• dbGVOSCC: a comprehensive data...

Treffer: dbGVOSCC: a comprehensive database of genetic variation for systems genetics research on oral squamous cell carcinoma.

Title:
dbGVOSCC: a comprehensive database of genetic variation for systems genetics research on oral squamous cell carcinoma.
Authors:
Zhou Y; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Wu Y; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.; State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Engineering Research Center of Oral Translational Medicine, Ministry of Education & National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China., Shi W; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.; 01life Institute, Shenzhen, China., Zhang Y; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Liu X; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Zhang Y; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Zhan C; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Chen B; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China., Tian W; State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Engineering Research Center of Oral Translational Medicine, Ministry of Education & National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China., Shen B; Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Source:
Frontiers in oncology [Front Oncol] 2025 Oct 31; Vol. 15, pp. 1692732. Date of Electronic Publication: 2025 Oct 31 (Print Publication: 2025).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101568867 Publication Model: eCollection Cited Medium: Print ISSN: 2234-943X (Print) Linking ISSN: 2234943X NLM ISO Abbreviation: Front Oncol Subsets: PubMed not MEDLINE
Imprint Name(s):
Original Publication: [Lausanne : Frontiers Research Foundation]
References:
Int J Med Sci. 2025 May 31;22(11):2792-2801. (PMID: 40520893)
Oral Oncol. 2010 Jul;46(7):543-8. (PMID: 20435510)
Cancer Rep (Hoboken). 2024 Mar;7(3):e2045. (PMID: 38522008)
Curr Top Microbiol Immunol. 2017;407:153-189. (PMID: 28550454)
Clin Epidemiol. 2019 Aug 19;11:733-741. (PMID: 31695503)
Int J Mol Sci. 2019 Dec 08;20(24):. (PMID: 31817996)
Cancer Metastasis Rev. 2021 Mar;40(1):141-152. (PMID: 33403469)
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W518-22. (PMID: 23703206)
Cancer Discov. 2013 Jul;3(7):770-81. (PMID: 23619168)
Am J Hum Genet. 2010 Mar 12;86(3):399-410. (PMID: 20170901)
Oral Oncol. 2010 Sep;46(9):e47-53. (PMID: 20656543)
Semin Cancer Biol. 2020 Apr;61:71-83. (PMID: 31542510)
Bioinformatics. 2016 Jun 15;32(12):1907-10. (PMID: 26883486)
Bioinformation. 2011 May 07;6(4):169-70. (PMID: 21572887)
EBioMedicine. 2019 Dec;50:203-210. (PMID: 31761620)
Int J Oral Sci. 2022 Feb 14;14(1):9. (PMID: 35153296)
Cancer Chemother Pharmacol. 2013 Jun;71(6):1395-409. (PMID: 23443307)
N Engl J Med. 2020 Jan 2;382(1):60-72. (PMID: 31893516)
Oral Oncol. 2020 Dec;111:104930. (PMID: 32745900)
Carcinogenesis. 2018 May 28;39(6):778-787. (PMID: 29668903)
Eur Radiol. 2023 Jan;33(1):162-171. (PMID: 36070090)
Med Sci (Basel). 2023 Jun 13;11(2):. (PMID: 37367741)
Addict Health. 2020 Jul;12(3):225-234. (PMID: 33244399)
Int J Oral Sci. 2023 Sep 22;15(1):44. (PMID: 37736748)
Database (Oxford). 2021 May 28;2021:. (PMID: 34048545)
Precis Clin Med. 2021 Apr 16;4(2):80-84. (PMID: 35694156)
JCO Clin Cancer Inform. 2020 Mar;4:210-220. (PMID: 32142370)
J Stomatol Oral Maxillofac Surg. 2025 Jun;126(3S):102166. (PMID: 39603507)
Mol Cancer. 2024 Dec 19;23(1):273. (PMID: 39696340)
Oral Oncol. 2012 Nov;48(11):1171-7. (PMID: 22818823)
Nat Rev Genet. 2014 Jan;15(1):34-48. (PMID: 24296534)
Nucleic Acids Res. 2019 Jul 2;47(W1):W587-W593. (PMID: 31114887)
Br J Cancer. 2020 Oct;123(9):1456-1463. (PMID: 32830199)
PLoS One. 2021 Jan 20;16(1):e0245715. (PMID: 33471836)
J Cancer Res Clin Oncol. 2025 Jan 28;151(2):53. (PMID: 39875744)
Front Immunol. 2024 Dec 03;15:1493377. (PMID: 39691710)
Front Oncol. 2025 May 29;15:1531799. (PMID: 40510139)
Sci Rep. 2023 Aug 28;13(1):14033. (PMID: 37640804)
N Engl J Med. 2006 Feb 9;354(6):567-78. (PMID: 16467544)
Contributed Indexing:
Keywords: cancer heterogeneity; dbGVOSCC database; genetic variations; oral squamous cell carcinoma; precision oncology
Entry Date(s):
Date Created: 20251117 Date Completed: 20251117 Latest Revision: 20251120
Update Code:
20251121
PubMed Central ID:
PMC12616376
DOI:
10.3389/fonc.2025.1692732
PMID:
41244916
Database:
MEDLINE

Weitere Informationen

Introduction: Oral squamous cell carcinoma (OSCC) is a highly aggressive malignancy of the oral epithelium, marked by a high rate of lymph node metastasis and a profound negative impact on patients' quality of life. Despite its severity, no routine screening program currently exists for OSCC. To address the genetic heterogeneity underlying OSCC, we have developed a database of genetic variation in oral squamous cell carcinoma (dbGVOSCC; http://www.sysbio.org.cn/dbGVOSCC/).
Methods: OSCC literature (1991-2024) was queried from PubMed and screened manually and via PubTator, following predefined inclusion/exclusion criteria. Entities and relations were extracted from qualifying articles and organized into tables. The database adopted a browser/server architecture using HTML and XAMPP. Front-end was built with HTML and CSS for web display; server-side used Apache for infrastructure, MySQL for data management, and PHP/JavaScript for backend-frontend integration. Bioinformatics included mapping genes to STRING (confidence >0.9), hub gene identification via PPI degree centrality, and GO/KEGG enrichment with clusterProfiler (FDR-corrected). Usability was assessed using SUS and NPS surveys.
Results: dbGVOSCC comprises 1,788 somatic genetic variation entries from 400 original studies and 106,079 clinical samples, covering epimutations/methylations (329), SNPs (411), point mutations excluding SNP (258), indels (98), CNVs (348), LOH (28), one locus mutation, plus 333 unspecified mutations. We curated 817 biomarker-linked variations (diagnostic n=71, therapeutic n=175, prognostic n=291; 277 multi-application). PPI analysis highlighted 15 key genes (e.g., TP53, CTNNB1, AKT1, EGFR, PIK3CA). Enrichment implicated proliferation, adhesion/migration, p53/DNA damage response, and PI3K-Akt signaling. User testing showed SUS 88.75 (grade A) and NPS 90.
Discussion: dbGVOSCC represents a robust and reliable knowledge base, offering clinicians and researchers an open-source platform for personalized genotype-phenotype association studies and systems genetics research into the mechanisms of OSCC.
(Copyright © 2025 Zhou, Wu, Shi, Zhang, Liu, Zhang, Zhan, Chen, Tian and Shen.)

Author WS was employed by company 01life Institute. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.