A panoramic view of gene expression in the human kidney

Abstract

To gain a molecular understanding of kidney functions, we established a high-resolution map of gene expression patterns in the human kidney. The glomerulus and seven different nephron segments were isolated by microdissection from fresh tissue specimens, and their transcriptome was characterized by using the serial analysis of gene expression (SAGE) method. More than 400,000 mRNA SAGE tags were sequenced, making it possible to detect in each structure transcripts present at 18 copies per cell with a 95% confidence level. Expression of genes responsible for nephron transport and permeability properties was evidenced through transcripts for 119 solute carriers, 84 channels, 43 ion-transport ATPases, and 12 claudins. Searching for differences between the transcriptomes, we found 998 transcripts greatly varying in abundance from one nephron portion to another. Clustering analysis of these transcripts evidenced different extents of similarity between the nephron portions. Approximately 75% of the differentially distributed transcripts corresponded to cDNAs of known or unknown function that are accurately mapped in the human genome. This systematic large-scale analysis of individual structures of a complex human tissue reveals sets of genes underlying the function of well-defined nephron portions. It also provides quantitative expression data for a variety of genes mutated in hereditary diseases and helps in sorting candidate genes for renal diseases that affect specific portions of the human nephron.

Fig. 1.

A microdissected human nephron. Blue boxes indicate the eight structures analyzed in the present study. Solid and dotted arcs indicate the kidney surface and limits of kidney zones, respectively. Glom, glomerulus; PCT, proximal convoluted tubule; PST, proximal straight tubule; DTL, descending thin limb; ATL, ascending thin limb; MTAL, medullary thick ascending limb of Henle's loop; CTAL, cortical thick ascending limb of Henle's loop; CNT, connecting tubule; CCD, cortical collecting duct; OMCD, outer medullary collecting duct; and IMCD, inner medullary collecting duct; DCT, distal convoluted tubule.

Fig. 2.

Expression pattern of markers for different nephron portions. Tag abundance indicates mRNA tag counts in libraries normalized to 50,000 tags. PODXL, podocalyxin-like; AQP1, aquaporin 1; UMOD, uromodulin; AQP3, aquaporin 3; SLC12A3, thiazide-sensitive Na-Cl cotransporter.

Fig. 3.

Overview of mRNA tag differential distribution. The number of mRNA tags displaying a significant differential distribution (P < 0.01, and ≥7-fold difference as compared with three libraries) is indicated for each library. The sum of all differences (n = 998) corresponds to 773 unique tags because of overlapping between libraries. The y axis indicates the number of differentially distributed tags common to clustered structures.

Fig. 4.

Quantitative RT-PCR analysis of mRNAs distribution along the nephron. RNAs were extracted from the five indicated structures, obtained in sufficient amounts to perform both SAGE and RT-PCR validations. RT-PCR data are displayed relative to the structure where expression is maximal. The value below each column indicates the result of the SAGE analysis and corresponds to tag counts for 50,000 tags. (a) Expression of candidate genes for IgA nephropathy (CTGF, GJA1) or PHA2A (DKFZp761N1114). (b) Selected examples of genes predicted by SAGE to be predominantly expressed in the glomerulus (SPARC, DKFZp564B076), the proximal tubule (BC001573, BC004360), or the thick ascending limb (FLJ31166).