High-Throughput Bisulfite Sequencing Method for Exploring the Breast Cancer Epigenome

PUBLIC ABSTRACT

The Human Genome Project has been touted as the greatest scientific achievement of our time. The project resulted in defining the sequence of more than 90% of the three billion DNA base pairs present in the human genome. While genomic information is uniform in the different cells of complex organisms, epigenetic processes initiate and maintain heritable patterns of gene expression in specific cells without changing the sequence of the genome. The programming of gene expression profiles is therefore dependent on the epigenome.

Breast cancer is increasingly being recognized as an epigenetic disease. These are compelling reasons for applying innovative technologies to decipher the breast cancer epigenome in its entirety. Such an epigenetic "map" would facilitate a greater understanding of the role of epigenetic modifications in normal and pathologic processes and offer considerable information of direct relevance to eradicate breast cancer. The epigenome is composed of two modules, DNA methylation and histone modifications. In breast cancer cells, the DNA methylation pattern is often defective. Before we are able to properly target DNA methylation in cancer therapy, we ought to understand which of the changes in the DNA methylation pattern are causal for cancer initiation and progression. Therefore, we propose to develop an innovative technology that is capable of conducting high-throughput and quantitative DNA methylation analysis at a single DNA base resolution. This innovative method will be established using a highly parallel sequencing system capable of analyzing tens of millions bases in a single reaction. We will apply a multidisciplinary approach involving both elegant experimental design and computational software development. All the experimental protocols and software developed in this project will be made available to other researchers.

This study could potentially become the first-ever large-scale digital scanning of the DNA methylation landscape across the breast cancer epigenome. We believe that the technology developed will revolutionize the current analytical methods of DNA methylation. With this highly informative method, we may identify genes critical in breast tumor formation that are influenced by aberrant DNA methylation changes. Since epigenetic alterations of breast cancer genome are in principle reversible, these identified genes represent potential targets for therapeutic intervention, and they could be developed into DNA methylation biomarkers for reliable and cost-effective early detection, diagnosis, prognosis, and monitoring the response to therapy in breast cancer. The support for this proposal will not only significantly promote the interdisciplinary collaboration between two principal investigators, but also bring two groups of update investigators to the field of breast cancer research.