Effects of probenecid on gene expression.

<p>A: Genes up-regulated in cells incubated in pre- and post dialysis plasma returned toward baseline with added probenecid. B: Genes down-regulated in cells incubated in pre- and post dialysis plasma returned toward baseline with added probenecid. Each line represents the average of 5 or 10 gene arrays.</p

Comparison of microrray findings with Nanostring assay (22 genes).

<p>2A: Changes in gene expression estimated by microarray. 2B: Changes in gene expression estimated by Nanostring. 2C: Comparison between microarray estimate and Nanostring shown on a coordinate plot. Pearson correlation coefficient, pre-D/Control = 0.98, post-D/Control = 0.92.</p

The expression of genes in the TGF receptor pathway identified by Pavlidis Template Matching [27] in the DAVID data base [31] and subjected to Gene Set Enrichment Analysis (GSEA) [32,33].

<p>The 10 uremic patients were dichotomized into those without RRF (n = 5) on the left and those with RF (n = 5) on the right. The GSEA enrichment score curve (top panel) for TGF-beta receptor signaling (34 genes), indicates 10 genes as core-enriched (mapped on ranked list left of the peak on the enrichment score curve). The activation of these 10 genes was greater following incubation in pre- and post- dialysis (Pre-Dial, Post-Dial) plasma of subjects without RRF than in subjects with RRF (bottom panels, red in heat map = high mRNA abundance, blue = low abundance).</p

Gene expression in reporter renal tubular cells.

<p>A: Genes that returned to baseline post-dialysis. Each individual line represents the average value in the 10 uremic subjects for each gene that was dysregulated. 282 genes were upregulated (displayed as yellow to red lines) and 255 genes were downregulated (displayed as green to blue lines) in the pre-dialysis samples as compared to normal controls. Post-dialysis these values returned to baseline. B: Genes that remained dysregulated after dialysis treatment. 843 genes were upregulated and 532 genes were downregulated. C: Genes expressed following incubation in normal plasma spiked with indoxyl sulfate compared with their expression levels in cells treated with pre-dialysis and post-dialysis plasma. 908 genes were upregulated and 571 genes were downregulated. D: 81.5% of upregulated genes that were not normalized by dialysis were mimicked by addition of indoxyl sulfate to normal plasma. E: 80.4% of downregulated genes that were not normalized by dialysis were mimicked by addition of indoxyl sulfate to normal plasma.</p

Plasma indoxyl sulfate concentration pre- and post—hemodialysis.

<p>Patients with and without residual renal function exhibited a decrease in circulating total indoxyl sulfate levels post-dialysis. Total indoxyl sulfate concentration was greater in both pre- and post-dialysis plasma in subjects without Residual Renal Function (anuric) than in subjects with Residual Renal Function.</p

Comparison of gene microarray and Nanostring stimates of IS.

<p>22 Genes are listed in descending order from greatest up-regulated to greatest down-regulated.The pre-and post dialysis values, used to create <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118703#pone.0118703.g002" target="_blank">Fig. 2A and 2B</a> are presented. Gene symbols are shown on the left; gene names are shown on the right.</p><p>Comparison of gene microarray and Nanostring stimates of IS.</p

Changes in pH and bicarbonate during isohydric and standard dialysis.

<p>Changes in pH and bicarbonate during isohydric and standard dialysis.</p

Changes in free fraction.

<p>Solute concentration and plasma clearance during isohydric and standard dialysis.</p

Proportion of variation accounted for by mixed models predicting free concentration from either pH or total concentration.

<p>Proportion of variation accounted for by mixed models predicting free concentration from either pH or total concentration.</p

Clinical characteristics of subjects.

<p>Clinical characteristics of subjects.</p