Decoding Cancer Through Epigenetics



Conquer cancer by treating it as an epigenetic/chromatin disease.

Our five strategic priorities

Our culture

We embrace diversity as our greatest asset. It spurs our creativity, galvanizes our collaborations and drives our innovations.

Our four organizational pillars

"De notre multitude naît notre richesse."

- Elisapie

Why chromatin & epigenetics

“Cancer is a disease of the chromatin, because the genetic contributions to phenotypes are entrusted to the chromatin.” - Mathieu Lupien Ph.D.

A human consists of trillions of cells with different functions to form different tissues & organs. While genetic differences account for the phenotypic traits unique to individuals, cells from different tissues & organs isolated from one individual each carry a copy of the same genome, a sequence of 6 billion DNA base pairs. Cells across tissues & organs appear and function very differently from one another because each uses different sections of the 6 billion DNA base pairs they carry.

In cells, DNA is packaged with proteins to form chromatin. Chromatin ranges from being “compacted” to “accessible”, the latter associated with sections of the genome driving cell identity. Tissues & organs develop from gradual changes in chromatin accessibility occurring over different DNA base pairs in a stem cell that differentiates into one of many mature cell types. While some DNA base pairs fall in compacted chromatin, others will lie in accessible chromatin to serve as templates for biological functions. Along the way, changes to chromatin accessibility are bookmarked with hundreds of different chemical modifications, such as DNA methylation. These chemical modifications are commonly referred to as “epigenetic” marks. Different combinations of these epigenetic marks over sections of DNA define epigenetic states. Epigenetic states differ across accessible and compacted chromatin and provide information complementary to DNA sequences. DNA base pairs that transition between chromatin accessibility or epigenetic states over development correspond to chromatin variants. Identifying chromatin variants specific to a cell type can therefore identify the genetic basis of a cell’s phenotype.

Cancer is a disease of the chromatin because it arises when a patient’s normal cell acquires the wrong chromatin variants, such as when a normal cell loses control over which sections of the genome are in accessible versus compacted chromatin. Such chromatin variants can originate from inherited or acquired genetic variants, including risk-associated single nucleotide polymorphism (SNPs) or somatic mutations respectively. They can also originate from environmental stresses, such as metabolic stress. Cancer-specific chromatin variants reveal which misused DNA sequences contribute to oncogenesis. Understanding the nature of DNA sequences found in cancer-specific chromatin variants reveals genetic dependencies to oncogenesis and by extension the Achilles heel of cancer needed to guide precise treatment decisions. This is why our research is focused on chromatin and the epigenetics of cancer.

Finding the determinants of cancer cell states from chromatin variants

Tumours are composed of cancer cells in different states, that differ in their ability to propagate. Cancer stem cells (CSCs), also known as Tumour Initiating Cells are the most dangerous type because of their ability to self-renew and seed new or recurrent tumours. Our goal is to study the chromatin & epigenetic states of CSCs to identify the DNA sequences that allow for self-renewal and tumour initiation. From these DNA sequences we can find the determinants of cancer stemness and use this information to guide the development of new therapies specifically aimed at eliminating the seeding cells.

Cancer types: Leukemia, Glioblastoma, Breast and Prostate Cancer

Defining how chromatin state impact the function of mutations in cancer

Cancer is commonly conceived to be a genetic disease, with mutations taking centre stage. However, not all mutations drive cancer development. Our goal is to identify cancer driver DNA elements, taking into account the mutational load within chromatin state defined DNA elements, such as regulatory elements, gene regulatory plexus or cistromes. This work is required to find mutations that can guide precision medicine based on genetic markers.

Cancer types: Prostate and Breast Cancer

Developing chromatin-guided targeted therapy against aggressive forms of cancer

Standard therapy fails for too many cancer patients and leads to deadly recurrent tumours. Our goal is to identify weaknesses in recurrent tumours based on chromatin variants and characterize their epigenetic and genetic composition. Based on their composition, we then identify weaknesses to therapies by repurposing existing drugs or guiding the design of new agents.

Cancer types: Triple-Negative (TNBC) and Proliferative ER-positive Breast Cancer

"Le merveilleux est la source de l’imaginaire"


Lupien lab github



“We embrace diversity as our greatest asset. It spurs our creativity, galvanizes our collaborations and drives our innovations.”


Dr. Mathieu Lupien

"I commit to creating an environment that gets the genius out of the box of those around me and lays the foundation of their professional advancement."

  • Post-doctoral fellow – Dana-Farber Cancer Institute/Harvard Medical School, Dr. Myles Brown alumnus
  • PhD – McGill University, Experimental Medicine, Dr. Sylvie Mader alumnus
  • PLDA – Harvard Business School alumnus

Dr. Mathieu Lupien is a Senior Scientist at the Princess Margaret Cancer Centre, a Professor at the University of Toronto and holds a cross-appointment with the Ontario Institute for Cancer Research. He serves on the Research Executive and the Research Council on Oncology to the Princess Margaret Cancer Centre.

Dr. Lupien’s research is demonstrating that cancer is a disease of the chromatin. Amongst key discoveries, Dr. Lupien’s research revealed a new type of genomic variation, known as chromatin variants, to pioneer the identification of cancer drivers in the non-coding cancer genome. His work also showed that cancer-specific chromatin variants could support oncogenesis independently of genetic variants (mutations). Finally, Dr. Lupien’s research showed the efficacy of epigenetic therapy that targets chromatin variants to block cancer development and progression. Among other honours, Dr. Lupien is a recipient of the Allan Slaight Collaborator Award, the Mona Gauthier Award, the Canadian Cancer Society Bernard and Francine Dorval Award for Excellence, a three-time recipient of the Investigator Award from the Ontario Institute for Cancer Research, is a two times recipient of the Till and McCulloch Discovery of the Year award and co-founder of CoBE.

Dr. Lupien earned his PhD in experimental medicine at McGill University under the leadership of Dr. Sylvie Mader and carried out postdoctoral training in medical oncology as an Era of Hope Fellow at the Dana-Farber Cancer Institute/Harvard Medical School under the mentorship of Dr. Myles Brown followed by a PLDA at Harvard Business School. Dr. Lupien joined the Princess Margaret Cancer Centre and the University of Toronto in 2012.

Email: mlupien(at)

Image Image Image Image Image Image

Lab diversity

Lab Members


Natalia Mukhina

Administrative Assistant

Email: Natalia.Mukhina(at)


Tina Keshavarzian

PhD Candidate (2020/09-present)

Research interest: Epigenetics, Breast cancer, and Computational biology


Shalini Bahl

PhD Candidate (2020/01-present)

Research interest: Triple-negative breast cancer, GBM, and chemoresistance.


Jocelyn Chen

PhD Candidate (2019/01-present)

Research interest: Triple-negative breast cancer, chemoresistance.


Chufan Zhang

PhD Candidate (2021/11-present)

Research interest: Breast cancer, chemoresistance.


Dr. Chu Pan

Post-doctoral fellow (2021/10-present)

Research interest: Single cell multi-omics.


Dr. Lisanne Mout

Post-doctoral fellow (2021/07-present)

Research interest: Prostate cancer.


Dr. med. Kira Kornienko

Visiting Post-doctoral fellow (2020/11-present)

Research interest: Urooncology, Prostate cancer, Precision medicine, Epigenetics.


Dr. Catherine Xu

Post-doctoral fellow (2021/08-present)

Research interest: Breast cancer.


Dr. Gislaine Curty Ferreira

Post-doctoral fellow (2023/11-present)

Research interest: Transposable elements.


Mostafa Shahhosseini

Research Intern (2023/08-present)

Research interest: Computational Biology.


Komaldeep Kaur Kang

Research Technician (2024/04-present)

Research interest: Cell Assay Development.


Ankita Nand

Bioinformatician (2020/02-present)

Research interest: Data analysis and pipeline development.




Bansri Patel

Research Technician (2019/04-2024/03)


Khrystany Isebia, MD

Visiting scientist (2023/05-2023/07)
Current: PhD candidate Medical Oncology
Erasmus University Medical Center


Kyle White

Summer Student (2022/05-2022/12)


Lucie Cressot

Intern Student (2022/01-2022/07)
Current: PharmD - ENS de Lyon,
Institute for Pharmaceutical Sciences and Biology


James Hawley

PhD Candidate (2017/01-2021/12)
Current: Computational Biologist,


Stanley Zhou

PhD Candidate (2016/01-2020/05)
Current: Arsenal Bio


Seyed Ali Madani Tonekaboni

PhD Candidate (2016/01-2020/03)
Current: Cyclica


Parisa Mazrooei

PhD Candidate (2014-2019/09)
Current: Genentech


Ingrid Kao

MSc student (2015-2017)
Current: Law student


Aislinn Treloar

MSc student (2013-2016)
Current: Exopharm Ltd, Australia


Kinjal Desai

PhD Candidate (2011-2016)
Current: Post-doctoral fellow, SickKids


Surbhi Goel-Bhattacharya

PhD Candidate (2010-2012)
Current: Intellia Therapeutics


Xiaoyang Zhang

PhD Candidate (2009-2013)
Current: Assistant Professor, Huntsman Cancer Centre, University of Utah, USA


Richard Sallari

PhD Candidate (2009-2012)
Current: Retired… for now


Dr. Giacomo Grillo

Post-doctoral fellow (2018/01-2023/01)
Current: Senior Scientist
T-ONE Therapeutics


Dr. Sarina Cameron

Post-doctoral fellow (2017/01-2022/12)


Kip Arlidge

Research Technician
Current: Professor,
Canadore College


Dr. Qin Wu

Post-doctoral fellow (2016/03-2020/12)
Current: Assistant Professor, Institute of Basic Medicine and Cancer, Chinese Academy of Science, China


Dr. Nergiz Dogan Artun

Post-doctoral fellow (2016/11-2020/10)


Dr. Bettina Nadorp

Post-doctoral fellow (2019/01-2020/01)
Current: Assistant Professor, New York University


Dr. Aditi Qamra

Post-doctoral fellow (2018/01-2019/04)
Current: Roche


Dr. Genevieve Deblois

Post-doctoral fellow (2015/01-2018/11)
Current: Assistant Professor, Université de Montréal


Dr. Paul Guilhamon

Post-doctoral fellow (2015/01-2018/08)
Current: Principal Scientist at Boehringer-Ingelheim


Dr. Alexander Murison

Post-doctoral fellow (2014/09-2018/04)
Current: Post-doctoral fellow, UHN


Dr. Ken Kron

Post-doctoral fellow (2013/01-2018/06)
Current: Deep Genomics


Dr. Swneke D. Bailey

Post-doctoral fellow (2012/01-2016/12)
Current: Assistant Professor, McGill University


Dr. Marco Gallo

Post-doctoral fellow (2012-2015)
Current: Assistant Professor, University of Calgary


Dr. Nadia M. Penrod

Post-doctoral fellow (2013-2015)
Current: Post-doctoral fellow, University of Pennsylvania


Dr. Xue Wu

Post-doctoral fellow (2013-2014)
Current: CEO at Geneseeq


Dr. Luca Magnani

Post-doctoral fellow (2009-2013)
Current: Professor, Imperial College London


Join us

The Lupien Lab offers a multi-disciplinary team setting. The lab brings together enthusiastic scientists with diverse backgrounds, providing a wide range of perspectives to each research project. This translates into the ideal research environment to push the boundaries of our imagination. Prospective post-doctoral fellows should send their C.V. along with three references to Dr. Mathieu Lupien by email at mlupien(at)

Prospective graduate students (MSc or PhD candidates) interested in joining the Lupien Lab first need to register through the Department of Medical Biophysics, part of the Temerty Faculty of Medicine
 at the University of Toronto.


Scientific Talks

Lupien lab YouTube channel


Lupien lab playlist



Mathieu Lupien Research Laboratory
Princess Margaret Cancer Centre
University Health Network
University of Toronto,
Department of Medical Biophysics

The MaRS Center, PMCRT room 11-706
101 College Street,
Toronto, ON,
M5G 1L7, Canada
Email: mlupien(at)
Email: Natalia.Mukhina(at)