ESR08 – Catarina Salgado – based in Leiden

Project Title: Examining tumour cell heterogeneity in melanoma metastasis using single cell genomic technologies.
PhD Award Expected: Summer 2020

I was born in Porto, Portugal’s 2nd largest city, best known for its unique historical landscape, exquisite cuisine and world-renowned wines.

Back when I was 8-years old, my teacher brought a book with biographies of historical characters. That day, my homework was to do a summary of Marie Curie’s life. This homework brought to life my dream of becoming a scientist in awe of Curie’s perseverance. Eventually, the dream came true, and I applied for a First Degree in Biology and afterwards to a Master Degree in Molecular Oncology granted by University of Porto. In 2011, I joined Ipatimup as a trainee, to develop my master’s thesis, focused on familial thyroid carcinoma. Alongside I have also contributed to other oncobiology research projects at Ipatimup. These first steps into scientific research showed me how challenging yet fulfilling this world can be. Consistent with my professional goals, I applied and was accepted into MELGEN network as a PhD student.

Apart from science, spending time with family and friends and finding new and quaint restaurants are my favourite hobbies. I also enjoy travelling and reading. Sports are also an essential part of my life as a way of managing the daily stress.


Research Summary

Catarina Salgado is working at Leiden (LUMC, The Netherlands). Her PhD project focuses on the epigenetics of melanoma.

Schematic representation of the development and progression of melanoma
Figure 1. Schematic representation of the development and progression of melanoma. This figure was built using Servier Medical Art images (https://smart.servier.com/)

Melanoma is the most aggressive and lethal type of skin cancer since it has the ability to spread to other organs in the body making it harder to control the disease.

It is very common to hear about cells, chromosomes, DNA, genes, and alterations when we talk about cancer. The chromosomes are confined to the nucleus of our cells and consist of long strands of DNA containing many genes. The most common alterations described in cancer are related to the DNA sequence, the so-called mutations, changes that impair the correct proteins to be produced. The latter may have different implications for the cell and can for instance predispose to cancer.

What does epigenetics stand for?

Mutations are alterations in the DNA strand itself. However, the components of the DNA strand can stay unchanged but be affected by many modifications triggering a similar impact in the generation of  a new (and defect?) protein. The set of these modifications affecting the “behaviour” of the DNA components is called “epigenetics”. The Greek prefix “epi” means “on top of” or “in addition to” the traditional genetics. The term “epigenetics” was originally proposed by Conrad Waddington in 1942 to describe the molecular mechanisms independent of alterations in the DNA sequence. There are three main epigenetic mechanisms: DNA methylation, histone modification and chromatin remodeling.

In this PhD project we aim to explore the degree to which epigenetics play a role in melanoma progression and survival.

Structure of DNA
Figure 2. Structure of DNA. The chromosomes are confined to the nucleus of the cells and consist of long strands of DNA containing many genes. Chromosomes have proteins called histones that bind to DNA. DNA is made up of four components called nucleotides (yellow, red, blue and purple). DNA methylation (m) and DNA hydroxymethylation (hm) are the epigenetic alterations represented [Adapted from © 2015 Terese Winslow LLC, U.S. Govt. has certain rights and Dictionary of Cancer Terms PDQ Cancer Information Summaries, National Cancer Institute (US)].

Therefore, we explore the above-mentioned DNA methylation (m in Fig.2) and its opposite process, DNA demethylation, also known as hydroxymethylation (hm in Fig.2), in the entire genome of benign (normal naevus) and malignant samples (melanoma) of different patients. The intent is to broaden knowledge of the degree to which methylation modifies key biological mechanisms and survival of cells and which processes are therefore potentially modifiable. In this project, we were able to identify specific sites/regions in the genome that might be valuable indicators to help the diagnosis along with regions localized in genes that might contribute to development of melanoma.

Additionally, we also studied the role of a mutation in melanoma development. This alteration in the DOT1L gene was found in a family with many melanoma-affected cases. We performed many cell-based experiments to see which biological processes were affected by adding the desired alteration in these cells. We conclude based on our and previous results, that the study of this alteration deserves further study, since mutations in DOT1L gene seem to affect UV exposure sensitivity, which may enhance malignant transformation.

Another project aims to assess whether the epigenetic alterations can be the cause of melanoma in a great proportion of the familial cases for which a genetic cause has not been identified. Different epigenetic mechanisms were investigated in the DNA from 2 melanoma-affected family members from 5 families. Our results show that heritable DNA methylation alterations are not likely to be a cause of familial melanoma.

Since both genetic and epigenetics modifications often ‘work’ side-by-side to trigger malignant transformation, in our last project we explored the combined contribution of epigenetics (DNA methylation and chromatin remodelling) and genetic (promoter mutations) mechanisms in regulating an important gene involved in cancer, TERT gene. TERT can prevent cell death and promote uncontroled proliferation, two important characteristics of cancer cells. We could observe a complex interplay among mutations, methylation and chromatin organization that explains the distinct biological origins of healthy/benign samples and tumour samples.

Publications

Salgado C, Kwesi-Maliepaard EM, Jochemsen AG, Visser M, Harland M, van Leeuwen F, van Doorn R, Gruis N. A novel germline variant in the DOT1L gene co-segregating in a Dutch family with a history of melanoma. Melanoma Res. 2019; 29(6):582-589.

Salgado C, Oosting J, Janssen B, Kumar R, Gruis N, van Doorn R. Genome-wide characterization of 5-hydoxymethylcytosine in melanoma reveals major differences with nevus. Genes Chromosomes Cancer. 2020 Feb 3. Available at: https://onlinelibrary.wiley.com/doi/full/10.1002/gcc.22837

Salgado C, Gruis N, BIOS Consortium, Heijmans BT, Oosting J, van Doorn R. Genome-wide analysis of constitutional DNA methylation in familial melanoma. Clinical Epigenetics 2020. Mar 6; 12(43) https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-020-00831-7