Research Pillar: Biomedical

Structural characterization of the architecture and assembly of the bacterial type III secretion system injectisome

Gram-negative bacteria such as E.coli, salmonella, shigella, pseudomonas aeruginosa, and yersina pestis are responsible for a wide range of diseases. A common trait shared by these bacteria is their capacity to inject toxins directly into the cells of infected individuals using a syringe-shaped “nano-machine” called the Type 3 Secretion System injectisome. Preventing the injectisome from performing its function would effectively prevent these bacteria from causing a disease.  

The injectisome is an important target for the development of novel treatments against bacterial infection. This research project will attempt to obtain a “map” of the injectisome at the level of individual atoms. Such a map will allow us to understand how different components interact to assemble such a “nano-machine” at the surface of the bacteria, and the mechanism by which the injectisome can inject toxins into human cells.

To map the injectisome at the level of individual atoms, Dr. Bergeron will use a range of biophysical methods, such as X-ray crystallography, nuclear magnetic resonance, electron microscopy, and molecular modelling.

A map of the injectisome could be used to design novel antibiotics or vaccines, which would function against a wide range of bacteria. In addition, understanding the mechanism of this nano-machine could allow the development of microscopic targeted injection devices with a wide range of potential applications.

Pharmacogenomic prediction of anthracycline-induced cardiotoxicity

Anthracyclines are a class of drugs used world-wide for the treatment of most cancers. However, their clinical utility is limited by a high risk of cardiac toxicity and congestive heart failure.

Dr. Aminkeng aims to identify genetic markers that can predict anthracycline-induced cardiotoxicity and congestive heart failure using a genome-wide association study (GWAS). The goal is to develop a clinical test that will allow for better identification of risk factors and improved treatment and monitoring that will increase the safety of anthracycline therapy.

Study participants have been recruited via the Canadian Pharmacogenomics Network for Drug Safety. Patients will be genotyped using the GWAS Illumina Infinium assay. In vitro, in vivo, and pharmacokinetic studies and pharmacodynamics modelling will be used to study the functional relevance of identified genes.

A highly predictive test for anthracycline-induced cardiotoxicity and congestive heart failure would significantly benefit patients, families and physicians by improving counselling and treatment options. For example, a patient at high risk could receive more aggressive echocardiogram monitoring for toxicity, receive a cardio-protective drug such as dexrasoxane, or be treated with an alternative chemotherapy protocol.

HIV adaptation to immune selection pressures: historic trends and future implications

HIV has tremendous capacity to mutate and evolve due to the body’s immune response. However, the extent to which the virus has adapted to its human hosts over the course of the pandemic remains poorly understood. Repeated cycles of immune selection and transmission may allow the accumulation of key “escape mutations” — changes in the viral genome that help HIV evade the body’s defences. If immune targets in the HIV genome were disappearing over time due to the accumulation of these mutations, our ability to generate natural and vaccine-induced protective immune responses would diminish as the epidemic progresses.

Furthermore, the extent to which immune escape has influenced HIV pathogenesis remains unknown. Studies investigating the evolution of HIV virulence have largely focused on population-level trends in clinical markers over time, but few have addressed this issue using biological assessments of replication capacity or viral protein function.

Dr. Zabrina Brumme’s research team will undertake the first large-scale investigation of immune-driven HIV evolution and its implications over the 30-year history of the epidemic in North America. Host and viral genetic sequences from 1979 to the present will be analyzed to characterize the extent of population-level HIV adaptation over the epidemic’s course. Functional assessments of viral replication capacity and protein function will be performed to determine whether HIV is evolving towards increased virulence, gradual attenuation, or simply adapting to changing host-pathogen pressures over time.

With this study, Brumme is poised to answer two key questions of HIV biomedical research, namely, to what extent the virus has adapted to its hosts since AIDS was first recognized, and what implications this has for the future of the epidemic. Results have the potential to significantly advance HIV vaccine research.

Characterization of the formation of protein aggregates induced by the inhibition of the ubiquitin proteasome system

Protein aggregation is a pathological feature of a large number of diseases with a strong preponderance in age-related neurodegenerative disorders like Parkinson’s disease. Failure to eliminate aberrant proteins in the cell plays a major role in these pathologies and is often linked to the impairment of the ubiquitin proteasome system, which degrades proteins labeled (or modified) with ubiquitin. The overall goal of Dr. Thibault Mayor’s research is to further define the involvement of the ubiquitin proteasome system in aggregation diseases using proteomic and cell biology approaches.

Mayor’s team has developed a new cellular assay to monitor the formation of aggregates induced by proteasome inhibition. They have identified by mass spectrometry more than 500 proteins that localize in these structures. Using a computational approach, Mayor will determine which features are shared among these proteins to give better insight into the mechanisms leading to aggregation. The UCHL1 enzyme may also be a major player in the aggregation process, and Mayor’s team will use the cell assay and mass spectrometry to further characterize UCHL1 and determine whether other enzymes related to the ubiquitin proteasome system may promote aggregation.

Current treatments for most aggregation diseases are primarily based on symptom management instead of directly treating the cause. Mayor’s work may potentially lead to a better understanding of the aggregation mechanism and identify novel targetable pathways to prevent formation or favor clearance of protein aggregates that could be used for new therapeutics.

A wearable assistive device for improving quality of life

Mobility of the upper extremities has a significant impact on independence and quality of life. For individuals with neuromuscular disorders due to aging, stroke, injury, or other diseases, the activities of daily living (such as eating and dressing) can be very challenging. However, biomedical robotic technologies offer a promising tool with which to improve the mobility of individuals with impaired upper extremities.

Collaborating with experts in the field of neuromuscular rehabilitation, Dr. Carlo Menon is leading the design and development of a smart assistive medical device that is portable and wearable. The objective is to develop a device that will assist with functional movements and strengthen muscular tone of the weakened or impaired extremities. The device will have potential use for both upper extremity assistance and rehabilitation.

This research will improve the quality of life for individuals with neuromuscular disorders by restoring mobility of the upper extremities. The proposed project will include the following phases: a) interaction with the neuromuscular collaborators to iteratively reformulate the design; b) the engineering design and development of the biomedical robotic device; c) the engineering testing of the device; d) a study of the interactions between the device and both healthy volunteers and individuals with neuromuscular disorders to verify that the device can assist functional movements; e) technology transfer to neuromuscular scientists and clinicians.

Uncovering novel regulators of beta cell genesis, growth and function

To date, the only successful approach for curing type 1 diabetes is to replace the insulin-producing beta cells that have been destroyed by the disease. Pancreas- and islet-cell transplantation are promising therapeutic strategies; however, scarcity of transplantable tissue has limited their widespread use. One way to produce enough beta cells to cure type 1 diabetes is to determine how the cells develop normally within the embryo and apply this knowledge to the regeneration of beta cells in the culture dish or directly in people with diabetes.

Using human and mouse model systems, Dr. Francis Lynn’s research aims to enhance our understanding of normal regulatory pathways that govern pancreas- and insulin-producing pancreatic beta cell genesis and function. The hope is that a greater understanding will enable cell-based approaches for treating and curing diabetes. Lynn’s long-term objective is to understand how regulatory DNA-binding proteins called transcription factors drive beta cell formation and function. This research specifically focuses on one member of the Sox gene family of transcription factors named Sox4. Preliminary data suggest that Sox4 is instrumental in governing both the birth of beta cells and their replication later in life. These observations place Sox4 as a novel and previously unappreciated key regulator of beta cell biology.

Lynn hopes that a thorough characterization of the pathways through which Sox4 regulates beta cell formation and function will inform novel approaches for generation of large numbers of functional beta cells from human embryonic stem cells or induced pluripotent stem cells.

HIV vaccine immunogen design to elicit broadly neutralizing antibodies

Existing viral vaccines provide immunity against a number of important infectious diseases. The technologies used to develop these vaccines generally work best against viruses that do not mutate very much in nature. However, conventional vaccine design approaches have proven inadequate for viruses such as HIV-1 that continuously evolve in order to evade our immune defenses. Thus, new vaccine design strategies are needed to tackle viruses like HIV.

Dr. Ralph Pantophlet’s research program is developing novel strategies for the design of vaccines that will induce broad immunity to HIV infection. Specifically, Pantophlet seeks to better understand molecular and immunological conditions that impact the elicitation of antibodies with the capacity to block the infectivity of a wide variety of HIV strains. This research focuses on these types of antibodies, dubbed “broadly neutralizing antibodies,” because of their demonstrable ability to block HIV infection in animal models. Another component of this program of research will be systematic studies to define neutralizing antibody target sites on HIV and investigate exposure of these sites at the molecular level. As part of the proposed research program, knowledge gained from the studies outlined above will be incorporated into the design of formulations to elicit target site-specific broadly neutralizing antibodies upon immunization. Thus, insight gained from this work is expected to advance HIV vaccine design efforts and be of significant interest to the field.

Although the focus will be on HIV, knowledge gained from this work may be applicable to other viruses for which conventional vaccine design approaches are also not optimal. Examples include hepatitis C virus, which like HIV is highly mutable and for which a vaccine has yet to be developed, and influenza, for which better vaccines are urgently being sought due to the constant threat of the emergence of a pandemic strain.

Keywords: HIV, vaccine, neutralizing antibody, immunogen design, vaccine immunology, B cell epitope, adjuvant, glycoprotein, T cell epitope, animal model

SHIP’s roles in intestinal immune homeostasis and inflammation

Dr. Laura Sly’s research program aims to improve our understanding of inflammatory bowel disease pathology and to identify and validate novel therapeutic approaches that will improve patient care. Her team has been investigating the role of SH2-containing Inositol Phosphatase (SHIP) in intestinal inflammation. SHIP is a protein that regulates enzymes involved in immune cell signaling. Sly’s research has shown that SHIP-deficient macrophages are hyper-responsive to IL-4, which drives them to an alternatively activated or M2 phenotype.

Using mice as a genetic model of M2 macrophages, Sly reported that M2 macrophages are protective against induced intestinal inflammation. Since then, her team has characterized a complimentary genetic model of M1-polarized macrophages and has identified key anti-inflammatory mediators that may be responsible for protection. Future investigations will focus on whether adoptive transfer of polarized macrophages or targeting macrophage polarization in situ can reduce intestinal inflammation in pre-clinical models of inflammatory bowel diseases.

Sly’s team has also developed a new mouse model of intestinal inflammation that shares key pathological features with Crohn’s disease. They have reported that SHIP-deficient mice develop spontaneous, discontinuous ileal inflammation accompanied by excessive collagen deposition and muscle thickening. Current research goals include targeting macrophage polarization or polarized macrophage products to reduce intestinal inflammation in pre-clinical models of inflammatory bowel disease, and identifying cell types and biochemical mechanisms that contribute to intestinal inflammation in SHIP-deficient mice. Together, these studies will identify cellular and biochemical targets and investigate new immunotherapeutic approaches that may useful in reducing intestinal inflammation in people with inflammatory bowel diseases.