Sequencing the human genome has led to the realization that a relatively small number of genes can give rise to an enormously complex living organism. This can be explained by the fact that proteins can be modified after their initial assembly to have multiple functions in multiple locations in the co-ordination of cell growth and function. One such modification called O-GlcNAc has been shown to be involved in many cellular processes, however, its precise function has not yet been determined. Malfunctions in the regulation of O-GIcNAc-modified proteins have been implicated in such diverse diseases as diabetes, Alzheimer’s, Parkinson’s, and a variety of cancers. For example, diabetic patients have been found to have elevated O-GlcNAc levels, although it is not clear whether these high levels are a cause or an effect of diabetes. Using techniques including mass spectrometry, chemical synthesis and mouse models, Matthew Macauley’s goal is to develop a method for identifying proteins modified by O-GlcNAc. This will give valuable insights into how this modification process affects normal cell function and may provide new knowledge about its precise role (i.e. is it a cause or an effect) in diabetes. In turn, such knowledge may contribute to the development of more effective preventive and treatment strategies.
Research Pillar: Biomedical
Stress and adult neurogenesis: neuroprotection by dehydroepiandrosterone (DHEA)
Mood disorders such as depression and post traumatic stress disorder are a major health concern in British Columbia, and around the world. Understanding the role of stress related to depression is a crucial step towards developing treatment strategies. From a biological perspective, stress-induced decreases in neuron (nerve cell) production in the adult brain have been associated with depressive symptoms. One line of research into treatment options is the use of a steroid hormone called dehydroepiandrosterone (DHEA) which has been shown to alleviate symptoms of depression. Steroid hormones are critical for the nervous system to develop and function normally, but relatively little is known about the actions of DHEA on the nervous system and how DHEA acts at the cellular and molecular level. Amy Newman is investigating how physiological levels of DHEA buffer the effect of stress in organisms in the brain. She is examining the effects of DHEA on stress-induced changes in the nervous system and on adult neurogenesis (development of nerve tissues). Ultimately, findings from this study may lead to the development of therapeutic advances to decrease neuronal loss in response to stress, and alleviate symptoms of depression.
In silico approaches for investigating mechanisms of gene regulation
More than 95% of the human genome is made up of non-coding DNA, historically dismissed as ‘junk DNA’ of unknown function. It is now known that the so-called junk DNA isn’t junk at all; in fact, it contains important information specifying how genes are regulated. Non-coding DNA sequences located adjacent to genes typically contain binding sites for proteins that act like regulatory switches, turning genes on or off in the appropriate cell types and under particular conditions. Errors in this process have been linked to diseases ranging from cancer to obesity. Recent studies have determined that there are a surprisingly large number of non-coding sequences that are highly conserved across the vertebrate lineage. These regions, termed ‘ultraconserved sequences’, are almost identical in humans, rodents and fish. They have been minimally explored but appear to have an important role in regulating the expression of key developmental genes. Shannan Ho Sui is studying the properties of ultraconserved regions in the human genome to assess their potential role in gene regulation. Her research involves using bioinformatics techniques to find and analyze patterns in DNA sequences. By determining the properties of genes associated with ultraconserved regions, evaluating how frequently recombination occurs in these regions, and locating similarly highly conserved non-coding sequences in the fly and worm genomes, Shannan hopes to develop a model describing how and why these regions are maintained in the genome. Her research results will provide valuable insights into mechanisms of gene regulation that play important roles in development and disease.
Effect of drugs on the tumour microenvironment
One challenge with treating solid tumours is ensuring the effective delivery of chemotherapy drugs to all the cells within a tumour. Inefficient penetration of an anti-cancer drug results in insufficient doses reaching cells distant from the tumour’s blood vessels. As a result, these cells may survive and proliferate, allowing the tumour to re-grow. In addition, a low drug exposure may actually contribute to tumour cells developing resistance to a drug. Lynsey Huxham is examining the tumour microenvironment after drug administration and determining which drugs penetrate well. She is focusing on the effects of a drug by examining dividing cells and those undergoing apoptosis (cell death) in relation to their distance from blood vessels. By understanding the process of extra-vascular drug distribution, she hopes to aid efforts to improve the administration and delivery of cancer drugs, as well as offer insight into the design of new chemotherapy drugs.
Glutamate regulation at the Drosophila larval neuromuscular junction: a model for excitatory synaptic function
The human brain is composed primarily of two cell types – neurons, which extend axons that make contact with other neurons at synapses, and glia, which wrap around neurons, protecting them and regulating their function. An electrical signal is conducted through the axon to the synapse where neurotransmitters are released to electrically excite the next neuron. The termination of this chemical signal is controlled by nearby glia, which remove the neurotransmitter using transporter proteins on their cell surfaces. A malfunction in this activity may lead to excessive levels of neurotransmitter accumulating in the synapse, over-exciting nearby neurons and glia and eventually leading to cell degeneration and death. This type of glial malfunction has been linked to many common neurodegenerative diseases (e.g. stroke, Alzheimer’s, multiple sclerosis and muscular dystrophy). Glutamate, the neurotransmitter at most brain synapses, is also present at many synapses of the fruit fly (Drosophila melanogaster). As in humans, fly glia have glutamate transporters that are thought to regulate synaptic communication. Robert Parker is studying glial neurotransmitter transporter function in the fruit fly, altering the amount of glutamate transporter present in glial cells near the Drosophila neuromuscular junction (a synapse between a neuron and a muscle cell) which may cause the over-excitation, degeneration and death of nearby cells. By studying the basic function of glutamate transporters in flies, he hopes to gain a greater understanding of the clinical importance of glutamate transporters in many human neurodegenerative diseases.
High resolution analysis of rearrangements in follicular lymphoma genomes using high-throughput BAC clone fingerprinting
Follicular lymphoma is a cancer of the lymphocytes (cells of the immune system) and is the most prevalent type of lymphoma in Canada. Most follicular lymphomas are associated with defective cells resulting from the gene regulation process (the process through which the cell determines when and where genes will be activated) resulting in increased production amounts of the protein Bcl-2. This protein prevents lymphocytes from dying at the end of their natural lifespan, causing these altered cells to persist in the body, gain abnormal alterations in their genomes, and eventually develop into cancerous cells. Anca Petrescu is examining how chromosomes in follicular lymphoma are structurally different and rearranged relative to the normal genome, and how these differences may cause cancer. She is studying ten follicular lymphoma genomes and will profile each to discover the rearrangements they harbour. Common rearrangements will be analyzed in detail to determine their exact properties, and their effect on genes. Anca hopes her research will provide insight into the role of recurrent rearrangements in follicular lymphoma, and allow for further research to identify key genes that may be may be of potential diagnostic or therapeutic use.
Tracking the differentiation fate of islets from pancreatic endocrine progenitors via expression of lentivirally transduced fluorescent reporter genes
The recent success of a pancreatic islet cell transplantation procedure known as the ‘Edmonton Protocol’ gave new hope for a better treatment of type 1 diabetes (insulin dependent diabetes), compared to the current treatment via insulin therapy. However, a shortage of donor pancreatic tissue means an alternate source of transplantable cells is needed. Insulin-producing islet cells are created from pancreatic precursor cells through a process called differentiation. However, not all pancreatic precursor cells give rise to insulin-producing islet cells. Further, the optimal conditions for differentiating these cells have not been determined. This poses a challenge for researchers attempting to identify and isolate the specific precursor cells needed for producing transplantable islet cells on a large scale in the laboratory. Marta Szabat is working to develop a functional assay for tracking the differentiation fate of islets from pancreatic precursor cells using fluorescent reporter genes. This cell marking technique would flag only those cells with specific genetic characteristics, allowing for purification and further characterization of labeled cells. Using this functional assay, her long term objective is to determine the optimal conditions to support (culture) the differentiation of pancreatic progenitors into insulin-producing cells.
Computational identification and quantitative modeling of dynamic cellular pathways
The ability of cells to carry out life functions arises from the collective behavior of interacting molecules. Cells are able to integrate multiple internal and external messages simultaneously and respond reliably with a predefined set of outcomes. This adaptability and robustness is based on a complex system of signaling and regulatory molecules, which interact in dynamic circuits to regulate and support all aspects of cell growth and function. James Taylor brings a background in engineering physics to the study of molecular biological systems. He is using mathematical and computational modeling to simulate information flow through dynamic molecular circuits. In parallel, he is designing microfluidic platforms for the experimental testing of these circuits on the single cell level. James hopes to increase the efficiency of biological discovery and the use of predictive modeling in drug discovery. Employing filamentous form cell differentiation in yeast as a model system, he is characterizing the dynamics of a new circuit within the MAP Kinase cascade, a common signaling system that plays a central role in integrating the signals from a diverse group of external stimuli to regulate processes such as cell proliferation, cell differentiation, cell movement and cell death. Using a double headed approach of modeling and experimentation, he is continuing to research how this complex circuit enables the cell to robustly integrate multiple internal and external molecular messages simultaneously.
The function of Pyk2 on Rap-GTPase mediated cell spreading and cell migration
B cells make antibodies that help combat pathogens. The B cell receptor, chemokine receptors and integrins on the cell surface are molecules that send signals to regulate B cell migration and adhesion. These processes are essential for B cells to enter the lymphatic system and to identify and adhere to foreign molecules (antigens) for the purpose of mounting a protective immune response. Proteins called Rap GTPases and Pyk2 are important in controlling B cell migration and adhesion, but the mechanisms involved are not well understood. Kathy Tse is investigating how Rap regulates Pyk2 and how Pyk2 promotes B cell migration and adhesion. Specifically, she is examining the localization and activity of Pyk2 during cell migration and adhesion. Knowledge from this study will allow better understanding of normal B cell movement and activation, and has potential for identifying drug targets for treating immune system diseases, including cancer.
Reducing pain and complications following total knee arthroplasty by minimizing patellofemoral contact loads intra-operatively
The primary reason for someone to undergo a knee replacement is to reduce pain due to arthritis. Unfortunately, some people who have the surgery will have similar, or even more, pain after their knee replacement. It is difficult to predict which patients will have this outcome and it is difficult to treat the pain post-operatively. Much of the pain is likely related to points of high pressure (high contact loads) between the kneecap (patella) and the thigh bone (femur), or unusually stretched soft tissues between the bones. A potential way to minimize pain and other problems following surgery would be to detect these points of high pressure during the operation and make adjustments to the positions of the implants or the tensions of the soft tissues to reduce the contact loads. If the contact loads could be minimized during the surgery, the outcome would be less pain and fewer subsequent surgeries due to wear, loosening or fracture of the components. Dr. Carolyn Anglin intends to reduce pain and improve the outcome of knee replacement surgery by developing a computer-aided system to help identify pressure points during surgery. In addition to performing a cadaver study to investigate the effects of different placements of the artificial components on cadaver specimens, she will review X-rays, patient charts and patient-completed questionnaires to determine the relationship between the placement of components and the resulting quality of life after surgery. Her ultimate goal is to develop a system that can measure the forces between the kneecap and the thigh bone, then display them on a computer screen. This will allow the surgeon to choose the best positions for the components. Such a system could dramatically reduce the incidence of pain and complications following knee replacement surgery.