Analysis of kidney glomerular and microvascular transcriptomes

Abstract: Kidney glomeruli play a crucial role in the maintenance of body homeostasis. Many diseases attack the kidney function by primarily affecting glomeruli. However, the transcriptome profiles and the function of the glomerulus is poorly understood. Microvascular pericytes are multifunctional cells and they are actively involved in angiogenesis at different aspects. But shortage of molecular markers for pericyte has hampered the studies for its identification, origin and function. In order to explore the transcriptome of kidney glomeruli and microvascular pericytes, several genomics and bioinformatics approaches were applied. First, we constructed and large scale sequenced four Express Sequence Tag (EST) libraries generated from pure preparations of newborn and adult mouse glomeruli. EST sequence analysis produced direct expression profiles of kidney glomerulus and revealed glomerulus-specific expression patterns (GlomBase). By comparing the transcript abundance profiles in the glomerulus EST libraries with public whole kidney libraries, we identified 497 glomerulus-enriched mouse transcripts in the newborn and/or adult mouse glomerulus, eight of which were confirmed by individual experiments. The glomerular ESTs were printed on glass slides in order to generate cDNA microarrays with broad representation of glomerulus-expressed genes (GlomChip). Subsequently, by using GlomChip to compare the RNA samples from the glomerulus with non-glomerulus kidney tissues, we identified 357 mouse genes as glomerulus-enriched and some of them were individually studied in detail. Further, by combing the result from Affymetrix whole genome array study and published SAGE and Stanford cDNA array results, we did a meta analysis and merged the data into a catalogue of 1407 glomerulus-enriched genes. Based on this, a protein-protein interaction network in the glomerulus (GlomNet) was constructed. GlomChip was also applied to the analysis of the microvascular pericyte transcriptome. By comparing the expression profiles in microvascular fragments from wild-type and pericyte-deficient Pdgfb/Pdgfrb knockout mice, we identified 142 gene transcripts that were down-regulated in both mutants, which could be potential new pericyte markers. The transcript catalogues that we have generated provide information about the transcriptome profiles of the kidney glomerulus and the microvascular pericytes, and contribute new information about their function, physiology and disease. Also, GlomNet will contribute an integrated systematic understanding of the kidney glomerulus.