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Dr. Davide Pellacani Talks Epigenetics and Cancer Research

By July 19, 2017October 6th, 2023No Comments

Dr. Davide Pellacani is a postdoctoral fellow in the lab of Dr. Connie Eaves at the Terry Fox Research Institute. Approaching the end of his postdoc, Dr. Pellacani’s research has evolved throughout his career to include the merging of stem cell biology, epigenetics, bioinformatics, and cancer research. We sat down with Dr. Pellacani to discuss some of his current projects and where he plans to take them.

The majority of your research focuses on studying cancer and tumorigenesis using primary cells. Why were you drawn to this area of research?

Good question. Throughout my training, my research focussed mainly on breast and prostate cancer. These diseases are incredibly heterogeneous, both when we compare cancers from different individuals, and when we compare individual cells within the same tumour mass. Some of the models we have used for years in cancer research fail in many ways to recapitulate this heterogeneity, and are sometimes molecularly and biologically very distant from the actual disease. Therefore they don’t tell us the whole story. For instance, established cell lines are great for studying the fundamental mechanisms of gene regulation, but are generally more limited for studying context-specific gene regulation, as they acquire many molecular alterations due to culture adaptation.

As an example, our lab has recently shown that, from an epigenomic perspective, uncultured cells purified from normal human breast tissues are widely different from non-tumorigenic human mammary cell lines, which are frequently used as a normal comparator in cancer research studies. For these reasons, I decided to mostly use primary cells in my current and future research. This does make my research much more complicated, expensive and time consuming, but I believe it is the best way to really understand the molecular and biological heterogeneity of cancer.

How did you analyse the epigenomic properties of these cells and what was the main goal of the project?

We characterized the genomic distribution of six specific modifications on the tail of histone H3, which are generally correlated with either active or repressed genomic regions, together with DNA methylation and mRNA abundance. We performed these experiments on the three main cell populations that we can identify within the mammary epithelium. The goal of the study was actually to understand the differences in regulatory regions, especially enhancers, between these different cell populations. So that was my focus. I then bioinformatically identified transcription factors potentially bound to these regions that might be involved in the regulation of the biological properties of these cells. Of course, this was all computational, so “the proof will be in the pudding”. As a first step, I am planning to modulate the expression of these transcription factors in the same primary cells and observe whether they can actually alter their proliferative and differentiation potential.

Are you working on any other related projects?

Another project I’m working on is an in-depth characterization of the epigenetic marks within the same cell types of young and old donors. The breast undergoes massive changes throughout ageing, mainly due to the hormonal changes happening with menopause, and since breast cancer is a disease of age, we think that the molecular events occurring during the aging process of the breast and those crucial to the emergence of cancer might be linked.

Therefore, we want to relate the epigenetic changes occurring in older individuals with those that occur in the first few steps of transformation. We have recently developed a de-novo tumour model that allows us to make these comparisons. In this model, we take normal human mammary epithelial cells, and we introduce oncogenes via lentiviral transduction. The cells are then implanted in immunocompromised mice and assessed for tumour formation within a few months. We can profile the resulting tumours, understand changes that are occurring and compare them to those occurring in older women.

Have you already used this model successfully?

Yes. Our lab has previously shown that the oncogene known as KRASG12D can efficiently produce tumours from primary normal cells within 8 weeks. Although this specific mutation is quite rare in breast cancer, aberrant activation of the pathways in which KRAS is involved are found in many breast cancers. Interestingly, the two most common oncogenes mutated in breast cancer, TP53 and PIK3CA, were, in our hands, much less efficient at producing tumours in the same settings, compared to KRAS.

Since then we have identified at least two other oncogenes that can independently produce a tumour mass. This is really exciting, as we can now study the both the commonalities and the differences in how these oncogenes alter the cells’ programs to produce a tumour. These studies would be extremely difficult, if not impossible, to conduct directly on cancer tissues from patients. In fact, once a tumour has reached a detectable size, it has already acquired multiple genomic and epigenomic changes. So, by the time you have a tumour, it’s really difficult to understand what has happened throughout tumorigenesis at a molecular level.

We’re now at the point where we’re able to try to understand what’s going on in the first few steps of this process, which is incredibly intriguing.

You’re approaching the end of your postdoc, and have mentioned that you hope to run your own academic research group once you’re done. What specific questions do you wish to pursue?

Good question! I’m interested in how the tightly controlled transcriptional programs that normal cells put into place are slowly deregulated with time, changes in the cellular environment, and acquisition of mutations. Ultimately, I want to know how this can lead to cancer. Transformation is a slow and continuous process. I am excited at the possibility of understanding what could be the first few steps that ultimately make a normal cell become an overt tumour cell, and what is the role of epigenomic control of gene expression in this complex system. This research would contain a component of stem cell biology, epigenetics, and cancer biology.

What advice would you give to someone just starting out their postdoc, and hoping to follow a similar career path?

Throughout my postdoc, talking to peers about their and my research, seeking feedback on my progress and asking for help on specific techniques really helped me. I tried to nurture relationships with my colleagues and I was always excited at the possibility of learning something from them. I always felt incredibly lucky being around brilliant colleagues who were often available and happy to help. These relationships became important in the most difficult times, when things were really not working out. So, I would suggest not getting stuck in the lab too much and spending some time getting to know the people around you, if the environment permits it.

I also tried to never settle, and never say: “now that I have mastered technique X, I am done”. I am always excited by the next challenge and how I can expand my knowledge and improve my critical thinking.

Thank you for taking the time to speak with us, Dr. Pellacani! It’s exciting to know that this incredible research is happening here in Vancouver!