ONCOMINE™ Again Key to Prostate Cancer Discovery
News Jun 12, 2008
Compendia Bioscience, Inc. has announced the central role of their flagship product Oncomine™ in the discovery and identification of SPINK1 as a key new therapeutic target and biomarker for prostate cancer.
The company believes that the Oncomine is a rapidly growing compendium of nearly 26,000 gene expression and DNA copy number arrays coupled with analysis functions and a web application for data mining and visualization. Comprised of thousands of samples representing every major type of cancer, Oncomine exploits this data for therapeutic target discovery, validation, and prioritization.
Compendia CEO Daniel R. Rhodes, Ph.D., in his continued role as a research investigator at the University of Michigan, led the Oncomine analysis that identified SPINK1 as a candidate oncogene in prostate cancer. Further experimental work by many of the same scientists that previously identified ETS-family gene fusions in prostate cancer using Oncomine led to this discovery.
“We extended an approach called Cancer Outlier Profile Analysis (COPA) that had previously led us to identify ETS-family gene fusions in prostate cancer,” said Dr. Rhodes.
“We knew from that experience that true oncogenes are likely to appear in COPA results from multiple independent datasets. Therefore, we intentionally looked for genes that had high COPA ranks across multiple datasets and SPINK1 looked interesting. Further Oncomine analysis showed that SPINK1 over-expression was mutually exclusive with ETS-family gene fusion events and was not present in normal prostate tissue. So, we were pretty sure we had found something important.”
Published in the current edition of Cancer Cell (Volume 13 Issue 6: June 2008), this study shows that SPINK1 is detectable in the urine and that SPINK1-positive prostate cancers are a particularly aggressive molecular subset of prostate cancer with SPINK1 having a role in cancer invasion.
The analysis approach used to identify SPINK1 has been named Meta-COPA and will soon become a standard feature within the Oncomine platform. In the interim, Compendia Bioscience will provide scientific services to answer customers’ key research questions requiring Meta-COPA or other analyses not currently addressable through the Oncomine user interface.
Chinese researchers have developed interfacially polymerized porous polymer particles for low- abundance glycopeptide separation. These polymer particles - with hydrophilic-hydrophobic heterostructured nanopores - can separate low-abundance glycopeptides from complex biological samples with high-abundance background molecules efficiently.