Gene clusters and natural products from the human microbiota

Worldwide, prematurity is the leading cause of death for all infants, with almost one million deaths per year. Babies born before 32 weeks face the worst odds. These babies are only 2% of births, but they account for over 1/3 of all infant deaths. For these infants, a disease called necrotizing enterocolitis (NEC) can be one of the most deadly complications of prematurity after the first week of life. NEC is an acquired condition in which intestinal tissue suddenly becomes inflamed and then begins to die off. NEC has a high mortality rate, and, even if the baby survives NEC, they are subject to considerable life-long health problems, resulting in tremendous costs to the health care system. With rising rates of prematurity, NEC poses a significant health and financial burden on Canada.

Dr. Ryan's research will employ approaches from biochemistry, microbiology, and chemistry to identify the factors produced by beneficial bacteria found in the infant microbiome that protect against NEC. This work will provide essential information for the development of novel therapeutics and preventatives for this costly disease.

Dr. Ryan will also collaborate with the Centre for Drug Research and Development to investigate molecules identified potential new drug leads, and researchers at the Child & Family Research Institute at the BC Children's Hospital to further investigate the role of the microbiome in infant health.

Identifying the molecular mechanisms underlying sex differences in fat storage using Drosophila as a model

In Canada, metabolic diseases (e.g. cardiovascular disease, type 2 diabetes, obesity) are leading causes of death, disability, and hospitalization. Currently, more than 10 million Canadians suffer from metabolic disease, with direct and indirect costs to the economy estimated to be $20 billion each year. Approximately 40% more men than women suffer from metabolic disease. In addition, commonly prescribed drugs used to prevent and treat metabolic disease are more effective in one sex than the other (e.g. fenofibrates). Despite these known differences in metabolic disease between men and women, prevention and treatment guidelines remain largely the same for both.

The main reason doctors do not treat men and women differently is due to lack of vital information about the fundamental metabolic differences between the sexes. The next step forward in preventing and treating metabolic disease is identification of the genes and pathways that control metabolism in each sex. This will provide researchers with a pool of promising new targets that will assist in developing therapies that will be effective in men and women, and eventually help in designing sex-specific treatment guidelines.

Dr. Rideout's research will work towards discovery of these genes and pathways using fruit flies as an innovative model, integrating the unparalleled genetic toolkit available to fly researchers with cutting-edge high-throughput metabolic analysis to answer three fundamental questions: firstly, which genes and pathways are essential for metabolic control in each sex; second, how sex-specific metabolic programs are established and maintained; and lastly, how sex differences in metabolism change in distinct contexts. Dr. Rideout will focus on sex differences in the regulation of fat storage, a key aspect of metabolism. 

Dr. Rideout's research outputs will be the identification of a pool of candidate genes that affect fat storage in each sex. Building on this vital starting point by translating this knowledge into pre-clinical models, and eventually humans, she will collaborate with world-leading experts in diabetes, obesity and cardiovascular disease in the Diabetes Research Group at The University of British Columbia. The innovative approach of this research program will make important strides towards developing personalized therapies for men and women, an important goal in modern medicine.

Studying genetic mechanisms of treatment resistance in non-Hodgkin lymphomas

Dr. Morin's research program will develop and apply laboratory and computational genomic methodologies that use DNA sequencing and other sensitive platforms to study the drivers of tumour onset, progression and treatment resistance in solid cancers in order to understand the somatic drivers of non-Hodgkin lymphomas (NHLs). Using massively parallel (next-generation) DNA and RNA sequencing, Dr. Morin will be able to identify somatic alterations and gene expression signatures in tumour tissue and liquid biopsies (circulating tumour DNA). To properly study such large data sets, he will utilize cutting-edge bioinformatics techniques and develop novel analytical approaches and pipelines that will allow leverage of unique sample processing techniques and applications.

Moving forward, this research will investigate aggressive subtypes of NHL including patients who typically fail standard-of-care treatments. Dr. Morin will rely on features of this malignancy such as high somatic point mutation rate, a well established list of known lymphoma-related genes, and the presence of clonal immunoglobulin rearrangements to develop assays to study the genetics of specimens from NHL patients in various ways. These include deep sequencing using a novel molecular barcoding system and digital PCR-based methods. He will continue to push the limits of sequencing technology by applying deep sequencing and whole exome sequencing to circulating tumour DNA. Under this research program, he will also continue to use a variety of laboratory and computational approaches to understand the clonal structure of NHLs, especially in the context of serial samples collected over the course of disease progression and after treatment failure or relapse. 

Dr. Morin's lab, along with the BC Cancer Agency, plan to pursue options to commercialize these strategies so that a broader group of users can use these techniques for research and clinical applications. Some of the research under this program will involve evaluating the performance of novel ctDNA-based methods to study tumour genetics and evaluate treatment responsiveness. This will be conducted in the context of prospective and retrospective samples from multi-centre clinical trials in Canada. This engagement with clinicians and publications describing these trials will help accelerate the adoption of such emerging technologies to the clinic.

Genetic dissection of neuronal pattern formation

Neurological diseases and disorders have been estimated to affect 3.6 million Canadians living in the community and over 170,000 Canadians living in long-term care facilities, including in British Columbia. However, we have limited information about the molecular mechanisms that cause many of those neurological conditions, largely because of the complexity of our nervous system. Therefore, understanding the mechanical processes that impart precise neural circuit formation using a simple model organism is critical to try to find ways to prevent neurological diseases and cure patients.

 

Toward this goal, Dr. Mizumoto will use nematode Caenorhabditis elegans as a model system to investigate the mechanisms that underlie neuronal circuit development. C. elegans has a short life cycle (3 days/generation) with a simple nervous system consisting of only 302 neurons, making it a great genetic model system to study the fine neural circuit formation. Most importantly, countless studies have shown that mechanisms and molecular machineries underlying the development of the nervous system are remarkably conserved between C. elegans and humans. It is likely that the knowledge obtained from our research will be directly applicable to the human nervous system and to diseases associated with nervous system defects.

 

Using C. elegans, Dr. Mizumoto will explore how neurons communicate with their neighboring neurons/cells to form a stereotyped neuronal pattern at the level of single synapse, which is a specialized interface between neurons or between neurons and other type of cells (such as muscle cells), to transmit electrical signals. Using a combination of C. elegans genetics, molecular biology and microscopy, this research will move towards an understanding of the fundamental principles of neural network formation.These studies will advance health-related knowledge by providing direct targets for other researchers to test in fruit fly (Drosophila) and mammalian models of neurodevelopmental disorders affected by Sema/Plexin signaling and others, and ultimately the development of therapeutic strategies for the treatment of these disorders.


End of Award Update: April 2023

Most exciting outputs

Many of the genes that we discovered from our research in specifying synapse formation are heavily associated with various neurological conditions, which suggest that our work may have potential to better understand the disease conditions affected by mutations in these genes.

 

Impact so far

As our work is fundamental and basic, we do not expect the impact of our work to be immediate.

 

Potential influence

We hope that our discoveries would lead to the development of therapeutics to treat neurological conditions in 20 years.

 

Next steps

We will continue to uncover the fundamental mechanisms of synapse pattern formation and specificity using C. elegans as a model organism.

Optimizing lifestyle approaches for the prevention and treatment of type 2 diabetes

The rising incidence of type 2 diabetes (T2D) puts financial stress on health care systems in British Columbia and across the world. Lifestyle interventions can improve cardiometabolic health to prevent or treat T2D, but optimal lifestyle strategies (e.g. exercise intensity, type, timing; diet composition) are not well-defined and adherence is notoriously poor.

The goals of Dr. Little's research are to optimize lifestyle interventions for improving cardiometabolic outcomes and uncover potential mechanisms underlying these health benefits. The research program aims to improve cardiometabolic health and reduce inflammation via a series of translational studies to define the optimal exercise and diet strategies and uncover cellular mechanisms underlying the benefits. To translate findings for true health impact, YMCA has partnered to implement an HIIT walking intervention in the community. In addition, a randomized controlled trial will be implemented to evaluate the effectiveness of a pharmacist-led intervention, implemented through a network of 13 BC pharmacies, to teach patients with T2D how to follow a low-carb, high-fat (LCHF) diet while also reducing their medications. This has tremendous potential to change diabetes management in BC through an innovative pharmacist-led therapeutic nutrition program using LCHF diets.

The long-term goals of this research will be to develop optimal evidence-based exercise and diet interventions that improve patient health and inform clinical practice guidelines for the prevention and treatment of T2D. Elucidation of the cellular and molecular mechanisms underlying the anti-inflammatory effects of exercise and diet approaches will also be used to define the best anti-inflammatory lifestyle interventions, and identify potential therapeutic targets for prevention and treatment of T2D.

Improving maternal and perinatal health outcomes in high risk mothers

Among women who give birth in industrialized countries maternal age, obesity, twin or triplet pregnancy, and presence of chronic diseases such as diabetes and hypertension continue to increase. For example, 34% of mothers in Canada today are overweight or obese, and approximately 20% of births are to women over 34 years. These demographic trends highlight the need for increasingly complex obstetric care with careful prenatal monitoring and timely obstetric intervention if necessary. 

Dr. Lisonkova's research will quantify the risk of severe maternal morbidity by developing a score system that will accurately distinguish between high, moderate, and low risk women. This score calculator will help, for example, women in rural areas to decide about transport to higher-level obstetric care, as these women may face geographical barriers to timely transfer. Determinants of these elevated risks will be examined, as well as whether these risks increase with distance to maternity care, seasonally (for example in winter), or occur only among women in selected geographically specific areas.

The results of this research will provide information to women who are contemplating delaying childbirth, who are overweight or obese, or have chronic health problems. This information will also help health care providers in pre-pregnancy and pregnancy counselling, and health care administrators to identify maternal care needs with respect to maternal-fetal medicine specialists and intensive care units. The maternal morbidity risk score calculator can also be used to adjust for baseline risks (maternal comorbidity, etc.) when comparing hospital performance and evaluating new safety measures in maternal care.

This project will be conducted in collaboration with the Society of Obstetricians and Gynaecologists of Canada, Public Health Agency of Canada, and the Department of Family Medicine & Midwifery, University of British Columbia. The collaboration between midwifery, family physicians and obstetricians will be beneficial especially for women in rural areas, for whom accurate risk identification is crucial.

Addressing HIV/AIDS, sexual health, and substance use among gay and other men who have sex with men

New HIV diagnoses are 71 times higher among gay, bisexual and other men who have sex with men (GBM) than other men in Canada. Since 2010, BC has adopted Treatment as Prevention (TasP) as a policy to increase HIV testing and engage more HIV-positive individuals in effective treatment to reduce transmission at a population level. However, the number of new diagnoses among GBM in BC has remained largely unchanged. Further, surveillance shows an increase of HIV diagnoses among the youngest birth cohorts of GBM. HIV pre-exposure prophylaxis (PrEP) is a new preventive tool for HIV-negative GBM, but inaccurate information, sub-optimal adherence or risk-compensation could result in a false sense of security, paradoxically leading to increased HIV transmission. In addition to HIV, infectious syphilis is now epidemic among GBM in BC.

This research program will address the HIV and sexually transmitted infection (STI) epidemics among GBM in Metro Vancouver and BC. Dr. Lachowsky will measure HIV risk behaviour over time, determine how PrEP affects bacterial STI incidence, and analyze shifting attitudes about HIV, challenges with HIV prevention and treatment, and changes in sexual negotiation and practices. Results will directly inform population-specific, age-relevant public health policy, programming, and interventions to reduce the burden of HIV for GBM, especially young GBM.

Dr. Lachowsky will employ a bidirectional, integrated knowledge translation approach, with a Community Engagement Committee and key academic, public health, and community partners. An interactive Web 2.0 hub will allow for knowledge dissemination and generation with community and service providers, and will be complemented with more traditional presentations, workshops, and publications.This single research project is part of a larger program of research examining health disparities amongst GBM in BC and Canada using interdisciplinary, community-based approaches.

Improving substance use treatment trajectories for men who have sex with men

British Columbia is currently in the process of developing and implementing new evidence-based policies and clinical reforms to address problematic substance use, including new: (i) pharmacotherapy approaches (e.g., replacement therapies); (ii) clinical practice guidelines; and (iii) integrated service delivery models of care. While men who have sex with men (MSM) represent a key group with historically high levels of substance use disorder and subsequent social and health-related sequelae (e.g., increased rates of HIV and sexually transmitted and blood-borne infections), there remains a gap in our knowledge about how best to design and implement services for today's generations of various sub-groups of MSM who use drugs (e.g., MSM who are: young; Indigenous; economically deprived).

Dr. Knight's five-year population health research program will adapt health policy and service delivery practices to improve substance use treatment trajectories for key groups of MSM who use drugs and are at risk for severe health and/or social consequences (i.e., the criteria for substance use disorder, as defined under DSM-V criteria). The aim will be to identify the most efficacious and scalable combinations of strategies to adapt interventions that respond to MSM's individual needs and broader social and structural conditions. This approach to implementation science offers a way to go beyond describing the problem and to focus on building an evidence base for implementing and adapting context-sensitive and population-specific solutions into routine policy and practice.

With collaborators representing the BC Ministry of Health, Vancouver Coastal Health, BC Centre for Disease Control and YouthCO HIV/Hep C Society and the BC Centre for Excellence in HIV/AIDS, as well as through the engagement of the BC Centre on Substance Use's Community Advisory Board, Dr. Knight's findings will be used to inform the development of policies (including clinical and provincial guidelines) to effectively scale up and integrate services that have the capacity to improve substance use treatment trajectories for MSM. Contributions to new knowledge will include the identification of the individual, social and structural factors shaping MSM's ability to reduce problematic drug use and prevent severe health and social outcomes (e.g., HIV and/or Hep C). Study outputs will also be assessed at an annual Stakeholder Workshop in which recommendations will be developed and refined for clinical and provincial guidelines.

Innovative addiction research program: Addressing polysubstance use

British Columbia (BC) faces a mental health and addiction crisis with an estimated cost of $100 million annually. In April 2016, a public health emergency was declared due to an alarming increase in opioid-related overdose deaths in recent years.

People who use illicit drugs (PWUD) bear a great burden of preventable morbidity and mortality from drug overdoses as well as other comorbidities including mental disorders and infectious diseases. While opioid agonist therapies (OAT) have proven effective in reducing heroin use, concomitant use of opioids and stimulant drugs (e.g., heroin and cocaine) is common among PWUD. Furthermore, recent research has suggested that many PWUD also suffer from untreated chronic pain, which may be driving prescription opioid (PO) misuse among this population. However, little is known about patterns of concomitant use of illicit opioids, POs and stimulants, and how OAT and other health services may serve to mitigate potential harms associated with such polydrug use. Currently, no approved pharmacotherapies exist for stimulant use disorder, necessitating urgent research effort in this area.

Dr. Hayashi's research will inform policies, programs and clinical practice to reduce harms associated with polydrug use. The primary research objectives are:

  • To investigate and address the impact of PO misuse, untreated chronic pain and concomitant opioid and stimulant use on patterns of drug-related harm.
  • Evaluate "naturally occurring" interventions and policy changes (i.e., new opioid addiction-related services and Vancouver Coastal Health's Downtown Eastside Second Generation Strategy) that are relevant to polydrug users.
  • Evaluate the efficacy of a novel pharmacotherapy to treat polydrug users. 

The research will employ vast longitudinal behavioural and biological data collected since 1996 via three ongoing prospective cohort studies of over 3000 PWUD in Vancouver. The findings are expected to inform care development and overdose prevention efforts for a high needs population in BC. One objective will involve implementing a clinical trial to evaluate whether an amphetamine-based medication reduces powder/crack cocaine use among 130 patients on OAT, who have both opioid and cocaine use disorders. If the study medication proves effective, Dr. Hayashi's research will potentially contribute to the identification of the first proven medication for cocaine addiction.

Incentivizing the delivery of sustainable care of chronic diseases in Canada: Case studies in musculoskeletal disease

Concerns about the sustainability of publicly funded health systems and the rising cost of care abound, yet there is little research that explores health care efficiency. Simple cost-saving exercises (i.e. cutting services) may risk harming patients, while more sophisticated, efficiency-saving approaches aim to provide health care at a greater benefit per unit of cost. Encouraging quality and value of health care delivery, whilst reducing waste, is also an indirect way to control health care costs. Undertreatment (failure to use best available care), overtreatment (treatment contrary to best-available evidence or preferences of patients), and poor coordination of care are three key clinical sources of waste. Many large-scale schemes aim to incentivize better health care, but show mixed results.

Dr. Harrison’s research will translate aspects of successful schemes and inform sustainable health care provision in Canada, focusing on musculoskeletal (MSK) diseases as they have been central to successful schemes. MSK diseases affect 11 million Canadians, and contribute hugely to the economic burden of disease in Canada. They have extensive impacts on people’s lives, including their health-related quality of life, ability to work, financial situation and reliance on the health care system. Additionally, high quality care of rheumatic disease requires early access to treatments which are often complex and considerably different from one another. Therefore, it is increasingly recognized that patients need coordinated, multidisciplinary support and care.

Dr. Harrison’s program will encompass policy-focused health economics and outcomes research to inform the design of financial and non-financial incentives to improve the efficiency of health care delivery.


End of Award Update: September 2022

Most exciting outputs

The project allowed me to explore whether a change to introduce a billing code for multidisciplinary care in rheumatology changed the experience of patients visiting rheumatologists in BC. We found that rheumatologists who used multidisciplinary care were able to expand services for patients.

 

Impacts so far

Our work adds to the evidence around incentives for multidisciplinary care in chronic disease. This will help inform future policy decisions.

 

Next steps

I continue to work on the evaluation of incentives and changes in policy for health care. I am currently co-leading a project evaluating the biosimilars initiative in BC.

 

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