Integrative genomics to identify novel therapeutics and biomarkers for COPD

Chronic obstructive pulmonary disease (COPD) affects 300 million people worldwide and is the third leading cause of death, responsible for over 3 million deaths per year. It is the number one reason why adults end up in hospitals. However, we do not have good drugs to treat patients with COPD. This is because we do not fully understand how and why COPD develops and progresses.

Smoking can cause COPD but not all smokers get the disease; our genes also play a role. Identifying which genes cause some people to get COPD or lead to disease worsening over time will allow us to understand these processes more and to develop new drugs to treat the disease.

This project will use sophisticated analysis tools called integrative genomics. First, we will identify regions of our DNA that are important for COPD risk and worsening over time. This will be done through studying DNA regions from thousands of subjects with and without the disease and on whom we have information on how well their lungs work. We will then identify the function of these DNA regions by uncovering their effect on gene products and proteins in tissues that are important and relevant for COPD such as lung and blood. These genes and their products will be tested in laboratories to confirm the findings. The goal is to use this information to monitor disease and will additionally allow us to interfere with these gene products to treat disease.

IgE-mediated inflammation generated by the airway epithelium is antigen independent: A cause of a novel asthma phenotype

Asthma is the most common chronic disease in childhood and continues to increase through adulthood. When a patient has asthma, airways in the lungs become swollen and tight causing symptoms such as shortness of breath, wheezing, chest tightness, and cough. Current therapies for asthma relieve symptoms but do not restore airways back to normal function or cure the disease. 

Asthma is influenced by many different genetic and environmental factors, so despite having many drugs available and more in development it is extremely difficult to match patients to the right treatment. To better match patients to the right therapies we need to understand the process by which allergies lead to asthma. 

This project aims to find new ways to predict the response of asthmatic patients to existing and new drugs by better understanding how allergies cause asthma symptoms. We will look at several molecules in the blood known to be important in asthma, and measure them in airway tissues and cells obtained from asthmatic and non-asthmatic patients. This will give us a much better picture of what these important molecules are doing directly at the source of the allergic inflammation.

The role of PCSK9 in clearance of bacterial lipids and the development of anti-PCSK9 treatment for sepsis

Sepsis, which is characterized as an uncontrolled inflammatory response to severe infection, is the leading cause of death in intensive care units. In Canada, sepsis led to a total of 13,500 deaths in 2011, which translates to approximately one in 18 deaths in Canada involving sepsis. Despite this pressing medical need, there are currently no effective treatments for sepsis. 

It is well established that bacterial lipids, such as lipopolysaccharide (LPS) in Gram-negative bacteria and lipoteichoic acid (LTA) in Gram-positive bacteria, induce aberrant inflammatory response in sepsis and they associate with various lipoprotein fractions in the blood. Recent research has revealed that septic patients with Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) loss-of-function mutations have better survival rates due to increased bacterial lipid clearance. It is likely that inhibition of PCSK9 leads to enhanced clearance of bacterial lipids and thus an improved chance of survival. 

Dr. Leung will characterize the role of PCSK9 in these two major pathways of bacterial lipid clearance by utilizing a novel in vivo imager to monitor the distribution of fluorescently-tagged LPS and LTA in mice. He will assess the therapeutic potential of PCKS9 inhibition by examining the ability of anti-PCSK9 monoclonal antibodies to clear bacterial lipid-laden LDL and VLDL through the LDLR and VLDLR pathways, respectively. 

Dr. Leung’s research will address a current knowledge gap in the role of lipoprotein pathways in the clearance of inflammatory bacterial lipids from circulation. 

 

Cardiovascular genetics: Phenotypes, genotypes and cellular mechanisms

Cardiovascular disease (CVD) is the leading cause of death of Canadians, and is strongly influenced by genetic factors. Integrating basic biomedical research into how specific gene variants influence the function of cardiac cells, with clinical research of patients and families with early onset CVD, will lead to important advances in translating the results of genetics research to improved care for patients and families with CVD.

Understanding the aging HIV lung from dysbiosis to cell injury

Patients with human immunodeficiency virus (HIV) are now living to older ages thanks to effective anti-HIV medicines. Despite these gains, many of them suffer from chronic lung disease that greatly impacts their ability to carry out their daily activities and impairs their quality of life. The type of lung disease they face is similar to what longtime smokers develop, a progressive narrowing of the airways and destruction of the lung. However, in HIV, the process appears to be accelerated and more severe. It's not unusual, for instance, to see patients in their 30s and 40s develop this lung disease (which is approximately 30-40 years earlier than expected). Also, it's not unusual for HIV patients who have never smoked before to develop this kind of disease. Unfortunately, the traditional medications we use to treat lung disease often interact with anti-HIV medicines, causing severe side effects. Management of breathing symptoms in HIV patients is therefore difficult and it is imperative that we find better agents to combat lung disease in this population. Only by understanding what causes and drives this lung injury process can this goal be achieved, though.

Multiple studies have now shown that smoking alone cannot explain the lung disease phenomenon in HIV. I believe that HIV injures the lung in a two phase process. First, the virus directly breaks down the protective layer of the airway known as the epithelium. Second, over time, as patients develop repeated lung infections due to their weakened immune systems, the bacterial community of the lung or microbiome shifts. I believe that this community disruption results in molecular changes that age the lung faster. My approach is to perform an in-depth investigation into the epithelium of the airway using two innovative methods. To explore the injury that HIV inflicts on the airway, I have created a novel model of the HIV airway using HIV-infected cells co-cultured on a cell culture model of the airway epithelium. We will use this model to see how HIV-infected cells break down the protective barrier of the lung. To explore the shifts in the microbiome, I have collected airway cells from HIV-infected and uninfected patients to not just describe what bacteria exist in the airway but also to determine what effect the community differences between the two groups have on the function of genes in the cells. We will measure how 'old' these cells are and compare these findings to uninfected patients.

Developing personalized anti-arrhythmic drug therapy for atrial fibrillation

Atrial fibrillation (AF) is the most common heart rhythm disorder. With an aging population, the number of people with AF is expected to rise dramatically. People with AF are twice as likely to die, are five times more likely to have a stroke, can develop worsening heart muscle function, and have a lower quality of life. We have learned that a person's genetic makeup, or DNA, has a major impact on their risk of developing AF; but we have a limited understanding of why, or how to use this information to treat people in a safer and more effective way. People with AF first receive drugs to control their irregular heart rhythm. Even people who have procedures to treat AF are also prescribed drugs. This is particularly important in the group of patients who have persistent AF, who require electrical or chemical therapy to change their heart rhythm, as the success of surgical procedures in this population is well below 50%. Unfortunately our current drugs are generally ineffective, and can be unsafe, with little progress in drug development over the last two decades.

With these challenges in mind, the first goal of my research program is to identify and understand the genes that play a role in the development and progression of AF, and determine which are most common and most important in the Canadian population. To do this, I am gathering a biobank of AF patients and performing the largest scale detailed genetic testing in this population to date. I am also focused on understanding the effect that genes can have on the safety and efficacy of rhythm controlling drugs, and have already started a trial, funded by the Canadian Cardiovascular Society, that will link a person's genetic makeup to these important outcomes. I will then be able to take this large clinical and genetic data set to the laboratory where we have developed the unique ability to generate patient-specific stem cell disease models of AF. The ultimate goal of my research program is to directly tailor therapy for AF patients based on their genetic makeup, using information from clinical research and personalized disease modeling.