Journal of the Korean Association of Oral and Maxillofacial Surgeons

  • 제48권1호
  • /
  • Pages.3-12
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  • 2022
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  • 2234-7550(pISSN)
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  • 2234-5930(eISSN)
대한구강악안면외과학회 (The Korean Association of Oral and Maxillofacial Surgeons)
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Next generation sequencing-based salivary biomarkers in oral squamous cell carcinoma

  • Sodnom-Ish, Buyanbileg (Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University) ;
  • Eo, Mi Young (Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University) ;
  • Myoung, Hoon (Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University) ;
  • Lee, Jong Ho (Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University) ;
  • Kim, Soung Min (Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University)
  • 투고 : 2021.12.06
  • 심사 : 2022.01.11
  • 발행 : 2022.02.28
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초록

Selection of potential disease-specific biomarkers from saliva or epithelial tissues through next generation sequencing (NGS)-based protein studies has recently become possible. The early diagnosis of oral squamous cell carcinoma (OSCC) has been difficult, if not impossible, until now due to the lack of an effective OSCC biomarker and efficient molecular validation method. The aim of this study was to summarize the advances in the application of NGS in cancer research and to propose potential proteomic and genomic saliva biomarkers for NGS-based study in OSCC screening and diagnosis programs. We have reviewed four categories including definitions and use of NGS, salivary biomarkers and OSCC, current biomarkers using the NGS-based technique, and potential salivary biomarker candidates in OSCC using NGS.

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과제정보

This study was supported by grant No. 03-2021-0045 from the SNUDH Research Fund.

참고문헌

  1. Nguyen TTH, Sodnom-Ish B, Choi SW, Jung HI, Cho J, Hwang I, et al. Salivary biomarkers in oral squamous cell carcinoma. J Korean Assoc Oral Maxillofac Surg 2020;46:301-12. https://doi.org/10.5125/jkaoms.2020.46.5.301
  2. Salazar C, Nagadia R, Pandit P, Cooper-White J, Banerjee N, Dimitrova N, et al. A novel saliva-based microRNA biomarker panel to detect head and neck cancers. Cell Oncol (Dordr) 2014;37:331-8. https://doi.org/10.1007/s13402-014-0188-2
  3. Pfaffe T, Cooper-White J, Beyerlein P, Kostner K, Punyadeera C. Diagnostic potential of saliva: current state and future applications. Clin Chem 2011;57:675-87. https://doi.org/10.1373/clinchem.2010.153767
  4. Schulz BL, Cooper-White J, Punyadeera CK. Saliva proteome research: current status and future outlook. Crit Rev Biotechnol 2013;33:246-59. https://doi.org/10.3109/07388551.2012.687361
  5. Genco RJ. Salivary diagnostic tests. J Am Dent Assoc 2012;143(10 Suppl):3S-5S. https://doi.org/10.14219/jada.archive.2012.0340
  6. Fabryova H, Celec P. On the origin and diagnostic use of salivary RNA. Oral Dis 2014;20:146-52. https://doi.org/10.1111/odi.12098
  7. Campuzano S, Yanez-Sedeno P, Pingarron JM. Electrochemical bioaffinity sensors for salivary biomarkers detection. TrAC Trends Anal Chem 2017;86:14-24. https://doi.org/10.1016/j.trac.2016.10.002
  8. Malon RS, Sadir S, Balakrishnan M, Corcoles EP. Saliva-based biosensors: noninvasive monitoring tool for clinical diagnostics. Biomed Res Int 2014;2014:962903. https://doi.org/10.1155/2014/962903
  9. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A 1977;74:560-4. https://doi.org/10.1073/pnas.74.2.560
  10. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463-7. https://doi.org/10.1073/pnas.74.12.5463
  11. Adams J. DNA sequencing technologies. Nat Educ 2008;1:193.
  12. Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975;94:441-8. https://doi.org/10.1016/0022-2836(75)90213-2
  13. Behjati S, Tarpey PS. What is next generation sequencing? Arch Dis Child Educ Pract Ed 2013;98:236-8. https://doi.org/10.1136/archdischild-2013-304340
  14. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17:333-51. https://doi.org/10.1038/nrg.2016.49
  15. Gabusi A, Gissi DB, Tarsitano A, Asioli S, Marchetti C, Montebugnoli L, et al. Intratumoral heterogeneity in recurrent metastatic squamous cell carcinoma of the oral cavity: new perspectives afforded by multiregion DNA sequencing and mtDNA analysis. J Oral Maxillofac Surg 2019;77:440-55. https://doi.org/10.1016/j.joms.2018.09.014
  16. Todorovic E, Dickson BC, Weinreb I. Salivary gland cancer in the era of routine next-generation sequencing. Head Neck Pathol 2020;14:311-20. https://doi.org/10.1007/s12105-020-01140-4
  17. Massive parallel sequencing [Internet]. San Francisco (CA): Wikipedia [cited 2021 May 30]. Available from: https://en.wikipedia.org/wiki/Massive_parallel_sequencing
  18. Harrington CT, Lin EI, Olson MT, Eshleman JR. Fundamentals of pyrosequencing. Arch Pathol Lab Med 2013;137:1296-303. https://doi.org/10.5858/arpa.2012-0463-RA
  19. The Next Generation Sequencing Platform of Roche 454 [Internet]. Shirley (NY): Biogene Blog [cited 2021 May 30]. Available from: https://www.creative-biogene.com/blog/index.php/2017/02/02/the-next-generation-sequencing-platformof-roche-454/#:~:text=Roche%20454%20sequencing%20system%20is,the%20next%20generation%20sequencing%20technology.&text=DNA%20Library%20construction%20in%20454,different%20adapters%20at%20both%20ends
  20. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011;12:245. https://doi.org/10.1186/1471-2164-12-245
  21. 454 Life sciences [Internet]. San Francisco (CA): Wikipedia [cited 2021 May 30]. Available from: https://en.wikipedia.org/wiki/454_Life_Sciences
  22. Ravi RK, Walton K, Khosroheidari M. MiSeq: a next generation sequencing platform for genomic analysis. Methods Mol Biol 2018;1706:223-32. https://doi.org/10.1007/978-1-4939-7471-9_12
  23. Illumina. HiSeqTM sequencing systems: redefining the trajectory of sequencing [Internet]. San Diego (CA): Illumina [cited 2021 May 30]. Available from: https://www.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
  24. Illumina. Genome AnalyzerIIx system: the most proven, widely adopted next-generation sequencing platform [Internet]. San Diego (CA): Illumina [cited 2021 May 30]. Available from: https://support.illumina.com/content/dam/illumina-marketing/documents/ products/datasheets/datasheet_genome_analyzeriix.pdf
  25. Castellana S, Romani M, Valente EM, Mazza T. A solid quality-control analysis of AB SOLiD short-read sequencing data. Brief Bioinform 2013;14:684-95. https://doi.org/10.1093/bib/bbs048
  26. ABI Solid Sequencing [Internet]. San Francisco (CA): Wikipedia [cited 2021 May 30]. Available from: https://en.wikipedia.org/wiki/ABI_Solid_Sequencing
  27. Thermo Fisher Scientific. Ion ProtonTM System for next-generation sequencing [Internet]. Seoul: Thermo Fisher Scientific [cited 2021 May 30]. Available from: https://www.thermofisher.com/kr/ko/home/life-science/sequencing/next-generation-sequencing/iontorrent-next-generation-sequencing-workflow/ion-torrent-nextgeneration-sequencing-run-sequence/ion-proton-system-for-nextgeneration-sequencing.html
  28. Complete genomics [Internet]. San Francisco (CA): Wikipedia [cited 2021 May 30]. Available from: https://en.wikipedia.org/wiki/Complete_Genomics
  29. Thompson JF, Steinmann KE. Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol 2010;Chapter 7:Unit7.10. https://doi.org/10.1002/0471142727.mb0710s92
  30. Helicos single molecule fluorescent sequencing [Internet]. San Francisco (CA): Wikipedia [cited 2021 May 30]. Available from: https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing
  31. PacBio. SMRT sequencing [Internet]. Menlo Park (CA): PacBio [cited 2021 May 30]. Available from: https://www.pacb.com/smrtscience/smrt-sequencing/
  32. Wong DT. Salivaomics. J Am Dent Assoc 2012;143(10 Suppl):19S24S. https://doi.org/10.14219/jada.archive.2012.0339
  33. Shah FD, Begum R, Vajaria BN, Patel KR, Patel JB, Shukla SN, et al. A review on salivary genomics and proteomics biomarkers in oral cancer. Indian J Clin Biochem 2011;26:326-34. https://doi.org/10.1007/s12291-011-0149-8
  34. Singh P, Verma JK, Singh JK. Validation of salivary markers, IL1β, IL-8 and Lgals3bp for detection of oral squamous cell carcinoma in an Indian population. Sci Rep 2020;10:7365. https://doi.org/10.1038/s41598-020-64494-3
  35. Li Y, Zhou X, St John MA, Wong DT. RNA profiling of cell-free saliva using microarray technology. J Dent Res 2004;83:199-203. https://doi.org/10.1177/154405910408300303
  36. Park NJ, Zhou H, Elashoff D, Henson BS, Kastratovic DA, Abemayor E, et al. Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection. Clin Cancer Res 2009;15:5473-7. https://doi.org/10.1158/1078-0432.CCR-09-0736
  37. Patel RS, Jakymiw A, Yao B, Pauley BA, Carcamo WC, Katz J, et al. High resolution of microRNA signatures in human whole saliva. Arch Oral Biol 2011;56:1506-13. https://doi.org/10.1016/j.archoralbio.2011.05.015
  38. Rapado-Gonzalez O, Lopez-Cedrun JL, Lopez-Lopez R, Rodriguez-Ces AM, Suarez-Cunqueiro MM. Saliva gene promoter hypermethylation as a biomarker in oral cancer. J Clin Med 2021;10:1931. https://doi.org/10.3390/jcm10091931
  39. Viet CT, Schmidt BL. Methylation array analysis of preoperative and postoperative saliva DNA in oral cancer patients. Cancer Epidemiol Biomarkers Prev 2008;17:3603-11. https://doi.org/10.1158/1055-9965.EPI-08-0507
  40. Nakahara Y, Shintani S, Mihara M, Hino S, Hamakawa H. Detection of p16 promoter methylation in the serum of oral cancer patients. Int J Oral Maxillofac Surg 2006;35:362-5. https://doi.org/10.1016/j.ijom.2005.08.005
  41. Viet CT, Jordan RC, Schmidt BL. DNA promoter hypermethylation in saliva for the early diagnosis of oral cancer. J Calif Dent Assoc 2007;35:844-9. https://doi.org/10.1080/19424396.2007.12221293
  42. Liao PH, Chang YC, Huang MF, Tai KW, Chou MY. Mutation of p53 gene codon 63 in saliva as a molecular marker for oral squamous cell carcinomas. Oral Oncol 2000;36:272-6. https://doi.org/10.1016/s1368-8375(00)00005-1
  43. Shpitzer T, Hamzany Y, Bahar G, Feinmesser R, Savulescu D, Borovoi I, et al. Salivary analysis of oral cancer biomarkers. Br J Cancer 2009;101:1194-8. https://doi.org/10.1038/sj.bjc.6605290
  44. Zimmermann BG, Wong DT. Salivary mRNA targets for cancer diagnostics. Oral Oncol 2008;44:425-9. https://doi.org/10.1016/j.oraloncology.2007.09.009
  45. Franzmann EJ, Reategui EP, Carraway KL, Hamilton KL, Weed DT, Goodwin WJ. Salivary soluble CD44: a potential molecular marker for head and neck cancer. Cancer Epidemiol Biomarkers Prev 2005;14:735-9. https://doi.org/10.1158/1055-9965.EPI-04-0546
  46. TP53 tumor protein p53 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/7157
  47. Grunewald I, Vollbrecht C, Meinrath J, Meyer MF, Heukamp LC, Drebber U, et al. Targeted next generation sequencing of parotid gland cancer uncovers genetic heterogeneity. Oncotarget 2015;6:18224-37. https://doi.org/10.18632/oncotarget.4015
  48. DAPK1 death associated protein kinase 1 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/1612
  49. Rettori MM, de Carvalho AC, Bomfim Longo AL, de Oliveira CZ, Kowalski LP, Carvalho AL, et al. Prognostic significance of TIMP3 hypermethylation in post-treatment salivary rinse from head and neck squamous cell carcinoma patients. Carcinogenesis 2013;34:20-7. https://doi.org/10.1093/carcin/bgs311
  50. TIMP3 TIMP metallopeptidase inhibitor 3 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/7078
  51. Sun W, Zaboli D, Wang H, Liu Y, Arnaoutakis D, Khan T, et al. Detection of TIMP3 promoter hypermethylation in salivary rinse as an independent predictor of local recurrence-free survival in head and neck cancer. Clin Cancer Res 2012;18:1082-91. https://doi.org/10.1158/1078-0432.CCR-11-2392
  52. Cristaldi M, Mauceri R, Di Fede O, Giuliana G, Campisi G, Panzarella V. Salivary biomarkers for oral squamous cell carcinoma diagnosis and follow-up: current status and perspectives. Front Physiol 2019;10:1476. https://doi.org/10.3389/fphys.2019.01476
  53. CDKN2A cyclin dependent kinase inhibitor 2A [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/1029
  54. MGMT O-6-methylguanine-DNA methyltransferase [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/4255
  55. CCND1 cyclin D1 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/595
  56. Ku BM, Jung HA, Sun JM, Ko YH, Jeong HS, Son YI, et al. High-throughput profiling identifies clinically actionable mutations in salivary duct carcinoma. J Transl Med 2014;12:299. https://doi.org/10.1186/s12967-014-0299-6
  57. SERPINB5 serpin family B member 5 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/5268
  58. Chattopadhyay I, Panda M. Recent trends of saliva omics biomarkers for the diagnosis and treatment of oral cancer. J Oral Biosci 2019;61:84-94. https://doi.org/10.1016/j.job.2019.03.002
  59. CXCL8 C-X-C motif chemokine ligand 8 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/3576
  60. Cheng J, Nonaka T, Wong DTW. Salivary exosomes as nanocarriers for cancer biomarker delivery. Materials (Basel) 2019;12:654. https://doi.org/10.3390/ma12040654
  61. L1B interleukin 1 beta [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/3553
  62. Lee YH, Kim JH, Zhou H, Kim BW, Wong DT. Salivary transcriptomic biomarkers for detection of ovarian cancer: for serous papillary adenocarcinoma. J Mol Med (Berl) 2012;90:427-34. https://doi.org/10.1007/s00109-011-0829-0
  63. S100P S100 calcium binding protein P [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/6286
  64. Cheng YS, Jordan L, Rees T, Chen HS, Oxford L, Brinkmann O, et al. Levels of potential oral cancer salivary mRNA biomarkers in oral cancer patients in remission and oral lichen planus patients. Clin Oral Investig 2014;18:985-93. https://doi.org/10.1007/s00784-013-1041-0 Erratum in: Clin Oral Investig 2014;18:995. https://doi.org/10.1007/s00784-013-1127-8
  65. MIR31 microRNA 31 [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/407035
  66. Liu CJ, Lin SC, Yang CC, Cheng HW, Chang KW. Exploiting salivary miR-31 as a clinical biomarker of oral squamous cell carcinoma. Head Neck 2012;34:219-24. https://doi.org/10.1002/hed.21713
  67. MIR125A microRNA 125a [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/406910
  68. MIR200A microRNA 200a [Homo sapiens (human)] [Internet]. Bethesda (MD): National Center for Biotechnology Information [cited 2021 Feb 21]. Available from: https://www.ncbi.nlm.nih.gov/gene/406983
  69. India Project Team of the International Cancer Genome Consortium. Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nat Commun 2013;4:2873. https://doi.org/10.1038/ncomms3873
  70. Shanmugam A, Hariharan AK, Hasina R, Nair JR, Katragadda S, Irusappan S, et al. Ultrasensitive detection of tumor-specific mutations in saliva of patients with oral cavity squamous cell carcinoma. Cancer 2021;127:1576-89. https://doi.org/10.1002/cncr.33393
  71. Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell 2018;173:291-304.e6. https://doi.org/10.1016/j.cell.2018.03.022
  72. Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, et al. Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov 2013;3:770-81. https://doi.org/10.1158/2159-8290.CD-12-0537
  73. Zammit AP, Sinha R, Cooper CL, Perry CFL, Frazer IH, Tuong ZK. Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: a prospective observational study. PLoS One 2018;13:e0205406. https://doi.org/10.1371/journal.pone.0205406
  74. Fadhil RS, Wei MQ, Nikolarakos D, Good D, Nair RG. Salivary microRNA miR-let-7a-5p and miR-3928 could be used as potential diagnostic bio-markers for head and neck squamous cell carcinoma. PLoS One 2020;15:e0221779. https://doi.org/10.1371/journal.pone.0221779
  75. Nisha KJ, Janam P, Harshakumar K. Identification of a novel salivary biomarker miR-143-3p for periodontal diagnosis: a proof of concept study. J Periodontol 2019;90:1149-59. https://doi.org/10.1002/JPER.18-0729
  76. Lu Z, He Q, Liang J, Li W, Su Q, Chen Z, et al. miR-31-5p is a potential circulating biomarker and therapeutic target for oral cancer. Mol Ther Nucleic Acids 2019;16:471-80. https://doi.org/10.1016/j.omtn.2019.03.012
  77. Wang Y, Zeng G, Jiang Y. The emerging roles of miR-125b in cancers. Cancer Manag Res 2020;12:1079-88. https://doi.org/10.2147/CMAR.S232388
  78. Korpal M, Kang Y. The emerging role of miR-200 family of microRNAs in epithelial-mesenchymal transition and cancer metastasis. RNA Biol 2008;5:115-9. https://doi.org/10.4161/rna.5.3.6558
  79. Kabzinski J, Maczynska M, Majsterek I. MicroRNA as a novel biomarker in the diagnosis of head and neck cancer. Biomolecules 2021;11:844. https://doi.org/10.3390/biom11060844
  80. Majewska H, Gorczynski A, Czapiewski P, Menon R, Mueller J, Lakis S, et al. ALK alterations in salivary gland carcinomas. Virchows Arch 2021;478:933-41. https://doi.org/10.1007/s00428-020-02971-w
  81. Kim S, Lee JW, Park YS. The application of next-generation sequencing to define factors related to oral cancer and discover novel biomarkers. Life (Basel) 2020;10:228. https://doi.org/10.3390/life10100228
  82. Sembler-Moller ML, Belstrom D, Locht H, Enevold C, Pedersen AML. Next-generation sequencing of whole saliva from patients with primary Sjogren's syndrome and non-Sjogren's sicca reveals comparable salivary microbiota. J Oral Microbiol 2019;11: 1660566. https://doi.org/10.1080/20002297.2019.1660566