Myelodysplastic syndrome (MDS) is one of the most frequent bone marrow malignancies, affecting around 1,500 Canadians every year. It is characterized by anemia and a high risk of transformation to acute myeloid leukemia (AML). The only curative option is bone marrow transplantation, which carries high mortality and morbidity. Other standard treatment modalities such as lenalidomide and 5-azacytidine are characterized by a short response and a high degree of relapse. The molecular causes of treatment resistance and disease transformation in this situation are not fully understood. Dr. Martin Jadersten aims to investigate the genetic changes associated with initiation of MDS and understand how these changes contribute to subsequent therapy failure or disease progression. He will investigate serial samples from 10 MDS patients before and after leukemic transformation. RNA and DNA will be extracted from bone marrow cells and marrow fibroblasts (non-malignant control cells), and global genetic investigations such as exome (DNA), transcriptome (RNA) and micro RNA (regulatory RNA) sequencing will be conducted. Powerful bioinformatics methods will be used to analyze the data and identify genomic alterations, including gene fusions, DNA insertions/deletions, and alternative expressions of genes (isoforms). These identified genetic alterations will be validated for recurrence in a large group of MDS patients, and candidate genes will be tested functionally with cell line experiments and mouse models. Dr. Jadersten’s work is already well underway. He has processed three samples from one MDS patient with all of the methods above and has shown that there are significant changes in micro-RNA expression between these time points. As the disease has progressed in this patient, a number of alternatively expressed genes appear, which potentially indicates alterations in the RNA-splicing machinery. By the time the patient develops AML, there is almost a complete loss of two clusters of important regulatory genes involved in embryogenesis and cancer. As this patient sequentially received the only two registered drugs for MDS (lenalidomide and 5-azacytidine), Dr. Jadersten will attempt to determine potential resistance mechanisms using the data already obtained. Identification of key mediators of disease development, leukemic transformation and drug resistance may sharpen our prognostic tools, improve clinical management and provide a basis for development of targeted therapy.
Research Pillar: Biomedical
Insight into motor cortex function from in vivo imaging of individual neurons
The cortex is a thin layer on the surface of the brain where most information processing takes place. The cortex is separated into several layers. There are large numbers of neural interconnections that exist between the different cortical layers, as well as many connections with neurons of the spinal cord. In the somatosensory cortex, where the perception of touch is analyzed, there is a spatial representation of the body on its surface. The same type of spatial organization exists in the motor cortex, controlling the body's muscles; however, the spatial organization of the motor cortex is not as well defined, and this characteristic allows for more change and adaptation during learning or in motor recovery after a stroke.
Dr. Matthieu Vanni will explore the participation of independent neurons in the different layers of the motor cortex of the mouse. The mouse is a model that will be used in these studies because it provides opportunities to manipulate the genome, which will be a major asset in stages of this project. Dr. Vanni will be measuring the activation of identified neurons using two-photon microscopy, which achieves a sub-cellular resolution in living tissue. The neuronal activation in the motor cortex will be measured in response to natural movements and/or following excitation/inactivation of individual neurons of the network.
The results of this study will help to better understand the information processing of motor tasks in the brain. This knowledge could have an impact on the understanding of how the brain adapts during learning and after stroke. Furthermore, understanding these cellular aspects will have important implications in the design of therapeutic rehabilitations such as prosthetic or brain stimulation, limiting post-stroke physical disability. This project will use novel applied optical methods: two-photon microscopy and optogenetics. The exceptional resolution and specificity of these new methods will have a strong impact in many other fields as well; for example, they may be applied to study neural compensation mechanisms observed in neurodegenerative diseases such as Alzheimer's or Parkinson's.
The role of the airway epithelium NLRP3 inflammasome in asthma pathogenesis
Asthma is a respiratory disease that afflicts more than two million Canadians. Asthmatics experience both airway inflammation and changes in the airway structure, called airway remodeling, when they inhale allergens, pollutants and other insults, and this leads to an exacerbation. The airway epithelium is the first site of contact for inhaled substances and has been shown to be different in asthmatics than in non-asthmatics. In specific cells of the body, including the airway epithelium, a danger sensor called the “inflammasome” can signal as part of the immune system to produce inflammation in response to an insult. Currently, we do not know if this airway epithelium danger sensor functions differently in asthmatics than in members of the general population and if this contributes to the development and progression of asthma.
Dr. Jeremy Hirota's hypothesis is that if the airway epithelium danger sensor is present, it increases airway inflammation and contributes to development and progression of asthma. His research goal is to determine the specific mechanisms responsible for airway epithelium danger sensor activation and to find out if it is more active in asthmatics. He is using three distinct approaches for his proposed research: 1) Using lungs that have been donated for medical research, he will compare the danger sensor between non-asthmatics and asthmatics. 2) Using the same donated lungs, he will grow human airway epithelial cells and expose them to an allergen or mechanical wound and then measure the resulting inflammation. 3) He will explore the role of the airway epithelium danger sensor during periods of allergen exposure by comparing normal mice to mice with a dysfunctional danger sensor.
The increasing prevalence of asthma in Canada demonstrates a requirement for a greater understanding of mechanisms leading to disease development and for new approaches to prevent or treat this disease. This research has the potential to highlight new therapeutic targets to control both excessive airway inflammation and the development of asthma.
Allele-specific silencing of the mutant huntingtin gene in a mouse model of Huntington disease
Huntington disease is a fatal and inherited neurodegenerative disease. It is characterized by diminished voluntary motor control, cognitive decline and psychiatric disturbance. Symptoms of the disease first appear in the thirties to fifites, with death usually occurring 15 to 20 years later. While there are still no effective therapies for this disease, recent research discoveries have provided insight into how the disease develops. The normal huntingtin gene encodes a protein that is important for neuronal health. Although everyone has two copies of the huntingtin gene, people with Huntington disease have one normal copy and one mutated copy. When a person has a mutated version the gene, the huntingtin protein accumulates within cells and engages in a variety of aberrant interactions that cause disease symptoms.
Dr. Amber Southwell is working to develop a strategy for turning off the mutant copy of a patient's huntingtin gene in order to prevent or delay the onset of the disease. Her lab has identified genetic characteristics that are more common in mutant than in normal huntingtin genes and have generated therapeutic reagents that specifically target these mutant variations. This effectively switches off the mutant but not the normal gene in cellular models of Huntington disease and results in the selective reduction of the mutant huntingtin protein.
Dr. Southwell will test the efficacy of these candidate therapeutics by measuring their ability to reduce the level of the mutant but not the normal protein in the living brains of a mouse model of Huntington disease. She will also evaluate how the therapeutic reagents influence the behavior and brain pathology of these mice. This targeted approach of selectively silencing the mutant gene while sparing the normal gene is preferable to other approaches that prevent the expression of any huntingtin protein. The normal huntingtin protein is important for neuronal health, and long-term reduction of this protein may not be well tolerated. Hopefully this targeted approach will lead to new therapies to prevent or delay Huntington disease onset.
Elucidating the functions of MCL-1 in DNA repair
Mammalian cells have developed elaborate DNA damage response (DDR) and DNA repair systems in order when to protect and repair their DNA encountering toxic agents. In tumour cells, activation of these molecular events can make tumour cells resistant to chemotherapy or radiotherapy-induced DNA damage. Therefore, decoding how the DDR and DNA repair mechanisms are controlled is very important for understanding how cells become resistant to chemotherapy and to find ways to improve conventional cancer therapies. MCL-1 is a pro-survival protein that has multiple roles within the cell and has been shown to protect cells from death. It can interact with multiple important nuclear proteins involved in DDR response. Loss of MCL-1 increases genome instability after DNA damage. These studies indicate that MCL-1 may be an important component of the DDR machinery to regulate the repair of DNA lesions. Dr. Yemin Wang is investigating how MCL-1 regulates DDR and DNA repair. He is taking an intracellular approach to understand how MCL-1 is delivered into the nucleus after DNA damage and will also use this approach to investigate how MCL-1 regulates crucial events in DDR and DNA repair machinery. Dr. Wang will also examine whether the presence of MCL-1 in the nucleus affects how the cell responds to chemotherapy and whether the role of MCL-1 in DDR affects tumor development. The results of Dr. Wang’s work will provide us with a better understanding of MCL-1 in DDR and DNA repair processes, explain its essential function in vertebrate development, and help us to design improved therapeutic interventions for cancer treatment.
Analysis of the influence of retroelements on activation of oncogenes in primary human lymphomas using high-throughput sequencing
Endogenous retroviruses (ERVs) are viral DNA sequences that have repeatedly inserted themselves through the course of primate evolution and in turn become an integral part of the human genome. The human genome contains more than 200 families of ERVs, which together comprise approximately 8 percent of our chromosomal DNA. A growing body of evidence indicates that ERVs have been a major player in molecular evolution and continue to impact the mammalian genome by acting as insertional mutagens, inducing DNA rearrangements and altering gene regulation. Given the potential for harmful effects, it is not surprising that mammals have evolved multiple lines of defense against these endogenous retroviruses, such as modifying the DNA or chromatin structure to prevent the genes from being expressed. In theory, if the ERVs are de-repressed, they could become active and then cause disruptive events leading to cancer. Although the structure, function and impact of human ERVs (HERVs) on the human genome has been studied in detail, their potential contribution to cancer has not been systematically examined. Dr. Mohammed Mahdi Karimi will be applying his experience in bioinformatics methods and high-throughput epigenetic analyses to study HERV families in human cancers. He will examine gene expression patterns and different types of epigenetic modifications, including histone modifications and DNA methylation, in primary lymphocytes isolated from lymphoma patients as well as in cell lines. By identifying the epigenetic changes in the genomes of HERV families, he hopes to determine how abnormal gene expression leads to the development of human lymphomas. Dr. Karimi expects that the results from this initial analysis will reveal genes that are misregulated in cancer as a result of the de-repression of HERVs, and this misregulation will be reflected in changes to the DNA or chromatin modification. The ultimate goal of Dr. Karimi’s research is to identify molecular or epigenetic pathways that are perturbed in different types of human lymphomas, which in turn may potentially be targeted with new therapeutic strategies.
Mechanisms underlying protective effects of HDL and ABCA1 in beta cell survival
Diabetes is a major cause of disease and death in BC. According to a report from the Canadian Diabetes Association, 7 percent of BC residents currently have a diagnosis of diabetes, and this number is expected to rise to more than 10 percent by 2020, by which time diabetes-associated heath care costs in BC are expected to rise to $1.9 billion per year. Diabetes and cardiovascular disease are intimately related, and having one of these diseases is a strong risk factor for the other. Altered blood cholesterol levels increase the risk of developing both cardiovascular disease and diabetes. Blood cholesterol is carried in two types of particles: low density lipoprotein (LDL) particles and high density lipoprotein (HDL) particles. The HDL is known as the “”good”” cholesterol, as it removes excess cholesterol from tissues and is therefore considered to be protective in the development of cardiovascular disease and diabetes, and people with low levels of the good HDL cholesterol have an increased risk to develop these diseases. Dr. Willeke de Haan is working to understand how these diseases are related at the molecular level. She is specifically examining the interaction between HDL and two cholesterol transporters, ABCA1 and ABCG1. Previous studies have shown that ABCA1 and ABCG1 are both involved in insulin secretion in cells of the pancreas; this provides insight into how HDL cholesterol influences and may contribute to diabetic metabolism. Her research involves both cultured beta cells, a type of cell that secretes insulin from the pancreas, as well as various mouse models of diabetes. Using these models, Dr. de Haan will determine how altering HDL cholesterol levels contributes to diabetes development by analyzing inflammation, stress, death and markers for underlying mechanisms. Her work will also provide essential insights about the function of HDL, ABCA1 and ABCG1 in the development of diabetes and cardiovascular disease, and will validate these molecules as potential targets in the development of novel therapeutic approaches to these diseases.
Characterization of moonlighting proteins as novel MMP substrates
Signalling pathways that control the development and function of T regulatory cells
Autoimmune diseases, such as inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis and psoriasis, arise from an overactive immune response against one’s own substances and tissues. If this overreaction against the body persists for an extended period of time, it results in chronic inflammation. Currently, there are no cures for autoimmune diseases; at best there are only treatments that mildly alleviate the symptoms. A patient with an autoimmune disease is typically treated with drugs to suppress the immune system, which diminishes immune responses in general. This type of treatment means that the individual becomes susceptible to infection and cancer as their immune system is effectively turned off. Dr. Scott Patterson’s research project focuses on an immune cell called a T regulatory cell (Treg). These cells have the ability to suppress immune responses and normally prevent autoimmune diseases. Since the method by which Tregs turn immune responses off is not clearly understood, Dr. Patterson’s goal is to characterize the molecular mechanisms that allow Tregs to work. In parallel, he will study how Tregs interact with other types of immune cells. Using animal models of inflammatory bowel disease and multiple sclerosis, this work will investigate the interactions Tregs have with immune cells in the body during autoimmune diseases. Gaining a greater understanding of how the actions of Tregs are controlled will be a big step in developing new therapies for autoimmune diseases and reducing the dependency on non-specific immunosuppressive drugs. Inflammatory bowel disease and diabetes each affect more than 200,000 people in Canada alone; thus, this research aims to improve the quality of life for this segment of the Canadian population.
Immunobiosensor-Based Analysis of Antigen-Specific B-Cell and Plasmablast Responses during HIV-1 Infection
The study of the cellular basis of antibody-mediated immunity in infection is an exciting, emerging field of research that has profound implications for our understanding of host-virus interactions, protective immunity and HIV vaccine design. Antibodies are proteins that are produced by plasma cells and bind to molecules on the surface of invading pathogens, flagging them for destruction. Research in the field of HIV/AIDS has shown that antibodies, which neutralize a broad range of HIV isolates in test tubes, also protect animals from HIV-like pathogens, such as simian immunodeficiency virus (SIV). Thus, there has been a concerted effort to design vaccines that elicit broadly neutralizing antibodies targeting HIV. HIV-infected people rarely produce protective antibodies against a broad range of viral variants; this is of great concern to those attempting to produce a vaccine. Currently, there is no way of isolating the blood plasma cells that produce and secrete antibodies against a particular molecule or pathogen (antigen).
Dr. Naveed Gulzar's research involves an innovative approach to identify single, live HIV-specific plasma cells whose secreted antibodies bind proteins associated with HIV. He is working with a multidisciplinary team to develop an immunobiosensor that will allow him to locate single cells that secrete HIV-specific antibodies from thousands of antibody-secreting cells from the blood of HIV-infected people, and to isolate them for subsequent analyses. His goal will be to characterize the antibody response against HIV envelope proteins, and see how these change during the course of infection. The genes encoding these antibodies will be analyzed and their features compared. The results may provide new insights into our understanding of the immune response against HIV infection.
Dr. Gulzar's team includes Dr. Jamie Scott and several different analytical chemistry, physics and engineering research groups at Simon Fraser University and the University of Victoria, along with Cangene, a Canadian industrial partner. They anticipate that by understanding the genetic and cellular features associated with antibodies that neutralize a broad range of viral variants, they will be able to better inform the design of an HIV vaccine that elicits broadly neutralizing antibodies.