Gene expression patterns in chronic periodontitis

Objectives: Key features of the pathogenesis of chronic periodontitis (CP) remain to be elucidated. High throughput technology such as gene expression microarray has the potential to provide new information relevant to the pathogenesis of CP. We conducted a clinical study to identify differences in gene expression patterns of gingiva collected from subjects with CP and healthy volunteers.

Methods: Clinical measures and gingival biopsies were collected from 28 patients with untreated CP and 14 volunteers without CP. Standard Affymetrix GeneChip (Santa Clara, CA) protocols were used to analyze RNA extracted from biopsies using HG-U95Av2 GeneChip (Affymetrix, Santa Clara, CA) arrays. CEL files were converted to analyzable form using the GC-robust multi-chip analysis. The resulting expression data were log transformed and grouped by periodontal disease status for comparison. Hierarchical clustering and significance analysis were performed using Arrayassist (Stratagene, La Jolla, CA).

Results: Hierarchical clustering was able to distinguish CP and healthy samples with notable exceptions. 5 of 28 hybridizations of PD samples clustered into the predominantly healthy group, while 3 of 14 healthy samples clustered into the CP group. Significance analysis revealed 110 differentially expressed genes. Inspection of this list led to the identification of genes of well known and lesser-known function which were related to the following biological pathways; immune response(n=26), transcription processes(16), cell cycle and signaling(13), ecto and mesodermal development(10), protein transformation(9), intracellular reactions(9), transport of ions(5), apoptosis related(3), complement activation(1), lectin pathway(1), co-translational protein membrane targeting(1), phosphoenolpyruvate-dependent sugar phosphotransferase system(1), biological process not identified(15).

Conclusion: Gene expression microarray technology differentiated chronic periodontitis and healthy samples in most but not all cases. Differentially expressed genes were identified that may prove to be useful in the identification of new pathways of tissue destruction. Interpretation of these biological networks may lead to better understanding of the pathogenesis of chronic periodontitis.