A novel technology for streamlined synthesis, screening, and sequencing of privileged cyclic peptide scaffolds (2011)

Overview

Over the past several years there has been increasing interest in drugs that are peptides and proteins. The reason that peptides and proteins appear promising is that they are made of amino acids, which humans naturally have, and are therefore less likely to cause unwanted side effects. Peptides control a vast range of processes in human cells. The vast majority of peptides are linear: they are built of amino acid building blocks into longer molecules that are flexible akin to spaghetti. Despite the biological significance of these flexible molecules, they are not good as therapeutic agents because our bodies have found a way to rapidly degrade them back into the amino acid constituents. If one could “tie up the loose ends” and create a circular peptide molecule out of a linear one, it may still have the desired biological effect. However, the stability is expected to be drastically increased because the body does not know how to chop circular molecules as efficiently as their linear counterparts.

One may, therefore, ask a question: “why don’t we see more circular peptides as drugs on the market?” The answer lies in extreme technical difficulties in making these circular molecules out of linear ones. In 2010, Dr. Andrei Yudin and his students at the University of Toronto found that the molecules of cyclic peptides can be readily made using novel chemistry developed in the Yudin lab. Funded in part by OGI (SPARK), the Yudin lab has made an exciting discovery that not only the stability but also the ability to enter human cells is increased when circular molecules are made with their method. With this important finding in hand, the Yudin lab is extremely excited about asking the next logical question: “now that your molecules can enter human cells, can they also kill disease-associated proteins found in infected cells?”. The SPARK grant has enabled us to build a much needed momentum that has resulted in several other grants, most notably – CQDM. Additionally, the Yudin group has initiated a collaboration with Eric Marsault (Department of Pharmacology, University of Sherbrooke). The stage is now set for an exciting path towards real therapeutics. For more information, please click here.

Instrumentation for automated pronuclear microinjection (2011)

Overview

Pronuclear microinjection is a technique for creating transgenic mice, an important tool in genetics/genomics and developmental biology research. Due to the inherent difficulties of manipulating delicate mouse embryos, pronuclear injection has been conducted by a handful of professional microinjectionists at Mouse Core Facilities that typically only large research institutions possess. To non-professionals, pronuclear injection of mouse embryos has high skill requirements, a long learning curve, and low success rates. Since regular lab technicians or graduate students are not up to the task, researchers usually turn to professional services provided by Mouse Core Facilities. Advanced Micro and Nanosystems Laboratory (AMNL)

In order to automate pronuclear microinjection, this project under Drs. Yu Sun and Zhe Lu at the University of Toronto developed several key technologies. Based on computer vision microscopy and precision motion control, the system prototype is capable of 3D orienting individual mouse embryos. Dynamic autofocusing techniques were embedded in the system for aligning the holding pipette, pronuclei, and the injection micropipette. Techniques based on motion history images were also implemented and proven effective for detecting the contact between cell and pipette tip. The proof-of-concept system also demonstrated the feasibility of performing pronuclear injection via computer mouse clicking. Building on the results from this project, the team will pursue partnership with industry to further develop the technology for translating it to industry.

First-of-a-kind web tool for exploring splicing misregulation in human disease (2011)

Overview

The human genome can be thought of as a computer program that controls the generation of biological complexity and the activities within living cells. While the text comprising the genome was revealed 10 years ago when the genome was ‘sequenced’, deciphering the genetic code hidden within the genome has been difficult. Recently, Drs. Brendan Frey and Benjamin J. Blencowe at the University of Toronto have developed a method that enabled them to identify the instructions comprising a ‘splicing code’ within the genome (Barash et al, Nature 2010 Website for Alternative Splicing Prediction). In this pilot project, they examined the potential for using the splicing code to enable biomedical research. They re-oriented their analysis toward the causes of human disease, invented a methodology for predicting the effects of genetic mutations, and developed a prototype web tool that demonstrates how the tool can be used to enable medical research. This pilot project was successful and led to 1) the development of a $1 million proposal to scale up the approach to fully support medical research, 2) a collaboration between the University of Toronto, Cold Spring Harbor to investigate the causes and therapeutic treatment of spinal muscular atrophy, the leading cause of infant mortality, and 3) the training of graduate students and postdoctoral fellows who are now working to scale up the methodology to support medical research. The exploratory research enabled by this project has opened the door to a new major direction of research in the Canadian genomics community.

MedSavant: A platform for identifying causal variants from disease sequencing studies (2011)

Overview

Using the Ontario Genomic’s SPARK award, Dr Budno and Mr Fiume of the University of Toronto have been developing MedSavant, a high-performance software platform for the analysis of DNA data that helps researchers pinpoint the causes of genetic diseases. The platform serves as a repository and search engine for huge volumes of genomic mutations that are being gathered through genome sequencing. It harnesses the information collected from many patients and studies, and provides a flexible interface for organizing data, performing sophisticated analyses, and generating reports. MedSavant continues to be developed with the aim of making genomic analysis powerful yet easy, and making the wealth of genome sequencing data being generated accessible to researchers without informatics backgrounds, including physicians and clinical geneticists.

During the SPARK grant, two beta version of the software have been publically released, and a full release is being developed. MedSavant is currently being deployed for use in leading genomic initiatives, both at the Hospital for Sick Children and as part of the nationwide FORGE consortium for finding the genes involved in rare diseases affecting Canadians. Going forward, MedSavant is expected to become central to the Hospital of Sick Children’s Genome Clinic, a large scale effort to develop the informatics, workflows, as well as ethical and legal frameworks necessary to bring whole-genome sequencing to the bedside.

BANGS: A tool for Bayesian analysis of next-generation sequencing data (2012)

Overview

This SPARK project will develop robust statistical data analysis tools for next generation sequencing (NGS), which refers to a set of high throughput technologies for measuring signals across the genome.  Those signals may represent which genes in the genome are active, where certain regulatory molecules bind to the DNA, or even something about the state of the DNA itself. However, NGS technologies do not measure the genomic signals perfectly — there are omissions, uncertainty, and in some cases, bias in the measurements.  Dr. Theodore Perkins’ project through the Ottawa Hospital Research Institute proposes a novel approach to reconstructing genomic signals represented in NGS data using Bayesian statistics.  The main features of this approach are that the team is able to put forth a best estimate of the signal, and also to quantify the uncertainty in the estimate. Quantifying uncertainty is useful for visualization of genomic signals, and is critical for comparing them under different conditions.  This statistical approach will be implemented in efficient, open-source, well-documented software, for the benefit of the NGS community.

Development of highly diverse but fully defined phage display libraries (2012)

Overview

Protein interactions are at the basis of all cellular processes. This project from Dr. Philip Kim and Dr. Sachdev Sidhu at the University of Toronto is developing a novel technology platform and associated methodology that can probe such interactions in a high-throughput manner. They are combining oligonucleotide chips with combinatorial chemistry and computational methods to create a powerful technology that directly scans biologically relevant interactions. The team will create novel software that will allow custom design of oligonucleotide sequences that encode for large numbers of different protein fragments.  Custom oligonucleotide chips will be ordered and used to generate the specifically designed protein fragments.  Finally they will establish protocols for making and assessing the binding of hundreds of protein fragments. This is the first time oligonucleotide chips have been used in this fashion. Initially, this project will test proteins involved in cancer, which could lead to new insights for cancer therapy. Furthermore, the platform is particularly well suited to test interactions between viral or bacterial proteins and their human targets. This project will result in new insights into the biology of viral infections and novel routes to treatment. Project deliverables are the completed technology platform as well as completed libraries suited for detection of interactions for both human and viral proteins.

Monomeric genome-editing nuclease (2012)

Overview

The ability to alter the genetic material of mammalian cells in a precise and time-effective manner will enhance our ability to understand the molecular basis of disease and facilitate treatment options. Altering the genetic makeup relies on the development of biochemical reagents that interact with DNA in a site-specific manner, with minimal interactions at unwanted sites. Developing these reagents is not trivial given the size of the human genome. The biochemical reagents in question are “molecular scissors”, site-specific DNA endonucleases that make a break in DNA at defined sites. The lab under Dr. David Edgell and Dr. Gregory Gloor at The University of Western Ontario has recently developed a new type of molecular scissor based on the nuclease (or cutting domain) from the phage T4 protein I-TevI that is fused to the TAL effector targeting domain which encodes DNA sequence specificity. The Tev-TAL fusions promise to be more specific and smaller than existing reagents. To realize the potential of the Tev-TAL nucleases, the DNA recognition “code” of the Tev-TAL scissors must be fully understood. That is, we must know what DNA sequences we can and cannot target with the Tev-TAL scissors. Knowing this code will allow us to design Tev-TAL scissors that will facilitate both basic and applied research. For instance, it will allow researchers to use Tev-TALs to knockout candidate genes in mouse models of human diseases, accelerating our basic understanding of complex human diseases.

Enhanced metabolite profiling for newborn screening (2012)

Overview

Newborn screening (NBS) programs represents one of the few proven strategies to prevent infant mortality and long-term disabilities associated with rare yet treatable genetic diseases. Early detection allows for prompt therapeutic intervention that improves clinical outcomes for infants. The recent advent of tandem mass spectrometry (MS/MS) has revolutionized NBS by enabling rapid metabolite profiling of dried blood spot samples collected via a heel prick of every newborn in Ontario. Despite the remarkable success of MS/MS technology, sample pretreatment currently limits the range of metabolites and classes of genetic diseases that can be reliably screened. This project, under Drs. Philip Britz-McKibbin (McMaster University) and Osama Aldirbashi (Newborn Screening Ontario, Children’s Hospital of Eastern Ontario), will develop a novel chemical reagent that permits efficient labeling of clinically relevant metabolites under mild/ambient conditions while potentially boosting sensitivity over two orders of magnitude. This is crucial for expanding NBS to encompass trace levels of metabolites that are difficult to analyze by MS/MS yet serve as primary biomarkers of various genetic disorders. To translate these findings into a marketable product for the clinical laboratory, the metabolomics team at McMaster University will optimize a chemical reagent kit which will be evaluated and validated at Newborn Screening Ontario in the Children’s Hospital of Eastern Ontario. This project will not only enhance the analytical performance of metabolite profiling by MS/MS for additional genetic diseases at minimal incremental costs, but also improve the efficacy of NBS programs by replacing classical biochemical assays that are prone to false-positives.

Creating a non-invasive Norway Maple (2014)

Overview

Led by Travis Banks and Darby McGrath of Vineland Research and Innovation Centre, this project will initiate work to develop a Norway maple tree that is no longer invasive, in an effort to keep our cities green. Pests and disease are destroying city trees and there are no alternatives suitable to survive the extreme conditions of Ontario urban environments. Having fallen out of favour because of invasiveness, Norway maple was used extensively as an urban tree, which thrives in polluted and compact soils, withstands hot summers and cold winters, and suffers few diseases. SPARK funding will enable DNA sequencing of the Norway maple genome and update methods to identify new Norway maple plants that are unable to create fertile seeds.

Genomic ancestry in a non-model wildlife species at risk, the Eastern Wolf (2014)

Overview

Led by Brent Patterson and Linda Rutledge, Trent University and the Ontario Ministry of Natural Resources & Forestry (OMNRF), this project aims to improve wolf conservation in Ontario. The research team will be collaborating with scientists at Princeton University to validate and optimize a rapid and efficient genetic mapping approach on the Eastern Wolf, which has the potential to make genomics more accessible to labs with limited resources and provide researchers with an effective, low-cost methodology for genomic analysis of fish and wildlife populations.