Year: 2013

Placental proteomics: Gaining a system-wide understanding of the dynamic protease networks in normal placental tissue and upon inflammation to identify diagnostic signatures as biomarkers for preterm labor

Preterm birth affects approximately 12 percent of all deliveries. Prematurity is the leading cause of neo-natal mortality in Canada and is a major risk factor for impaired growth and development. There is a pressing need for tests to predict the risk of premature delivery accurately enough to provide the best treatment to prevent pre-term delivery and avoid unnecessary interventions.

It is thought that preterm labour can result from infection and inflammation of the placenta. Fetal and/or maternal inflammatory proteins in threatened preterm labour may form a diagnostic signature that can be used to predict whether preterm delivery is imminent or not. The Overall lab has developed several techniques to identify diagnostic inflammatory signatures in tissues. Using these methods, Dr. Eckhard aims to establish a functional, system-wide understanding of infection-induced inflammation in preterm labour using human placentas as a model of infection and inflammation.

Dr. Eckhard will elucidate placental molecular pathways that are activated in response to escalating infection resulting from the rupture of placental membranes. Collection of placentas from various documented times following membrane rupture to delivery will capture a range of inflammatory responses to infection — these “timed infection” placentas will be compared to non-inflamed placentas from full-term caesarean section deliveries and to placentas from defined pre-term deliveries to establish biomarkers and determine how infection-induced inflammation leads to pre-term labour.  

The role of histone methyltransferase SETD2 in the development of acute myeloid leukemia

Acute myeloid leukemia (AML) results from genetic defects. Recurrent  variations in chromosomal structures are common in AML, and several genes have been identified to be recurrently mutated in AML. Identification of these genetic defects in AML patients has improved diagnosis and treatment. However, more than twenty-five percent of AML patients carry no mutations in the known leukemia-associated genes, and the heterogeneity of AML and various survival outcomes suggest that as yet, undiscovered genes and pathways contribute to AML.

Dr. Gerben Duns performed high-throughput RNA sequencing and resequenced whole exomes, a portion of the genome, on 92 AML clinical samples to discover novel genes involved in AML. Mutations were identified within a gene called SETD2 in 7.6 percent of samples, suggesting a role for SETD2 in a subset of AML samples. The nature of the identified mutations suggests that these mutations are inactivating, which is in concordance with the recent identification of inactivating SETD2 mutations in several other cancer types.

Through in vitro and in vivo studies, Dr. Duns will examine the effects of the inactivating and mutating gene SETD2 as it contributes to AML development. Bioinformatic approaches are also used to investigate the potential association between the presence of SETD2 mutations and the response to therapy and disease outcome.

This study will provide insights into the mechanisms of AML pathogenesis, and will potentially reveal novel diagnostic and prognostic markers, as well as therapeutical targets.

Harnessing natural product biosynthetic machinery

Cladoniamide, a new alkaloid originally isolated from a bacterial strain found on the surface of a British Columbia lichen, has attracted attention as a potential new colorectal cancer drug.

The objective of this proposal is to harness the cladoniamide biosynthetic pathway to produce cladoniamide and new derivatives at high levels and generate new “hybrid” compounds by genetic manipulation of cladoniamide and related indolocarbazole biosynthetic pathway

This proposal aims to use biological and chemical tools to access new therapeutic molecules, specifically targeting colon cancer. The approach uses biosynthetic machinery from microorganisms to make complex natural products and their “unnatural” derivatives. Dr. Du will develop engineered biological platforms for the production of molecules that cannot be acquired in sufficient quantities through either organic synthesis or cultivation of a natural producer.

This project represents a unique approach that combines genomic and chemical tools to develop new drug leads from the cladoniamide scaffold. Results from this work will lay the groundwork for future, collaborative efforts in drug research, development, formulation, testing and commercialization.

Evaluating the impact of moral arguments on societal values for orphan drug coverage

As a member of the CIHR New Emerging Team for Rare Diseases, Nick is exploring citizens’ attitudes and behaviour as they relate to the challenge of providing accessible treatments for patients suffering from rare diseases. The development of accessible orphan drugs poses a dual problem. On the one hand, the small potential market for orphan drugs for rare diseases makes it difficult for many innovators to access sufficient private capital to develop new orphan drugs, resulting in a lack of treatment options for many rare disease patients. Nick is exploring how patient groups and the general public may be able to address this funding gap. Specifically, he is investigating the extent to which crowdfunding – an emerging approach to online fundraising – might be used to help “de-risk” early-stage orphan drug research by allowing investigators to fund exploratory studies that make it possible for them to attract subsequent grant funding or private investment.

On the other hand, provincial health insurance plans are faced with a decision-making challenge due to the fact that orphan drugs for rare diseases are often very expensive. This poses a moral dilemma, since the same funds used to treat one individual with a rare disease could provide less costly medications for many more Canadians. Because taxpayers must ultimately bear the cost of funding these treatments through the public insurance system, empirically estimating society’s willingness to pay for expensive treatments for rare diseases, despite the significant opportunity costs, is a key element of democratic decision-making. Using data from an online survey of adult Canadians, Nick is exploring societal preferences for orphan drug funding by analyzing respondents’ choices in different scenarios in which provincial health authorities must decide whether or not to fund a specific treatment through the provincial insurance system.

New indications for old drugs: Do statins, angiotensin converting enzyme inhibitors or proton pump inhibitors impact long-term disease progression in multiple sclerosis?

The most widely prescribed drugs for multiple sclerosis (beta interferons) have been shown to be only partially effective while carrying high costs and adverse side-effects. However, statins, angiotensin converting enzyme (ACE) inhibitors, and proton pump inhibitors (PPIs), which are effective against lipids, blood pressure, and acid, respectively, are safe, relatively inexpensive, and also have anti-inflammatory and immunomodulating properties that may be beneficial in the treatment of MS. There is a shortage of clinical data supporting the beneficial effects of these drugs in MS treatment.

This project will study the real-world therapeutic potential of statins, ACE inhibitors, and PPIs in the treatment of multiple sclerosis.

Dr. de Jong will examine the impact of statins, ACE inhibitors, and PPIs on multiple sclerosis disease progression, alone or in combination with beta interferon therapy, in a large cohort of patients with relapsing-onset MS from British Columbia. She will also describe the safety and tolerability of these drugs in patients with MS treated with and without a beta interferon. In both studies, a time-dependent Cox proportional hazards model will be used. Results will be expressed as hazard rates with 95 percent confidence intervals.

This research has the potential to improve the treatment of multiple sclerosis by establishing the efficacy, safety, and tolerability of alternative drugs for the treatment of MS.

Targeting androgen receptor dimerization as a potential therapy for prostate cancer

Prostate cancer is a leading cause of death in men. Treatment involves reducing production of di-hydro-testosterone (DHT) or blocking the interaction of this hormone with the androgen receptor (AR), a transcription factor responsible to drive expression of genes responsible for tumour growth. This treatment is unfortunately temporary and tumours eventually undergo genetic changes to become castration-resistant and able to grow in the absence of DHT.

This research project aims to use drugs to block AR activity in castration-resistant prostate cancer. Within the nucleus, two androgen receptor molecules must self-associate (“dimerize”) before binding DNA and initiating transcription. Dr. Dalal hypothesizes that slowing tumour growth can be achieved by preventing the AR-DNA interaction directly or by interfering with AR dimerization.

Cell biology and biochemistry approaches will allow Dr. Dalal to study the molecular mechanism of DNA-blocking or dimer-interfering compounds. Several compounds targeting both processes have been optimized to show potent and specific inhibition of the androgen receptor in cultured prostate cancer cells. Gel shift assays, calorimetry methods and confocal microscopy are now being used to gauge the effects of drugs on both DNA binding and AR dimerization. Site-directed mutagenesis of amino acids on the AR protein surface will validate the binding location of inhibitors. Promising compounds will be tested in mice to show effects on the size of prostate tumours.

Targeting transcription factor dimerization and DNA binding is a novel strategy that holds great promise to treat advanced forms of prostate and other cancers.

Beyond the known genome: long non-coding RNAs as novel therapeutic targets and biomarkers for metastatic prostate cancer

Recent evidence indicates that non-coding RNAs (NC-RNAs) play crucial functions in physiological and pathological cellular processes. Long non-coding RNAs (lncRNAs) are the most abundant NC-RNA class, accounting for 10–20,000 genes. Despite this, the role of only a few of them (approxim. 40) has been characterized. Many lncRNAs show a tissue-specific expression pattern and are altered in cancer cells. For this reason, it has been suggested that they may be useful as biomarkers in oncology.

We performed RNA-Seq. on non-metastatic and metastatic prostate cancer (PCa) tumor tissue xenografts. Our analysis revealed 159 up- and 77 down-regulated lncRNAs in the metastatic samples. We validated the differential expression of 7 up-regulated lncRNas in metastatic xenografts (QPCR). Using pooled plasma samples from 3 three patient groups (normal, localized PCa and metastatic PCa) one lncRNA (JUPITER) assayed to date differentiates amongst the three groups. We hypothesize that lncRNAs play critical roles in PCa progression and can be exploited as biomarkers and therapy targets. To address these hypotheses we will: 1: Characterize the function of selected lncRNAs. We will select the most up-regulated lncRNAs in metastatic vs. primary PCa xenografts and assay their expression in a panel of PCa cell lines. Once we identify 2-3 cell lines expressing the highest levels of a transcript, we will silence it using siRNAs. Silenced and control-treated cells will be assayed for proliferation, migration, invasion, apoptosis, and cell cycle progression. 2: Measure by QPCR the expression of selected lncRNas on RNA extracted from freshly frozen prostate samples (normal prostate, prostate intraepithelial neoplasia, local and metastatic PCa). For each gene, we will statistically compute correlations with clinico-pathological variables (grade, stage, PSA level). 3: Further analyze lncRNAs as biomarkers. The expression of JUPITER (and other differentially expressed lncRNAs) will be assayed in individual plasma samples from patients with different PCa stages, in order to estimate the optimal threshold values for early detection of metastatic PCa (ROC curve).

While localized PCa is a treatable disease, progression to a metastatic and drug-resistant cancer accounts for 4000 deaths annually in Canada. Understanding the mechanisms of Pca progression and identifying new molecular markers and therapeutic targets will allow better disease management and ultimately reduce deaths. In brief, we discovered a long non-coding RNA (PCAT18) that is expressed exclusively by prostate cancer cells and is required for prostate cancer cell growth and motility. This gene can be used as a biomarker and as a therapeutic target for metastatic prostate cancer.

Mechanisms of cardiovascular disease in children with mental health conditions

Prescriptions of second-generation antipsychotic  (SGA) medication for children in British Columbia increased 22-fold from 1996 to 2010. These medications treat the underlying mental health issues (e.g. psychosis, depression, attention deficit/hyperactivity disorder) but often come with side-effects, including metabolic syndrome.

Metabolic syndrome is a cluster of clinical features that includes excess weight around the middle, high blood pressure, and high blood sugar or triglyceride concentrations. Given that metabolic syndrome is a risk factor for cardiovascular disease, there are serious implications for the long-term health of these children. Development of a secondary chronic disease such as CVD, on top of an existing mental health condition, further marginalizes the life-long health of these children.

Accordingly, there is a need to develop a means by which to distinguish children at risk for developing metabolic syndrome from those who are not. The goal of this research is to identify genetic markers that will indicate which children will develop risk factors for heart disease and stroke when treated with SGAs so that appropriate prevention strategies may be implemented in these children.