12 Oct NimbleGen to be part of new cancer study
Madison, Wis. – A Madison company will participate newly funded research to map regulatory pathways in cancer. The company, NimbleGen Systems Inc., will participate in the research with a number of other groups that together have been approved for a National Cancer Institute grant that could total $1.7 million over four years.
NimbleGen will work with the University California, San Diego (UCSD) Branch of the Ludwig Institute for Cancer Research (LICR) and Iceland Genomics Corp. on the research.
In the first phase, NimbleGen and LICR researchers will collaborate on optimizing chromatin immunoprecipitation (ChIP)-chip methodologies to increase by threefold the number of samples that can be studied on a single microarray as well as reduce experimental costs.
The second phase will utilize the optimized ChIP-chip technology to map transcription factor (TF) binding sites throughout the human genome and screen TF binding in a large sample set from Iceland Genomics’ clinical cancer collection. The process will also feature high-throughput NimbleGen ChIP-chip array reuse, further reducing experimental costs.
ChIP-chip is a rapidly emerging technology in the study of gene regulation and represents the next phase in unraveling the complexities of the human genome.
The collaboration between investigators from NimbleGen and LICR is an extension of prior collaborative research on ChIP-chip technology, associated with the ENCODE consortium, which resulted in the genome-wide mapping of human TF binding sites. According to Roland Green, NimbleGen vice president of research and development, the investigators hope to gain insights on TF patterns that represent unique signatures in specific tumor types.
“Most human cancers are caused by abnormal activities of a class of proteins called transcription factors,” said Bing Ren, head of the Laboratory of Gene Regulation at LICR. “These proteins are molecular switches that control the program of gene expression in the human genome. This project represents the most comprehensive analysis of the function of several transcription factors involved in breast and colon cancers, and the results should help us understand the molecular basis of two of the most common and deadly forms of human cancers.”
Iceland Genomics, a participant in the Icelandic Cancer Project, provides expertise in cancer research and has built a comprehensive database containing clinical data and genealogy records on all cancer patients who participate in their research program.
“Mapping the binding sites of transcription factors in tumors can give us important information on why cancer cells differ from normal cells. Such information can then be applied to identify targets for treating the disease,” said Eirikur Steingrimsson, chief scientific officer of Iceland Genomics. “This is the ultimate goal of the Icelandic Cancer Project.”
(The research already under way between NimbleGen and LICR resulted in the Nature publication “A High-Resolution Map of Active Promoters in the Human Genome,” Kim, TH et al. Nature 436, 876-880, Aug. 11, 2005.)
¥ See previous WTN coverage of NimbleGen:
—NimbleGen identifies human genome sequences
— NimbleGen presents new tech for comparing microbe DNA
— Madison biochip research offers geneticists a big view through a small window