DelCancer

Specific regions in the chromosome are commonly lost in the development and progression of cancer, yet much remains to be learned about the role of these deletions in the disease. Researchers in the DelCancer project are using gene editing techniques and experimental models of cell transformation to shine new light on the development and progression of breast cancer, as Dr Anna Sablina explains

The loss of DNA in the genome is a common feature of the development and progression of cancer. While alterations and changes to some regions of the genome are thought to play a role in tumourgenic transformation, much remains to be learned about the loss of heterozygosity that is commonly observed in cancer genomes, an area that forms the primary research focus for the ERC-backed DelCancer project. “The main goal of the project is to investigate the consequences to patients of large-scale chromosomal deletions,” says Dr Anna Sablina. This is not an easy question to study, as typically multiple genes are lost simultaneously when large areas of chromosome are deleted. “Some of those genes can suppress the proliferation of cancer cells, but others can confer a selective growth advantage. That’s why it’s really difficult to define the role of these large-scale deletions in the development of cancer,” explains Dr Sablina.

The development of sophisticated new genetic engineering tools is an important step forward in these terms. The project is using both TALEN and CRISPR technologies, which allow researchers to cut DNA at specific locations and manipulate the genome of human cells. “We can mimic the situations that we can see in cancer patients. So we can introduce the same large-scale deletions that we see in cancer patients, then assess the role of these deletions on cancer development and progression,” outlines Dr Sablina. Researchers are working mainly with patient cells derived from mammaplasty procedures, and genetically engineering these cells to model the alterations associated with cancer. “We use the TALEN or CRISPR gene-editing techniques

to introduce the genetic alterations that we commonly see in breast cancer patients,” continues Dr Sablina.

Researchers are deleting an entire region of the chromosome, rather than a smaller area or specific parts of the chromosome, aiming to establish a protocol for editing the genome on a large scale. The goal then for Dr Sablina and her colleagues is to assess how disrupting the chromosomal network in this way affects cells. “If we have such a large-scale chromosomal deletion, how will it affect gene expression? And will this contribute to cell transformation?” she outlines. The project is using experimental models of cell transformation to investigate the impact of deleting specific chromosomal regions. “We introduce these chromosomal alterations into the model, then we try to figure out what is going on in the cells by looking for different assays and different pathways,” explains Dr Sablina. “We look at whether these large-scale chromosomal deletions can lead to the formation of cancer.”

This research relates to both the early stages of cancer development and its later progression. Some chromosomal alterations may occur at an early stage of cancer development, while others may take place later, an issue which Dr Sablina and her colleagues are investigating. “First of all, we are looking at the cancer genomes. We aim to figure out which alterations recur, to define the border of the deletions, and to define whether the specific deletion is an early event or a late event,” she says. Data from the cell models can also lead to new insights into the molecular mechanisms behind cancer

that we can see in cancer patients. These model systems allow us to assess the role of these deletions on cancer development and progression

development. “We can look at whether a specific alteration is associated with drugresistant or metastatic phenotypes for example. It’s then easier for us to figure out which phenotypes we should look at in our models,” continues Dr Sablina.

This work also holds wider relevance in terms of diagnosis and prognosis for breast cancer patients. Breast cancer is a highly complex condition, and it is currently classified across several different categories in order to identify the best course of treatment for each individual case; Dr Sablina says deeper knowledge about chromosomal aberrations could bring real benefits in this regard. “We can see that some of these chromosomal aberrations could serve as prognostic marker for certain therapeutic decisions. Some of them could act as indicators of sensitivity to a particular type of therapy,” she says. These prognostic markers could potentially be used in the clinic in future; Dr Sablina plans to investigate this further, using tissue taken from patients during surgery. “We will introduce these pieces of tissue into a mouse, so we can look at a primary tumour in a humanized mouse. Then we will characterise the different chromosomal alterations we observe in this tumour, which will affect the response to specific drugs,” she continues.

The wider goal in this research is to investigate how particular chromosonal deletions lead to the initiation and progression of cancer. While the project is focused primarily on breast cancer, Dr Sablina says this approach could potentially be used to investigate other forms of cancer. “I’m mainly familiar with breast cancer, but this could be applied to any other kind of tissue,” she says. Researchers will continue to investigate the underlying mechanisms behind cancer development over the coming years, which could also help in the identification of new therapeutic targets to help improve treatment. “With effective drug screening, we can really identify compounds or drugs to reach our modified cells. Then we can go back to the patient data, and see which chromosomal organisation can be used as a predictive marker for sensitivity to a particular type of therapy,” outlines Dr Sablina.

Loss of chromosome 8p governs tumor progression and drug Response by altering lipid metabolism.

The role of loss-of-heterozygosity in cancer development and progression (DelCancer)

One-fourth of a typical breast cancer genome is affected by chromosome arm deletions. By genetically engineering human cells, we generated clinically relevant models of large-scale chromosomal deletions. Our results demonstrate that experimental models mimicking cancerassociated deletions provide a powerful system for functional annotation of the cancer genome. The generated models also represent a platform to identify drugs that selectively kill tumor cells harboring a particular chromosomal abnormality.

ERC Starting Grant DelCancer

Dr Anna Sablina VIB Laboratory for Mechanism of Cell Transformation KU Leuven O&N Campus Gasthuisberg Herestraat 49 bus 602 3000 LEUVEN T: +32 16 37 69 27 E: anna.sablina@cme.vib-kuleuven.be W: http://www.vib.be/en/research/ scientists/Pages/Anna-Sablina-Lab.aspx

Dr Anna Sablina

Dr Anna Sablina is a Group Leader in the VIB Laboratory for Mechanism of Cell Transformation at the University of Leuven. Her main research interests are focused on understanding the cooperative interactions that conspire to promote tumorigenic transformation.