Oral Biology pp 307-326 | Cite as

Genome-Wide Analysis of Periodontal and Peri-Implant Cells and Tissues

  • Moritz KebschullEmail author
  • Claudia Hülsmann
  • Per Hoffmann
  • Panos N. Papapanou
Part of the Methods in Molecular Biology book series (MIMB, volume 1537)


Omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, are powerful means of generating comprehensive genome-level data sets on complex diseases. We have systematically assessed the transcriptome, miRNome and methylome of gingival tissues from subjects with different diagnostic entities of periodontal disease, and studied the transcriptome of primary cells ex vivo, or in vitro after infection with periodontal pathogens. Our data further our understanding of the pathobiology of periodontal diseases and indicate that the gingival -omes translate into discernible phenotypic characteristics and possibly support an alternative, “molecular” classification of periodontitis.

Here, we outline the laboratory steps required for the processing of periodontal cells and tissues for -omics analyses using current microarrays or next-generation sequencing technology.

Key words

Periodontal disease Gene expression Transcriptome MicroRNA DNA methylation Microarray Next-generation sequencing Gingiva 



This work was supported by grants from the German Society for Periodontology (DG PARO) and the German Society for Oral and Maxillofacial Sciences (DGZMK) to M.K. and by grants from NIH/NIDCR (DE015649, DE021820, and DE024735) and by an unrestricted gift from Colgate-Palmolive Inc. to P.N.P.


  1. 1.
    Chung CH, Bernard PS, Perou CM (2002) Molecular portraits and the family tree of cancer. Nat Genet 32(Suppl):533–540CrossRefPubMedGoogle Scholar
  2. 2.
    Quackenbush J (2006) Microarray analysis and tumor classification. N Engl J Med 354:2463–2472CrossRefPubMedGoogle Scholar
  3. 3.
    Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Glickman JN, Ikeda K, Hashimoto M, Watanabe G, Daidone MG, Roayaie S, Schwartz M, Thung S, Salvesen HB, Gabriel S, Mazzaferro V, Bruix J, Friedman SL, Kumada H, Llovet JM, Golub TR (2008) Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 359:1995–2004CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Haslett JN, Kunkel LM (2002) Microarray analysis of normal and dystrophic skeletal muscle. Int J Dev Neurosci 20:359–365CrossRefPubMedGoogle Scholar
  5. 5.
    Colangelo V, Schurr J, Ball MJ, Pelaez RP, Bazan NG, Lukiw WJ (2002) Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling. J Neurosci Res 70:462–473CrossRefPubMedGoogle Scholar
  6. 6.
    Haroutunian V, Katsel P, Schmeidler J (2009) Transcriptional vulnerability of brain regions in Alzheimer‘s disease and dementia. Neurobiol Aging 30:561–573CrossRefPubMedGoogle Scholar
  7. 7.
    Thornton S, Sowders D, Aronow B, Witte DP, Brunner HI, Giannini EH, Hirsch R (2002) DNA microarray analysis reveals novel gene expression profiles in collagen-induced arthritis. Clin Immunol 105:155–168CrossRefPubMedGoogle Scholar
  8. 8.
    van der Pouw Kraan TC, van Baarsen LG, Rustenburg F, Baltus B, Fero M, Verweij CL (2007) Gene expression profiling in rheumatology. Methods Mol Med 136:305–327CrossRefPubMedGoogle Scholar
  9. 9.
    Burke W (2003) Genomics as a probe for disease biology. N Engl J Med 349:969–974CrossRefPubMedGoogle Scholar
  10. 10.
    Izuhara K, Saito H (2006) Microarray-based identification of novel biomarkers in asthma. Allergol Int 55:361–367CrossRefPubMedGoogle Scholar
  11. 11.
    Demmer RT, Behle JH, Wolf DL, Handfield M, Kebschull M, Celenti R, Pavlidis P, Papapanou PN (2008) Transcriptomes in healthy and diseased gingival tissues. J Periodontol 79:2112–2124CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Jonsson D, Ramberg P, Demmer RT, Kebschull M, Dahlen G, Papapanou PN (2011) Gingival tissue transcriptomes in experimental gingivitis. J Clin Periodontol 38:599–611CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Kebschull M, Guarnieri P, Demmer RT, Boulesteix AL, Pavlidis P, Papapanou PN (2013) Molecular differences between chronic and aggressive periodontitis. J Dent Res 92:1081–1088CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Papapanou PN, Behle JH, Kebschull M, Celenti R, Wolf DL, Handfield M, Pavlidis P, Demmer RT (2009) Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiol 9:221CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Kebschull M, Papapanou PN (2011) Periodontal microbial complexes associated with specific cell and tissue responses. J Clin Periodontol 38:17–27CrossRefPubMedGoogle Scholar
  16. 16.
    Kramer B, Kebschull M, Nowak M, Demmer RT, Haupt M, Korner C, Perner S, Jepsen S, Nattermann J, Papapanou PN (2013) Role of the NK cell-activating receptor CRACC in periodontitis. Infect Immun 81:690–696CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Nowak M, Kramer B, Haupt M, Papapanou PN, Kebschull J, Hoffmann P, Schmidt-Wolf IG, Jepsen S, Brossart P, Perner S, Kebschull M (2013) Activation of invariant NK T cells in periodontitis lesions. J Immunol 190:2282–2291CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Kebschull M, Demmer RT, Grun B, Guarnieri P, Pavlidis P, Papapanou PN (2014) Gingival tissue transcriptomes identify distinct periodontitis phenotypes. J Dent Res 93:459–468CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Stoecklin-Wasmer C, Guarnieri P, Celenti R, Demmer RT, Kebschull M, Papapanou PN (2012) MicroRNAs and their target genes in gingival tissues. J Dent Res 91:934–940CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Papapanou PN, Sedaghatfar MH, Demmer RT, Wolf DL, Yang J, Roth GA, Celenti R, Belusko PB, Lalla E, Pavlidis P (2007) Periodontal therapy alters gene expression of peripheral blood monocytes. J Clin Periodontol 34:736–747CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Hummon AB, Lim SR, Difilippantonio MJ, Ried T (2007) Isolation and solubilization of proteins after TRIzol extraction of RNA and DNA from patient material following prolonged storage. Biotechniques 42(467-470):472Google Scholar
  22. 22.
    Spiess AN, Mueller N, Ivell R (2003) Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 4:44CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Moritz Kebschull
    • 1
    • 2
    Email author
  • Claudia Hülsmann
    • 1
  • Per Hoffmann
    • 3
    • 4
  • Panos N. Papapanou
    • 2
  1. 1.Department of Periodontology, Operative and Preventive Dentistry, Faculty of MedicineUniversity of BonnBonnGermany
  2. 2.Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation SciencesColumbia University College of Dental MedicineNew YorkUSA
  3. 3.Department of Genomics, Institute of Human GeneticsUniversity of BonnBonnGermany
  4. 4.Human Genomics Research Group, Department of BiomedicineUniversity of BaselBaselSwitzerland

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