Human prostate epithelial cell-type cDNA libraries and prostate expression patterns.

Background: Transcriptome analysis is a powerful approach to uncovering genes responsible for diseases such as prostate cancer. Ideally, one would like to compare the transcriptomes of a cancer cell and its normal counterpart for differences.

Methods: Prostate luminal and basal epithelial cell types were isolated and cell-type-specific cDNA libraries were constructed. Sequence analysis of cDNA clones generated 505 luminal cell genes and 560 basal cell genes. These sequences were deposited in a public database for expression analysis.

Results: From these sequences, 119 unique luminal expressed sequence tags (ESTs) were extracted and assembled into a luminal-cell transcriptome set, while 154 basal ESTs were extracted and assembled into a basal-cell set. Interlibrary comparison was performed to determine representation of these sequences in cDNA libraries constructed from prostate tumors, PIN, cell lines.

Conclusions: Our analysis showed that a significant number of epithelial cell genes were not represented in the various transcriptomes of prostate tissues, suggesting that they might be underrepresented in libraries generated from tissue containing multiple cell types. Although both luminal and basal cell types are epithelial, their transcriptomes are more divergent from each other than expected, underscoring their functional difference (secretory vs. nonsecretory). Tumor tissues show different expression of luminal and basal genes, with perhaps a trend towards expression of basal genes in advanced diseases.