LSI researchers awarded funding through Fall 2023 CIHR Project Grant competition

Five LSI researchers were awarded funds in the CIHR Fall 2023 Project Grant competition. Listed below are the LSI-based PIs and a description of the funded projects, including two Priority Announcement and one Bridge grant. In total, these grants were awarded > $4.5 million from this competition.

Dr. Carolyn Brown

Carolyn Brown

Functional characterization of genomic DNA elements regulating epigenetic silencing

Most females have two X chromosomes while males generally have one and the sex-determining Y chromosome. To minimize the impact of having double dose of the almost 1000 genes on the X chromosome, there is a process called X-chromosome inactivation (XCI) that silences most of the X chromosome. Once this silencing occurs it is maintained through cell division, so we call it ‘epigenetic’ – control above the genetic instructions. For 75% of the genes on the X chromosome this silencing is complete, but we seek to understand how the other 25% are skipped by this chromosome-wide silencing. From our previous grant we have found important differences in how these ‘escape’ genes are controlled. We can put a human transgene into the future inactive X chromosome of a mouse, or a mouse embryonic stem cell, and when the X inactivates we have defined a critical 6 kilobases of DNA sequence that keeps the gene expressed. We will now refine those elements both by manipulation of the DNA in the transgene and also by computational analysis of the regulatory elements. Overall, understanding how genes escape from XCI lets us understand the epigenetic rules and also will provide tools to keep genes active if they are put into cells as a therapy or for research.

Kota Mizumoto

Elucidating the novel role of Calcium/calmodulin-dependent protein kinase II (CaMKII) in presynaptic assembly

Our brain consists of billions of nerve cells that communicate with each other to conduct complex tasks. Nerve cells use a cellular interface called synapse to send and receive information. The synapse contains many different types of proteins, each playing different roles for a synapse to function properly. If the synaptic structure is abnormal, nerve cells cannot communicate correctly, and brain function will be severely affected. Indeed, abnormal structure and function of synapses are often observed in the brains of patients with various neurological disorders, including intellectual disability. Currently, few therapeutics are available for these neurological disorders, partly because of the lack of understanding of how synapse is assembled and how its abnormality leads to these diseases. Therefore, we urgently need to increase our knowledge of the basic mechanisms of synapse formation. We tackle this important issue using nematode (C. elegans) as a genetic model organism. C. elegans has a simple nervous system, yet its nerve cells and synapses are highly similar to those of humans. Historically, many studies have proven that the discoveries made in C. elegans nerve cells and synapses can be directly transferred to understand how our nerve cells and synapses develop. Specifically, we focus on studying a gene called Calcium/calmodulin-dependent protein kinase II (CaMKII), whose mutations in humans are highly associated with various neurological disorders including intellectual disabilities. Our current data strongly suggests that CaMKII plays a crucial role in assembling multiple proteins into a functional synapse. Uncovering the novel functions of CaMKII in synapse formation will help us better understand how our brain develops, and how mutations in CaMKII cause various neurological diseases, which are the first steps toward the future development of the therapeutics.

Selena Sagan

How do flaviviruses orchestrate viral RNA replication and virion assembly?

Flaviviruses, including Zika virus and Dengue virus, are mosquito-borne pathogens of public health concern, with more than 2.2 billion people at risk of infection. While many cases remain asymptomatic, symptomatic infections lead to rash, fever, arthralgia, myalgia, headache, retro-orbital pain, and conjunctivitis. More serious complications include hepatitis, vascular shock syndrome, encephalitis, acute flaccid paralysis, congenital abnormalities, and fetal death. Despite decades of research, our understanding of the fundamental biology of flaviviruses, including how they replicate their genomes and build viral particles, remains rudimentary. Today, the technologies exist to allow us to tease apart the roles of the main viral proteins in mediating these processes. Herein, we are studying two viral proteins known to participate in both the process of viral genome replication and viral particle assembly, and are therefore highly lucrative targets for antiviral intervention. Insight into these processes, and how the viral proteins interact with one another and with the viral genome, will allow us to develop novel antiviral strategies and design new vaccination approaches for these important human pathogens. Moreover, given the conservation of these viral proteins across the flavivirus genus, our results are likely to be applicable to several other important human pathogens.

Dr. Sheila Teves stands in front of a green leafy shrub. She has long black hair that drapes over her camel coloured blazer.

Sheila Teves

Defining mechanisms for TBP-independent transcription

Cells are the basic building blocks of living organisms, and all cellular activities are encoded by genes in DNA. The genes are then “transcribed” to form RNAs that are “translated” to proteins, which in turn do most of the work in the cell. The enzymes that convert DNA to RNA in transcription are called RNA Polymerases. Cells require at least three different kinds of RNA polymerases to generate all the different types of RNA. Moreover, each of the RNA Polymerases requires other proteins to direct them to the correct places in the DNA. One of these proteins is called TBP. Found in virtually all organisms, TBP is an essential protein, and without it, organisms do not survive. Importantly, decades of research have shown that TBP is required for transcription by all three RNA Polymerases, providing further testament to its central role in transcription. Despite what we know about TBP, we found that TBP is not required for transcription of protein-coding genes in mouse embryonic stem cells. This finding stands in contrast to one of the main dogmas of molecular biology. If transcription can occur without TBP, what do we really know about how genes are transcribed? Our research project will address this question for each of the three main RNA Polymerases in mouse embryonic stem cells. We will tackle this question through different approaches, combining molecular biology, advanced DNA sequencing, and live- cell microscopy. This multi-pronged approach will allow us to redefine the central role of TBP and generate new insights into how genes are transcribed. Since transcription underlies how cells function, and therefore how organisms develop, the results from this study will have a broad impact in cell and developmental biology. Importantly, many diseases arise from transcription errors, and by understanding precisely how transcription works, we can better identify problems and find solutions when things go wrong during disease.

Photograph of Dr. Carolina Tropini

Carolina Tropini

Impact of endoscopy bowel preparation on microbiota-mucosal interactions in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a debilitating condition characterized by continuous inflammation and intense recurrences, or flares. There is no cure for IBD, and the surveillance regimen involves routine endoscopy to monitor disease. Endoscopy requires bowel preparation, which is performed by administering a laxative and clearing intestinal contents. Some studies have shown that bowel preps in IBD patients can worsen inflammation. The goal of this project is to define the effects of bowel preparation on gut inflammation in IBD via its impact on the gut microbiota. Our microbiota is a unique, constantly evolving consortium of trillions of bacteria that live in and on our bodies. Gut microbes produce compounds that are absorbed into our blood, providing nourishment, and affecting diverse functions such as digestion, immunity, and neurodevelopment. Importantly, the microbiota is impacted in IBD and some bacterial species that are present in IBD patients are thought to promote inflammation and can thrive due to the disruption caused by bowel prep. This project will use a combination of cutting-edge experimental and computational techniques to study the connection between the IBD gut microbiota, bowel prep and inflammation. We have previously shown that exposure to bowel prep laxatives can cause the diversity of microbes in the gut of experimental animals to decrease, such that certain key species completely disappear, and the host becomes more susceptible to infection by pathogens. We will now measure the effects of bowel prep on IBD patients and measure changes in gut microbes. Furthermore, we will identify the mechanisms by which some microbes survive in the altered gut environment during bowel prep to increase inflammation. New knowledge from this project may inform and impact the use and frequency of bowel prep in IBD patients.

Dr. Leonard Foster

Leonard Foster

Development and Commercialization of a Safe and Effective Mpox Subunit Vaccine with Global Impact

Priority Announcement

In a rapidly changing global landscape characterized by expanding human populations, diminishing habitats, and evolving disease patterns influenced by climate change, the likelihood of zoonotic diseases transitioning to humans has escalated. The recent COVID-19 pandemic underscored our unpreparedness, leading to significant health and economic impacts. While rapid solutions such as first-generation mRNA vaccines were developed, their payload capacity may not suffice to counter novel threats from Orthopoxviruses like monkeypox (Mpox). Concurrently, existing attenuated vaccines for poxviruses can be ineffective and, at times, induce adverse side effects, particularly in immunocompromised individuals. Here we propose to use innovative vaccine platforms to develop a safer and more effective Mpox vaccine than what is currently available by creating a subunit vaccine that retains a large number of immunologically important targets while removing the toxic side effects. In collaboration with Eyam Vaccines and Immunotherapeutics Ltd., we aim to create the first Mpox vaccine crafted by Canadian scientists and manufactured and distributed globally. This breakthrough will not only help protect vulnerable populations but also establish a rapid vaccine response system for other emerging pandemics caused by zoonotic diseases. Finally, the past pandemic has provided profounds evidence that Canada should be in control of its own vaccine supplies and this proposal will facilitate this goal.

Hugh Kim

Pro-inflammatory platelet signaling: identifying novel therapeutic targets for periodontitis

Priority Announcement

Periodontitis, or gum disease, is a very common infection of the mouth that causes chronically inflamed gum tissues and tooth loss. Periodontitis also increases the risk for serious diseases such as heart disease and diabetes. During periodontal infection, the immune cells that circulate in our bloodstream release signaling molecules known as cytokines. Some cytokines aggravate disease by driving up inflammation. The goal of this grant application is to study blood platelets, which are normally known as cells that control blood coagulation (clotting). However, platelets also release cytokines that contribute to inflammation. We will focus our studies on a specific cytokine called platelet factor 4 (PF4), and determine exactly how PF4 increases the “inflammatory” behaviour of other cells around the teeth and in the gum tissues. This information will give us a better idea of how platelets drive inflammation and may eventually lead to improved treatments for many chronic inflammatory diseases including arthritis, inflammatory bowel disease and periodontitis.

Dr. Elitza Tocheva in the LSI

Elitza Tocheva

Characterization of the ESX-3 and ESX-4 secretion systems in Mycobacterium abscessus

Bridge Grant

Mycobacterium abscessus (Mab) is an emerging global health threat, causing infections in people with lung inflammations and respiratory disorders. Mab is ubiquitously found in the environment and can spread directly through contaminated water, surgical tools and other shared materials which make it widely implicated in hospital-acquired infections. Mab is intrinsically resistant to many antibiotics and thus, extremely difficult to treat. It uses an arsenal of tools, or virulence factors, to colonize the lungs, including secretion systems, that inject molecules into host cells and cause harmful symptoms, including inflammation and decline in lung function. The detailed mechanisms by which Mab causes these infections, however, are largely unknown. This proposal aims to characterize the role of two newly-discovered secretion systems in Mab that are essential for pathogenesis. By characterizing the structures and roles of these systems, we can identify novel targets for the treatment of mycobacterial infections.