Scientists at The Institute of Cancer Research, London (U.K.) have used a high-throughput genetic analysis technique known as Capture Hi-C (CHi-C) to link 110 genes with an increased risk of breast cancer. The high-resolution technique can identify how regulatory genetic elements physically interact with distant protein-coding genes, even when separated by megabases (Mb) of DNA. The ICR researchers used CHi-C to analyze 63 genome regions that previous genome-wide association studies (GWAS) had linked with breast cancer. Among the 110 genes identified using CHi-C, 32 were subsequently linked with breast cancer survival.

“Our study took the high-level maps of breast cancer risk regions and used them to pull out specific genes that seem to be associated with the disease,” explains Olivia Fletcher, Ph.D., team leader in functional genetic epidemiology at The Institute of Cancer Research, and co-corresponding author of the team’s published paper in Nature Communications. “We studied how DNA forms loops to allow physical interactions between a DNA sequence in one part of the genome and a risk gene in another. Identifying these new genes will help us to understand in much greater detail the genetics of breast cancer risk. Ultimately, our study could pave the way for new genetic tests to predict a woman's risk, or new types of targeted treatment.”

The ICR team and colleagues at The London School of Hygiene and Tropical Medicine, the University of Leicester, and the Babraham Institute in Cambridge, report their findings in a paper entitled “Capture Hi-C Identifies Putative Target Genes at 33 Breast Cancer Risk Loci.

Prior GWAS, large-scale replication studies, and fine-mapping studies have identified about 100 breast cancer loci, the researchers write. Within these regions, most of the risk-related single-nucleotide polymorphisms (SNPs) have been mapped to nonprotein-coding regions of the genome, and are thought to play a role in regulating gene transcription. Other sites of interest are within regions of the genome known as gene deserts, which may be hundreds of kilobases away from the nearest known protein-coding gene. Figuring out which genes are responsible for increased risk is challenging because genes and their regulatory elements may be distant from each other and only interact when the DNA loops to allow the sites to interact.

The ICR researchers developed the high-throughput, high-resolution Capture Hi-C technique to identify the physical interactions between regulatory elements and their target genes, however far apart they are. They applied the technique to analyze the 63 genetic loci previously linked with breast cancer.

The results of CHi-C analysis in breast cancer cells and normal cells identified 110 putative target genes in 33 loci, including 94 protein-coding genes and 16 noncoding RNAs. No specific genes were identified in the remaining 30 gene regions. Previous studies have suggested a role for 14 of the 110 genes—including the estrogen receptor gene ESR1—in breast cancer risk, but most of the genes identified using CHi-C had not been associated with breast cancer risk before. One of those identified, FADD, has previously been linked to head and neck cancer and lung cancer.

The team evaluated their results in the context of three publicly available breast cancer data sources, to determine whether the genes identified using CHi-C might have a causal role in breast cancer. They found that 32 of the 97 CHi-C genes for which patient data were available were associated with survival in estrogen-receptor positive (ER+) disease, although none were linked with survival in ER disease.

“In all data sources combined there were support for 48 CHi-C target genes mapping to 32 loci from at least one additional source and there was support for six genes mapping to six loci from at least two additional sources,” the authors write. “These data suggest that a substantial proportion of the CHi-C putative target genes are likely to influence breast cancer risk and warrant further investigation.”

The authors acknowledge that it could take years to categorize which genes play definitive roles in cancer risk or development, but they suggest that the first stage will be to short-list candidates for follow-up studies. “…we would argue that a high-throughput CHi-C analysis can contribute to on-going efforts to functionally annotate GWAS risk loci and that CHi-C target genes that are supported by additional data sources are strong candidates for in depth functional follow up studies.”

Paul Workman, Ph.D., chief executive of The Institute of Cancer Research, London, comments, “Large-scale genomic studies have been instrumental in associating areas of our DNA with an increased risk of breast cancer. This study brings these regions of DNA into sharper focus, uncovering a treasure trove of genes that can now be investigated in more detail. The ways in which particular genes influence cancer risk are highly complex. In the future, a better understanding of the genes identified in this study could lead to the discovery of new targeted drugs, or new strategies to improve diagnosis or prevention of the disease.”

The research was funded by U.K. breast cancer charity Breast Cancer Now. The organization’s chief executive, Baroness Delyth Morgan, added, “These are really important findings. We urgently need to unravel how the genetic changes in the building blocks of our DNA influence a woman’s risk of breast cancer, and this study adds another vital piece to this jigsaw….Many of these genes have been relatively undocumented to date, and we now hope further research will untangle their exact role in breast cancer risk, and how we could use them to stop more women developing the disease.”


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