Differential DNA methylation and mRNA transcription in gingival tissues in periodontal health and disease
Hyunjin Kim
Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Systems Biology, Columbia University, New York, New York, USA
Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
Search for more papers by this authorFatemeh Momen-Heravi
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Search for more papers by this authorSteven Chen
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Search for more papers by this authorPer Hoffmann
Institute of Human Genetics, University of Bonn, Bonn, Germany
Search for more papers by this authorMoritz Kebschull
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
Search for more papers by this authorCorresponding Author
Panos N. Papapanou
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Correspondence
Panos N. Papapanou, Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University College of Dental Medicine, 630 W 168th Street, PH 7 E 10, New York, NY 10032.
Email: [email protected]
Search for more papers by this authorHyunjin Kim
Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Systems Biology, Columbia University, New York, New York, USA
Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
Search for more papers by this authorFatemeh Momen-Heravi
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Search for more papers by this authorSteven Chen
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Search for more papers by this authorPer Hoffmann
Institute of Human Genetics, University of Bonn, Bonn, Germany
Search for more papers by this authorMoritz Kebschull
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
Search for more papers by this authorCorresponding Author
Panos N. Papapanou
Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University, New York, New York, USA
Correspondence
Panos N. Papapanou, Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University College of Dental Medicine, 630 W 168th Street, PH 7 E 10, New York, NY 10032.
Email: [email protected]
Search for more papers by this authorFunding information: NIH/NIDCR:, Grant/Award Numbers: DE015649, DE021820, DE024735, NCATS: TR000040, Colgate Palmolive Company
Abstract
Aim
We investigated differential DNA methylation in gingival tissues in periodontal health, gingivitis, and periodontitis, and its association with differential mRNA expression.
Materials and methods
Gingival tissues were harvested from individuals and sites with clinically healthy and intact periodontium, gingivitis, and periodontitis. Samples were processed for differential DNA methylation and mRNA expression using the IlluminaEPIC (850 K) and the IlluminaHiSeq2000 platforms, respectively. Across the three phenotypes, we identified differentially methylated CpG sites and regions, differentially expressed genes (DEGs), and genes with concomitant differential methylation at their promoters and expression were identified. The findings were validated using our earlier databases using HG-U133Plus2.0Affymetrix microarrays and Illumina (450 K) methylation arrays.
Results
We observed 43,631 differentially methylated positions (DMPs) between periodontitis and health, and 536 DMPs between gingivitis and health (FDR < 0.05). On the mRNA level, statistically significant DEGs were observed only between periodontitis and health (n = 126). Twelve DEGs between periodontitis and health (DCC, KCNA3, KCNA2, RIMS2, HOXB7, PNOC, IRX1, JSRP1, TBX1, OPCML, CECR1, SCN4B) were also differentially methylated between the two phenotypes. Spearman correlations between methylation and expression in the EPIC/mRNAseq dataset were largely replicated in the 450 K/Affymetrix datasets.
Conclusions
Concomitant study of DNA methylation and gene expression patterns may identify genes whose expression is epigenetically regulated in periodontitis.
CONFLICT OF INTEREST
The authors declare no conflict of interests.
Open Research
DATA AVAILABILITY STATEMENT
The Affymetrix HG-U133Plus 2.0 microarray dataset is available at the Gene Expression Omnibus (GSE #16134). The EPIC- and 450K- DNA methylation data, as well as the RNA seq data are available at the Gene Expression Omnibus (GSE #173082).
Supporting Information
| Filename | Description |
|---|---|
| jcpe13504-sup-0001-Supinfo01.xlsxPDF document, 15.6 KB | Appendix S1: Supporting Information. |
| jcpe13504-sup-0002-Supinfo02.xlsxPDF document, 584.2 KB | Appendix S2: Supporting Information. |
| jcpe13504-sup-0003-Supinfo03.docxWord 2007 document , 14.3 KB | Appendix S3: Supporting Information. |
| jcpe13504-sup-0004-FigureS1.pngPNG image, 28.3 KB | Figure S1: Supporting Information. |
| jcpe13504-sup-0005-FigureS2.pngPNG image, 230.5 KB | Figure S2: Supporting Information. |
| jcpe13504-sup-0006-FigureS3.pngPNG image, 173.2 KB | Figure S3: Supporting Information. |
| jcpe13504-sup-0007-FigureS4.pngPNG image, 148.8 KB | Figure S4: Supporting Information. |
| jcpe13504-sup-0008-FigureS5.pngPNG image, 139.5 KB | Figure S5: Supporting Information. |
| jcpe13504-sup-0009-FigureS6.pngPNG image, 27.8 KB | Figure S6: Supporting Information. |
| jcpe13504-sup-0010-TableS1.xlsxPDF document, 10.4 MB | Table S1: Supporting Information. |
| jcpe13504-sup-0011-TableS2.xlsxPDF document, 169.9 KB | Table S2: Supporting Information. |
| jcpe13504-sup-0012-TableS3.xlsxPDF document, 588.9 KB | Table S3: Supporting Information. |
| jcpe13504-sup-0013-TableS4.xlsxPDF document, 15.7 KB | Table S4: Supporting Information. |
| jcpe13504-sup-0014-TableS5.docxWord 2007 document , 26.3 KB | Table S5: Supporting Information. |
| jcpe13504-sup-0015-TableS6.docxWord 2007 document , 23.8 KB | Table S6: Supporting Information. |
| jcpe13504-sup-0016-TableS7.xlsxPDF document, 10.9 KB | Table S7: Supporting Information. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- Axelsson, P., & Lindhe, J. (1981). Effect of controlled oral hygiene procedures on caries and periodontal disease in adults. Results after 6 years. Journal of Clinical Periodontology, 8(3), 239–248. https://doi.org/10.1111/j.1600-051x.1981.tb02035.x
- Barros, S. P., Fahimipour, F., Tarran, R., Kim, S., Scarel-Caminaga, R. M., Justice, A., & North, K. (2020). Epigenetic reprogramming in periodontal disease: Dynamic crosstalk with potential impact in oncogenesis. Periodontology 2000, 82(1), 157–172. https://doi.org/10.1111/prd.12322
- Barros, S. P., & Offenbacher, S. (2009). Epigenetics: Connecting environment and genotype to phenotype and disease. Journal of Dental Research, 88(5), 400–408. https://doi.org/10.1177/0022034509335868
- Bartold, P. M., & Van Dyke, T. E. (2013). Periodontitis: A host-mediated disruption of microbial homeostasis. Unlearning learned concepts. Periodontology 2000, 62(1), 203–217. https://doi.org/10.1111/j.1600-0757.2012.00450.x
- Beeton, C., Wulff, H., Standifer, N. E., Azam, P., Mullen, K. M., Pennington, M. W., Kolski-Andreaco, A., Wei, E., Grino, A., Counts, D. R., Wang, P. H., LeeHealey, C. J., Andrews, M. W., Sankaranarayanan, A., Homerick, D., Roeck, W. W., Tehranzadeh, J., Stanhope, K. L., Zimin, P., … Chandy, K. G. (2006). Kv1.3 channels are a therapeutic target for T cell-mediated autoimmune diseases. Proceedings of the National Academy of Sciences of the United States of America, 103(46), 17414–17419. https://doi.org/10.1073/pnas.0605136103
- Bittner, S., & Meuth, S. G. (2013). Targeting ion channels for the treatment of autoimmune neuroinflammation. Therapeutic Advances in Neurological Disorders, 6(5), 322–336. https://doi.org/10.1177/1756285613487782
- Brait, M., Munari, E., LeBron, C., Noordhuis, M. G., Begum, S., Michailidi, C., Gonzalez-Roibon, N., Maldonado, L., Sen, T., Guerrero-Preston, R., Cope, L., Parrella, P., Fazio, V. M., Ha, P. K., Netto, G. J., Sidransky, D., & Hoque, M. O. (2013). Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma. Cell Cycle, 12(7), 1058–1070. https://doi.org/10.4161/cc.24050
- Cavalli, G., & Heard, E. (2019). Advances in epigenetics link genetics to the environment and disease. Nature, 571(7766), 489–499. https://doi.org/10.1038/s41586-019-1411-0
- Chapple, I. L. C., Mealey, B. L., Van Dyke, T. E., Bartold, P. M., Dommisch, H., Eickholz, P., Geisinger, M. L., Genco, R. J., Glogauer, M., Goldstein, M., Griffin, T. J., Holmstrup, P., Johnson, G. K., Kapila, Y., Lang, N. P., Meyle, J., Murakami, S., Plemons, J., Romito, G. A., … Yoshie, H. (2018). Periodontal health and gingival diseases and conditions on an intact and a reduced periodontium: Consensus report of workgroup 1 of the 2017 world workshop on the classification of periodontal and Peri-implant diseases and conditions. Journal of Clinical Periodontology, 45(Suppl 20), S68–S77. https://doi.org/10.1111/jcpe.12940
- Chen, Y. A., Lemire, M., Choufani, S., Butcher, D. T., Grafodatskaya, D., Zanke, B. W., Gallinger, S., Hudson, T. J., & Weksberg, R. (2013). Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 8(2), 203–209. https://doi.org/10.4161/epi.23470
- Chen, Y. A., Lemire, M., Choufani, S., Butcher, D. T., Grafodatskaya, D., Zanke, B. W., Gallinger, S., Hudson, T. J., & Weksberg, R. (2013). Potassium channels Kv1.3 and KCa3.1 cooperatively and compensatorily regulate antigen-specific memory T cell functions. Nature Communications, 8, 14644. https://doi.org/10.1038/ncomms14644
- Chiang, E. Y., Li, T., Jeet, S., Peng, I., Zhang, J., Lee, W. P., DeVoss, J., Caplazi, J., Chen, J., Warming, S., Hackos, D. H., Mukund, S., Koth, C.M., Grogan, J. L. (2017). Potassium channels Kv1.3 and KCa3.1 cooperatively and compensatorily regulate antigen-specific memory T cell functions. Nat Commun, 8, 14644. https://doi.org/10.1038/ncomms14644
- Darveau, R. P. (2010). Periodontitis: A polymicrobial disruption of host homeostasis. Nature Reviews Microbiology, 8(7), 481–490. https://doi.org/10.1038/nrmicro2337
- Di, L., Srivastava, S., Zhdanova, O., Ding, Y., Li, Z., Wulff, H., Lafaille, M., & Skolnik, E. Y. (2010). Inhibition of the K+ channel KCa3.1 ameliorates T cell-mediated colitis. Proceedings of the National Academy of Sciences of the United States of America, 107(4), 1541–1546. https://doi.org/10.1073/pnas.0910133107
- Di Spirito, F., Toti, P., Pilone, V., Carinci, F., Lauritano, D., & Sbordone, L. (2020). The association between periodontitis and human colorectal cancer: Genetic and pathogenic linkage. Life (Basel), 10(9). https://doi.org/10.3390/life10090211
- Gocke, A. R., Lebson, L. A., Grishkan, I. V., Hu, L., Nguyen, H. M., Whartenby, K. A., Chandy, K. G., & Calabresi, P. A. (2012). Kv1.3 deletion biases T cells toward an immunoregulatory phenotype and renders mice resistant to autoimmune encephalomyelitis. Journal of Immunology, 188(12), 5877–5886. https://doi.org/10.4049/jimmunol.1103095
- Guzeldemir-Akcakanat, E., Sunnetci-Akkoyunlu, D., Orucguney, B., Cine, N., Kan, B., Yilmaz, E. B., Gumuslu, E., & Savli, H. (2016). Gene-expression profiles in generalized aggressive periodontitis: A gene network-based microarray analysis. Journal of Periodontology, 87(1), 58–65. https://doi.org/10.1902/jop.2015.150175
- Haffajee, A. D., Cugini, M. A., Dibart, S., Smith, C., Kent, R. L., Jr., & Socransky, S. S. (1997). Clinical and microbiological features of subjects with adult periodontitis who responded poorly to scaling and root planing. Journal of Clinical Periodontology, 24(10), 767–776.
- Haffajee, A. D., Dibart, S., Kent, R. L. J., & Socransky, S. S. (1995). Clinical and microbiological changes associated with the use of 4 adjunctive systemically administered agents in the treatment of periodontal infections. Journal of Clinical Periodontology, 22(8), 618–627.
- Heitz-Mayfield, L. J., Schatzle, M., Loe, H., Burgin, W., Anerud, A., Boysen, H., & Lang, N. P. (2003). Clinical course of chronic periodontitis. II. Incidence, characteristics and time of occurrence of the initial periodontal lesion. Journal of Clinical Periodontology, 30(10), 902–908.
- Juodzbalys, G., Kasradze, D., Cicciu, M., Sudeikis, A., Banys, L., Galindo-Moreno, P., & Guobis, Z. (2016). Modern molecular biomarkers of head and neck cancer. Part I. epigenetic diagnostics and prognostics: Systematic review. Cancer Biomark, 17(4), 487–502. https://doi.org/10.3233/CBM-160666
- Karolchik, D., Hinrichs, A. S., & Kent, W. J. (2009). The UCSC genome browser. Current Protocols in Bioinformatics– 28, 1.4.1–1.4.26. https://doi.org/10.1002/0471250953.bi0104s28
10.1002/0471250953.bi0104s28 Google Scholar
- Kebschull, M., Guarnieri, P., Demmer, R. T., Boulesteix, A. L., Pavlidis, P., & Papapanou, P. N. (2013). Molecular differences between chronic and aggressive periodontitis. Journal of Dental Research, 92(12), 1081–1088. https://doi.org/10.1177/0022034513506011
- Kebschull, M., & Papapanou, P. N. (2015). Mini but mighty: microRNAs in the pathobiology of periodontal disease. Periodontology 2000, 69(1), 201–210. https://doi.org/10.1111/prd.12095
- Kinane, D. F., Stathopoulou, P. G., & Papapanou, P. N. (2017). Periodontal diseases. Nature Reviews. Disease Primers, 3, 17038. https://doi.org/10.1038/nrdp.2017.38
- Lalla, E., & Papapanou, P. N. (2011). Diabetes mellitus and periodontitis: A tale of two common interrelated diseases. Nature Reviews Endocrinology, 12, 738–748. https://doi.org/10.1038/nrendo.2011.106
- Lappalainen, T., & Greally, J. M. (2017). Associating cellular epigenetic models with human phenotypes. Nature Reviews. Genetics, 18(7), 441–451. https://doi.org/10.1038/nrg.2017.32
- Larsson, L., Castilho, R. M., & Giannobile, W. V. (2015). Epigenetics and its role in periodontal diseases: A state-of-the-art review. Journal of Periodontology, 86(4), 556–568. https://doi.org/10.1902/jop.2014.140559
- Lee, J. Y., Lee, W. K., Park, J. Y., & Kim, D. S. (2020). Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers. Genes Genomics, 42(5), 571–579. https://doi.org/10.1007/s13258-020-00925-9
- Lindhe, J., Hamp, S. E., & Löe, H. (1973). Experimental periodontitis in the beagle dog. International Dental Journal, 23(3), 432–437.
- Lindhe, J., Westfelt, E., Nyman, S., Socransky, S. S., Heijl, L., & Bratthall, G. (1982). Healing following surgical/non-surgical treatment of periodontal disease. A clinical study. Journal of Clinical Periodontology, 9(2), 115–128.
- Löe, H., Theilade, E., & Jensen, S. B. (1965). Experimental gingivitis in man. Journal of Periodontology, 36, 177–187.
- Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8
- McCall, M. N., Jaffee, H. A., Zelisko, S. J., Sinha, N., Hooiveld, G., Irizarry, R. A., & Zilliox, M. J. (2014). The gene expression barcode 3.0: Improved data processing and mining tools. Nucleic Acids Research, 42(1), D938–D943. https://doi.org/10.1093/nar/gkt1204
- Momen-Heravi, F., Friedman, R. A., Albeshri, S., Sawle, A., Kebschull, M., Kuhn, A., & Papapanou, P. N. (2021). Cell type-specific decomposition of gingival tissue transcriptomes. Journal of Dental Research, 22034520979614. https://doi.org/10.1177/0022034520979614
- Nibali, L., Bayliss-Chapman, J., Almofareh, S. A., Zhou, Y., Divaris, K., & Vieira, A. R. (2019). What is the heritability of periodontitis? A systematic review. Journal of Dental Research, 98(6), 632–641. https://doi.org/10.1177/0022034519842510
- Orban, C., Bajnok, A., Vasarhelyi, B., Tulassay, T., & Toldi, G. (2014). Different calcium influx characteristics upon Kv1.3 and IKCa1 potassium channel inhibition in T helper subsets. Cytometry. Part A, 85(7), 636–641. https://doi.org/10.1002/cyto.a.22479
- Ostrow, K. L., Hoque, M. O., Loyo, M., Brait, M., Greenberg, A., Siegfried, J. M., Grandis, J. R., Gaither Davis, A., Bigbee, W. L., Rom, W., & Sidransky, D. (2010). Molecular analysis of plasma DNA for the early detection of lung cancer by quantitative methylation-specific PCR. Clinical Cancer Research, 16(13), 3463–3472. https://doi.org/10.1158/1078-0432.CCR-09-3304
- Palmer, R. M., Wilson, R. F., Hasan, A. S., & Scott, D. A. (2005). Mechanisms of action of environmental factors—tobacco smoking. Journal of Clinical Periodontology, 32(Suppl 6), 180–195.
- Papapanou, P. N., Behle, J. H., Kebschull, M., Celenti, R., Wolf, D. L., Handfield, M., Pavlidis, P., & Demmer, R. T. (2009). Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiology, 9, 221. https://doi.org/10.1186/1471-2180-9-221
- Papapanou, P. N., Sanz, M., Buduneli, N., Dietrich, T., Feres, M., Fine, D. H., Flemmig, T. F., Garcia, R., Giannobile, W. V., Graziani, F., Greenwell, H., Herrera, D., Kao, R. T., Kebschull, M., Kinane, D. F., Kirkwood, K. L., Kocher, T., Kornman, K. S., Kumar, P. S., … 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 Clinical Periodontology, 45(Suppl 20), S162–S170. https://doi.org/10.1111/jcpe.12946
- Petronis, A. (2010). Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature, 465(7299), 721–727. https://doi.org/10.1038/nature09230
- Piovesan, A., Antonaros, F., Vitale, L., Strippoli, P., Pelleri, M. C., & Caracausi, M. (2019). Human protein-coding genes and gene feature statistics in 2019. BMC Research Notes, 12(1), 315. https://doi.org/10.1186/s13104-019-4343-8
- Reimand, J., Kull, M., Peterson, H., Hansen, J., & Vilo, J. (2007). G:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research, 35(Web Server issue), W193–W200. https://doi.org/10.1093/nar/gkm226
- Riggs, A. D., Martienssen, R. A., & Russo, V. E. A. (1996). Introduction. In V. E. A. Russo, R. A. Martienssen, & A. D. Riggs (Eds.), Epigenetic mechanisms of gene regulation (Vol. 32, pp. 1–4). Cold Spring Harbor Laboratory Press.
- Shungin, D., Haworth, S., Divaris, K., Agler, C. S., Kamatani, Y., Keun Lee, M., Grinde, K., Hindy, G., Alaraudanjoki, V., Pesonen, P., Teumer, A., Holtfreter, B., Sakaue, S., Hirata, J., Yu, Y. H., Ridker, P. M., Giulianini, F., Chasman, D. I., Magnusson, P. K. E., … Johansson, I. (2019). Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data. Nature Communications, 10(1), 2773. https://doi.org/10.1038/s41467-019-10630-1
- Tschritter, O., Machicao, F., Stefan, N., Schafer, S., Weigert, C., Staiger, H., Spieth, C., Haring, H. U., & Fritsche, A. (2006). A new variant in the human Kv1.3 gene is associated with low insulin sensitivity and impaired glucose tolerance. The Journal of Clinical Endocrinology and Metabolism, 91(2), 654–658. https://doi.org/10.1210/jc.2005-0725
- Valverde, P., Kawai, T., & Taubman, M. A. (2004). Selective blockade of voltage-gated potassium channels reduces inflammatory bone resorption in experimental periodontal disease. Journal of Bone and Mineral Research, 19(1), 155–164. https://doi.org/10.1359/JBMR.0301213
- Vicente, R., Escalada, A., Coma, M., Fuster, G., Sanchez-Tillo, E., Lopez-Iglesias, C., Soler, C., Solsona, C., Celada, A., & Felipe, A. (2003). Differential voltage-dependent K+ channel responses during proliferation and activation in macrophages. The Journal of Biological Chemistry, 278(47), 46307–46320. https://doi.org/10.1074/jbc.M304388200
- Waddington, C. H. (1942). The Epigenotype. Endeavour, 1, 18–20.
- Willyard, C. (2018). New human gene tally reignites debate. Nature, 558(7710), 354–355. https://doi.org/10.1038/d41586-018-05462-w
- Xu, J., Wang, P., Li, Y., Li, G., Kaczmarek, L. K., Wu, Y., Koni, P. A., Flavell, R. A., & Desir, G. V. (2004). The voltage-gated potassium channel Kv1.3 regulates peripheral insulin sensitivity. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 3112–3117. https://doi.org/10.1073/pnas.0308450100
- Zoghbi, H. Y., & Beaudet, A. L. (2016). Epigenetics and human disease. Cold Spring Harbor Perspectives in Biology, 8(2), a019497. https://doi.org/10.1101/cshperspect.a019497
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