Drs Ragavan and Martin rightly indicate that it is difficult to differentiate between the PZ and TZ based on H&E staining only. In our study, zonal origin was mainly based on the location of the tissue within the transverse prostate section. Macroscopically, the different zones can easily be located. The 5-mm thick transverse section was sliced into 1.5 × 1.5 cm fragments, keeping track of orientation and location of this fragment with respect to the macroscopic location of the zones. With this information, H&E cryostat sections were used to pinpoint normal transition or peripheral tissue.

This lack of clear distinguishing morphological differences between the PZ and TZ indeed supports our hypothesis that the dissimilarity in gene expression is caused by a qualitative distinction in cell-type characteristics. As some genes preferentially expressed in the different zones were stroma-specific, we propose that particularly this cell type is different between the zones. The contribution of other cell types (such as stem cells) to zonal-specific gene expression was not investigated, but is definitely worth assessing. Previous work on gene expression differences between the zones, as described by Drs Ragavan and Martin, and others, was confirmed by our microarray analyses. Besides the zonal-preferential genes mentioned in Table 3, also the PZ preferential expression of CYP1B1 was substantiated in our assays (Appendix, Table, ID 303).