Mutational drivers of metastatic colorectal cancer

Each human cell contains instructions — in the form of genetic material or the genome — to direct its growth, function and death. The genome is made up of three billion molecules called nucleotide pairs, which are joined in a specific sequence. Sometimes the nucleotide sequence in a cell’s genome can become altered, or mutated, and these mutations can lead to changes in the cell that cause cancer. The spread of cancer cells from the primary tumor is known as metastasis. Relatively little is known about the mutations in the genome that create, control and direct metastasis. Next-generation sequencing allows researchers to rapidly “read” the sequence of the three billion nucleotide pairs in the genome of cancer cells. Using this technology, Dr. Jill Mwenifumbo aims to identify the sequence mutations that are unique to, and perhaps essential for, colorectal cancer metastasis. Ultimately, discovering the genetic mutations that drive metastasis will help identify potential drug targets, which will lead to more effective treatments for this disease. Given that colorectal cancer is the second leading cause of cancer death in Canada, effective treatment has enormous potential to improve personal and population health.

Investigating the role of endometriosis-associated inflammatory signalling in ovarian clear cell carcinoma development

Ovarian cancer is the most lethal cancer of the female reproductive system and the fifth leading cause of cancer-related death in Canadian women. Ovarian cancer is not one disease, but rather comprises several tumour types that likely develop through unique mechanisms from different cell types. Previous research suggests two types of ovarian cancer — clear cell carcinoma (CCC) and endometrioid carcinoma (EC) — may develop from ovarian endometriosis, a condition associated with increased inflammation. Dr. Alicia Tone is investigating how endometriosis-associated inflammation can influence the development of CCC and EC by looking at the specific role that the ARID1A gene plays in inflammation. ARID1A has been shown to increase the activity of the glucocorticoid receptor, which plays a crucial role in reducing the duration and intensity of an inflammatory response. In addition, the ARID1A gene was recently found to be mutated in both CCC/EC, and the mutated gene is associated with endometriosis lesions. Dr. Tone intends to 1) identify which specific inflammatory genes are altered in CCC/EC cells and associated endometriosis; 2) compare the response of cells obtained from endometriosis and CCC specimens with and without mutations in the ARID1A gene; and 3) determine the mechanism by which ARID1A regulates the response to inflammatory mediators. This study will help our understanding of how endometriosis may develop into ovarian cancer (CCC and EC); more importantly, pointing to the development of new preventive strategies. Research aimed at understanding what is involved in the early stages of development of these different cancers may reduce the number of deaths associated with ovarian cancer.

Identification of antigens for disease associated public T-cells

Circulating T-cells are the key players in our adaptive immune system and are particularly important for recognizing and killing cells that are infected with viruses or carry cancer-causing mutations. T-cells have the ability to potentially recognize vast numbers of different infectious agents and cancer- or tumour-associated mutations. The T-cell receptor, on the surface of the T-cell, is responsible for this task, and the variation required for recognition is generated mainly by shuffling the large number of short DNA segments that comprise T-cell receptor genes. Although the central importance of the T-cell receptor in adaptive immunity is well established, the actual number and diversity of T-cells that exist in an individual (i.e. the T-cell repertoire), how this changes in response to immune challenge, and how it varies from one individual to the next, remains a mystery. Dr. Rob Holt’s lab is using the latest DNA sequencing technologies to directly sequence T-cell receptor genes in order to examine the T-cell repertoire in a given blood sample. Using this approach, the lab has identified populations of unique T-cell repertoires in bone marrow stem cell transplant patients and in colorectal cancer patients. Dr. Kristoffer Palma’s research project is to take this approach one step further by developing a novel, high-throughput screen for the molecular patterns (antigens) recognized by donor T-cells and to find out how these are related to transplant success in bone marrow transplants. The second application of his research is to determine if there are T-cell receptor commonalities in patients with colorectal cancer tumours, how T-cell receptor commonalities relate to disease prognosis, and what tumour-associated antigens may be recognized by T-cells in patients with high survival rates. In the case of bone marrow transplants, Palma anticipates that his research will lead towards the earlier diagnosis and intervention in graft versus host disease, which is the most immediate and life-threatening complication of bone marrow transplant, affecting 30 to 80 per cent of patients. With regard to colorectal cancer, Palma hopes his research will contribute to the creation of a high-resolution diagnostic screening test to identify early stage cancer that would be undetectable with current assays and aid in the eventual development of cancer-specific vaccines.

Investigation of breast cancer genome heterogeneity in predictive models of drug action

A common method of testing new cancer drugs is to use human breast tumour cells that have been transplanted into mice. How this transplantation process and drug treatments affect the grafted cells is not known. In particular, we need to know if certain types of mutation within the tumour may survive the process of engraftment better than others, resulting in a transplanted tumour that has a different composition and different properties from the original human tumour. Dr. Peter Eirew's aim is to study in detail how the “landscape” of different gene mutations in the tumor evolves when tumour cells undergo transplantation and subsequent treatment with anti-cancer drugs. Dr. Eirew will sequence the entire DNA and RNA (a measure of the active genes in a cell) of breast cancer patients' tumours before and after transplantation into mice to see how the frequency of each mutation changes over time. Dr. Samuel Aparicio's group has already read the entire DNA sequence of human breast cancer — both the original tumour and a recurrence in a different part of the patient's body nine years later — and showed that the type and frequency of the mutations changed over time. In the second part of the study, he will sequence these human tumour cells before and after the drug treatment to determine the types of mutations that survive. This will set the stage for a follow-on clinical study to determine how closely the drug response of these human cells predict how tumours in patients respond to the same drugs. This study will be the first attempt to define how grafted breast cancer cells behave in mice and how this behaviour is affected by the choice of grafting methods and treatment with existing drugs. This information will be used to improve the methods that are currently used to test potential new cancer drugs, with the ultimate aim of bringing new breast cancer treatments into routine use more quickly than in the past. Knowing the types and combination of mutations that are present in a tumour and how this combination changes during treatment will be the key to developing new and more effective drugs. The study may also identify new mutations in breast tumours, which have the potential to answer more specific questions about how these cancers arise, progress and become resistant to treatment.

Investigating biochemical signatures of radiation resistance in human breast and prostate cancers via single cell Raman spectroscopy

Radiation therapy is the recommended treatment for about one-third of all cancer patients, including those with breast and prostate cancer. One factor limiting the use of radiation therapy is the considerable difference in radiation response between patients. There are currently no proven biochemical or imaging methods to assess a cancer patient's radiation response during an extended radiation therapy treatment. There is a need to develop customized radiation treatments to accommodate the variations in radiation response from individual patients; however, implementing such personalized treatments requires a better understanding of the fundamental biochemical responses of human tumour cells to ionizing radiation. Dr. Quinn Matthews is investigating the use of Raman spectroscopy as a way to monitor radiation responses in cancer patients undergoing radiotherapy. Raman spectroscopy is a non-invasive technique that shows great promise for the biochemical analysis of cellular radiation responses, as it can provide sensitive molecular information from biological samples, such as human cells or tissues. Recent laboratory studies have shown that single-cell Raman spectroscopy techniques applied to irradiated cells can detect radiation-induced changes in certain proteins, lipids and nucleic acids within human prostate, breast and lung tumour cells. These results suggest that certain types of radiation-induced biochemical changes measured with Raman spectroscopy are correlated with tumour-cell resistance to radiation treatment. The goal of Dr. Matthews' research project is to apply the proven capabilities of Raman spectroscopy to investigate the biochemical radiation response of a variety of human breast and prostate cancers, irradiated both in vitro (in the lab) and in vivo (in the organism). The results of this research will lead to increased effectiveness of radiation therapy by facilitating the development of personalized adaptive treatments designed to account for individual radiation response.

Functional characterization of MLL2 mutations in follicular and diffuse large B-cell lymphomas

Lymphomas are cancers of the immune system. Canadian cancer statistics estimated around 8,100 newly diagnosed cases and 3,300 deaths from lymphoma in 2009. Lymphomas develop as the result of errors, or mutations, in the proteins that regulate the rate of cell division. These types of mutations are found in many different cancer types; however, certain mutations are found only in a specific cancer type. When the same mutation is found in several patients of a specific cancer type, it is likely to be a cancer-causing or cancer-driving mutation. The aim of Dr. Maria Mendez-Lago’s research is to investigate the impact of mutations found in the gene MLL2 on the formation and progression of lymphomas. Her research team discovered mutations in MLL2 by using next-generation sequencing of 127 non-Hodgkin lymphoma cases. Based on the pattern and distribution of the mutations, they believe MLL2 is a new tumour suppressor that might be acting through de-regulation of gene expression. Next-generation sequencing has allowed Dr. Mendez-Lago’s team to do whole genome, exome, and transcription sequencing using limited amounts of DNA from cancer tissues – an approach that was not possible only four years ago. They are applying this technology to different applications, such as the targeted sequencing approach used to detect mutations in MLL2. MLL2 has only recently been linked to cancer, so there is a great need to study the gene in further detail to understand how mutations in this gene promote cancer. To explore the impact of these mutations, Dr. Mendez-Lago’s team will culture and study all lines similar to the cancer cells from patients. Their findings will likely determine new candidates for designing drugs to treat cancers.

Identification and characterization of leukemia stem cells in T-cell acute lymphoblastic leukemia (T-ALL)

The traditional view of cancer is that tumours are composed of identical cells, and thus the goal of treatment is to kill every one of those cancer cells in the body. In a tumour, it is estimated that a very small fraction of cells (perhaps 1 in 10,000) are ""cancer stem cells"", which are the cells that have the capacity to self-renew or to create progeny that carry the same properties as the parent cell. A new cancer treatment theory hypothesizes that to treat cancer, the only cells that need to be killed off are these cancer stem cells, and once they are gone the rest of the tumour should regress on its own. The challenge becomes to first identify the cancer stem cells and then design a drug that would specifically kill those cancer stem cells only. Dr. Vincenzo Giambra's lab has recently shown that cancer stem cells exist in a particular type of blood cancer called T-cell acute lymphoblastic leukemia (T-ALL). Although T-ALL is not a common form of cancer, it is unique in that more than 50 per cent of cases carry mutations that inappropriately activate a gene called Notch1, which plays an important role in normal stem cell maintenance. Dr. Giambra's research objectives are to identify how cancer stem cells are able to evade the immune system and thrive in T-ALL, and to design a drug that specifically kills those cancer stem cells. He will be isolating cancer stem cells from a unique mouse model that has Notch1-induced T-ALL, using specific molecules on the surface of cancer stem cells. He will also compare leukemias generated from mice of different ages to see if they express different genes, with the goal of using this information to design new drugs that may help to cure more patients with leukemia. These studies will allow Dr. Giambra to define the genetic programs and pathways that are responsible for conferring self-renewal upon the leukemia stem cells; they will also provide rationale for the design of new therapies that specifically target the stem cells. In focusing his efforts toward killing only the cancer stem cells, Dr. Giambra expects these therapies will be more effective for achieving a cure and less toxic to the patient. Finally, he anticipates that some of the genetic programs and pathways he will identify will be critical for self-renewal of Notch T-ALL stem cells and may be important for self-renewal of all cancer stem cells in general. Thus, these results may prove useful to investigators studying other cancers as well.

Integrative analysis of epigenetic signatures in stem cells

The billions of cells in your body share the same DNA sequence and yet display a vast array of morphologies and functions. Understanding how this same genetic material is interpreted in diverse cell types remains a challenge. Epigenetic modifications are those that change how DNA is expressed without altering the genome sequence. For example, chemical modification of histones, the proteins that bind DNA into the large chromosome structures, can influence how genes are expressed.

In a related process, DNA itself can become methylated, which is typically thought to be a gene-silencing signal. Understanding how epigenetic modification influences gene expression has significant therapeutic potential and may provide us with insights into how we can disrupt abnormal cell divisions in cancer or promote self-renewal in stem cells for clinical use in repairing damaged or diseased tissue.

Dr. Cydney Nielsen aims to characterize epigenetic changes of stem cells, from which all other cells in the body arise. Stem cells can either self-renew to form identical daughter cells or can divide and differentiate into specialized cell types. Dr. Nielsen will use next-generation sequencing technologies and develop new data analysis techniques to examine the epigenetic changes and determine gene expression patterns in stem cells before and after differentiation.

Using these data sets, she will determine if characteristic epigenetic modification patterns exist for self-renewing cells. She will also use this information to determine if certain therapeutics are able to induce self-renewal in stem cells, to determine what the epigenetic changes are in this case, and if this ''reprogramming'' of cellular state opens up promising therapeutic applications. Such an approach will be valuable in evaluating the extent to which chemically induced cells have been reprogrammed and are appropriate for therapeutic use for regenerative medicine.

Bioinformatic approaches for the interpretation of cancer genomes

The rapidly developing field of genomics is providing increasingly powerful tools to investigate our genetic make-up and provide a fundamental understanding into how cells and organisms function. Previously funded by an MSFHR Scholar award, Dr. Steven Jones’ ongoing research focus is to apply genomic and bioinformatic technologies to cancer research. Next-generation DNA sequencing machines at Canada’s Michael Smith Genome Sciences Centre provide the underlying technology platform for Jones to conduct a number of studies that will expand our knowledge about the fundamental mechanisms underlying health and disease. Jones will develop a number of studies around three key themes: • Understanding the genetic changes present in human cancer cells, as compared to the normal human genome, to improve drug screening and testing methods. • Investigating the changes that occur in cells in response to drug treatments to identify ways to improve the efficacy of these drugs. • Using the mouse liver as a model, identifying active regions of the genome in order to further understand the functional elements within our genetic material and how, in concert, they are able to coordinate and maintain the activity of a tissue or organ.

Population-Based Genetic Studies of Cancer and Healthy Aging

The number of elderly Canadians is increasing as the baby boomers age. Insight into how to promote healthy aging, coupled with advice that can be provided to our population as it ages, will influence Canada’s healthcare costs, as well as the quality of life of a large segment of our population. Cancer and aging are intimately connected. Cancer incidence rises with age, and this increase accelerates dramatically over 60 years of age. Cancer and other aging-associated diseases like cardiovascular disease are thought to result from the interaction of numerous genetic and environmental or lifestyle factors. Population-based studies that use large groups of affected and unaffected individuals are now the preferred method to study the genetics of complex diseases. This program has clinical relevance and involves close collaboration with clinical experts to study healthy aging and two specific cancers, non-Hodgkin lymphoma and cervical cancer. The overall objective is to discover genetic factors that contribute to susceptibility to cancer or confer long-term good health. The program will use state-of-the-art genetic analysis methods, and over the next 5 years will expand these projects and add additional types of cancer. This coordinated study of cancer and healthy aging is a unique and innovative approach by which we will increase our understanding of the connection between cancer and aging and benefit from new knowledge regarding the basis of common aging-associated diseases like cancer. This research will lead to development of clinically useful markers that will help individuals avoid developing diseases as they age.