Journal of Periodontal and Implant Science

Korean Academy of Periodontology (대한치주과학회)
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Standard operating procedures for the collection, processing, and storage of oral biospecimens at the Korea Oral Biobank Network

  • Young-Dan Cho (Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital) ;
  • Eunae Sandra Cho (Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry) ;
  • Je Seon Song (Department of Pediatric Dentistry, Yonsei University College of Dentistry) ;
  • Young-Youn Kim (Department of Oral and Maxillofacial Surgery, Apple Tree Institute of Biomedical Science, Apple Tree Dental Hospital) ;
  • Inseong Hwang (Docsmedi Co., Ltd.) ;
  • Sun-Young Kim (Department of Conservative Dentistry, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital)
  • Received : 2022.09.06
  • Accepted : 2022.12.12
  • Published : 2023.10.30
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Abstract

Purpose: The Korea Oral Biobank Network (KOBN) was established in 2021 as a branch of the Korea Biobank Network under the Korea Centers for Disease Control and Prevention to provide infrastructure for the collection, management, storage, and utilization of human bioresources from the oral cavity and associated clinical data for basic research and clinical studies. Methods: To address the need for the unification of the biobanking process, the KOBN organized the concept review for all the processes. Results: The KOBN established standard operating procedures for the collection, processing, and storage of oral samples. Conclusions: The importance of collecting high-quality bioresources to generate accurate and reproducible research results has always been emphasized. A standardized procedure is a basic prerequisite for implementing comprehensive quality management of biological resources and accurate data production.

Keywords

Acknowledgement

This work was supported by the Korea Disease Control and Prevention Agency, "Collaborative Subnetwork for Specific Disease-targeted Future Biobanking (No. KBN4_A04)" and Bio & Medical Technology Development Program of the National Research Foundation (NRF) and funded by the Korean government (MSIT) (No. 2022M3A9F3082330).

References

  1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007;449:804-10. https://doi.org/10.1038/nature06244
  2. Cho YD, Kim WJ, Ryoo HM, Kim HG, Kim KH, Ku Y, et al. Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives. Clin Epigenetics 2021;13:92.
  3. Birch K, Dove ES, Chiappetta M, Gursoy UK. Biobanks in oral health: promises and implications of post-neoliberal science and innovation. OMICS 2016;20:36-41. https://doi.org/10.1089/omi.2015.0123
  4. Cho YD, Kim KH, Lee YM, Ku Y, Seol YJ. Oral microbiome and host health: review on current advances in genome-wide analysis. Appl Sci (Basel) 2021;11:4050.
  5. Balic A. Biology explaining tooth repair and regeneration: a mini-review. Gerontology 2018;64:382-8. https://doi.org/10.1159/000486592
  6. Zhai Q, Dong Z, Wang W, Li B, Jin Y. Dental stem cell and dental tissue regeneration. Front Med 2019;13:152-9. https://doi.org/10.1007/s11684-018-0628-x
  7. Miletich I. Introduction to salivary glands: structure, function and embryonic development. Front Oral Biol 2010;14:1-20. https://doi.org/10.1159/000313703
  8. Tiwari M. Science behind human saliva. J Nat Sci Biol Med 2011;2:53-8. https://doi.org/10.4103/0976-9668.82322
  9. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 2012;13:R42.
  10. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-14. https://doi.org/10.1038/nature11234
  11. Ciurli A, Liebl M, Derks RJ, Neefjes JJ, Giera M. Spatially resolved sampling for untargeted metabolomics: a new tool for salivomics. iScience 2021;24:102768.
  12. Jo R, Nishimoto Y, Umezawa K, Yama K, Aita Y, Ichiba Y, et al. Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water. Sci Rep 2019;9:16124.
  13. Maruyama Y, Nishimoto Y, Umezawa K, Kawamata R, Ichiba Y, Tsutsumi K, et al. Comparison of oral metabolome profiles of stimulated saliva, unstimulated saliva, and mouth-rinsed water. Sci Rep 2022;12:689.
  14. Kuboniwa M, Tribble GD, Hendrickson EL, Amano A, Lamont RJ, Hackett M. Insights into the virulence of oral biofilms: discoveries from proteomics. Expert Rev Proteomics 2012;9:311-23. https://doi.org/10.1586/epr.12.16
  15. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol 2010;192:5002-17. https://doi.org/10.1128/JB.00542-10
  16. Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, et al. The personal human oral microbiome obscures the effects of treatment on periodontal disease. PLoS One 2014;9:e86708.
  17. Bowen WH, Burne RA, Wu H, Koo H. Oral biofilms: pathogens, matrix, and polymicrobial interactions in microenvironments. Trends Microbiol 2018;26:229-42. https://doi.org/10.1016/j.tim.2017.09.008
  18. Eley BM, Cox SW. Proteolytic and hydrolytic enzymes from putative periodontal pathogens: characterization, molecular genetics, effects on host defenses and tissues and detection in gingival crevice fluid. Periodontol 2000 2003;31:105-24. https://doi.org/10.1034/j.1600-0757.2003.03107.x
  19. Subbarao KC, Nattuthurai GS, Sundararajan SK, Sujith I, Joseph J, Syedshah YP. Gingival crevicular fluid: an overview. J Pharm Bioallied Sci 2019;11:S135-9.
  20. Cetinkaya G, Arat S. Cryopreservation of cartilage cell and tissue for biobanking. Cryobiology 2011;63:292-7. https://doi.org/10.1016/j.cryobiol.2011.09.143
  21. Sivolella S, Scanu A, Xie Z, Vianello S, Stellini E. Biobanking in dentistry: a review. Jpn Dent Sci Rev 2022;58:31-40. https://doi.org/10.1016/j.jdsr.2021.12.002
  22. Hartman V, Matzke L, Watson PH. Biospecimen complexity and the evolution of biobanks. Biopreserv Biobank 2019;17:264-70. https://doi.org/10.1089/bio.2018.0120
  23. Watson PH. Biospecimen complexity-the next challenge for cancer research biobanks? Clin Cancer Res 2017;23:894-8. https://doi.org/10.1158/1078-0432.CCR-16-1406
  24. Yong WH, Dry SM, Shabihkhani M. A practical approach to clinical and research biobanking. Methods Mol Biol 2014;1180:137-62. https://doi.org/10.1007/978-1-4939-1050-2_8
  25. Srinivasan M, Sedmak D, Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol 2002;161:1961-71. https://doi.org/10.1016/S0002-9440(10)64472-0
  26. Ericsson C, Franzen B, Nister M. Frozen tissue biobanks. Tissue handling, cryopreservation, extraction, and use for proteomic analysis. Acta Oncol 2006;45:643-61. https://doi.org/10.1080/02841860600818047
  27. Chu TY, Hwang KS, Yu MH, Lee HS, Lai HC, Liu JY. A research-based tumor tissue bank of gynecologic oncology: characteristics of nucleic acids extracted from normal and tumor tissues from different sites. Int J Gynecol Cancer 2002;12:171-6. https://doi.org/10.1136/ijgc-00009577-200203000-00006
  28. Yasojima K, McGeer EG, McGeer PL. High stability of mRNAs postmortem and protocols for their assessment by RT-PCR. Brain Res Brain Res Protoc 2001;8:212-8. https://doi.org/10.1016/S1385-299X(01)00119-2
  29. Micke P, Ohshima M, Tahmasebpoor S, Ren ZP, Ostman A, Ponten F, et al. Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab Invest 2006;86:202-11. https://doi.org/10.1038/labinvest.3700372
  30. Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, et al. Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol 2013;20:1737-44. https://doi.org/10.1245/s10434-012-2440-1
  31. Leonard S, Logel J, Luthman D, Casanova M, Kirch D, Freedman R. Biological stability of mRNA isolated from human postmortem brain collections. Biol Psychiatry 1993;33:456-66. https://doi.org/10.1016/0006-3223(93)90174-C
  32. Shabihkhani M, Lucey GM, Wei B, Mareninov S, Lou JJ, Vinters HV, et al. The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. Clin Biochem 2014;47:258-66. https://doi.org/10.1016/j.clinbiochem.2014.01.002
  33. Zhang X, Han QY, Zhao ZS, Zhang JG, Zhou WJ, Lin A. Biobanking of fresh-frozen gastric cancer tissues: impact of long-term storage and clinicopathological variables on RNA quality. Biopreserv Biobank 2019;17:58-63. https://doi.org/10.1089/bio.2018.0038
  34. Kelly R, Albert M, de Ladurantaye M, Moore M, Dokun O, Bartlett JM. RNA and DNA integrity remain stable in frozen tissue after long-term storage at cryogenic temperatures: a report from the Ontario Tumour Bank. Biopreserv Biobank 2019;17:282-7. https://doi.org/10.1089/bio.2018.0095
  35. Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P. Unlocking the archive--gene expression in paraffin-embedded tissue. J Pathol 2001;195:66-71. https://doi.org/10.1002/1096-9896(200109)195:1<66::AID-PATH921>3.0.CO;2-F
  36. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS One 2007;2:e1261.
  37. Hewitt SM, Lewis FA, Cao Y, Conrad RC, Cronin M, Danenberg KD, et al. Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Arch Pathol Lab Med 2008;132:1929-35. https://doi.org/10.5858/132.12.1929
  38. Conti CJ, Larcher F, Chesner J, Aldaz CM. Polyacrylamide gel electrophoresis and immunoblotting of proteins extracted from paraffin-embedded tissue sections. J Histochem Cytochem 1988;36:547-50. https://doi.org/10.1177/36.5.3282007
  39. Metz B, Kersten GF, Hoogerhout P, Brugghe HF, Timmermans HA, de Jong A, et al. Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem 2004;279:6235-43. https://doi.org/10.1074/jbc.M310752200
  40. Klockenbusch C, O'Hara JE, Kast J. Advancing formaldehyde cross-linking towards quantitative proteomic applications. Anal Bioanal Chem 2012;404:1057-67. https://doi.org/10.1007/s00216-012-6065-9