Home   >   CSC-OpenAccess Library   >    Manuscript Information
Gene Expression Meta-Analysis Reveals Gene Associated with Periodontitis
Laura K. Harris, Mingi Kim
Pages - 1 - 17     |    Revised - 31-01-2024     |    Published - 29-02-2024
Volume - 17   Issue - 1    |    Publication Date - February 2024  Table of Contents
MORE INFORMATION
KEYWORDS
Periodontitis, Microarray, Gene Expression, Meta-Analysis, Gene Set Enrichment Analysis.
ABSTRACT
Background: Periodontitis is a severe form of gum disease which in flames and destroys tissues supporting the teeth and leading to potential loss of teeth. If untreated, it could lead to heightened risk of serious health issues and other complications. This study was performed to meta-analyze gene expression data from Periodontitis infected samples to possibly identify clinically targetable genes associated with Periodontitis.

Methods: This study defined 8 gene signatures between Periodontitis infected and mock infected from 2 datasets and compared them through Gene Set Enrichment Analysis (GSEA). Positive and negative panels were defined from GSEA identified leading-edge genes in each query set. GSEA was then utilized to calculate enrichment and identify differentiation in gene expression of Periodontitis and compared it with other gene signatures.

Results: GSEA identified 93 and 127 probes, representing 71 and 114 unique positive and negative panels, respectively, from the GSE10334 dataset. Also, GSEA identified 110 and 112 probes, representing 92 and 108 unique positive and negative panels, respectively, from the GSE16134 dataset. Non-random significant enrichment was observed between each identified panel and all verification gene signatures derived from both datasets and 23 overexpressed and 33 under expressed genes were found out to be shared across all verification gene signatures. The final genes identified to have significant association with Periodontitis consisted of few genes that were found to be associated with periodontitis in previous studies and also showed new genes that have not been identified to have connection with periodontitis previously.

Conclusion: Gene Set Enrichment Analysis identified genes associated with Periodontitis with prior or no prior known connection with Periodontitis. These results might be useful as potential therapeutic targets for Periodontitis disease.
Abusleme, L., Hoare, A., Hong, B. Y., & Diaz, P. I. (2021). Microbial signatures of health, gingivitis, and periodontitis. Periodontology 2000, 86(1), 57-78. https://doi.org/10.1111/prd.12362.
Cho, Y. D., Kim, W. J., Ryoo, H. M., Kim, H. G., Kim, K. H., Ku, Y., & Seol, Y. J. (2021). Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives. Clinical Epigenetics, 13(1), 1-14. https://doi.org/10.1186/s13148-021-01074-w.
Gao, S., Lin, M., Chen, W., Chen, X., Tian, Z., Jia, T., & Wu, L. (2024). Identification of potential diagnostic biomarkers associated with periodontitis by comprehensive bioinformatics analysis. Scientific Reports, 14(1), 93. https://doi.org/10.1038/s41598-023-50410-y.
Hajishengallis, G., & Korostoff, J. M. (2017). Revisiting the Page & Schroeder model: the good, the bad and the unknowns in the periodontal host response 40 years later. Periodontology 2000, 75(1), 116-151. https://doi.org/10.1111/prd.12181.
Hetta, H. F., Mwafey, I. M., Batiha, G. E., Alomar, S. Y., Mohamed, N. A., Ibrahim, M. A., Elkady, A., Meshaal, A. K., Alrefai, H., Khodeer, D. M., & Zahran, A. M. (2020). CD19+ CD24hi CD38hi Regulatory B Cells and Memory B Cells in Periodontitis: Association with Pro-Inflammatory and Anti-Inflammatory Cytokines. Vaccines, 8(2), 340. https://doi.org/10.3390/vaccines8020340.
Jeon, Y. S., Cha, J. K., Choi, S. H., Lee, J. H., & Lee, J. S. (2020). Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients. Journal of Periodontal & Implant Science, 50(5), 313. https://doi.org/10.5051/jpis.1905460273.
Jepsen, S., Caton, J. G., Albandar, J. M., Bissada, N. F., Bouchard, P., Cortellini, P., ... & Yamazaki, K. (2018). Periodontal manifestations of systemic diseases and developmental and acquired conditions: Consensus report of workgroup 3 of the 2017 World Workshop on the Classification of Periodontal and Peri‐Implant Diseases and Conditions. Journal of clinical periodontology, 45, S219-S229. https://doi.org/10.1038/sj.bdj.2018.616.
Kebschull, M., Demmer, R. T., Grn, B., Guarnieri, P., Pavlidis, P., & Papapanou, P. N. (2014). Gingival tissue transcriptomes identify distinct periodontitis phenotypes. Journal of dental research, 93(5), 459468. https://doi.org/10.1177/0022034514527288.
Kim, Y. G., Kim, M., Kang, J. H., Kim, H. J., Park, J. W., Lee, J. M., & Lee, Y. (2016). Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns. Human genomics, 10, 1-10. https://doi.org/10.1186/s40246-016-0084-0.
Kukurba, K. R., & Montgomery, S. B. (2015). RNA sequencing and analysis. Cold Spring Harbor Protocols, 2015(11), pdb-top084970. https://doi.org/10.1101/pdb.top084970.
Kwon, T., Lamster, I. B., & Levin, L. (2021). Current concepts in the management of periodontitis. International dental journal, 71(6), 462-476. https://doi.org/10.1111/idj.12630.
Li, Y., He, J., He, Z., Zhou, Y., Yuan, M., Xu, X., & Zhou, X. (2014). Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. The ISME journal, 8(9), 1879-1891. https://doi.org/10.1038/ismej.2014.28.
Lundmark, A., Gerasimcik, N., Bge, T., Jemt, A., Mollbrink, A., Salmn, F., ... & Yucel-Lindberg, T. (2018). Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics. Scientific reports, 8(1), 9370. https://doi.org/10.1038/s41598-018-27627-3.
Papapanou, P. N., Sanz, M., Buduneli, N., Dietrich, T., Feres, M., Fine, D. H., ... & Tonetti, M. S. (2018). Periodontitis: Consensus report of workgroup 2 of the 2017 World Workshop on the Classification of Periodontal and Peri‐Implant Diseases and Conditions. Journal of periodontology, 89, S173-S182. https://doi.org/10.1111/jcpe.12946.
Park, A., & Harris, L. K. (2021). Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. Frontiers in immunology, 12, 694355. https://doi.org/10.3389/fimmu.2021.694355.
Peymani, F., Farzeen, A., & Prokisch, H. (2022). RNA sequencing role and application in clinical diagnostic. Pediatric Investigation, 6(01), 29-35. https://doi.org/10.1002/ped4.12314.
Roky, M., Tan, J., Sztukowska, M. N., Trent, J. O., & Demuth, D. R. (2020). Identification of small-molecule inhibitors targeting Porphyromonasgingivalis interspecies adherence and determination of their in vitro and in vivo efficacies. Antimicrobial Agents and Chemotherapy, 64(11), 10-1128. https://doi.org/10.1128/aac.00884-20
Sanz, M., Herrera, D., Kebschull, M., Chapple, I., Jepsen, S., Beglundh, T., Sculean, A., Tonetti, M. S., & EFP Workshop Participants and Methodological Consultants (2020). Treatment of stage I-III periodontitis-The EFP S3 level clinical practice guideline. Journal of clinical periodontology, 47 Suppl 22(Suppl 22), 4–60. https://doi.org/10.1111/jcpe.13290.
Sczepanik, F. S. C., Grossi, M. L., Casati, M., Goldberg, M., Glogauer, M., Fine, N., & Tenenbaum, H. C. (2020). Periodontitis is an inflammatory disease of oxidative stress: We should treat it that way. Periodontology 2000, 84(1), 45-68. https://doi.org/10.1111/prd.12342.
Tettamanti, L., Gaudio, R. M., Iapichino, A., Mucchi, D., & Tagliabue, A. (2017). Genetic susceptibility and periodontal disease: a retrospective study on a large italian sample. ORAL & implantology, 10(1), 20-27. https://doi.org/10.11138/orl/2017.10.1.020.
Tonetti, M. S., Greenwell, H., & Kornman, K. S. (2018). Staging and grading of periodontitis: Framework and proposal of a new classification and case definition. Journal of periodontology, 89, S159-S172. https://doi.org/10.1002/jper.18-0006.
Trombelli, L., Farina, R., Silva, C. O., & Tatakis, D. N. (2018). Plaque‐induced gingivitis: Case definition and diagnostic considerations. Journal of clinical periodontology, 45, S44-S67. https://doi.org/10.1002/jper.17-0576.
Wang, X., Zou, Y., & Zhang, J. (2023). Identification of biomarkers related to prognosis and diagnosis of periodontitis by bioinformatics based on public database. Oral Diseases. https://doi.org/10.1111/odi.14740.
Dr. Laura K. Harris
Lumiere Education Inc. Wilmington, 48824 - United States of America
Mr. Mingi Kim
Harris Interdisciplinary Education, Dewitt, 48820

Lumiere Education Inc., Wilmington, 48824 - United States of America
mingikim1628@gmail.com


CREATE AUTHOR ACCOUNT
 
LAUNCH YOUR SPECIAL ISSUE
View all special issues >>
 
PUBLICATION VIDEOS