Research

1. GENOMICS OF NERVOUS SYSTEM TUMOURS

OVERVIEW: My clinical area of expertise is focused on managing skull base tumors that are typically considered to be benign tumors by world health organization (WHO) classification, however due to their intimate involvement and invasion of critical neurological structures pose a considerable challenge for the care and outcome of patients. Research in the area of skull base tumors is extremely limited and consequently targeted therapies have not been identified to date. This is an area of extreme unmet need and my lab is dedicated to advancing the molecular and genomic understanding of these tumors.

Schwannomas are tumors that arise from nerves in the skull base, peripheral nerves and spine. Schwannomas can result in significant debilitating morbidities. Schwannomas can occur either sporadically or in the setting of a genetic predisposing condition, such as NF2. We performed an integrated molecular analysis of schwannomas to determine the somatic landscape of sporadic schwannomas and NF2 related schwannomas. Exome sequence analysis with validation by targeted DNA-sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19Mb chromosomal inversion on chromosome 10q. The presence of the fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma.  Methylation and gene expression profiling identified molecular subgroups that correlated with fusion status. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated-ERK, increased proliferation, increased invasion, in vivo transformation and increased tumorgenesis. Targeting of the MEK/ERK was effective in fusion-positive schwann cells, suggesting a possible therapeutic approach for this subset of tumors. Impact: This study was published in Nature Genetics, 2016 (senior author). It is the first comprehensive molecular analysis of schwannomas, identifying a novel fusion protein that can be used for diagnostic, prognostic and therapeutic benefit. In addition, providing evidence that repurposing MEK inhibitors can be a viable therapeutic option.

Meningiomas are the most common type of brain tumor and paradoxically remain one of the most understudied brain tumor type. There is a huge clinical need to better understand the biology of these tumors in order to be able to identify targets of therapy so that treatments options can be expanded beyond the current limited options of surgery and radiation therapy. The main limitation in management of meningiomas is that while WHO histopathological classification is useful, it is hampered in its ability to predict and prognosticate. Despite WHO classification there exists a subgroup of clinically aggressive meningiomas (CAMs) that exhibit extremely high recurrence rates. Therefore, we need to identify factors beyond histopathological grading that can more effectively and with precision determine outcome so that we can tailor treatments better. Individual centres will not have sufficient numbers of CAMs to allow a robust and in-depth analysis of the biology of this tumor. Therefore, it is necessary to combine efforts across institutions. I have therefore focused on building an international meningioma consortium giving us access to a large number of samples, databases, collaborations and expertise throughout the world.  I have a substantial commitment to conducting an integrated multiplatform molecular analysis of the clinically aggressive meningiomas to be able to better identify predictors of prognosis and response to therapy.

Additionally, using epigenomic – specifically methylation data – we have developed a predictive model to help guide decision-making around adjuvant therapy (you can access this program on our website – Methylation Program).

A specific research focus borne out of my clinical interest and focus is on a unique subpopulation of patients that are the Radiation Induced Meningiomas. This work was published in Nature Communications, 2017 (senior author). Impact: this project is the first to document a comprehensive genomic landscape of childhood radiation induced meningiomas and we have demonstrated that there is a distinct genomic landscape to these tumors compared to their sporadic counterparts, shedding light on the biological targets.

2. TUMOUR ANGIOGENESIS: MECHANISMS OF RESISTANCE TO THERAPY

OVERVIEW: The overall goal of this research stream is to understand impact of anti-angiogenic therapy (AATx). In specific we are studying the contribution of bone marrow derived progenitor cells (BMDC) to tumour neo-vascularization in order to identify novel therapeutic strategies that can predict and improve response to AATx. We have established the mechanisms of BMDC recruitment, migration, differentiation and integration into the tumour vasculature and microenvironment, and in response to radiation therapy (RT). Results from this proposal will provide insights into as yet unidentified mechanisms of tumour neo-vascularization and provide the basis for translational studies that will examine the benefits of targeting BMDC to restrict tumour growth. This study was published in Cancer Research, 2015. The continued research is focused on determining the interaction of bone marrow derived macrophages with tumor endothelial cells in directing resistance to therapy. We have identified a few key predictors of response to AATx, in specific TNFa as a key factor in directing recruitment of macrophages to the tumor vasculature and activating endothelial cells that in turn form a resistant cell phenotype. The project is now centred on application of the predictive markers to determine best responders to AATx in clinical practice.

3. TUMOUR METABOLISM

OVERVIEW: Altered cancer cell metabolism is recognized as a critical mechanism by which cancer cells survive unfavorable micro-environmental conditions. A classic biochemical adaptation is the metabolic shift to aerobic glycolysis rather than mitochondrial oxidative phosphorylation, regardless of oxygen availability, a phenomenon traditionally referred to as the “Warburg Effect”. Aerobic glycolysis, characterized by high glucose uptake, low oxygen consumption and elevated production of lactate is a feature of cancer cells. One of the key regulators of the Warburg Effect is hexokinase-2 (HK2). We have shown that HK2 is aberrantly expressed in and is an important mediator of aerobic glycolysis in malignant brain tumours, providing a proliferative and cell survival advantage to cancer cells. These works have been published in Oncotarget, Cancer Research, and Clinical Cancer Research. Furthermore, we have shown that HK2 is responsible for the highly invasive nature of malignant brain tumours, which is one of the key factors responsible for malignant brain tumours being resistant to therapy and exhibiting an extremely rapid recurrence rate. We have used an in-silico drug screen to identify drugs that can be repurposed to modulate tumor metabolism. Ongoing work: A second focus of this research program is the multi-integrated genomic and metabolomics analysis of 150 gliomas that has allowed us to establish distinct subclasses of gliomas with respect to the metabolic and genomic profile of tumors, introducing a new dimension in glioma classification that can be used to better understand and response to therapy.

BASIC SCIENCE RESEARCH          CLINICAL RESEARCH         CLINICAL TRIALS

Basic Science Research

Molecular Profiling of Aggressive Meningiomas.

Meningiomas are the most common primary brain tumor, but are severely understudied. Although most patients can be cured with surgery alone, some patients exhibit relentless recurrence of disease despite multiple rounds of surgical and radiation therapies. We are learning that these aggressive meningiomas have a different biology than those that are cured with surgery alone. Using state-of-the-art genetic sequencing techniques, we are studying the biology of meningiomas in order to better define those tumors that are aggressive with hopes of finding new medical treatment options that are in dire need for these patients. Our lab is amongst the first to identify a methylation signature in meningiomas that can more accurately predict risk of recurrence than the standard classifications that routinely used in clinical care. For more information on this please visit our Methylation Program page.

Metabolism of Gliomas.

Gliomas are the most deadly brain tumors. Recent genetic studies have demonstrated that most gliomas harbour a mutation in the isocitrate dehydrogenase (IDH) gene. This mutation results in accumulation of the 2-hydroxyglutarate metabolite which facilitates tumor growth and invasion. It is clear that the metabolism of gliomas can be altered by this mutation. We are using High-performance liquid chromatography combined with mass spectrometry techniques in order to better understand the implications of altered metabolism in the context of other genetic changes in gliomas.

Molecular characterization of the full spectrum of peripheral nerve sheath tumors

Neurofibromatosis Type 1 (NF1) is a hereditary tumor predisposition syndrome that afflicts 1 in 3500 people and results in the development of innumerable peripheral nerve sheath tumours. These tumours fall within a spectrum of benign and malignant tumours. Although a large number of these tumours are benign, the cause significant morbidity such as intractable pain, physical disfigurement and neurological deficits. In addition, a subset of these tumours have a risk of malignant transformation into a high grade sarcoma called malignant peripheral nerve sheath tumours (MPNSTs); however, the mechanism of malignant transformation is poorly understood. We will leverage a multi platform integrated molecular analysis of the full spectrum of peripheral nerve sheath tumours to better understand the biology of oncogenesis and identify novel therapeutics as potential treatments.

Proteogenomics of Recurrent Gliolastoma Multiforme (GBM)

Our research focuses on better understanding the changes that occur to GBM between initial diagnosis and recurrence. Currently, these tumours inevitably recur and there is no standard treatment for recurrent disease. We will be utilizing a multi-omics approach to identify new biomarkers and better understand recurrent GBM. This will allow us to better predict response to treatment, recurrence, and prognosis and identify novel therapeutic targets.

Application of Novel Machine Learning Approaches for Recurrence Risk Prediction in Meningioma Based on Methylome Analysis:

Our goal is to develop clinical machine-learning tool to predict early recurrence risk in each meningioma patient using DNA methylation signatures and prognostic clinical factors. The approaches for the predictor are based on (1) GBM (generalized boosting machine) classification model to calculate the probability of recurrence over a time cut-off, (2) continuous survival random-forest modelling to calculate the probabilities of a recurrence over various time frames, (3) Integrate two models (continuous time or cut off time based) to create a robust/improved classifier, and (4) finally choose important minimal signatures possible from the methylation data for different years of cut-off (expected features to be less than number of events / recurrence).

Survival Stratification of IDH Mutant Glioma Using Methylation and mRNA based Integrated Approach:

Diffuse Glioma is genomically separated into IDH mutant (IDHmut) and IDH wild type tumors which defines prognosis in gliomas. We aim to characterize IDHmut LGG multi-omic platforms and identify methylation signature of outcome, and validate them with external test set. Initial results showed that multiple platform based integrated approach provided a clinically and biologically relevant subtypes that showed a strong correlation with patient survival and somatic mutations.

Comprehensive Methylome Analysis of EGFR-mutant Primary Lung Adenocarcinoma and Matched Brain Metastasis:

Lung Adenocarcinomas (LUAD) are the most common lung tumours and EGFR-mutant LUAD have a higher risk of brain metastasis development, which leads to poorer survival. Genetic, epigenetic or mutational signatures of brain metastasis from LUAD have not been WELL characterized yet. In this project, we are interested in (1) comparing the EGFR-mutant primary LUAD to matched brain metastasis to understand mechanisms of brain metastasis, (2) comparing FIRST (initial) BM and recurrent BM pairs to identify genomic alterations.

Epigenomics of Brain Metastases and their Primary Tumours.

The metastasis of lung, breast, and melanoma cancer to a patient’s brain significantly worsens their prognosis. Unfortunately, there is no reliable method to determine which patients will develop brain metastases currently. We are identifying DNA methylation signatures that predict which patients will develop brain metastases from their primary lung, breast and melanoma cancers and are also characterizing DNA methylation differences between brain metastases and the corresponding primary tumours. This work may allow for the identification of new treatment targets to prevent brain metastases and for clinicians to match the extent of treatment to a patient’s risk of poor oncological outcomes. It may also improve our understanding of the mechanisms that allow for tumour spread to the brain.

Epigenomic Drivers of Chordoma Recurrence.

Chordomas represent 20% of primary spine and skull base tumours and survival remains poor despite standard treatment of surgery and post-operative radiotherapy. Patients that develop a recurrence of their chordoma experience poorer survival and unfortunately there is no robust approach to predict which patients will have a recurrence. We are identifying DNA modifications, including methylation signatures and histone marks, that predict which patients will experience chordoma recurrence. We are also screening drugs which target the epigenetic signatures that we are identifying. This work may provide clinicians with information allowing them to balance the extent of a patient’s treatment with their risk of having poor outcomes and it may also lead to the identification of new chordoma treatments.

Non-invasive Diagnosis of Central Nervous System Tumours.

Currently, after the diagnosis of an intra-axial brain tumour on imaging, surgery is required in order to provide a definitive diagnosis from a wide differential ranging from benign to malignant lesions before treatment is planned. Recent work has shown that DNA methylation alterations in central nervous system tumours can be utilized for diagnostic purposes. We are identifying DNA methylations alterations non-invasively, using cell-free tumour DNA found in patient blood, and exploiting these signatures to classify different brain tumour types. This work may lead to the diagnosis of brain tumours without the need for invasive tissue sampling and thereby allow for the coordination of appropriate patient treatment, including radiotherapy or targeted therapies, without surgery.

Investigating the role of macrophages in glioblastoma angiogenesis and treatment resistance.

Glioblastoma (GBM) is characterized by pathologically altered vessels that are tortuous, hyperdilated, and leaky. Tumour vascularization is highly dependent on the tumour microenvironment and our laboratory, among several others, have shown that bone marrow-derived macrophages are actively recruited to perivascular regions within the tumour where they are thought to provide a supportive role for blood vessels. However, the specific role of macrophages in GBM angiogenesis and underlying molecular mechanisms have not been well-characterized. Preliminary data from our lab has now shown that glioma-associated macrophages (GAMs) secrete TNF-alpha to upregulate genes involved in endothelial cell activation, a pro-inflammatory response that may drive aberrant tumour angiogenesis. The overall objective of this project is to further elucidate the molecular mechanisms and functional impact of GAMs on endothelial cells (EC) to gain a better understanding of their role in tumour angiogenesis and resistance to therapy.

Generation and characterization of a novel syngeneic GBM mouse model

We have previously generated a novel transgenic Glioblastoma Multiforme (GBM) mouse model that recapitulates the genetic mutations found in ‘classical’ subtype of human GBM. This mouse model, called GEC3, overexpresses EGFRvIII under the astrocyte-specific promoter, GFAP, in combination with heterozygous knockout of CDKN2A. These mice spontaneously acquire brain tumours around 2-5 months of age. However, for drug studies it is ideal to use a xenograft model where all tumours can be implanted at the same time and progress along the same time course so that treatment can be initiated at a specific time point to determine response to therapy. We have isolated and cultured glioma stem cells from GEC3 tumours, which we will now implant into GEC3 genotype negative mice to validate the tumourigenicity of these cells and generate a syngeneic mouse model that can be used for drug studies.

Clinical Research

Effects of Meningioma on Quality of Life

Previous studies have shown patients with a meningioma may have limitations to their quality of life and daily functioning after receiving treatment for their meningioma. These limitations and problems may impact their quality of life for years after treatment and into their journey to recovery. The purpose of this study is to learn how patients with meningioma feel during and after their treatment and what concerns they may have after their treatment. Additionally, we aim to learn about quality of life concerns of patients who do not receive treatment for their meningioma, where their tumour is monitored with imaging. This additional information may help find better ways to cope with the effects of having a meningioma.

Clinical Trials

Combination Adenovirus + Pembrolizumab to Trigger Immune Virus Effects (CAPTIVE).

Glioblastomas are the most deadly brain cancer. Treatment options for patients with glioblastoma after recurrence are extremely limited. We are the lead Canadian site investing the role of intratumor injection of a novel adenovirus that kills tumor cells in combination with immunotherapy (pemborlizumab) for patients with recurrent glioblastoma as part of the CAPTIVE clinical trial https://clinicaltrials.gov/ct2/show/NCT02798406

Azoles Targeting Recurrent High Grade Gliomas

High grade gliomas (HGGs) are the most common and aggressive brain tumors. Right now, average survival is only 14 months. Our treatments have not changed in years. We desperately need treatments that specifically target tumor cells, especially for patients with HGGs. We will give either KCZ or PCZ a few days before surgery to patients who have the tumor and need surgery. Then we will take the tumor out during surgery and see how much drug actually got in to the tumor. Our plan is to study each drug separately in 5 different individuals with HGG tumor. If we can show that the drug got into the tumor, then we will plan on studies that use higher doses of drug to see if we can safely increase the dose to achieve maximum effect. This would then allow us to test either drug in a larger group of HGG patients to see if we can increase patient survival. If we can show improved survival by specifically targeting tumor metabolism, there is promise of ultimately finding a more effective method of managing this fatal disease. https://clinicaltrials.gov/ct2/show/NCT03763396