Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis

Abstract

Background: Interstitial cystitis (IC), a chronic bladder disease with an increasing incidence, is diagnosed using subjective symptoms in combination with cystoscopic and histological evidence. By cystoscopic examination, IC can be classified into an ulcerative and a non-ulcerative subtype. To better understand this debilitating disease on a molecular level, a comparative gene expression profile of bladder biopsies from patients with ulcerative IC and control patients has been performed.

Results: Gene expression profiles from bladder biopsies of five patients with ulcerative IC and six control patients were generated using Affymetrix GeneChip expression arrays (Affymetrix--GeneChip Human Genome U133 Plus 2.0). More than 31,000 of > 54,000 tested probe sets were present (detection p-value < 0.05). The difference between the two groups was significant for over 3,500 signals (t-test p-value < 0.01), and approximately 2,000 of the signals (corresponding to approximately 1,000 genes) showed an IC-to-healthy expression ratio greater than two. The IC pattern had similarities to patterns from immune system, lymphatic, and autoimmune diseases. The dominant biological processes were the immune and inflammatory responses. Many of the up-regulated genes were expressed in leukocytes, suggesting that leukocyte invasion into the bladder wall is a dominant feature of ulcerative IC. Histopathological data supported these findings.

Conclusion: GeneChip expression arrays present a global picture of ulcerative IC and provide us with a series of marker genes characteristic for this subtype of the disease. Evaluation of biopsies from other bladder patients with similar symptoms (e.g. patients with non-ulcerative IC) will further indicate whether the data presented here will be valuable for the diagnosis of IC.

Figures

Figure 1

Gene expression array correlation plot. Gene expressions of 16 bladder biopsies were compared. Bladder tissue was taken from six healthy controls ("healthy") and from five IC patients ("ulcus" and "ni"). From each IC patient, two samples have been analyzed, one from an ulcer (ulcus) and one from a non-ulcer (ni) area. Only probe sets defined as "present" have been included in this comparison, and the metric was the Pearson correlation coefficient. White or light-grey squares represent a similar gene expression, and black or dark-grey squares represent a difference in gene expression. Ulcer tissue (ulcus); non-ulcer tissue in patients with Hunner's ulcers (ni).

Figure 2

Scatter plot: ni-vs-healthy. The scatter plot illustrates the data selection set by the statistical requirements in the ni-vs-healthy comparison. The average expression values of condition "healthy" (patients 2, 5, 7, 9, 10, 11; x-axis) and condition "ni" (patients 4, 12, 13, 14, 15; y-axis) were compared. For this graph, all normalized data (54,613 probe sets) were used. Grey dots correspond to "not present" probe sets (criteria for "present": detection p-value < 0.05). Black dots correspond to "presents", and blue dots correspond to "presents" and "significants" (criteria for "significant": p-value for differential expression < 0.01). Non-ulcer tissue in patients with Hunner's ulcers (ni).

Figure 3

Heatmap visualization of the top 100 B- and T-cell markers. Using a biomarker search with Genevestigator [33] we identified the top 100 probe sets that were specific for "B-lymphocytes" (A) and "T-lymphocytes" (B), respectively, and visualized them as a heatmap. For each probe set the heatmap shows the log2-ratio against the average of our entire data set. For both the B- and T-lymphocytes, a large proportion of the probe sets was upregulated in "ni" and "ulcus" as compared to the healthy tissue. Additional file 6 (Blympho-top100 cluster) and Additional file 7 (Tlympho-top100 cluster) list the top 100 probe sets and their corresponding gene names. Ulcer tissue (ulcus); non-ulcer tissue in patients with Hunner's ulcers (ni).

Figure 4

Histopathology data. Representative histopathology findings of bladder biopsies from IC patient 15 (A, B), from IC patient 4 (C), and from control patient 2 (D). (A) Cross-section of an entire biopsy (60× magnification). The HE stain shows a focally accentuated lymphoplasmocytic inflammatory infiltration. The inner bladder surface is denudated from the urothelial lining (lower right), thus showing an ulcer area. (B) Giemsa staining (200×). Arrowheads point to numerous mast cells in the mixed lymphoplasmocytic inflammatory infiltration. Blood vessels show active hyperemia with dilated lumina. There is evidence of a substantial interstitial edema. (C) The HE stain (100×) shows a marginal urothelial layer (on the left) and substantial inflammation in deep areas of the biopsy. (D) The HE stain (100×) shows the urothelial layer on the left side and signs of a mild unspecific subepithelial inflammation.

Figure 5

Map of BCR-pathway. The process "Immune_BCR pathway" turned out to be significant (p-value 3.48E-13) in ulcerative IC (MetaCore analysis). The map shows a B-cell with the signal transduction from the membrane receptors to the transcription factors in the nucleus. The five columns on the right of an individual signaling component indicate the expression results of the five patient samples (4 ni, 12 ni, 13 ni, 14 ni, 15 ni) relative to the healthy controls. Up-regulated gene expressions are shown in red.