Flow cytometry (FCM) is a method of sorting and measuring types of cells by fluorescent labelling of markers on the surface of the cells. It plays a critical role in basic research and clinical therapy in the areas of cancer, HIV and stem cell manipulation. For example, it can be used to diagnose some types of cancer, based on which labelled antibodies bind to a particular cell’s surface. It is widely recognized that one of the main stumbling blocks for FCM analysis is in data processing and interpretation, which heavily relies on manual processes to identify particular cell populations and to find correlations between these cell populations and their clinical diagnosis and outcome (e.g. survival). Manual analysis of FCM data is a process that is highly tedious, time-consuming (to the level of impracticality for some datasets), subjective and based on intuition rather than standardized statistical inference. Dr. Ali Bashashati has developed a “pipeline” for automatic analysis of FCM data – a computational platform that can identify cell populations, find biomarkers that correlate with clinical outcomes, and label the samples as normal or diseased. Preliminary evaluations of this pipeline have shown accuracy levels of more than 90 per cent in identifying some sub-types of lymphoma. Moreover, a biomarker that contributes to a more aggressive behaviour of a specific sub-type of lymphoma has been discovered. Bashashati is now testing and refining the platform to improve its analytical power and applicability to a range of FCM data, testing its performance across a number of ongoing FCM studies in BC. Ultimately, he hopes to provide an accurate, powerful computational platform to increase the efficiency of using FCM for research and clinical purposes.
Program: Trainee
CD34 in development of lung inflammatory diseases
Ever since its discovery more than 20 years ago, the CD34 antigen has been widely used as a marker to identify stem cells, precursor cells that give rise to all types of specialized cells. However, the exact function of CD34 expression on hematopoietic precursors and mature cells is still not well understood. Dr. Marie-Renée Blanchet and colleagues have uncovered some fascinating details about the role of CD34 in allergy and asthma. The team recently demonstrated that CD34 is expressed on mature mast cells and eosinophils – two types of cell that respond to injury during inflammation of the body’s tissues – and that the CD34 antigen is involved in their recruitment to the lung and peritoneum. They showed that mice without the CD34 antigen are protected against development of airway hyper-responsiveness and airway inflammation, which are two major hallmarks of allergic asthma. Finally, in preliminary experiments, these mice also showed protection in hypersensitivity pneumonitis, another model of lung inflammation. Now, Blanchet is working to better understand the mechanisms behind these recent findings. Many cell types involved in asthma and hypersensitivity pneumonitis express CD34, some in which the role of this protein remains unknown (eg. fibrocytes and dendritic cells). She plans to use models to elucidate the role of CD34 expression in these cells. Ultimately, she hopes her studies will reveal potential targets for treatment of allergy and inflammation.
Epigenetic mechanisms regulating the acquisition and extinction of conditioned fear: exploring the neurobiology of relapse
A major obstacle in the treatment of fear-related anxiety disorders is their likelihood for relapse. Fear-related behaviour can be inhibited with extinction therapy (repeated exposure to specific fear-inducing cues). This is, however, a temporary fix because fear often returns after exposure to cues associated with the original learning. In the case of post-traumatic stress disorder, fear can also “incubate” or sensitize over time and further exacerbating symptoms of the disorder. These phenomena likely reflect long-term neural adaptation that occurs during learning – changes that may be based on lasting epigenetic modification of genes responsible for maintaining fear memories. Epigenetic modifications influence the way a gene functions without altering the underlying DNA sequence- processes now recognized to participate in the regulation of gene expression in the adult brain. Rapidly emerging evidence suggests that epigenetic mechanisms play an important role in psychiatric disease and in disorders of learning and memory. Dr. Timothy Bredy is employing state-of-the-art technologies to investigate the fundamental epigenetic mechanisms of associative fear memory. He is using a genome-wide approach to examine epigenetic machinery involved in regulating critical gene targets during the acquisition and extinction of conditioned fear. Dr. Bredy hopes his findings will provide insight into the molecular basis of relapse and its prevention and that this research will ultimately contribute to the design of novel pharmacotherapeutic treatment approaches for fear-related anxiety disorders.
The role of H2AX in non-Hodgkin lymphoma
Non-Hodgkin lymphoma (NHL) is a specific type of cancer where an abnormal growth of immune cells produces what is known as a lymphoid tumour. Since the 1970s, NHL has become increasingly common, indicating that lifestyle and environment are likely causative factors. However, certain individuals may also have a genetic make-up that makes them more susceptible. NHL tumours often show a type of DNA damage called a translocation, where two chromosomes are incorrectly joined together. In NHL tumours, translocations are generally found near genes that are important for the development of immune cells. They cause changes in how these genes are regulated (turned on or off), that result in abnormal cell growth. Certain genes are responsible for repairing damaged DNA. If these genes are not functioning properly, DNA breaks will not be repaired and harmful translocations may occur. Previous studies have found that a common DNA sequence change at one of these DNA repair genes, called H2AX, was much more frequent among the NHL patients than unaffected individuals. Individuals who carry this gene variant have twice the risk of NHL as those who do not carry it. Dr. Karla Bretherick is interested in how common genetic variants influence risk for complex diseases. MSFHR has previously funded her graduate training, which involved studying the genetic factors that contribute to premature menopause. Now, she is looking at why individuals with the H2AX gene variant have increased risk of NHL. She will look at how this DNA sequence change affects H2AX gene regulation, modifies protein binding, and affects the ability of the cell to repair DNA damage. Ways to understand, prevent, and avoid NHL and other cancers are of increasing importance for the Canadian healthcare system. Understanding how and why this specific gene variant increases risk for NHL will lead to a better knowledge of how this cancer develops. This information will eventually be useful for identifying new drug targets and therapies for NHL, and may also provide insight into the development of cancers in general.
Degradation of tumour suppressor ING3: Pathway and its role in cell cycle progression
Cutaneous malignant melanoma is a life-threatening skin cancer that is very resistant to conventional radio- and chemotherapy and has a low survival rate. Thus, it is important to understand the molecular changes underlying the onset and progression of the disease. The novel tumour suppressor ING3 acts to inhibit cell growth. A number of previous studies have demonstrated that ING3 switches on and off during normal cell division, and that it enhances cell death in melanoma cells when they are exposed to UV-light. Dr. Guangdi Chen has identified that the expression of ING3 degrades (or decreases) much faster in melanoma cells than in regular melanocytes (healthy melanin-producing cells) during the cell cycle. This rapid degradation may be an important cause of aberrant ING3 expression and the loss of its tumour suppressing function. However, the mechanism of ING3 protein degradation and its role in cell cycle progression remain unclear. Chen is investigating the pathway of ING3 protein degradation and assessing its role in cell cycle progression. By understanding the molecular mechanisms of ING3 tumour suppressive functions in cell cycle progression, he hopes his work could help in the design of novel strategies for cancer prevention and treatment. Chen’s post-doctoral fellowship is jointly funded by MSFHR and the VGH & UBC Hospital Foundation.
The role of AMP-activated protein kinase on glycolysis and myocardial remodeling in the hypertrophied heart
A heart that has become enlarged in response to a pressure overload, such as with high blood pressure, has reduced function compared to a normal heart. This impaired function is particularly apparent during and after interruption of the blood supply, which can occur when a blood clot blocks a diseased coronary artery, or during open heart surgery. This reduced heart function can be very dangerous for the patient. Enlarged hearts use glucose to a greater extent than normal, a situation that appears to contribute to their exaggerated dysfunction. The mechanisms responsible for the accelerated utilization of glucose in enlarged hearts are not yet known. Dr. Minnie Dai was previously funded by MSFHR for her doctoral training. Currently, she is working to determine the mechanisms behind accelerated rates of glucose utilization in enlarged hearts. Using molecular biology techniques, she will selectively and specifically alter the activity of potentially relevant proteins in order to determine their role in causing accelerated glucose utilization. Her studies are unique in that the activity of proteins will be altered at specific times and will be altered only in the heart – ensuring that changes observed are truly related to alterations in these proteins. Many people suffer ill health because of an enlarged heart. By understanding the mechanisms responsible for their accelerated use of glucose, researchers may be able to identify targets for the development of drugs designed to altered glucose use by enlarged hearts, thereby improving their function.
Proteomics of natural substrates of PMN and macrophage proteases in inflammation
Chronic obstructive pulmonary disease (COPD) is a serious lung disease that is predicted to become the fifth leading cause of death by 2020. It is marked by inflammation of the airways. Currently, there is no efficient drug for treatment for this disease. A promising area of COPD research is focused on matrix metalloproteases (MMP), a family of proteins that digest or cut other proteins (known as substrates) into smaller pieces. These cleavages modify the biological functions of the substrate. MMPs are implicated in many inflammatory diseases, including COPD. Dr. Alain Doucet is studying how two specific MMPs, MMP-8 and MMP-12, contribute to the development of COPD. He is conducting studies to validate his hypothesis that MMP-8 and -12 regulate inflammation by cleaving immune cell mediators such as cytokines, chemokines and their cellular receptors. He is conducting a proteomic identification of MMP-8 and -12 biological substrates and assessing the effect of the substrate cleavage on its biological activity. This work could lead to identification of new, more refined targets for COPD treatment. The identification of MMP-8 and -12 biological substrates will indicate their cleavage specificity and will help in the design of more specific inhibitors. Anti-inflammatory drugs developed for COPD treatment also have the potential to be applied to other inflammatory-associated diseases, such as cancer and arthritis.
Wnt signalling during avian facial morphogenesis
It is estimated that 1 in 800 babies is born with cleft lip with or without a cleft palate, making CL/P the most common craniofacial malformation in humans. The lip forms during the early embryonic period in utero, at which time the face is very different from its appearance after birth. Initially, there are separate swellings that surround the oral cavity, several of which grow together and fuse in order to make a continuous smooth upper lip. Dr. Poongodi Geetha-Loganathan is determining the molecules that are required for normal lip fusion, focusing the roles of Wnt genes in the control of facial growth. She is using chickens as a model for facial development, observing through windows made in the shell how the beak develops, and the role of different proteins or DNA. This work will help researchers find those changes in genes that give rise to clefts. In the long term these discoveries will lead to identification of new genes that cause human orofacial clefts, potentially suggesting ways to prevent this common birth defect.
Dissection of O-glycosylation of nuclear and cytoplasmic proteins
The recent decoding of the human genome surprisingly revealed that humans possess a relatively small number of genes. Yet despite this apparently small number, we are rather complex beings. Genes are a special code that can be read out to form proteins, which are responsible for the vast majority of biochemical process within our bodies. This apparent inconsistency between the number of genes and the complexity of humans can be, in part, accounted for by various ‘post-translational modifications’ of human proteins. These types of modification are often additional molecule groups that are added onto certain positions in the protein and can change its activity. Dr. Tracey Gloster is interested in a modification where there is addition and removal of a sugar called ‘N-acetylglucosamine’. Disruptions to this modification are implicated in conditions such as diabetes, cancer and neurodegenerative diseases. The enzyme responsible for adding the N-acetylglucosamine modifies a large number of completely different target proteins. Little is known about how the enzyme recognizes its targets and modifies them at the correct position to ensure they carry out their proper function. Gloster is investigating a specific domain on this enzyme that could hold the answer. There are multiple sites on this interacting domain which she believes each recognize different sets of target proteins. By finding proteins that are modified by this protein and determining the exact region of the target protein that binds to the enzyme, it may be possible to block the enzyme’s action. This could open up new therapeutic approaches in the treatment of diabetes and other diseases.
Immunomodulation of regulatory mechanisms in mucosal immunity
Inflammatory bowel diseases (IBD) are chronic conditions characterized by severe inflammation of parts of the bowel, causing significant symptoms, such as diarrhea, pain and intestinal bleeding. There are two main types of IBD: Crohn’s disease and ulcerative colitis. IBD is prevalent in Canada, with an estimated 170,000 people suffering from the disease. Despite years of effort, the causes of these disorders remain incompletely and inadequately understood. The intestinal inflammation in IBD is thought to result from abnormal responses to the bacteria that live normally in the gut. In healthy individuals, the immune system is able to distinguish between harmless (commensal) bacteria and those that cause infections (pathogens). In IBD patients, the immune system elicits an aberrant and aggressive response against components of host commensal bacteria. Dendritic cells (DC) and regulatory T cells (nTreg) are two types of cells important in maintaining a healthy intestinal immune system. Defects in the development or function of these cells could ultimately lead to inappropriate responses to commensal bacteria, or certain commensal bacteria or pathogens could perturb the normal immune state of the gut. Dr. Gijs Hardenberg is investigating the interplay between host commensal bacteria and the immune system in IBD. He is studying the roles of nTreg and immune responses, focusing on the bacterial protein flagellin, which has been shown to be the major target of intestinal immune responses in Crohn’s disease patients. His work aims to understand how IBD begins and persists how it might ultimately be treated or even prevented. The findings from these studies may also be broadly applicable to other autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and lupus.