Identifying clinically relevant biomarkers in lymphoma using next-generation sequencing

Lymphomas are a class of cancers that generally derive from blood cells known as B-cells that are present within organs called lymph nodes. Similar to other cancers, lymphoma tumours can be surgically removed. However, patients often relapse after surgery because, inevitably, a small number of cancer cells remain in the body. Diffuse large B-cell lymphoma (DLBCL), is one of the most common types of lymphoma. Sophisticated techniques that allow one to view the abundance of genes (expression,) or the genetic code (DNA sequence), of cancer cells can reveal clinically relevant distinctions between cases of DLBCL. This type of grouping is important because, for example, patients with one subgroup of lymphoma known as the ABC variety appear to have an inferior response to current standard therapies compared to those with the more common GCB variety of DLBCL. The signals that define distinct subtypes of cancers are often referred to as biomarkers and their presence or absence can, in some cases, be tested in a clinical setting. Ryan Morin is focusing his research on the identification of new biomarkers in cancer cells from a clinically diverse group of lymphoma patients. Additionally, Mr. Morin’s research will focus on the identification of genes that have been damaged by somatic mutations, and thereby the identification of genes important to the development of DLBCL. By cataloguing the identified cancer driver mutations, it may be possible to use their signatures to define new subgroups of lymphoma with distinct characteristics. Marrying this information to new biomarkers may help determine whether any new biomarker is associated with positive (i.e. cure), or negative (i.e. relapse), clinical outcomes. Finally, the identification of biomarkers and specifically somatic mutations altering protein function may reveal possible vulnerabilities of a cancer cell to specific drugs. For example, a mutation that results in activation of an oncoprotein may allow a clinician to choose an appropriate drug that inhibits that protein. Further, if no drugs are available, these findings may spur the development of new drugs to specifically target the mutated or activated proteins responsible for malignancy.

Developing New Non-Invasive Optical Techniques for Detecting and Diagnosing Cancer

While cancer continues to affect thousands of Canadians, when detected at an early stage patients have a better chance of survival. Therefore, the development of sensitive diagnostic tools to enable early cancer detection and diagnosis is important. Dr. Anthony Lee is focusing his research efforts on the design and development of high resolution, non-invasive, in vivo optical imaging tools that will allow clinicians to perform so called ‘optical biopsies’ to detect and diagnose lung and skin cancers while the patient is being examined. Lung cancer is the leading cause of cancer mortality. The only reliable way to definitively diagnose the disease is to perform a lung biopsy for histological inspection by a pathologist. This technique is invasive and is associated with numerous problems. Dr. Lee’s Optical Coherence Tomography (OCT), is a technique that shows promise as a non-invasive diagnostic tool for lung cancer. Part of his project will be dedicated to developing a new OCT instrument designed specifically for use in patients’ lungs. OCT is similar in principle to ultrasound except that it uses light rather than sound as the imaging signal. It has higher resolution than ultrasound and sufficient penetration into tissue to examine the lung epithelial lining, where most cancers originate. The endoscopic probe being designed can image large segments of the bronchial tree in high resolution. Additionally, Dr. Lee is developing a Multiphoton Microscopy (MPM), instrument for use in diagnosing skin cancer, the most commonly diagnosed form of cancer. MPM has microscopic resolution and will be able to create 3-dimensional volumetric images of tissue. The results of Dr. Lee’s work will provide improved diagnostic tools to replace traditional biopsies which are time and resource intensive. Moreover, if cancer diagnoses can be confirmed in situ, immediate treatment becomes a possibility and may eliminate the need for subsequent patient visits.

Developing an innovative antibody-based nanopharmaceutical for treating cancer

Rituximab is an anti-CD20 monoclonal antibody (mAb), approved for use in combination with standard chemotherapeutic agents for treatment of patients with CD20-positive B cell lymphomas. Although it provides significant benefits for lymphoma patients, it is not curative, and for several specific forms of lymphoma, rituximab offers little or no benefit. To date, the mechanism(s) underlying the anti-tumour activity of this mAb in vivo are not clear. However, one area of particular interest is in activities that involve clustering of the CD20 molecule on the cell surface. Clustering of CD20 has been shown to elicit changes in cell signalling pathways that promote cell death, while enhancing sensitivity of lymphoma cell lines to cytotoxic agents. By better understanding this mechanism of antibody-induced tumour death it will be possible to determine the clinical basis for insensitivity to rituximab. Jesse Popov’s research is exploring this mechanism of activity by comparing a novel, highly active multivalent form of rituximab that he has developed, to the activity of rituximab. The results of his research will provide for improvements on the novel mAb he has developed and may also provide a possible therapeutic alternative to rituximab. Importantly, this novel agent can be made with any therapeutic antibody, not just rituximab, which means that it has the potential to be used for treating virtually any type of cancer. Such improvements over current therapies translate directly into a higher quality of life for cancer patients.

Treating breast cancer with a novel programmable fusogenic gene delivery system for small interfering RNA targeting integrin-linked kinase

Cancer is a disease characterized by specific functional capabilities that are not typically expressed by normal healthy cells. For example, cancer cells can grow in the absence of normal growth signals, build resistance to the detrimental effects of drugs, invade and spread to other sites of the body. These capabilities are a result of acquired or inherited genetic mutations to DNA within cells, damaging genetic information that defines normal cellular function. If these unique features of cancer cells can be altered or corrected using gene therapy, it may provide an effective strategy to treat cancer. Studies have shown that in both plants and animal cells, introduction of man-made molecules known as small interfering RNAs (siRNA) can result in the suppression (silencing) of specific genes that promote cancer growth. Ultimately, this weakens the cancer cells to cause cell death or make cancer cells more vulnerable to radiation and/or chemotherapy. One promising siRNA treatment targets breast cancer by suppressing integrin-linked kinase (ILK), a protein that is known to be over-expressed in breast cancer. However, the effectiveness of siRNA treatment is currently hampered by issues related to the way the drug is delivered to the tumour. Dr. Emmanuel Ho is working to develop and test a novel method to deliver the drug only to cancer cells, leaving healthy, non-cancerous cells unaffected. By doing so, he hopes that the siRNA will decrease the expression of ILK and result in a decrease of breast tumour growth. If this new drug delivery system proves successful, the technology will enhance breast cancer treatment and facilitate the development of other siRNAs that are safe and effective.

Conditional genetic screens to define gene-gene and gene-drug interactions in normal and malignant human cells

Approximately eight per cent of breast cancers are caused by inherited mutations in genes called BRCA1 and BRCA2 (BReast CAncer 1 and 2). Since the BRCA genes were first identified in patients with inherited breast cancer, it has become obvious that they are also mutated in many non-inherited cancers. Understanding their function in normal and tumour cells is therefore an important problem in breast cancer research. Genes usually carry out their functions through interactions with other genes, organizing the different steps into pathways. Cells often use two or more different pathways to respond to the same stimulus. For example, there are multiple pathways that repair damaged DNA; one involves BRCA2, while a gene called PARP1 is involved in other pathways. Even when radiation and chemotherapy disable the BRCA-2 pathway, the intact PARP1 repair pathways may compensate and enable the cancer cells to survive. PARP1 inhibitors are currently undergoing clinical trials at various centres, including the BC Cancer Agency. Dr. Hong Xu is identifying interactions between the BRCA2 and PARP1 DNA repair pathways. She is also screening for gene mutations that make normal and BRCA2-mutated breast cells more sensitive to PARP1 inhibitors, which could help physicians determine appropriate doses based on a tumour’s genetic profile. Xu’s work will enhance our understanding of the roles of BRCA2 and PARP1, and accelerate the development of new individually tailored therapeutic treatments for breast cancer.

Genetics of healthy cardiovascular aging

Statistics Canada projects that there will be more than 1.6 million seniors over 85 by the year 2041. Only a minority who reach this age maintain a good quality of life and are free of major age-related diseases such as cardiovascular disease (CVD), cancer, lung disease, diabetes, and Alzheimer’s disease. Advancing age is the biggest risk factor for cardiovascular disease. However, a minority of people older than 85 — called “”super seniors”” — seem resistant to the most common age-related diseases, including CVD. These people may represent a group that either lacks genetic susceptibility factors that contribute to disease in the majority of people or may possess genetic resistance factors that enhance their ability to resist disease and prolong lifespan. Dr. Maziar Rahmani seeks to answer whether people whose hearts remain healthy well into their 80s and 90s have “good genes.” He is studying more than one thousand residents in the Metro Vancouver area, using cutting-edge technologies to scan the entire genome of each study participant. He will look across more than a million potential variances to find genetic commonalities among super seniors in Vancouver, and compare these findings to other studies using European and other North American populations. Identifying and understanding genetic factors that influence resistance or susceptibility to heart problems could open the way for personalized, optimized disease prevention and treatment strategies.

Statistical models for clinical genomics of cancer

Ovarian cancer is the most fatal gynecological cancer in North American women and the fifth most common cause of cancer death. Breast cancer is the most common cancer in women worldwide. Recent approaches to improving clinical outcomes for these two diseases have focused on defining distinct subtypes within ovarian and breast tumours that differ in their clinical outcomes and responses to therapy. Preliminary evidence suggests that subtypes can be detected from biopsies by performing state-of-the-art molecular tests to determine specific molecules (called markers) that distinguish the subtypes. It is also expected that an even smaller subset of markers could be used as indicators for determining prognosis and for directing therapy tailored to the subtype. A number of BC research programs are currently working collaboratively to identify and characterize the subtypes of ovarian and breast cancers, using more than 2,000 breast cancer and 400 ovarian cancer tumours for which clinical outcomes are known. This work generates massive amounts of molecular data (more than 100,000 data points per tumour). Previously supported by MSFHR funding for his PhD training, Dr. Sohrab Shah focuses his post doctoral work on developing bioinformatics (the application of computer science tools and research to biology) and statistical modeling approaches that can help pinpoint potential markers among the reams of data. Shah’s research is key to developing tools that help uncover the molecular characteristics of the subtypes of breast and ovarian cancers, and provide state-of-the-art classifiers for improved outcomes for patients with these devastating diseases.

The role of SHIP in the development and function of myeloid immune suppressor cells

An important role of the immune system is to identify and eliminate tumour cells. When a tumour first forms, the immune system recognizes it as foreign and generates specialized T cells to attack and kill it. However, tumours have evolved a number of mechanisms that prevent the immune system from being able to function properly, resulting in cancer progression. One of the mechanisms by which tumours escape from the immune system is by secreting chemicals that promote the generation of cells that inhibit T cells from carrying out their normal functions. The presence of these suppressive cells is one of the most common reasons current cancer therapies fail. Melisa Hamilton is investigating a specific subset of these suppressive cells, called myeloid immune suppressor cells (MISCs). Previous research has shown that the protein known as SHIP is important in regulating the survival and proliferation of myeloid cells (white blood cells). Hamilton’s research is focused on investigating the specific role SHIP plays in MISC development and function. With a better understanding of how tumours stimulate the development of MISCs and how these cells suppress the immune system, researchers can design targeted therapies to prevent the formation and function of MISCs. These therapies would greatly increase the ability of the immune system to attack and eradicate tumours and would be especially effective in combination with current cancer immunotherapy treatments to improve cancer patient outcomes.

Identification of causal genetic alterations involved in the progression of epithelial cancers

Of the 227,000 newly diagnosed cancer cases in Canada in 2007, approximately 80 per cent were some type of carcinoma. Carcinomas (epithelial cancers) include a vast array of common cancers such as lung, breast, prostate, colorectal, oral, esophageal and cervical cancers. Patients with early stage cancer show the best response to therapies and exhibit the greater survival rate compared to those with the advanced stage disease. However, with current screening techniques, the majority of patients present with advanced stage disease at the time of diagnosis, limiting treatment options. The disruption of genes is responsible for cancer development. However, the accumulation of gene disruptions during cancer progression makes it difficult to distinguish which disruptions are the initiating events in this process. The discovery of these initiating events are crucial for gaining a better biological understanding of how cancer progresses. Conventional methods can only detect large DNA disruptions that may contain many genes, hindering precise identification of the genes responsible for cancer development. MSFHR funded William Lockwood for his early PhD research. He’s now continuing his comparison of DNA profiles of normal cells against cancerous cells. By labelling normal and tumour DNA with different dyes, he will be able to investigate the genetic changes that occur in progressing stages of cancer, in order to retrace the evolving patterns of gene disruption during cancer development. By distinguishing the initiating events, Lockwood’s research will shed light on the pathways driving the progression of cancer cells. This could lead to the identification of biomarkers to predict which early stage cancers are prone to develop into advanced tumours.

Investigating the molecular mechanisms of micrometastasis and tumour dormancy in pediatric sarcoma

Sarcomas are an aggressive type of childhood cancer arising from bone or soft tissue. Despite advances in cancer treatment, sarcomas remain a deadly disease because of their tendency to spread throughout the body (metastasis). Following cancer surgery to remove a malignancy, remnant sarcoma cells are often able to remain dormant in the body for months or years, in spite of efforts to eradicate them with chemotherapy. When such therapies are ineffective, these hibernating cells may revive and regrow as deadly metastases. Under laboratory conditions, cultured cancer cells are able to survive for long periods in the form of multi-cellular clusters called “”spheroids””. Interestingly, these spheroids also appear to enter a hibernation state, with cancer cells trading away their ability to grow rapidly in favour of the ability to survive for long periods. The cells use their “oncogenes” to suppress the expression of their growth-promoting genes, despite the fact that oncogenes are normally known for their cancer-promoting properties. It is believed that cancer cells and their oncogenes target a new set of genes to drive this hibernation. Tony Ng is screening all human genes for ones important in maintaining this hibernation. Using a technique called gene expression profiling, he will determine which genes become more active when cancer cells hibernate. He is also studying two genes, TXNIP and YB-1, which appear to be important for spheroid survival and dormancy. Laboratory results will be validated using clinical samples of dormant tumour cells from childhood cancers. Ng hopes that the genes identified in these studies will become the basis of chemotherapies to specifically kill these hibernating cells, resulting in therapies that are more effective and less toxic to patients.