Mapping of cancer regulatory pathways and identification of prognostic cancer biomarkers using ChIP-DSL promoter analysis

¹Jeffrey Falk, ¹Mingie Jin, ¹Dongyan Liu, ²Xiang-Dong Fu
¹Aviva Systems Biology, 11025 Roselle St, Suite 100, San Diego, CA 92121, United States of America, ²University of California, San Diego, Dept of Cellular and Molecular Medicine, 9500 Gilman Dr, La Jolla, CA 92093, United States of America

We have developed a novel promoter array technology, ChIP-DSL, that has specific applications to oncology target, biomarker, and drug discovery efforts. Studies will be presented demonstrating transcriptional profiling of histone deacetylation, demethylation, and estrogen receptor sites and how these interactions have pinpointed alternative regulatory pathways associated with cancer that have direct implications in cancer biomarker and therapeutic drug development efforts. Additional data will be presented demonstrating how estrogen receptor interactions can be correlated with clinical breast cancer data to prognostically define specific biomarkers and novel drug targets within distinct groups of patients. We will also describe key elements of the ChIP-DSL (Chromatin Immunoprecipitation - DNA Selection and Ligation) technology which enables genome-wide identification of key promoter interactions by screening 20,000 promoter interactions in a single array format using only 10⁶ cells, and provides a 2 orders of magnitude increase in sensitivity as compared to traditional ChIP-Chip studies.