Renal Transcriptomes: Segmental Analysis of Differential Expression

Abstract

Background/Aims: Progress accomplished by complete genomes and cDNA-sequencing projects calls for methods that fully use these resources to study gene expression patterns in characterized cell populations. However, since the number of functional genes cannot be readily inferred from the genomic sequence, it is highly desirable to make use of methods enabling to study both known and unknown genes. Methods: The method of serial analysis of gene expression provides short diagnostic cDNA tags without bias towards known genes. In addition, the frequency of each tag in the library conveys quantitative information on gene expression. A microassay was set-up to perform serial analysis of gene expression in minute samples such as those obtained by microdissecting nephron segments. Results: Studies carried out in the thick ascending limb of Henle’s loop and the collecting duct of the mouse kidney provided expression data for several thousand genes. Known markers were found appropriately enriched, and several of the thick ascending limb or collecting duct specific transcripts had no database match. Conclusions: The microassay for serial analysis of gene expression makes possible large-scale quantitative measurements of mRNA levels in nephron segments. The comprehensive picture generated by analyzing both known and unknown transcripts in defined cell populations should help to discover genes with dedicated functions.

A panoramic view of gene expression in the human kidney

“…However, as outlined previously (2,20), caution is required when extrapolating to human beings observations made on the kidneys of animals. Comparison of the present results to those obtained in the mouse kidney (12,33) confirms that marked differences indeed are present between species. For example, the mRNA levels for AQP2 and AQP3 are heavily different in the mouse outer medullary collecting duct (OMCD), reaching a 30:1 ratio (33), whereas in the human OMCD we found similar mRNA abundances for both aquaporins.…”

Large-scale identification of genes implicated in kidney glomerulus development and function

“…Here we used a platform for glomerulus transcription profiling in the mouse, which combines an efficient method for glomerulus isolation with a tailored array—GlomChip—covering over 6000 glomerulus‐expressed genes. Transcription profiling studies on healthy and diseased kidneys, including isolated glomeruli, have previously been reported (Virlon et al , 1999; Wada et al , 2001; Elalouf et al , 2002; Chabardes‐Garonne et al , 2003; Sarwal et al , 2003; Wilson et al , 2003; Baelde et al , 2004; Higgins et al , 2004; Peterson et al , 2004; Sadlier et al , 2004; Susztak et al , 2004). When comparing our study to the earlier reports, it becomes apparent that the detection of glomerulus‐specific transcripts, in particular those with podocyte‐specific expression, is notoriously problematic.…”