Gene Expression Analysis in Periodontitis Using a Novel RNA-sequencing Method

Objectives: Periodontitis is the most common chronic inflammatory disease in humans. It is the result of a complex interaction of periodontal microorganisms and the host inflammatory response, leading to destruction of the tooth-supporting structure, and ultimately tooth-loss. We have previously performed RNA-sequencing (RNA-seq) analyses in gingival tissue from patients with periodontitis and healthy controls, which identified differentially expressed genes. The aim of this study is to further analyze the gene expression in gingival tissue from periodontitis tissues at a high resolution, using a novel RNA-sequencing method that enables spatially resolved gene expression in tissue sections.
Methods: A novel RNA-seq method, which combines histological analyses of tissue sections with transcriptome analysis through RNA-seq was used. Fresh frozen gingival tissue sections were placed onto an array with spatially defined probes, designed to capture mRNA. By imaging the sections after H&E staining and converting the mRNA to sequencing libraries the transcriptome data from each cell could be coupled to the corresponding cell in the tissue section.
Results: The novel RNA-seq method identified a number of genes to be specifically expressed in epithelial cells and connective tissue. As a proof of concept keratin was shown to be expressed specifically in epithelial cells and collagen was expressed specifically in connective tissue. Genes that previously have been shown to be expressed in gingival tissue were identified, showing the potential of identifying novel genes involved in the disease.
Conclusions: The results lead to the conclusion that this RNA-seq method can be used to identify genes involved in periodontitis, while retaining the histological information about the biopsy, such as cell type and degree of inflammation. This will lead to a greater understanding of the disease and a possibility to identify genes that could be used as biomarkers for periodontitis.