Acute myeloid leukemia (AML) is a cancer in which blood cells grow out of control. Blood cells have to suffer at least two mutations to become cancerous: one to make them grow faster, and another to stop them developing normally. However, even with whole genome sequencing, in some patients we have been unable to find both mutations using existing methods, and we need to look deeper.
MicroRNAs are one place we can look. These are small pieces of RNA which reduce the production of proteins by targeting specific messenger RNAs. We know that cancers tend to have more or less of some microRNAs, and that many of these play important roles in cancer biology. However, whole-genome studies have mainly looked at the amounts of well-known microRNAs, without looking deeply at mutations of the microRNAs themselves, which can completely change their targets. Smaller studies have shown that microRNA mutations (as well as normal variations between people) can be important drivers of cancers, but nobody has investigated these at the genome-wide scale.
I will examine mutations of microRNAs in the genomes of around 200 AML and myelodysplastic syndrome patients. I will measure the effects of each mutation on messenger RNA levels. I will then look especially in patients in which two driver mutations could not be found to see whether any microRNA mutations could be oncogenic. The results will increase our understanding of the biology of AML, thereby leading to new research into improved therapies. They will also improve our ability to diagnose AML, which will give more information to doctors and patients making difficult decisions on treatments. After analysing our local dataset, I intend to similarly analyse all cancers in the Cancer Genome Atlas (TCGA) data set. Since the microRNA sequencing for the TCGA was performed at the Michael Smith Genome Science Centre in Vancouver, this is an excellent opportunity to extract further value from a locally-produced resource.
For knowledge translation activities, I intend to present this work at the annual meetings of the American Society for Hematology and the International Society for Computational Biology. Further, I will write up the AML analysis for submission to Genome Research or Leukaemia, and the later work applying the method to the TCGA data to a similar (or higher-impact) venue. Lastly, I will release the source code to perform the analysis as an open source software package.
Michael Smith Foundation for Health Research/The Pacific Alzheimer Research Foundation Post-Doctoral Fellowship Award
Millions people worldwide are currently afflicted with Alzheimer’s disease (AD). In the absence of a complete understanding of the disease, therapeutic trials have been unsuccessful and there still remains no cure. Biomarkers that can reliably detect AD at the earliest possible stage are essential for disease monitoring and drug therapy. The development of a biomarker for AD that can be translated to a rodent model of AD would also be useful in drug discovery. A validated biomarker could profoundly change the rate of the development and implementation of treatments for AD by enabling rapid high throughput screening of new drugs. Furthermore, the development of a robust method for biomarker detection which can be translated to a clinical laboratory setting would be an invaluable tool for AD diagnosis and monitoring. AD patients have deposits of proteinaceous plaques within their brains.
Our previous research has shown that a protein called melanotransferrin (MTf; also known as p97 or CD228) exists at high levels in humans with AD and is specifically expressed by immune cells associated with plaques in the brain. In contrast, healthy patients show a limited distribution of MTf. Of particular interest, the blood concentration of p97 is also elevated in AD patients compared to age-matched healthy human controls. These preliminary studies are promising but suffer from limited population size and the inherent uncertainty of current AD diagnostic methods (i.e. can only be truly diagnosed post mortem).
We plan to further validate MTf as an AD biomarker in mouse models of AD. This will be accomplished using a revolutionary diagnostic technology known as the SISCAPA assay. This platform offers reliable, robust absolute quantitation of proteins in complex biological fluids, and is already in use across the USA for the diagnosis of thyroid cancer. Using this clinically amenable method, we will monitor AD model mice, and wild type controls, throughout their life and correlate MTf concentration with the degree of neurodegeneration. It is expected that at a young age AD mice will be indistinguishable from healthy controls but as plaques appear in the brain, so too will MTf levels rise. These results will illuminate the timeline and intensity of MTf elevation as it relates to neuropathology. We will also establish the baseline for MTf in healthy or pre-AD subjects. These discoveries have the potential to change the course of detection and treatment of AD.
Michael Smith Foundation for Health Research/The Pacific Alzheimer Research Foundation Post-Doctoral Fellowship Award
Type 2 diabetes (T2D) patients have an increased risk of developing Alzheimer’s disease (AD). However, the underlying mechanism is poorly understood. Human islet amyloid polypeptide (hIAPP) aggregates, occurring in ~95% of T2D patients, induce a variety of pathological processes that are contributing factors to AD neuropathology. In current proposal, we attempt to investigate the effect of hIAPP aggregation on the Alzheimer’s development in T2D and the potential mechanism by conducting cell and animal experiments. Additionally, novel transgenic mouse models of diabetic AD will be generated to mimic the natural process of AD development in diabetics.
This study will help us to define the prevention and treatment of diabetic AD. Dissemination of the findings from this study will be done in different ways to make sure that the largest number of people will hear, understand and benefit from this novel research project. The experimental results will be published as research articles on academic journals and presented at scientific conferences, such as Society for Neuroscience annual meeting and Canadian Diabetes Association professional conference. Educational events and learning series will be held in the community, such as Cafe Science and public lecture series where we can engage the public with our research study, answer their questions directly and stimulate discussions.
End of Award Update
Source: CLEAR Foundation
Dr. Zhang’s research focused on creating a better understanding of why type 2 diabetes patients have an increased risk of developing Alzheimer disease. This research identified the important role of human islet amyloid polypeptide (hIAPP) in diabetes-induced dementia. Targeting hIAPP may be a valid approach for preventing and treating dementia in diabetes mellitus.
A dental implant is a screw-like device that is surgically placed in the jawbone to provide a foundation for artificial teeth. This involves precise removal of bone using drills, which is often risky because of proximity to delicate structures such as the maxillary sinus, orofacial nerves, and blood vessels. Mistakes in the drilling path may result in permanent nerve damage, life threatening hemorrhage, or injuries to adjacent teeth. This research project aims to reduce errors in the process by developing an objective and sensor-based method to assist practitioners in conducting the drilling process.
Our method will analyze the sounds generated during implant drillings to monitor the process and recognize different bone tissues, providing real-time feedback on whether the practitioner is taking the correct line. Proof of concept exists in that drilling sounds have already been used in similar applications to discriminate between tooth materials.
To collect the data, we will drill sample jawbones (pig or cow) as we would in typical implant surgeries. We will record the sounds produced by drilling bone tissues under different conditions such as direction, feed rate, speed, and applied forces. Advanced signal processing methods such as machine learning will analyze the data to allow us to discriminate between different bone tissues.
We will optimize the resulting algorithm to produce an aid for practitioners that will improve the safety and precision of their dental implant surgeries. Future work could include further customizing the algorithm to extend its use to other medical procedures that involve bone drilling such as orthopedics, spine, and ear surgeries.
Close to 5,000 Canadians are diagnosed with pancreatic cancer every year and it is the fourth most common cause of cancer-related deaths in Canada. Unfortunately, a majority of these patients die within a year of their diagnosis, due in part to late diagnosis and tumour resistance to chemotherapy. In addition, most patients who are successfully treated eventually recur and succumb to the disease.
There is a need for reliable blood tests for more routine diagnosis, monitoring treatment response, and detecting tumour recurrence in pancreatic cancer patients. We seek to develop such tests using cell-free DNA in the blood. Mutant forms of cell-free DNA that originate from tumours can be detected in the blood of patients with pancreatic cancer, and this project will explore how we can use it to:
- Diagnose pancreatic cancer earlier
- Detect cancer recurrence earlier
- Identify patients whose tumours do not respond to chemotherapy in order to help guide treatment decisions
We will collect blood from patients who have undergone surgical removal of pancreatic cancers and follow their progress over two years to examine whether we can detect cancer recurrence by monitoring the presence of mutant cell-free DNA after surgery. We will also collect blood from patients with advanced stage pancreatic cancer who are undergoing treatment to explore whether changes in mutant cell-free DNA levels predict whether their tumours respond to chemotherapy.
In these ways, a non-invasive blood test will help to improve quality of life and optimize treatment for thousands of Canadians diagnosed with pancreatic cancer.
In healthy humans, blood flow to the brain is regulated such that appropriate amounts of oxygen and glucose are delivered to brain tissue. Even when blood pressure changes or when a region of the brain becomes more active, brain blood vessels react in order to provide sufficient blood to their respective area of tissue. When these processes fail, disease states develop. For example, too little blood flow to the brain for even a few seconds causes fainting and too much blood flow can cause a stroke.
Our understanding of these processes is currently lacking, particularly with respect to the relationships between the sympathetic nervous system (associated with the "fight-or-flight" response), brain metabolism, and regulation of brain blood flow.
This project aims to develop a better understanding of the relationships between these processes.
Michael Smith Foundation for Health Research/Vancouver Coastal Health Research Institute Post-Doctoral Fellowship Award
Stroke is a debilitating disease and the third leading cause of death in Canada. It stems from disrupted blood flow to the brain, leading to cell death due to lack of oxygen and glucose. A major consequence of stroke is edema (swelling of brain cells and tissue), and is the principal cause of death in stroke patients. Current treatments for brain edema, such as osmotherapy and surgical decompression, are relatively crude and ineffective.
We have identified a new possible cause of stroke-induced edema in SLC26A11, an ion transporter that is expressed in neurons throughout the brain. Our previous work shows that it allows chloride ions to enter brain cells, bringing excess water into the cells by osmosis. This project will probe our theory that SLC26A11 is a critical trigger of cell death during stroke.
This work could lead to a better understanding of edema during stroke, which could ultimately aid in developing new drugs to treat it.
Atherosclerosis, caused by cholesterol buildup and inflammation in arterial blockages (plaques), is the leading cause of death in Canadians. Cholesterol-loaded cells (foam cells) that collect in plaques make it unstable, leading to heart attacks and strokes. White blood cells called macrophages have previously been thought to be the main cell type accumulating cholesterol in plaques. However, our studies found that at least half of foam cells in human plaques come from artery smooth muscle cells.
Mouse models are routinely used to study and test new therapies for atherosclerosis, but little is known about the contribution of smooth muscle cells to foam cell formation in mouse plaques. Our finding calls into question whether these models are truly applicable to understand the human disease.
We will compare the contribution of smooth muscle cells to foam cell formation in two commonly used mouse models of atherosclerosis to that in human plaque. This will provide valuable information about the utility of those models for understanding atherosclerosis in humans.
Furthermore, we will examine the differences between macrophage-derived and smooth muscle cell-derived foam cells that are related to disease progression, regression, and treatment efficiency.
This research may change how we understand, prevent, and treat atherosclerosis.
Michael Smith Foundation for Health Research/BC Cancer Foundation Post-Doctoral Fellowship Award
High-grade serous ovarian cancers (HGS) have a low five year survival rates at less than 40 percent. This is partly because of high relapse rates due to resistance to platinum-based therapies, which is the current standard of treatment. Although these therapies are effective at treating the primary tumour, cancers develop resistance to platinum drugs in almost all instances and the tumours recur.
How genomic instabilities evolve in HGS tumours and lead to platinum-resistance is poorly understood, and there are currently no biomarkers that give a reliable prognosis. We seek to identify effective genomic biomarkers for determining which HGS patients will respond more effectively to platinum-based chemotherapy.
This project will build on our research group's recent observations of differences in global genomic patterns between platinum-sensitive and platinum-resistant groups. We will analyze an HGS cohort of seventy cases composed of short- and long-term survivors with five year clinical follow-up data by:
- Comparing and contrasting the entire DNA sequence of tumours to the patient's normal DNA to identify global patterns of genomic instability
- Comparing and contrasting genomic profiles from the whole genome of the short-term and long-term survivors
- Studying diversity via deep-sequencing data of the tumours.
Ultimately, the results of this project and future work could allow for a long-term prognosis and optimized treatments for patients with HGS ovarian cancer.
Diarrheal illnesses remain a major cause of sickness and death worldwide, killing approximately 760,000 children under the age of five each year. This project seeks to better understand one major cause: bacteria known as attaching and effacing (A/E) pathogens. This group includes several classes of pathogens: i) a class that causes death primarily among children in developing countries, and ii) a class with potentially life-threatening complications such as kidney failure in both developing and developed countries.
First, the normal community of microbes inhabiting the healthy mammalian digestive tract (the gut microbiota) represents a major challenge for A/E pathogens by competing for nutrients and possibly by producing molecules that inhibit the A/E pathogens. We will investigate how A/E pathogens sense and adapt to the presence of the gut microbiota with a view to gaining insights into their overall infection strategy.
Second, we will seek out species within the gut microbiota that inhibit A/E pathogens. Chemicals that they produce could form the basis of drug discovery programs for novel antibiotics.
Our final objective is to characterize one genetic system that A/E pathogens use to sense their surroundings: the Cpx envelope stress response. This system triggers production of damage-repair proteins when it senses damage to the envelope of the bacterial cell. We will study whether and how these repair proteins are required for A/E pathogens to infect mice. If so, they represent a potential target for developing novel antibiotics.
This project will yield a better understanding of a major cause of illness and death and might give rise to new avenues of research for novel antibiotics to counter it.
