Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study.

To evaluate the utility of transcript profiling for prediction of protein expression levels, we compared profiles across the NCI-60 cancer cell panel, which represents nine tissues of origin. For that analysis, we present here two new NCI-60 transcript profile data sets (A based on Affymetrix HG-U95 and HG-U133A chips; Affymetrix, Santa Clara, CA) and one new protein profile data set (based on reverse-phase protein lysate arrays). The data sets are available online at http://discover.

Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery.

Transcriptomic techniques are valuable tools with which to validate genetic and biological hypotheses and are now widely available for research. However, with the exception of tumor biology, comparative genomics analyses have been difficult to use as discovery engines to describe biologically relevant expression changes. We propose that physical proximity of human genes correlates with similar mRNA expression, so that increased expression might include a disease-relevant gene and many other genes in the adjacent region.

Expression of SSX genes in the neoplastic cells of Hodgkin's lymphoma.

The cancer/testis antigen (CTA) group of tumor-associated proteins have been reported to be expressed in various cancers and in adult testis but they are essentially not found in any other normal adult nonneoplastic tissues. Prompted by the frequent detection of SSX1 in a previous comprehensive expression profile of the Hodgkin's lymphoma (HL) cell line L428, we analyzed SSX expression by nonnested reverse-transcription polymerase chain reaction (RT-PCR) in 4 HL cell lines (L428, L540, HD-MY-Z, and KM-H2) and 32 tumor samples of HL. The cellular localization of SSX expression in the tumor samples was further analyzed by in situ hybridization (ISH).