Medical Genomics Research Spotlight: Dr. Emma Bell

Dr. Emma Bell is a bioinformatician, postdoctoral researcher at the Princess Margaret Cancer Center, and guest lecturer in the M.H.Sc in Medical Genomics program. They combine biology, statistics, and information engineering to ask biologically and clinically meaningful questions as a bioinformatician. Dr. Bell’s long-term research aim is to improve gynecological healthcare outcomes, inclusive of trans and non-binary patients.

As a bioinformatician, Dr. Bell conducts research focused on a genome-wide DNA methylation profiling technique developed at University Health Network (UHN) called cell-free methylated DNA immunoprecipitation (cfMeDIP-seq). cfMeDIP-seq falls under a larger class of non-invasive methods called liquid biopsies – Emma notes, “in contrast to traditional tissue biopsy, liquid biopsies are a way of getting information about a tumor without having to do an invasive procedure like surgery.” By detecting DNA shed by tumours into the bloodstream, genetic profiling techniques like cfMeDIP-seq are employed to identify tumours and characterize them into classes based on their resistance or sensitivity to chemotherapies. A major advantage of cfMeDIP-seq is that it comes without the risks of pain, bleeding, and infection that come with traditional invasive tissue biopsy techniques. In the course MMG3003Y: Genomics Methodologies, Dr. Bell’s lecture on genome wide profiling of DNA methylation dives into the commonly used methods to profile DNA methylation in academic research and how these methods provide insights into how DNA methylation markings look different in cancer when compared to markings present during normal mammalian development.

By profiling DNA methylation across the human genome, we gain information about gene expression. Methylation markings detected at a promoter region near the beginning of a gene indicate repression, while markings found along the gene body are associated with the opposite – increased transcription of that gene. Unlike changes to the DNA itself, changes to DNA methylation are considered non-permanent and may change depending on the context of your environment. The study of how your environment influences gene expression through modifying the DNA (e.g., methylation) is called epigenetics. As Dr. Bell explains, “there are an awful lot of environmental features that will cause changes to DNA methylation.” They continued, “things like chemotherapy treatment, age, environmental exposures to alcohol and smoking all affect your DNA methylation profiles.” Since epigenetic profiles are typically complex with many data points, bioinformaticians like Dr. Bell have turned to computational modelling to better understand the epigenetic underpinnings of cancer: “I’m working on building accurate enough machine learning models to identify the informative parts of the genome, and we can use that information to help clinicians better understand the diagnosis and prognosis of the patient in front of them and what treatment protocols might be effective.” Using machine learning and cfMeDIP-seq, Dr. Bell hopes cancer treatments will become more precise: “Instead of trying chemotherapy A when the patient is resistant, we can skip that and go [directly] to chemotherapy B.”

Liquid biopsy techniques like cfMeDIP-seq show promise as a tool for diagnosis and surveillance of cancer, and Dr. Bell believes liquid biopsies hold the potential to close the in gaps in care for often overlooked conditions – especially in female health – such as polycystic ovarian syndrome (PCOS) and endometriosis: “Why does it take ten years to diagnose endometriosis in 2023? There is no reason that is should [take that long].” This delay can be incredibly impactful for patients, because as Emma notes, the condition is a “risk factor for certain types of endometrial cancer and the long-term inflammation [has] an effect on the DNA methylation profiles of the cell-free DNA (cfDNA) that the uterine lining cells are shedding.” A liquid biopsy approach cfMeDIP-seq - which profiles the methylation of cfDNA from blood sample - is thus “a good candidate diagnostic tool to reduce the time it takes to diagnose endometriosis.”

On the topic of improving women’s healthcare and gynecological healthcare for women and transgender and non-binary folks, Dr. Bell urges the importance of sex and gender education: “We need the very basic definitions of sex and gender to become common knowledge within healthcare and health care research.” They continued, “some of my colleagues – both research and clinical - use terms interchangeably, and if it was any other aspect of biology, we would be stressing that precision and accuracy are absolutely essential.” Furthermore, they reference a well-documented patient experience: “when female patients go to their general practitioner and talk about pain, they’re not believed in the same way as when a male patient does.” Dr. Bell also references similar negative experiences with healthcare professionals that have been documented by Black patients, pointing to how health equity training is so important for care providers to best respect patients’ needs, boundaries, and modes of communication.

Dr. Bell appreciates the flexible schedule that working at the cutting edge of research allows them, as they prefer to work differently in the context of their ADHD: “Sometimes I only manage one session of focused work, sometimes I only managed to do the administration work, but I always manage to keep things ticking over.” For those interested in biomedical research, Dr. Bell recommends “getting comfortable with not knowing,” and they emphasized that biology is “always more complicated than you initially thought it was.”

We are so honoured to have heard from Dr. Emma Bell and wish them success in their postdoctoral research position and beyond!