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Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset.

Lindenmeyer MT, Eichinger F, Sen K, Anders HJ, Edenhofer I, Mattinzoli D, Kretzler M, Rastaldi MP, Cohen CD - PLoS ONE (2010)

Bottom Line: This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus.Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance.In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons.

View Article: PubMed Central - PubMed

Affiliation: Division of Nephrology, University Hospital Zurich, Zurich, Switzerland.

ABSTRACT
Glomerular diseases account for the majority of cases with chronic renal failure. Several genes have been identified with key relevance for glomerular function. Quite a few of these genes show a specific or preferential mRNA expression in the renal glomerulus. To identify additional candidate genes involved in glomerular function in humans we generated a human renal glomerulus-enriched gene expression dataset (REGGED) by comparing gene expression profiles from human glomeruli and tubulointerstitium obtained from six transplant living donors using Affymetrix HG-U133A arrays. This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus. Genes with 'a priori' known prominent glomerular expression served for validation and were all found in the novel dataset (e.g. CDKN1, DAG1, DDN, EHD3, MYH9, NES, NPHS1, NPHS2, PDPN, PLA2R1, PLCE1, PODXL, PTPRO, SYNPO, TCF21, TJP1, WT1). The mRNA expression of several novel glomerulus-enriched genes in REGGED was validated by qRT-PCR. Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance. This finding was further validated by assessing the expression of the axon guidance molecules neuritin (NRN1) and roundabout receptor ROBO1 and -2. In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons. A systematic analysis of this glomerulus-specific gene expression dataset allows the detection of target molecules and biological processes involved in glomerular biology and renal disease.

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Evaluation of neuron-associated genes by real-time RT-PCR.Expression of NRN1, ROBO1, ROBO2, and NPDC1 mRNA in an independent cohort of microdissected samples of allograft donors normalized to the tubulointerstitial expression (n = 10). * p<0.05; ** p<0.01. The data shown are normalized to the mean of the two reference genes, GAPDH and 18S rRNA.
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pone-0011545-g003: Evaluation of neuron-associated genes by real-time RT-PCR.Expression of NRN1, ROBO1, ROBO2, and NPDC1 mRNA in an independent cohort of microdissected samples of allograft donors normalized to the tubulointerstitial expression (n = 10). * p<0.05; ** p<0.01. The data shown are normalized to the mean of the two reference genes, GAPDH and 18S rRNA.

Mentions: DDD as well as GO and KEGG analyses revealed axon guidance-related genes to be overrepresented in the renal glomerulus. We decided to focus on 4 selected neuronal associated genes in closer detail: neural proliferation differentiation and control 1 (NPDC1), neuritin (NRN1), roundabout receptor 1 and 2 (ROBO1, ROBO2, the latter not on the HG-U133A array and therefore not in REGGED, but found in rodent glomeruli by [42]). For initial further validation real-time RT-PCR was performed on an independent cohort of microdissected samples of allograft donors. Figure 3 displays the results for NPDC1, NRN1, ROBO1 and ROBO2 mRNA expression. The abundance of all these genes was significantly higher in glomeruli than in the tubulointerstitium ranging from approximately 9-fold (NPDC1) to 130-fold (ROBO2).


Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset.

Lindenmeyer MT, Eichinger F, Sen K, Anders HJ, Edenhofer I, Mattinzoli D, Kretzler M, Rastaldi MP, Cohen CD - PLoS ONE (2010)

Evaluation of neuron-associated genes by real-time RT-PCR.Expression of NRN1, ROBO1, ROBO2, and NPDC1 mRNA in an independent cohort of microdissected samples of allograft donors normalized to the tubulointerstitial expression (n = 10). * p<0.05; ** p<0.01. The data shown are normalized to the mean of the two reference genes, GAPDH and 18S rRNA.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2902524&req=5

pone-0011545-g003: Evaluation of neuron-associated genes by real-time RT-PCR.Expression of NRN1, ROBO1, ROBO2, and NPDC1 mRNA in an independent cohort of microdissected samples of allograft donors normalized to the tubulointerstitial expression (n = 10). * p<0.05; ** p<0.01. The data shown are normalized to the mean of the two reference genes, GAPDH and 18S rRNA.
Mentions: DDD as well as GO and KEGG analyses revealed axon guidance-related genes to be overrepresented in the renal glomerulus. We decided to focus on 4 selected neuronal associated genes in closer detail: neural proliferation differentiation and control 1 (NPDC1), neuritin (NRN1), roundabout receptor 1 and 2 (ROBO1, ROBO2, the latter not on the HG-U133A array and therefore not in REGGED, but found in rodent glomeruli by [42]). For initial further validation real-time RT-PCR was performed on an independent cohort of microdissected samples of allograft donors. Figure 3 displays the results for NPDC1, NRN1, ROBO1 and ROBO2 mRNA expression. The abundance of all these genes was significantly higher in glomeruli than in the tubulointerstitium ranging from approximately 9-fold (NPDC1) to 130-fold (ROBO2).

Bottom Line: This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus.Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance.In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons.

View Article: PubMed Central - PubMed

Affiliation: Division of Nephrology, University Hospital Zurich, Zurich, Switzerland.

ABSTRACT
Glomerular diseases account for the majority of cases with chronic renal failure. Several genes have been identified with key relevance for glomerular function. Quite a few of these genes show a specific or preferential mRNA expression in the renal glomerulus. To identify additional candidate genes involved in glomerular function in humans we generated a human renal glomerulus-enriched gene expression dataset (REGGED) by comparing gene expression profiles from human glomeruli and tubulointerstitium obtained from six transplant living donors using Affymetrix HG-U133A arrays. This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus. Genes with 'a priori' known prominent glomerular expression served for validation and were all found in the novel dataset (e.g. CDKN1, DAG1, DDN, EHD3, MYH9, NES, NPHS1, NPHS2, PDPN, PLA2R1, PLCE1, PODXL, PTPRO, SYNPO, TCF21, TJP1, WT1). The mRNA expression of several novel glomerulus-enriched genes in REGGED was validated by qRT-PCR. Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance. This finding was further validated by assessing the expression of the axon guidance molecules neuritin (NRN1) and roundabout receptor ROBO1 and -2. In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons. A systematic analysis of this glomerulus-specific gene expression dataset allows the detection of target molecules and biological processes involved in glomerular biology and renal disease.

Show MeSH
Related in: MedlinePlus