Transcriptomes in healthy and diseased gingival tissues

Abstract

Background: Clinical and radiographic measures are gold standards for diagnosing periodontitis but offer little information regarding the pathogenesis of the disease. We hypothesized that a comparison of gene expression signatures between healthy and diseased gingival tissues would provide novel insights in the pathobiology of periodontitis and would inform the design of future studies.

Methods: Ninety systemically healthy non-smokers with moderate to advanced periodontitis (63 with chronic periodontitis and 27 with aggressive periodontitis) each contributed at least two diseased interproximal papillae (with bleeding on probing [BOP], probing depth [PD] > or =4 mm, and attachment loss [AL] > or =3 mm) and a healthy papilla, if available (no BOP, PD < or =4 mm, and AL < or =2 mm). RNA was extracted, amplified, reverse-transcribed, labeled, and hybridized with whole genome microarrays. Differential expression was assayed in 247 individual tissue samples (183 from diseased sites and 64 from healthy sites) using a standard mixed-effects linear model approach, with patient effects considered random with a normal distribution and gingival tissue status considered a two-level fixed effect. Gene ontology analysis classified the expression patterns into biologically relevant categories.

Results: Transcriptome analysis revealed that 12,744 probe sets were differentially expressed after adjusting for multiple comparisons (P <9.15 x 10(7)). Of those, 5,295 were upregulated and 7,449 were downregulated in disease compared to health. Gene ontology analysis identified 61 differentially expressed groups (adjusted P <0.05), including apoptosis, antimicrobial humoral response, antigen presentation, regulation of metabolic processes, signal transduction, and angiogenesis.

Conclusion: Gingival tissue transcriptomes provide a valuable scientific tool for further hypothesis-driven studies of the pathobiology of periodontitis.

Figure 1

Visualization of the top 50 probe sets with increased expression in diseased, relative to healthy gingival tissue (A) and of the top 50 probe sets with decreased expression in diseased, relative to healthy gingival tissue (B). Gingival tissue samples are grouped according to clinical periodontal status with diseased tissues on the left (red horizontal bar) and healthy tissues on the right (green bar). The color of each pixel represents gene expression level with darker colors indicating lower relative expression values. Columns correspond to individual tissue samples and rows correspond to probe sets. Fold change (FC) describes the ratio of mean expression in diseased tissue over the mean expression in healthy tissue. Note that multiple probe sets map to a single gene. Due to space limitations, only one gene symbol and gene name per probe set are identified. A complete list of gene symbols and names per probe set is provided in the Online Supplement Table 1.

Figure 1

Visualization of the top 50 probe sets with increased expression in diseased, relative to healthy gingival tissue (A) and of the top 50 probe sets with decreased expression in diseased, relative to healthy gingival tissue (B). Gingival tissue samples are grouped according to clinical periodontal status with diseased tissues on the left (red horizontal bar) and healthy tissues on the right (green bar). The color of each pixel represents gene expression level with darker colors indicating lower relative expression values. Columns correspond to individual tissue samples and rows correspond to probe sets. Fold change (FC) describes the ratio of mean expression in diseased tissue over the mean expression in healthy tissue. Note that multiple probe sets map to a single gene. Due to space limitations, only one gene symbol and gene name per probe set are identified. A complete list of gene symbols and names per probe set is provided in the Online Supplement Table 1.

Figure 2

Ontology analysis of selected pathways. (A) MAPK signaling pathway; (B) cytokine-cytokine receptor interaction; (C) cell adhesion molecules; (D) apoptosis. Genes shown in red are over-expressed and genes shown in blue under-expressed in diseased gingival tissues when compared to healthy tissues. Genes in green are unchanged at the p<0.05 significance level.

Figure 2

Ontology analysis of selected pathways. (A) MAPK signaling pathway; (B) cytokine-cytokine receptor interaction; (C) cell adhesion molecules; (D) apoptosis. Genes shown in red are over-expressed and genes shown in blue under-expressed in diseased gingival tissues when compared to healthy tissues. Genes in green are unchanged at the p<0.05 significance level.

Figure 2

Ontology analysis of selected pathways. (A) MAPK signaling pathway; (B) cytokine-cytokine receptor interaction; (C) cell adhesion molecules; (D) apoptosis. Genes shown in red are over-expressed and genes shown in blue under-expressed in diseased gingival tissues when compared to healthy tissues. Genes in green are unchanged at the p<0.05 significance level.

Figure 2

Ontology analysis of selected pathways. (A) MAPK signaling pathway; (B) cytokine-cytokine receptor interaction; (C) cell adhesion molecules; (D) apoptosis. Genes shown in red are over-expressed and genes shown in blue under-expressed in diseased gingival tissues when compared to healthy tissues. Genes in green are unchanged at the p<0.05 significance level.