Epigenetic changes as modifiers of BRCA1/ BRCA2 cancer risk

Institution: Beckman Research Institute of the City of Hope
Investigator(s): Susan Neuhausen, Ph.D. -
Award Cycle: 2011 (Cycle 17) Grant #: 17IB-0015 Award: $251,128
Award Type: IDEA
Research Priorities
Etiology and Prevention>Etiology: the role of environment and lifestyle



Initial Award Abstract (2011)

This project was supported in part by a generous donation from the Katie Ann Buzbee Trust.

Non-technical overview of the research topic and relevance to breast cancer:
Women who have mutations in the high-risk breast cancer genes, BRCA1 and BRCA2, have a 40 to 80 percent risk of developing breast cancer. This level of risk is 4 to 8 times higher than that of the general population. Whatís more, not all women in the same family who carry the same mutation will develop cancer. So, there is a tremendous amount of uncertainty, and women simply donít have the facts regarding their own individual risks that would enable them to choose the best option to reduce their risks. Their options range from more intensive screening and magnetic resonance imaging (MRI) to prophylactic surgeries of the breast and ovary, resulting in loss of fertility and early menopause. Therefore, it is essential to better understand who develops cancer and thus be able to provide a more precise estimate of risk. In large collaborative research efforts aimed at discovering the germline genetic mutations that contribute to risk, we have identified a small number of candidates. However, they explain little of the variation in risk. We are proposing a new paradigm to identify modifications to DNA that do not involve changes to the DNA sequence but change genesí chemical structure and ability to function. The study of this type of heritable modifications of DNA or associated proteins (epigenetics) can be used in the future for better risk estimates, and to design prevention strategies. This proposed study will be the first to systematically focus on the discovery of epigenetic changes that modify the risk of cancer in BRCA1 and BRCA2 carriers.

The question(s) or central hypotheses of the research:
Methylation of cytosine residues is a mechanism which causes silencing of a gene and is the most characterized epigenetic mechanism. The hypothesis is that methylation changes modify the risk of developing breast cancer in women carrying deleterious mutations in BRCA1 and BRCA2. These changes also likely will play a role in non-familial breast cancer.

The general methodology:
The overall objective is to identify methylation changes in DNA that may be associated with risk of developing breast cancer in women who carry pathogenic BRCA1 and BRCA2 mutations. In the first phase, we will use methylation arrays to identify methylation changes in promoters of genes in 90 DNA samples. We will include samples from 13 extended BRCA1 or BRCA2 families studying DNA from 3 breast cancer patients and 2 other women in their families who have not been affected by cancer, as well as 20 healthy unrelated controls. We will then assess the methylation differences between the diagnosed and unaffected groups. By studying methylation differences within families, we can determine if the methylation changes are specific to those with cancer. Once we have results from these experiments, we will confirm that the identified regions are correct and then characterize the genes associated with those methylation changes, test whether these changes are associated with cancer in additional family members, as well as determine if those changes silence those specific genes where the methylation changes occurred.

Innovative elements of the project:
We are proposing a new paradigm of breast cancer in carriers of BRCA1 and BRCA2 mutations. This will be the first study to assess whether methylation is more frequent in blood in those who develop cancer than those who are still unaffected, and whether specific methylation changes can predict risk of developing cancer. By studying families, we will be able to determine whether the methylation change modifies breast cancer risk even though we are only studying a small number of women.

Advocacy involvement and relevance to the human issues associated with breast cancer:
For this project, we will be identifying epigenetic changes that modify the risk of developing breast cancer in women who carry pathogenic BRCA1 or BRCA2 mutations. It is our hope that this study will provide results that can then be validated in the future to provide women with more accurate risk estimates, and to develop more targeted prevention based on the epigenetic changes that we have observed and documented. Michele Rakoff, an advocate, will provide insight and direction with regard to how the results from this study can be moved into clinical practice. We will obtain initial results midway through the project, at which point we will discuss which changes are likely to be important and which should therefore be targeted for validation and future studies related to new preventative or risk-reducing strategies such as modification of diet or other preventive agents.




Final Report (2013)

Women who have mutations in the high-risk breast cancer genes, BRCA1 and BRCA2, have a 40 to 80 percent risk of developing breast cancer. This level of risk is 4 to 8 times higher than that of the general population. Whatís more, not all women in the same family who carry the same mutation will develop cancer. So, there is a tremendous amount of uncertainty, and women simply donít have the facts regarding their own individual risks to enable them to choose the best option to reduce their risks. Therefore, it is essential to better understand who develops cancer and thus be able to provide a more precise estimate of risk. In large collaborative research efforts to discover germline genetic modifiers of risk, we have identified a small number of those modifiers. However, they explain little of the variation in risk. In this study, we proposed research to study a new paradigm - that epigenetic effects can be modify the risk of developing cancer in women carrying mutations in BRCA1 and BRCA2. Epigenetics is the study of heritable modifications of DNA or associated proteins that lead to altered gene expression without changing the underlying DNA sequence. We studied methylation of cytosine residues which prevent the gene protein from being expressed and made.

In the first phase, we used arrays to identify methylation changes in promoters of genes in 92 DNA samples. The first method we used did not provide good enough discrimination, so we tried a different newer method that did not work well. The third method was methylation arrays and they worked well. We included 70 samples from 13 extended BRCA1 or BRCA2 families, as well as 23 healthy unrelated controls. We assessed the methylation differences between the diagnosed and unaffected groups. We found specific methylated genes within families that appear to increase the risk of cancer. There were fewer genes that appeared in common across families. In the second phase, we looked in-depth in families, and in some instances, we were able to confirm that the methylation changes were associated with development of cancer. We are using the Cancer Genome Atlas (TCGA) data to determine that the changes affect expression of the genes. We were able to accomplish the aims of the proposal, but not in the depth that we desired, due to the time and cost in overcoming the difficulties in determining the methylation differences.

The significant accomplishment is that this is the first study to assess whether methylation is more frequent in blood in those who develop cancer than those who are still unaffected, and whether specific methylation changes can predict risk of developing cancer. We found significant evidence that differences in methylation may modify risk. We also determined that a proportion of the methylation changes are due to underlying genetic changes that create or abolish the sites where methylation occurs. However, we need to do a more in-depth study involving a larger number of families and samples, and assess how much of a modifying effect on risk is due to methylation changes. This funding from CBCRP provided us with sufficient preliminary data that we can apply for further funding to investigate this paradigm more fully.