April 1, 2020
OICR-supported researchers quantify common prostate cancer outcome predictor
Advances in cancer research have opened the door to new tests to better assess tumours and help recommend the most appropriate course of treatment for a patient. Research pathologists play a critical role in turning scientific knowledge into tests that can be used in an everyday clinical setting.
“Scientists are constantly advancing our understanding of cancer, but that understanding cannot help patients unless it’s applied in practice,” says Dr. Tamara Jamaspishvili, Research Pathologist at Queen’s Cancer Research Institute. “Our role as research pathologists is to bridge that gap, and transform discoveries into more accurate diagnoses and prognoses for patients that could be implemented and actionable in practice.” Jamaspishvili’s work is supported by the Ontario Molecular Pathology Research Network, an OICR-funded province-wide network that conducts high-quality cancer research focussed on clinical impact.
An example of the challenge of clinical translation is found in PTEN testing. PTEN is a cancer-preventing gene that – when absent in a cell – may lead to uncontrolled tumour growth. Research has shown that the loss of PTEN within a prostate tumour could help predict the severity of a man’s prostate cancer, but PTEN is not routinely tested.
“Simply put, some cells in a tumour sample may have PTEN loss and some cells don’t, but nobody has clearly quantified how the ratio of cells with or without PTEN contribute to a patient’s health,” says Jamaspishvili.
Jamaspishvili teamed up with collaborators to address the subjectivity of PTEN testing. Her collaborators include Drs. David Berman, Palak Patel, Robert Siemens, Paul Peng, and Yi Niu from Queen’s Cancer Research Institute, Drs. Fred Saad and Anne-Marie Mes-Masson from the University of Montreal, Dr. Tamara Lotan from Johns Hopkins University, and Dr. Jeremy Squire and colleagues at the University of São Paulo.
Their study, recently published in the Journal of the National Cancer Institute, proposes a new quantitative approach to assess PTEN. They clarify how pathologists can predict the severity of a patient’s prostate cancer based on the number of cells with PTEN loss. These findings can help standardize PTEN testing, but their approach can also be applied to other pathology tests that are still highly subjective.
“Quantifying qualitative tests helps us move towards automated pathology techniques,” says Jamaspishvili. “This is the future of pathology.”
Jamaspishvili is now working to automate PTEN digital pathology analysis in collaboration with Dr. Stephanie Harmon and colleagues in Dr. Baris Turkbey’s lab as part of the National Cancer Institute’s Molecular Imaging Program.
“Now, we can apply machine learning image analysis tools to analyze PTEN loss and make better predictions for the benefit of patients. We look forward to using artificial intelligence in digital pathology to help fill the gaps between research and clinical practice.”
October 21, 2019
Internationally-recognized computational biologist, Dr. Anna Panchenko joins OICR as Senior Investigator
OICR welcomes Dr. Anna Panchenko, Tier I Canada Research Chair, to Ontario’s cancer research community as OICR’s newest Senior Investigator
Recently recruited to Canada as a Tier I Canada Research Chair and OICR Senior Investigator, Dr. Anna Panchenko has chosen to establish her lab at the Department of Pathology and Molecular Medicine, Queen’s University School of Medicine. OICR is proud to support Panchenko and her research endeavors with a Senior Investigator Award, which is given to researchers who have achieved national and international excellence and spent more than 10 years as independent investigators.
Panchenko joins the local research community with nearly two decades of experience at the National Institutes of Health’s National Center for Biotechnology Information. She is internationally recognized for her expertise in using computational biology to study cancer genomics and epigenetics, protein-protein interactions and nucleosome dynamics. Her methods have been widely used by thousands of scientists from around the world.
Here, she discusses her work and the opportunities that Ontario provides.
What is your research about?
Generally, there are two prongs to my research focus. The first is investigating cancer-related mechanisms. We’re looking at how mutations accrue – or accumulate – in cancer cells, which mutations are driving carcinogenesis and how these mutations may affect proteins and their interactions. The second is looking into how chromatin is dynamically regulated at a molecular level.
Both of these avenues are important to our understanding of cancer, and both areas of study need new computational methods and techniques. My group develops these methods and algorithms to better understand cancer progression to possibly come up with new targeted therapeutic strategies.
For example, some of my work focuses on identifying cancer-driving mutations – the changes in DNA that are at the root of cancers. Out of hundreds of point mutations, there are only a few that drive the disease. If we can find these mutations, we can discover new ways to predict the course of a patient’s disease, or new ways to treat the disease.
What excites you about your work?
I am excited by the beauty and complexity of biological systems. I am also excited by working with the dedicated, curious and smart people in our scientific community. My work isn’t just about making discoveries, it’s about designing methods to help other researchers to make their own discoveries.
What drew you to this field?
I grew up in Moscow and I was always interested in math and biology as a child. I was motivated to pursue science by my parents who are both scientists and the field of computational biology was a perfect combination of my two interests. Throughout my career, I met several other scientists who impressed me with their integrity, behavior and dedication to science. They inspired me to continue along this difficult but very gratifying path.
Why were you interested in coming to Canada? What’s next?
I love Canada, it feels like home. I’m now minutes away from Lake Ontario in a community of incredible scientists and clinicians. I feel like there are a lot of exciting opportunities here and I’m proud to be working in a high-caliber work environment. I appreciate the support from the government and I love the culture of collaboration. I’m excited to strengthen my collaborations with researchers at different departments of Queen’s University and across Ontario.
October 8, 2019
OICR is proud to welcome Dr. Tricia Cottrell to Ontario’s cancer research community.
Dr. Tricia Cottrell, who is an immunologist and pathologist by training, is focused on the interplay between cancer cells and the immune system. She maps these complex interactions, as patients undergo treatment, to develop new biomarkers that can better predict the course of a patient’s disease.
Joining OICR from Johns Hopkins University in Baltimore, MD, Cottrell brings unique expertise in studying the tumour immune microenvironment, specifically in lung cancer. Here, she discusses her transition and her new appointments at the Canadian Cancer Trials Group, Queen’s University and OICR.
How did you become interested in the field of immuno-oncology?
The idea of harnessing the immune system to control and eliminate cancer fascinates me.
My PhD research on the autoimmune disease scleroderma left me eager to find ways to study immune responses in human tissue. While pursuing this research through my anatomic pathology residency, I stumbled upon the revolution happening in cancer immunotherapy. There are a lot of interesting intersections between cancer immunology and autoimmunity, and I knew I wanted to dig in.
What problems and questions are you working to solve?
Generally, I look at different features of the immune response to cancer and find patterns in these features that are associated with a response to therapy. I’m addressing the question: can we predict which patients are most likely to respond to treatment?
When we have tools to answer that question, we can help patients decide which treatment is best suited for their unique disease.
How are you addressing those big questions?
As a pathologist, I start with simple observations made through a microscope. Then, I use techniques like multiplex immunofluorescence to understand the cells and molecules driving the patterns I see in the tissue. Finally, I integrate these observations with other –omics analyses of the same sample, like DNA or RNA profiling, in pursuit of better biomarkers. The ultimate goal is to have biomarkers that can accurately predict which therapy or combination of therapies is most likely to empower a patient’s immune system to eliminate their cancer.
Through these studies, we also identify patterns and molecular characteristics in the tumours of patients who respond poorly to treatment. We can use this knowledge to find mechanisms of resistance, or the ways that the cancer can evade treatment. Then we can develop new therapies to address these mechanisms.
You’ve been recognized and awarded for your research on several occasions. What is an achievement that most people don’t know about?
I never anticipated that my research as a pathologist would lead me to analyzing big data. I’m quite proud that I learned some computer programming and I continue to integrate new technologies and cutting-edge analytic approaches into my research.
A specific achievement I am proud of is developing a method to measure the response of lung cancer patients to checkpoint blockade therapy using microscopic features of their tumours. This method is now being validated in a large clinical trial and has been shown to work in other cancer types as well. We are currently investigating its potential as a pan-tumour biomarker that would allow unprecedented standardization of clinical trials across different cancer types.
Why did you choose to relocate to Kingston?
I was looking for an opportunity to expand my research focusing on patients enrolled in clinical trials. Kingston offered that opportunity through an appointment with the Canadian Cancer Trials Group (CCTG), which is based at Queen’s University where I am also an Assistant Professor.
At CCTG, I get to participate in the design of clinical trials, including arranging tissue collection and planning the correlative science (the study of the relationship between biology and clinical outcomes) that goes along with those trials. My goal is to make sure my research will be translatable to the clinic, or in other words – to find solutions that can be applied in practice.
I’m also personally very excited about the opportunity for my family to be here in Canada.
What are you looking forward to over the next year?
I look forward to maintaining my existing collaborations while broadening my research scope. I’ll be working to establish a laboratory-based platform that produces high-quality, large-scale multiplex immunofluorescence data from tumour tissue specimens. I also look forward to laying the groundwork for a data integration and analysis pipeline for tissue-based immunology studies.
Most of all, I’m excited to begin growing my own lab group. I hope to foster a collaborative team environment with individuals from diverse backgrounds in pathology, biology, immunology, bioinformatics and more.
April 13, 2017
Breast cancer is the most common form of cancer amongst women in Canada and worldwide, but despite its prevalence, a group of researchers believes that it should often be treated as a rare disease. Doing so would change clinical approaches and improve treatment for patients.
November 9, 2016
Men newly diagnosed with prostate cancer face a difficult dilemma: either wait and see how the growth develops and whether it is aggressive, or treat it fully right away and risk the many long-term side effects of treatment. Dr. Tamara Jamaspishvili is a young researcher at Queen’s University in Kingston who is working to change that.
September 29, 2016
Today OICR announced the launch of the Ontario Molecular Pathology Research Network (OMPRN), which will be based at Queen’s University and will bring together pathologists across the province.
Pathology is key to the early detection, diagnosis and treatment of cancer. An accurate diagnosis can provide better prognostic information and allow doctors to better target therapies. Pathology research can also lead to the development of new treatments that target specific cancer-driving mutations, genes and pathways, reducing the need for treatments with unwanted side effects.
August 17, 2016
Toronto (August 17, 2016) – Mr. Peter Goodhand, President of The Ontario Institute for Cancer Research (OICR), today announced a new collaborative research study in partnership with Thermo Fisher Scientific and Queen’s University to help bring more targeted diagnosis and treatment to breast cancer patients in the future.