Serial microanalysis of renal transcriptomes

Large-scale gene expression studies can now he routinely performed on macro amounts of cells, but it is unclear to which extent current methods are val uable for analyzing complex tissues, In the present study, we used the meth od of serial analysis of gene expression (SAGE) for quantitative mRNA profi ling in the mouse kidney. We first performed SAGE at the whole-kidney level by sequencing 12,000 mRNA tags. Most abundant tags corresponded to transcr ipts widely distributed or enriched in the predominant kidney epithelial ce lls (proximal tubular cells), whereas transcripts specific for minor cell t ypes were barely evidenced, To better explore such cells, we set up a SAGE adaptation for downsized extracts, enabling a 1,000-fold reduction of the a mount of starting material. The potential of this approach was evaluated by studying gene expression in microdissected kidney tubules (50,000 cells). Specific gene expression profiles were obtained, and known markers (e.g., u romodulin in the thick ascending limb of Henle's loop and aquaporin-2 in th e collecting duct) were found appropriately enriched. In addition, several enriched tags had no databank match, suggesting that they correspond to unk nown or poorly characterized transcripts with specific tissue distribution, It is concluded that SAGE adaptation for downsized extracts makes possible large-scale quantitative gene expression measurements in small biological samples and will help to study the tissue expression and function of genes not evidenced with other high-throughput methods.