,000 tons of plastic leak into the Canadian environment and oceans annually, creating severe environmental problems, including killing 100,000 marine mammals annually. Another 2.8 million tons of plastic are sent to Canadian landfills, which creates a latent problem for future generations, with only 9% of plastic being recycled.

With growing awareness of the detrimental impacts of plastic, governments and manufacturers are working towards a zero-plastic waste future. Under this paradigm, plastics will be made with recycled or biodegradable components. In this project, a Canadian-led team consisting of multiple universities, governments, and industries will drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics.

This team will identify and engineer bacteria and enzymes that can break down plastics into recyclable components or valuable fine chemicals more effectively than chemical conversion-based technologies. Additionally, they will conduct a holistic investigation into the impact of these new plastic biotechnologies on society, the economy, and the environment.

Preliminary estimates indicate recycling could save Canada $500 million annually in costs and create 42,000 jobs in new industries. The market for recovered waste plastic in the textiles sector alone is over $600 million per year. We could also save 1.8 million tons of CO2 equivalents per year in greenhouse gas emissions, ensuring that plastics continue to contribute to the economy without adversely impacting the environment.

“To reach zero plastic waste in Canada by 2030, the Open Plastic consortium will develop novel microbiological technology to support the breakdown of plastic waste into marketable recycled products. Our open science framework will empower trainees of the program and existing companies to build ventures for Canada and export.”

– Dr. Laurence Yang, Assistant Professor, Queen’s National Scholar in Systems Biology, Queen’s University.


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Stopping Foodborne Outbreaks Early

In Canada, consumption of contaminated food causes 4 million illnesses, over 14,000 hospitalizations, and more than 300 deaths each year, with an estimated annual economic burden of approximately $4 billion.

A major impediment to identifying contaminated food is that current surveillance methods rely on sick people to seek medical help instead of public health mechanisms detecting foodborne outbreaks.

The Public Health Agency of Canada (PHAC), the University of Guelph, and Université Laval, are developing a novel, integrated approach to improved foodborne outbreak detection, beginning with genomic detection of foodborne pathogens in raw sewage and monitoring of social media for keywords associated with enteric illness.

The tools, methods, and datasets generated through this project will be translated for downstream operational use into the network of Canadian foodborne surveillance programs through collaborations between PHAC and its federal, provincial, and territorial partners.

Implementation will reduce the number of illnesses and hospitalizations and increase economic savings due to decreased food recalls through faster detection of outbreaks. Another advantage is that this project can be scaled-up for rapid detection of other pathogens and is currently being utilized to monitor levels of SARS-CoV-2, the virus that causes COVID-19, in wastewater, as an early indicator of changing case numbers before clinical presentation.

“As the COVID-19 pandemic continues, we are seeing increasing emergence of variants of concern (VOCs) and variants of interest (VOIs) which threaten the health and wellbeing of Canadians. The funding provided by Ontario Genomics and Genome Canada is helping my team to develop a genomics-based surveillance platform based on analysis of wastewater, providing a customizable tool for use in controlling the spread of infectious diseases, whether they be food or waterborne, or respiratory borne like COVID-19.”

– Dr. Lawrence Goodridge, Director at Canadian Research Institute for Food Safety, University of Guelph.


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Precision Medicine in Early Breast Cancer

Breast cancer accounts for approximately 25% of new cancer cases each year and 13% of all cancer deaths in Canadian women. Breast cancer, which was once considered a homogenous tissue disease, is now known to be a complex, heterogeneous disease. Breast cancer in patients is individual and has different molecular make-ups; therefore, precision oncology promises to significantly improve treatment options.

To better comprehend the individual nature of breast cancer in patients, the implementation of integrated ‘omics solutions is needed to understand the combined effects of genomic and epigenomic changes in driving cancer progression and deliver on the promise of precision medicine.

Emerging research in breast cancer implicates epigenomics in the regulation of multiple cancer processes, including treatment response. Additionally, epigenomics data across cancer driver genes from different ethnic groups shows that molecular processes are influenced by differences in ethnicity. This highlights the diagnostic importance of epigenomic features for equitable delivery of healthcare to patients.

Ontario Institute for Cancer Research (OICR) and Thermo Fisher Scientific have collaborated to develop and validate novel panel-based targeted approaches for the evaluation of epigenetic alterations in breast cancer to address two major needs: improved predictive and prognostic assays for all breast cancer patients and a focused study comparing methylation profiles between cancers in ethnic minority groups.

“We’re investigating the impact of ethnicity in the biology of breast cancer. We are developing new tools to improve the diagnosis of breast cancer patients and accelerate personalized treatment based on the biology of their disease.”

– Dr. Melanie Spears, Principal Research Scientist, Ontario Institute for Cancer Research.


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