Abstract
BackgroundPeriodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing.MethodsThe pooled RNAs of 10 gingival tissues from both healthy and periodontitis patients were analyzed by deep sequencing followed by computational annotation and quantification of mRNA structures.ResultsThe differential expression analysis designated 400 up-regulated genes in periodontitis tissues especially in the pathways of defense/immunity protein, receptor, protease, and signaling molecules. The top 10 most up-regulated genes were CSF3, MAFA, CR2, GLDC, SAA1, LBP, MME, MMP3, MME-AS1, and SAA4. The 62 down-regulated genes in periodontitis were mainly cytoskeletal and structural proteins. The top 10 most down-regulated genes were SERPINA12, MT4, H19, KRT2, DSC1, PSORS1C2, KRT27, LCE3C, AQ5, and LCE6A. The differential alternative splicing analysis revealed unique transcription variants in periodontitis tissues. The EDB exon was predominantly included in FN1, while exon 2 was mostly skipped in BCL2A1.ConclusionsThese findings using RNA sequencing provide novel insights into the pathogenesis mechanism of periodontitis in terms of gene expression and alternative splicing.Electronic supplementary materialThe online version of this article (doi:10.1186/s40246-016-0084-0) contains supplementary material, which is available to authorized users.
Highlights
Periodontitis is a chronic inflammatory disease of periodontium, characterized by massive destruction of both soft and hard tissues surrounding the teeth [1]
RNA sequencing results Total RNA was extracted from 10 healthy gingival tissue samples and 10 chronic periodontitis-affected gingival tissues as described above
By applying the cutoff of at least twofold change in the number of reads with 5 % false discovery rate (FDR), we found a total of 462 genes differentially expressed between the samples (Fig. 1a, volcano plot)
Summary
Periodontitis is a chronic inflammatory disease of periodontium, characterized by massive destruction of both soft and hard tissues surrounding the teeth [1]. The current concept for the periodontal diseases involve complex interaction between the microbial biofilm and host immune responses that leads to the alteration of bone and connective tissue homeostasis [2, 3]. The analysis of transcriptome by microarrays has been a valuable tool to study the changes in gene expression profiles in gingival tissues of periodontitis patients [7,8,9]. Recent advances in the high-throughput RNA sequencing technology revolutionarily enhanced our understanding on the complexity of eukaryotic transcriptome [10, 11]. Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. High-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing
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