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TRIA-FoR: Transformative Risk Assessment and Forest Resilience Using Genomic Tools for the Mountain Pine Beetle Outbreak (2020)

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Overview

The current mountain pine beetle (MPB) epidemic has killed approximately 20 million hectares of mainly lodgepole pine forests in British Columbia and Alberta. Climate change and forest management practices have contributed to unprecedented range expansion of MPB. From its historic range in central British Columbia, MPB has spread through novel habitats in Alberta, establishing in a new host, the jack pine. Jack pine is a boreal forest species with a range that extends to the Atlantic Ocean, raising the spectre of continued eastward spread of MPB. Given the importance of lodgepole and jack pine to the forest industry, their central role in providing ecosystem services and their cultural importance, there is an urgent need to enhance resiliency of forests replacing MPB-killed stands, and to quantify eastward spread risk potential of MPB.

In TRIA-FoR, we will adopt a state-of-the-art multidisciplinary and integrative approach to develop genomics-informed knowledge, tools and application frameworks that mitigate risk for the present MPB epidemic and improve resiliency in future epidemics. Risk and resiliency will be investigated in the context of MPB-pine-climate interactions that affect MPB population dynamics, human dimensions in forest resource management, and impacts on diverse communities connected to forests at risk.

TRIA-FoR research encompasses three overarching goals. (1) Enhance lodgepole pine genetic resiliency to MPB. We will identify gene-based markers that predict MPB resiliency in lodgepole pine and identify traits that contribute to MPB resiliency. To understand how genetic resiliency translates into forest resiliency, we will model the impact of planting MPB-resilient lodgepole pine on outbreaking MPB populations. (2) Improve risk assessment efficacy for MPB northern and eastern spread into the boreal forest by examining MPB – pine host – climate interactions. We will test whether jack pine forests east of Alberta can support MPB populations, or whether expanding populations require immigration from the lodgepole x jack pine hybrid zone. In tandem, we will determine how overwintering temperatures and pine host characteristics in these marginal habitats affect MPB success. (3) Develop a social sciences framework of risk management planning and resilience building that can facilitate adoption of genomics-informed practices or technologies. We will investigate geographic, sociological, economic and policy aspects of risk related to the MPB epidemic, identifying factors that influence stakeholder willingness to adopt genomics-informed applications. This collaborative cross-scale research will enable a genomics-informed total risk and resilience management approach that can enhance forest health in the face of present and future MPB epidemics.

Optimizing a Microbial Platform to Break Down and Valorize Waste Plastic (2020)

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Overview

In Canada, 29,000 tonnes of plastic leak into the environment and oceans every year, creating severe environmental problems. Waste plastic kills 100,000 marine mammals annually, including whales, dolphins, seals, and sea lions, either through ingestion of plastic debris or entanglement in fishing gear. Another 2.8 million tonnes of plastic are sent to Canadian landfills, which creates a latent problem for future generations. Only 9% of plastic is recycled.

Despite the waste and environmental impact, plastic production is increasing in Canada, with an additional 4.8 million tonnes produced per year. Demand for plastic continues to grow because it is cheap to produce and has many important benefits. However, with a growing awareness of the environmental 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. For this change in paradigm to succeed, government, the public, and industry will all need to play a role.
In this project a Canadian-led team consisting of multiple universities, municipal governments, and industries will drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics. Our goal is to identify and engineer bacteria and enzymes that can break down plastics into recyclable components or into valuable fine chemicals more effectively than chemical conversion-based technologies. On a second front our team will conduct a holistic investigation into the impact of these new plastic biotechnologies on society, the economy, and the environment. Preliminary estimates indicate that if 90% of plastic is diverted to recycling instead of landfill, Canada could avoid $500 million per year in costs, and create 42,000 jobs in new industries. The market for recovered waste plastic in the textiles sector alone is up to $600 million per year. We could also save 1.8 million tonnes of CO2 equivalents per year in greenhouse gas emissions. Globally, stopping plastics from leaking into the environment would avoid up to $13 billion per year in damage to marine ecosystems. Ultimately, we envision a future where plastics continue to contribute to the economy in a positive way, but without the concomitant negative impact on the environment.

This project is affiliated with the Contaminants of Emerging Concern Research Excellence Network (CEC-REN) at Queen’s University, which is an interdisciplinary research and innovation initiative. CEC-REN is focused on the detection and treatment of emerging contaminants in the natural and built environment that pose environmental and human health risks.

BIOSCAN–Canada (2020)

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Overview

The Global Risks Report 2020 from the World Economic Forum ranked biodiversity loss as one of the top five threats confronting humanity. Stemming this loss requires understanding how species interact and respond to changes in their environment, but this is impossible to accomplish with traditional morphological methods. DNA barcoding first emerged 15 years ago as a rapid, accurate way to discriminate species based on the sequence characterization of short segments of DNA. The International Barcode of Life Consortium, led by the Centre for Biodiversity Genomics at Guelph, involves research organizations in 40 nations which share the goal of cataloging all species and establishing a global biosurveillance system before mid-century.

Its current research program, BIOSCAN, is harnessing new technologies to make DNA barcoding faster and less expensive, advances that will broaden its application. Importantly, the technologies normally used to sequence whole genomes can be employed to gather DNA barcodes from thousands of specimens at a time. BIOSCAN–Canada is a core component of this global effort; its work will increase the cost effectiveness of DNA-based identification systems while also providing new biodiversity data with direct relevance to Canadians. For example, new species will be revealed from under-explored regions such as the Arctic and the ocean floor off British Columbia. DNA barcoding will also be used to illuminate interactions among species, such as which flowers a bee visited, and to track the shifting distributions of species in response to environmental change at previously impossible scales. Through community engagement, BIOSCAN–Canada will incorporate Indigenous ways of knowing into an accounting method for “natural capital” that extends beyond conventional economic metrics like the GDP.
By combining genomics-based biodiversity data with this accounting system, it will enable effective, timely environmental impact assessments and policymaking for the forestry, mining, and agricultural sectors as well as for conservation planning. Through such action, BIOSCAN–Canada will slow biodiversity loss, improve Indigenous relations through consultation, increase the sustainability of our agricultural and forestry sectors, and strengthen Canada’s leadership in global conservation efforts.

SALMON and CHIPS – Commercial application of genomics to maximize genetic improvement of farmed Atlantic salmon on the East coast of Canada

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Overview

Aquaculture companies are increasingly incorporating genomics technology into their breeding programs to develop desirable stock traits for improved growth and disease resistance. To retain its ability to compete internationally, Cooke Aquaculture/Kelly Cove Salmon will partner with Dr. Elizabeth Boulding and her academic group from the University of Guelph to incorporate genomics marker technology into Kelly Cove Salmon’s current breeding program. This will allow the company to improve the effectiveness of its breeding program and increase the resistance of its salmon to diseases and parasites. The company aims to implement an advanced genomics technology known as SNP-chips, which when blended with conventional animal breeding techniques, can yield significant increases in the survival rates of eggs and juvenile stages, as well as improved saltwater performance. The implementation of this genomics technology is expected to increase the quality and sales of Kelly Cove’s salmon, and improve profitability by reducing expenditures on vaccines and medication. Strengthening Kelly Cove Salmon and its parent company, Cooke Aquaculture, will be good news for the more than 1,700 current employees in Atlantic Canada, and will lead to increased employment in rural and coastal communities.

Genomics for a competitive greenhouse vegetable industry

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Overview

Tomatoes, peppers and cucumbers generate more than $1 billion in annual sales for the Canadian greenhouse vegetable industry. These plants are susceptible to a number of diseases, which threaten crops and decrease profits for producers. In order to maintain a competitive edge, create growth and ensure future success, Canada’s greenhouse vegetable industry needs plant varieties that are resistant to disease. To address this challenge, Vineland Research and Innovation Centre will partner with Dr. Keiko Yoshioka, a leading academic from the University of Toronto, who has discovered a key gene involved in plant disease resistance. By using proven gene technologies to enhance disease resistance in greenhouse vegetables, this project aims to develop new commercial traits and varieties for Canada’s vegetable industry. These technologies will benefit Canada’s greenhouse vegetable industry by adding value to Canadian greenhouse vegetables, and fostering economic growth, increased exports, reducing competition from imports.

Development of low cost diagnostic platform for infectious disease testing

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Overview

Conventional lab testing for infectious diseases such as Hepatitis C, malaria and tuberculosis is inefficient and not cost-effective, particularly in developing countries. The development of fast and accurate point-of-care testing for these infections would significantly improve the clinical management of infectious diseases. For this research, Xagenic will partner with Dr. Shana Kelley, a leading academic from the University of Toronto, to leverage expertise in viral assay development, sensor technology and plastic chip fabrication. This project will lead to a single affordable and accurate genotyping test to screen for infectious pathogens, and will provide a new solution for rapid disease diagnosis. The low-cost, disposable, battery-powered testing device will identify pathogens in human blood in minutes, which could reduce infectious disease in Canada and around the world, and dramatically improve disease management. The launch of this new product line by Xagenic will result in increased revenues and significant job creation within the company.

Cardiovascular Biomarker Translation (CBT) program

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Overview

Heart failure (HF) is the most costly chronic disease in developed and developing countries. More than 26 million people worldwide are suffering from HF, placing great stresses on patients, caregivers and health care systems. The number of patients will be increasing in the next decades due to ageing populations, therefore improved diagnosis and therapy of HF are important goals of major healthcare organizations. In keeping with its mission to identify areas of unmet medical needs and develop innovative health care solutions, Roche Diagnostics is partnering with the University of Ottawa Heart Institute (UOHI) to develop a better way to identify and classify HF, based on testing novel biomarkers for the disease. To date, with previous Genome Canada funding, UHOI, University of Toronto and Roche Diagnostics have identified eight novel biomarker candidates for HF characterization and have filed for global patents for these candidates. Now, the partners will conduct further clinical evaluation of the biomarkers, with the intent of developing a HF biomarker panel and an accompanying clinical development program to translate the findings from basic research to clinical benefit of patients. Partnering with Roche has the strategic advantage that their diagnostic test might run on more than 40,000 Roche Diagnostic instruments worldwide. The Panel aims to assist physicians in earlier identification and classification of HF and support personalized HF treatment that might result in more effective therapies and better outcomes for HF patients. These are important aspects in view of patient burden and costs associated with HF, with particular focus on minimizing length of hospitalization, re-admissions, unnecessary treatments and adverse events. The project aims at promoting Canadian leadership in medical innovation and attracts additional partnerships and investments from major leaders in the global biotech industry.

Developing Vasculotide, a genomic/proteomic-derived treatment to target vascular inflammation and destabilization

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Overview

More than one million cardiac surgeries are carried out each year, usually successfully. Nearly one-third of high-risk patients, however, will experience a rapid loss of kidney function after surgery, known as Acute Kidney Injury, or AKI. AKI is the result of short-term interruptions in blood flow during surgery; 11 percent of patients who develop AKI after bypass surgery will die, compared to 2 percent of those who do not. Those who survive AKI are at risk of developing longer term kidney complications such as chronic kidney disease or End Stage Renal Disease. There is, therefore, a pressing need for better ways to prevent or treat AKI. Drs Dumont and Van Slyke conceptualized and designed a drug called Vasculotide (VT) that binds to the Tie2 receptor, which is responsible for maintaining vascular health (and thus blood flow). Vasomune Therapeutics, the company developing and commercializing the drug, is partnering with these researchers to develop VT to the point where it is ready for human clinical trials. At that point, Vasomune will be positioned to seek venture capital for further development. Within three-to-five years of the end of the project, Vasomune will be a venture-backed Ontario biotech company with a Phase II clinical program in renal disease. Being able to prevent or reverse AKI will save the healthcare system as much as $1 billion each year, in part because fewer patients will develop chronic kidney disease. Canadians will also have earlier access to VT. Commercializing VT will also bring financial returns to Canada and provide training and create jobs for highly qualified personnel.

Clinical utility and enhancements of a pharmacogenomic decision support Tool for Mental Health Patients

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Overview

One in five Canadians will experience some form of mental illness in their lifetime. Treatments are available but each person responds differently to them, in part because of their genes. A clinically proven genetic test, called GeneSight, analyzes an individual’s genes and recommends the optimal drugs for that person along with dose adjustments among the 33 most commonly prescribed antidepressant and antipsychotic drugs. Clinical testing in the United States has shown that GeneSight doubles the odds of a patient responding to antidepressant medication. More than 100,000 patients have received GeneSight tests in the United States. Now, Assurex Health, the company that developed GeneSight, is partnering with scientists at Toronto’s Centre for Addiction and Mental Health (CAMH) to develop the Enhanced GeneSight (E-GeneSight) genomic test. E-GeneSight will incorporate new genomic markers that scientists at CAMH have identified and characterized for their association with patient responses to psychiatric medications. Assurex Canada and CAMH will together validate these markers for their ability to predict efficacy and side effects of psychiatric medications; the most predictive markers will be integrated into E-GeneSight. E-GeneSight, when launched in 2017, is anticipated to reduce the need for “trial-and-error” approaches to prescribing and increase the likelihood that people will respond optimally to the medications prescribed for them, while reducing side effects. This will increase the proportion of patients who stay on their medications and improve their quality of life. It will also save the Canadian healthcare system $4,000 per year per treatment-resistant patient and will generate royalty revenues for CAMH as E-GeneSight is marketed internationally.

Novel rapid diagnostic tools for lung transplantation: Bringing omics to the bedside

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Overview

A considerable number of patients needing a lung transplant die due to a lack of donor organs deemed suitable for transplant. Now, a proposed genomics approach to assessing donor lungs has the potential to save thousands of lives while reducing healthcare costs. The project, led by Dr. Shaf Keshavjee of Toronto’s University Health Network (UHN) in collaboration with the U.S. biotech firm Lung Bioengineering Inc., a subsidiary of United Therapeutics Corp., intends to develop a genomics-based diagnostic test to determine whether a donor lung meets transplant requirements. At present, such evaluations are based on physiological assessments alone. As a result, less than 15 per cent of lungs, the healthiest, are deemed suitable for transplant, leaving unused countless “marginal” lungs that also could save lives. A genomics-based analysis could increase the number of transplant-acceptable lungs to nearly 50 per cent, resulting in a greater number of patients receiving this life-saving intervention. Using diagnostic test kits, donor lung conditions would be precisely monitored through biomarker analyses. Under Dr. Keshavjee’s research leadership, some biomarkers have already been isolated that can predict lung quality. Building on these findings, this new initiative will result in the creation of rapid diagnostic tools that could be used in transplant centres around the world. The world’s first successful clinical lung transplant took place at Toronto General Hospital in 1983. Today’s genome project has the potential to further cement Canada’s global leadership in this high-tech medical sector. This initiative may also reduce the economic burden on the Canadian healthcare system while improving overall quality of life for lung-transplant patients.