Decoding Cancer Through Epigenetics

Why chromatin & epigenetics

“Cancer is a disease of the chromatin, because the genetic contributions to phenotypes are entrusted to the chromatin.”

Pioneering the functional decoding of the non-coding cancer genome by revealing how chromatin determines genome interpretation, how genetic and environmental processes generate cancer-associated epigenomic variation, and how variation across both the unique and repetitive genome controls malignant cell states and drives cancer evolution.

Dr. Mathieu Lupien is a Senior Scientist at the Princess Margaret Cancer Centre, University Health Network, and Professor at the University of Toronto. His research has challenged the prevailing view of cancer as primarily a disease of genetic mutations by establishing that another layer of heritable information, the organization of DNA into chromatin, determines which portions of the genome a cell can use and, consequently, its identity and behaviour.

Dr. Lupien has pioneered the use of chromatin to functionally decode the non-coding genome, identify the regulatory consequences of inherited and somatic genetic variation, and uncover epigenomic alterations capable of driving malignant cell states. More recently, his work has defined how genetic alterations and environmental and metabolic pressures generate epigenomic variation that provides a substrate for cancer evolution, and has revealed a previously unrecognized role for the repetitive genome in controlling cancer-cell self-renewal and stemness. Collectively, his discoveries have helped move cancer research from cataloguing changes in DNA sequence to understanding variation in how the genome is interpreted.

The Work

The cells of the human body contain essentially the same DNA sequence, yet they acquire profoundly different identities because each uses different portions of that genome. Dr. Lupien recognized early that the organization of DNA around nucleosomes contains information that determines which genomic sequences are available for use by a particular cell.

In landmark work published in 2008, Dr. Lupien and colleagues demonstrated that the cell-type-specific function of the pioneer transcription factor FOXA1 is determined by the chromatin environment in which its DNA-recognition sequences reside. The study established that cell-type-specific regulatory elements could be distinguished by their chromatin state and that mapping these states could therefore provide a functional annotation of the non-coding genome. It showed that the same transcription factor can recognize the same DNA motif yet engage different genomic locations in different cell states because only selected sites are presented within a permissive chromatin context. This established chromatin as a fundamental layer of biological information that determines how the same genome is interpreted differently across cell types, thereby defining regulatory potential and cellular identity.

Dr. Lupien subsequently applied this principle to one of the major problems created by human genomics, understanding genetic variants that lie outside protein-coding genes. His group demonstrated that inherited cancer-risk variants preferentially reside within chromatin-defined regulatory elements and showed that individual variants can alter transcription-factor recruitment and gene regulation. He then extended this approach to mutations acquired during tumour development, demonstrating that somatic mutations distributed across non-coding regulatory elements can converge on the control of cancer genes. These studies helped establish a framework for interpreting genetic variation according to its function rather than simply its position in the DNA sequence.

This work also expanded the concept of what constitutes a cancer driver. Rather than requiring mutations to recur within an individual gene or at the same genomic position, Dr. Lupien and colleagues showed that alterations dispersed across multiple regulatory elements can converge on the same cancer gene or transcriptional program. This led to approaches that consider regulatory plexuses, comprising the regulatory elements controlling a gene, and cistromes, comprising the regulatory elements engaged by a transcription factor, as functional units in which cancer-driving alterations can accumulate.The work opened a route to identifying non-coding cancer drivers that are missed to conventional mutation-recurrence analyses.

A further challenge to the mutation-centred view of cancer came from Dr. Lupien's collaboration with Dr. Michael Taylor and colleagues studying pediatric ependymoma. Their work identified an aggressive childhood brain tumour characterized by profound epigenomic abnormalities despite an absence of recurrent genetic drivers, helping establish pediatric ependymoma as the first recognized human cancer driven predominantly by chromatin-based epigenomic alterations in the absence of recurrent genetic drivers. The finding demonstrated that disruption of genome interpretation, through epigenomic variations, can itself become a defining feature of malignancy rather than merely a downstream consequence of genetic mutation.

These discoveries prompted a further question, what generates cancer-associated chromatin variation? Dr. Lupien's work showed that both genetic alterations and environmental pressures can reshape the epigenome in cancer. His group demonstrated that structural variants can rewire chromatin states and regulatory activity across solid cancers. In triple-negative breast cancer, they showed that treatment-associated metabolic stress affecting the methionine cycle can drive epigenomic reprogramming during the acquisition of chemotherapy resistance. Work with Dr. Michael Taylor in pediatric ependymoma further connected the hypoxic tumour environment as a source of change to cellular metabolism to alter chromatin states.Together, these studies established metabolism as an important intermediary through which environmental pressures can reshape genome interpretation in cancer.

More recently, Dr. Lupien extended his studies to the repetitive genome. His group showed that transposable elements associated with pluripotent states can be reactivated and co-opted as oncogenic regulatory elements in solid cancer. In acute myeloid leukemia, working with Dr. John Dick and colleagues, his group demonstrated that epigenomic variation over transposable element distinguishes leukemia stem cells from differentiated cells and, through targeted chromatin editing, that specific elements are required to maintain leukemia stem-cell self-renewal.These discoveries established the repetitive genome as a previously overlooked reservoir of regulatory information capable of controlling pluripotency, cancer stemness and tumour propagation.

The Impact

Dr. Lupien's discoveries have contributed to a fundamental expansion of how the cancer genome is understood, from a DNA sequence containing genes and mutations to a functional genome whose interpretation depends on chromatin state. His early work helped establish the now widely used principle that chromatin annotation identifies cell-type-specific regulatory elements. This framework subsequently became central to interpreting the large number of disease-associated variants discovered through genome-wide association studies and to searching the non-coding genome for somatic cancer drivers.

His work has also broadened the mechanisms considered capable of generating cancer heterogeneity. Genetic mutations remain fundamental, but they cannot fully explain the diversity of cellular states found within tumours. By defining chromatin variants and demonstrating how genetic alterations and metabolic pressures can generate changes in genome interpretation, Dr. Lupien's research has helped establish epigenomic heterogeneity as an additional substrate for tumour evolution. This has important implications for precision oncology because genetically similar cancer cells can occupy distinct epigenomic states with different behaviours and therapeutic vulnerabilities.

The discovery that transposable elements can encode pluripotent regulatory programs and sustain cancer stem-cell self-renewal further expands the portion of the human genome considered functionally relevant to cancer. It connects two major advances in contemporary cancer biology, the recognition of non-mutational epigenetic reprogramming as a hallmark of cancer and the emerging realization that repetitive DNA carries regulatory information, to tumour plasticity, self-renewal and cancer evolution.

Where cancer genomics taught us to identify what is altered in the DNA sequence of a tumour, Dr. Mathieu Lupien's work has helped reveal how a tumour interprets that sequence. His discoveries have expanded cancer biology from genes to the non-coding and repetitive genome, from individual mutations to distributed regulatory systems, and from genetic alterations to chromatin variants that define selectable cell states. In doing so, his work has established variation in genome interpretation as a fundamental dimension of cancer biology, one that helps explain cancer initiation, heterogeneity and evolution while revealing new opportunities for precision cancer medicine.

From the Discovery of Stem Cells to Decoding the Cancer Epigenome

The roots of cancer epigenetics at Princess Margaret Cancer Centre can be traced to one of the institution’s greatest scientific legacies: the discovery that cells can exist in fundamentally different states, with profoundly different abilities to self-renew, differentiate and regenerate tissues. In the early 1960s, Drs. James Till and Ernest McCulloch provided the first functional demonstration of blood-forming stem cells. Their experiments established two defining properties of stem cells: the ability to self-renew, preserving their identity through cell division, and the capacity to differentiate into multiple specialized cell types. Their discoveries founded the modern field of stem-cell biology and ultimately provided the scientific foundation for regenerative medicine. Decades later, Princess Margaret scientist Dr. John Dick extended this concept directly into cancer. His landmark studies in human leukemia demonstrated that cancers could also be organized as cellular hierarchies, sustained by rare leukemia stem cells capable of both self-renewal and generating the diverse malignant cells within a tumour. These were the first human cancer stem cells to be functionally characterized and helped establish an entirely new way of thinking about cancer development, treatment resistance and recurrence.

Together, these discoveries raised a profound biological question: What allows one cell to remain a stem cell while another becomes a mature blood cell, or a cancer cell, even when they contain essentially the same DNA sequence? The answer could not lie in DNA sequence alone.

Cells must carry another layer of heritable biological information that determines which portions of the genome they use, which state they occupy and which future states remain available to them. That information must be stable enough to preserve cellular identity through cell division, yet flexible enough to allow cells to differentiate, respond to their environment or, in cancer, change state under the selective pressure of treatment. This is the fundamental territory of epigenetics. Epigenetic information is encoded in the organization and chemical modification of chromatin, the complex of DNA and histone proteins that determines how the genome is packaged and used within a cell. It provides a mechanism through which essentially the same DNA sequence can generate profoundly different cellular identities and behaviours. For cancer researchers at Princess Margaret, stem-cell and cancer-stem-cell biology therefore created a natural scientific foundation for a new field: understanding how the cancer genome is interpreted, how that interpretation becomes corrupted, and whether it can be therapeutically rewritten.

Building a Critical Mass in Cancer Epigenetics

Princess Margaret’s strength in cancer epigenetics did not arise by chance. It was deliberately built. Beginning in 2012, Princess Margaret identified epigenetics as an emerging area of scientific opportunity and assembled a group of investigators with highly complementary expertise. Drs. Daniel De Carvalho, Housheng Hansen He, Michael Hoffman and Mathieu Lupien joined an environment in which Dr. Cheryl Arrowsmith had already established internationally recognized leadership in the structural and chemical biology of proteins controlling chromatin. Together, they created an unusual concentration of expertise spanning the entire spectrum of cancer epigenetics.

Dr. Cheryl Arrowsmith reveals the three-dimensional structures of the molecular machinery that controls chromatin and develops chemical strategies to target these proteins, creating starting points for entirely new classes of cancer medicines.
Dr. Daniel De Carvalho investigates how epigenetic therapies can expose cancers to the immune system and pioneered epigenetic approaches to liquid biopsy that could transform how cancers are detected and monitored.
Dr. Housheng Hansen He has expanded the frontier from chromatin into the regulatory non-coding genome and RNA, revealing how overlooked regulatory elements, RNA molecules and RNA modifications can control cancer behaviour and create new therapeutic opportunities.
Dr. Michael Hoffman develops computational and artificial-intelligence approaches capable of interpreting the enormous complexity of the cancer epigenome, transforming millions of molecular measurements into biologically and clinically meaningful information.
Dr. Mathieu Lupien maps how cancer cells use their genomes, revealing how alterations in chromatin and the vast non-coding genome can initiate and sustain cancer and identifying previously unrecognized classes of cancer drivers.

Together, these scientists gave Princess Margaret the ability to interrogate cancer from the atomic structure of an individual chromatin protein to the regulatory architecture of the entire genome, the evolution of tumour-cell populations and ultimately the behaviour of cancers in patients.That breadth has enabled discoveries that have repeatedly changed what scientists believe can cause cancer, how cancer can be detected and how it might be treated.

From Milestone Discoveries To Clinical Impact
Redefining What Can Drive Cancer

One of Princess Margaret’s most consequential contributions challenged a fundamental assumption about cancer itself. For decades, the dominant model of cancer focused on mutations, changes in the DNA sequence, as the primary drivers of malignancy. In 2014, an international study involving Dr. Mathieu Lupien investigated posterior fossa ependymoma, a lethal childhood brain cancer. Genomic sequencing revealed something remarkable: these tumours contained extremely few mutations and lacked recurrent single-nucleotide mutations capable of readily explaining their aggressive behaviour. Instead, they displayed profound abnormalities in the epigenome. The findings provided compelling evidence that a cancer could be driven predominantly by disruption of how DNA is packaged and regulated rather than by recurrent mutations in conventional cancer genes. Importantly, these tumours also showed vulnerability to drugs targeting DNA and histone methylation, immediately connecting a new understanding of cancer biology with potential therapeutic strategies. The discovery expanded the central question of cancer research.It was no longer sufficient to ask: What has changed in the DNA sequence? Researchers also needed to ask: How is the cancer cell interpreting that DNA differently? This helped establish a broader view of cancer as a disease not only of DNA sequence, but also of chromatin, the regulatory system that determines how the genome is used. It also established new classes of cancer drivers, including across the non-coding genome.

Making Cancer Visible to the Immune System

Another Princess Margaret discovery created an unexpected bridge between epigenetics and cancer immunotherapy. In 2015, Dr. Daniel De Carvalho and his team discovered that removing DNA methylation from cancer cells could awaken ancient viral sequences embedded within the human genome. These sequences are remnants of viruses that entered the genomes of our ancestors millions of years ago and are normally kept silent by epigenetic mechanisms. When reactivated in cancer cells, they can make the cell behave as though it has been infected by a virus, triggering an antiviral immune response. The phenomenon became known as viral mimicry. Published alongside independent work from Johns Hopkins, the discovery helped establish that DNA-demethylating therapies could activate endogenous viral signals and provoke anti-tumour immunity. A finding that initially explained how an epigenetic drug worked opened an entirely new area of investigation at the intersection of epigenetic therapy and immunotherapy. Researchers around the world are now exploring ways to deliberately trigger viral mimicry to make tumours more visible to the immune system. At Princess Margaret, the work continues as researchers investigate how cancers suppress or escape this response, and whether those escape mechanisms can themselves become therapeutic vulnerabilities.

Reading Cancer in a Blood Draw

The same epigenetic biology led Princess Margaret researchers toward an entirely different clinical opportunity: detecting and monitoring cancer through a simple blood sample. Tumours continuously release tiny fragments of DNA into the bloodstream. Traditional liquid biopsies largely searched these fragments for mutations, an approach that becomes increasingly difficult when only minute amounts of tumour-derived DNA are present. Dr. De Carvalho’s group asked a different question: Instead of searching for a handful of altered DNA letters, could we recognize the epigenetic fingerprint left by the cancer?

Working with Dr. Michael Hoffman, the team developed cfMeDIP-seq, a technology sensitive enough to profile DNA methylation from the exceptionally small quantities of cell-free DNA circulating in blood.The innovation went beyond a new laboratory assay. By combining epigenetic measurements with computational and machine-learning approaches, researchers could transform hundreds of thousands of molecular signals into clinically interpretable information. In a landmark 2018 study, the Princess Margaret-led team demonstrated that methylation patterns in blood could distinguish samples from patients with multiple types of cancer from those without cancer and could provide information about the tissue from which the tumour originated. The next challenge was translation. Dr. De Carvalho and Princess Margaret clinician-scientist Dr. Scott Bratman worked to move the technology toward clinical application. Adela, launched in 2021, was created to develop epigenetic blood tests for applications including cancer detection and molecular residual disease. Clinical studies at Princess Margaret subsequently demonstrated the potential for methylation-based blood testing to identify molecular evidence of recurrent head and neck cancer before recurrence became clinically apparent in some patients.A fundamental question about how cancer cells package their DNA ultimately became a technology with the potential to change how patients are monitored after treatment.

Turning Molecular Structure into New Medicines

Princess Margaret’s impact on epigenetics also extends directly into drug discovery. Dr. Cheryl Arrowsmith pioneered the structural and chemical biology of proteins that regulate chromatin. Through her leadership within the Structural Genomics Consortium, her work helped transform proteins that were once difficult to study into molecules whose structure could be visualized, whose function could be understood and whose activity could potentially be controlled with drugs. The translational potential of this approach is powerfully illustrated by WDR5, an epigenetic protein implicated in cancer. Research involving Dr. Arrowsmith and collaborators helped enable the development of first-in-class chemical tools targeting WDR5. What began as fundamental structural biology and an openly shared chemical probe ultimately contributed to a proprietary drug-development program and biotechnology company creation. The significance extends beyond any single molecule. It demonstrates how understanding the fundamental molecular machinery controlling the cancer epigenome can create entirely new therapeutic opportunities. An investigation of an obscure chromatin protein can become a drug target.A chemical probe can become a therapeutic program. And fundamental discovery can attract the investment needed to bring a new class of medicines closer to patients.

Expanding the Epigenetic Frontier into RNA Medicine

Research by Dr. Housheng Hansen He has extended the boundaries of cancer epigenetics beyond DNA and chromatin into another previously underestimated layer of biology: RNA. Most of the human genome does not encode proteins, yet it produces a remarkable diversity of RNA molecules capable of controlling how cells behave. Dr. He’s research has helped reveal that long non-coding RNAs, circular RNAs and chemically modified RNAs can carry important regulatory information, influence cancer progression and create new therapeutic opportunities. Rather than viewing these RNAs as incidental products of the genome, his work has helped establish them as components of the regulatory machinery controlling cancer. This research is contributing to the foundation of RNA medicine at Princess Margaret: new approaches that use or target RNA to understand, diagnose and ultimately treat disease. It represents another expansion of what can constitute actionable cancer biology, from genes, to chromatin, to the non-coding regulatory genome, and now to RNA.

A Research Community Built to Create the Next First

Taken together, these accomplishments reveal a distinctive pattern. Princess Margaret scientists have repeatedly identified dimensions of cancer biology that were previously difficult or impossible to see, and then developed ways to exploit those discoveries for patients.

● Chromatin-driven cancers. ● Cancer drivers hidden within the non-coding genome. ● Ancient viral sequences that can expose cancer to the immune system. ● Epigenetic fingerprints of tumours circulating in blood. ● Chromatin proteins that can become drug targets. ● Regulatory RNAs that may form the basis of future medicines.

Each began as a fundamental scientific question. What makes Princess Margaret particularly powerful is that these questions are not pursued in isolation.Structural biologists, epigenomic scientists, computational researchers, artificial-intelligence experts, cancer biologists, clinician-scientists and drug developers work within an environment directly connected to one of the world’s leading cancer hospitals and to the patients whose cancers pose the questions science still needs to solve. Discovery therefore moves in both directions. Observations in patients generate fundamental scientific questions. Discoveries in the laboratory can be examined in human tumours, clinical studies and therapeutic-development programs. This creates an ecosystem designed not simply to understand cancer differently, but to translate that understanding into better ways to detect cancer earlier, anticipate its evolution, overcome treatment resistance and develop new therapies.

The Next Frontier

The next generation of cancer epigenetics may be even more consequential. New technologies can now measure gene activity, chromatin accessibility, DNA methylation, spatial organization and cellular identity at unprecedented resolution, even within individual cells in a tumour. Artificial intelligence offers the possibility of integrating these layers of information to understand not simply what a cancer looks like today, but where it may go next. The central challenge is shifting from describing the cancer epigenome to learning how to control it.

● Can we identify the epigenetic states that allow a cancer cell to survive therapy before resistance appears? ● Can we prevent tumour cells from changing identity to escape treatment? ● Can epigenetic information in blood reveal cancer before conventional imaging can detect it? ● Can we discover previously invisible cancer drivers within the non-coding genome? ● Can we deliberately push malignant cells out of dangerous states, or prevent them from entering those states in the first place?

Answering these questions could change the role of epigenetics in cancer medicine: from explaining tumour behaviour after it occurs to predicting, intercepting and ultimately controlling it. Princess Margaret has the scientific foundation, clinical environment and multidisciplinary community needed to lead that transition.

Why Philanthropy Matters

Transformative discoveries rarely announce their future importance at the beginning. The first experiment showing that an ancient viral sequence can awaken inside a cancer cell does not yet look like a new approach to immunotherapy. A study revealing the structure of an obscure chromatin protein does not yet look like the beginning of a major drug-development program. A methylation experiment performed on a few nanograms of DNA does not yet look like a blood test capable of detecting recurrent cancer. A map of regulatory elements across the non-coding genome does not yet look like the beginning of a new class of cancer drivers. And a map of chromatin states within individual tumour cells does not yet look like a strategy for preventing cancer from becoming resistant to therapy. This is precisely where philanthropy can have its greatest impact. Philanthropic support creates the freedom to pursue important questions before their clinical or commercial value is obvious. It allows scientists to test unconventional ideas that conventional funding mechanisms may consider too early or too risky. It provides the resources to generate the critical first evidence that can unlock major peer-reviewed grants, industry partnerships and clinical studies. It supports the technologies, computational infrastructure and shared platforms that allow multiple investigators to tackle problems no individual laboratory could solve alone. And critically, it helps recruit and train the exceptional young scientists who will make the discoveries that define the next generation of cancer research. Princess Margaret’s history in cancer epigenetics demonstrates the extraordinary leverage such investment can have.

● A fundamental discovery can create a new field. ● A molecular insight can become a medicine. ● A laboratory technology can become a diagnostic platform. ● A previously invisible cancer driver can become a new therapeutic opportunity. ● And a new way of understanding cancer can ultimately become a new way of caring for patients.

The opportunity now is to build on this extraordinary scientific foundation and move cancer epigenetics toward its next frontier: understanding not only what makes a cancer cell malignant, but what allows it to change, evolve and escape treatment, and learning how to intervene before it does. Philanthropy can provide the freedom, speed and ambition required to make that possible. It can help ensure that the breakthroughs that redefine cancer biology at Princess Margaret today become the diagnostics, medicines and cures of tomorrow.

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