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DNA Resource Core

The DNA Resource Core provides access to specialized resources such as rapid and user friendly high-throughput DNA sequencing, a cDNA/RNAi clone repository, and distribution services and informatics support. Under the direction of J. Wade Harper, PhD (HMS), the core sequences approximately 200,000 samples per year. Project examples include:

PI:  J. Brugge (HMS) (Breast and Cancer Cell Biology Program). The Breast Cancer 1000 (BC1000) is a collection of cDNAs encoding genes linked to breast and other cancers. This resource was one of the first clone collections made available to DF/HCC members through the Core. Genes were selected for this set using bioinformatics and data mining tools that identify genes associated with breast cancer. Greater than 1,000 cDNAs were assembled and sequence verified with high-throughput recombination-based cloning. The BC1000 represents the first publicly available sequence-validated human disease gene collection. J. Brugge (HMS) systematically assessed the functional activity of a subset of the BC1000 collection using cell-based assays that monitor changes in cell proliferation, migration and morphogenesis in MCF-10A mammary epithelial cells expressing a variant of ErbB2 that can be inducibly activated through dimerization. Using this approach, she then identified many cDNAs, encoding diverse classes of cellular proteins that displayed activity in one or more of the assays, thus providing insights into a large set of cellular proteins capable of inducing functional alterations associated with breast cancer development.

PI: B. Kaelin (DFCI) (Cancer Cell Biology, Kidney Cancer Program), E. Harlow (former member, Cancer Cell Biology Program), K. Munger (BWH) (Cancer Cell Biology Program). Systematic analysis of protein kinases in proliferation and cancer development. Protein kinases serve as major signaling molecules in eukaryotic cells and are frequent drivers of cancer development. Efforts of the Core led to the development of a human protein kinase gene repository. This repository was used in a high-throughput cell based screen for cell survival. In addition, the Core created a focused collection of shRNA vectors targeting protein kinases (using the TRC library resource in the core) and a multi-disciplinary team of Cancer Center members have used these tools to examine the kinase requirements of cancer cells for proliferation and for transformation via the HPV E7 oncoprotein, and for proliferation of VHL-/- cells. These studies revealed similar requirements for distinct kinases across particular related cell lines. In contrast, some commonly used cancer cell lines were distinct from others in their requirement for protein kinases. In some cases, even primary cells of different lineages isolated from distinct tissues displayed differences in kinase requirements. Additional studies identified kinases that are required for survival of cells expressing the E7 oncoprotein, a critical HPV oncogene involved in cervical cancer. These studies were greatly facilitated by the Core. Clones in the kinase collection are among the most highly requested clones in the PlasmID Repository.