Research Location: BC Cancer Research Centre

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.

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.

While the fundamental unit of life is the cell, it is the cell’s DNA which instructs how a cell is to function. These microscopic blueprints can be read. Reading DNA sequences has enabled genes to be identified and revealed insights about the causes of many human diseases such as Huntington’s and numerous cancers. Reading and understanding how DNA functions, however, is only half the challenge in genetics research. To correct genetic errors accumulated in diseased genes, it is necessary to also write in DNA. But while DNA is essential in all genetics research, it is difficult to produce. Methods to rewrite or create new DNA sequences from scratch are limited. Regions of DNA can be copied, but there are relatively few methods of generating new fragments. Nucleotides are the characters of the DNA language. A 1,000 nucleotide gene costs approximately $1,000 to construct. Given that the average human gene is more than 3,000 nucleotides long, and that regulatory regions of DNA can be tens of thousands of nucleotides long, the cost of producing DNA becomes daunting. Daniel Horspool is researching a new laboratory technique for DNA construction. While the primary method involves adding one nucleotide at a time chemically to the growing sequence, the new technique relies on stitching multi-nucleotide fragments together in parallel. This process could be much faster and less error prone than the conventional method, and by using microfluidic devices, DNA could be produced at a much lower cost. The research could lead to an approach for constructing complete genes, which would be an important new tool for basic and applied biomedical research. The research could ultimately contribute to efforts to realize the promise of genomic and personalized medicine.

Flow cytometry (FCM) is a method of sorting and measuring types of cells by fluorescent labelling of markers on the surface of the cells. It plays a critical role in basic research and clinical therapy in the areas of cancer, HIV and stem cell manipulation. For example, it can be used to diagnose some types of cancer, based on which labelled antibodies bind to a particular cell’s surface. It is widely recognized that one of the main stumbling blocks for FCM analysis is in data processing and interpretation, which heavily relies on manual processes to identify particular cell populations and to find correlations between these cell populations and their clinical diagnosis and outcome (e.g. survival). Manual analysis of FCM data is a process that is highly tedious, time-consuming (to the level of impracticality for some datasets), subjective and based on intuition rather than standardized statistical inference. Dr. Ali Bashashati has developed a “pipeline” for automatic analysis of FCM data – a computational platform that can identify cell populations, find biomarkers that correlate with clinical outcomes, and label the samples as normal or diseased. Preliminary evaluations of this pipeline have shown accuracy levels of more than 90 per cent in identifying some sub-types of lymphoma. Moreover, a biomarker that contributes to a more aggressive behaviour of a specific sub-type of lymphoma has been discovered. Bashashati is now testing and refining the platform to improve its analytical power and applicability to a range of FCM data, testing its performance across a number of ongoing FCM studies in BC. Ultimately, he hopes to provide an accurate, powerful computational platform to increase the efficiency of using FCM for research and clinical purposes.

Non-Hodgkin lymphoma (NHL) is a specific type of cancer where an abnormal growth of immune cells produces what is known as a lymphoid tumour. Since the 1970s, NHL has become increasingly common, indicating that lifestyle and environment are likely causative factors. However, certain individuals may also have a genetic make-up that makes them more susceptible. NHL tumours often show a type of DNA damage called a translocation, where two chromosomes are incorrectly joined together. In NHL tumours, translocations are generally found near genes that are important for the development of immune cells. They cause changes in how these genes are regulated (turned on or off), that result in abnormal cell growth. Certain genes are responsible for repairing damaged DNA. If these genes are not functioning properly, DNA breaks will not be repaired and harmful translocations may occur. Previous studies have found that a common DNA sequence change at one of these DNA repair genes, called H2AX, was much more frequent among the NHL patients than unaffected individuals. Individuals who carry this gene variant have twice the risk of NHL as those who do not carry it. Dr. Karla Bretherick is interested in how common genetic variants influence risk for complex diseases. MSFHR has previously funded her graduate training, which involved studying the genetic factors that contribute to premature menopause. Now, she is looking at why individuals with the H2AX gene variant have increased risk of NHL. She will look at how this DNA sequence change affects H2AX gene regulation, modifies protein binding, and affects the ability of the cell to repair DNA damage. Ways to understand, prevent, and avoid NHL and other cancers are of increasing importance for the Canadian healthcare system. Understanding how and why this specific gene variant increases risk for NHL will lead to a better knowledge of how this cancer develops. This information will eventually be useful for identifying new drug targets and therapies for NHL, and may also provide insight into the development of cancers in general.

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.

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.

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.