免疫介质中的遗传变异作为口腔癌评估的潜在分子生物标志物:通过计算分析和贝叶斯方法进行系统重估的见解

Juliana Campos Botelho , Samuel Arcebispo Brasileiro , André Victor Oliveira Monteiro , Alessandro Luiz Araújo Bentes Leal , Naum Neves da Costa dos Santos , Gabrielly Ribeiro Alves , Reyce Santos Koga , Haline Alves da Silva , José Rogério Souza Monteiro , Denis Vieira Gomes Ferreira , Adenilson Leão Pereira , Ana Carolina Alves de Oliveira , Márcia Socorro Silva Lima Duarte , Felipe Rodolfo Pereira da Silva
{"title":"免疫介质中的遗传变异作为口腔癌评估的潜在分子生物标志物:通过计算分析和贝叶斯方法进行系统重估的见解","authors":"Juliana Campos Botelho ,&nbsp;Samuel Arcebispo Brasileiro ,&nbsp;André Victor Oliveira Monteiro ,&nbsp;Alessandro Luiz Araújo Bentes Leal ,&nbsp;Naum Neves da Costa dos Santos ,&nbsp;Gabrielly Ribeiro Alves ,&nbsp;Reyce Santos Koga ,&nbsp;Haline Alves da Silva ,&nbsp;José Rogério Souza Monteiro ,&nbsp;Denis Vieira Gomes Ferreira ,&nbsp;Adenilson Leão Pereira ,&nbsp;Ana Carolina Alves de Oliveira ,&nbsp;Márcia Socorro Silva Lima Duarte ,&nbsp;Felipe Rodolfo Pereira da Silva","doi":"10.1016/j.oor.2025.100729","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><div>Oral cancer is a complex disease in which genetic variations in immune mediator play a relevant role in its pathophysiology. This study aimed at assessing the level of false-positive rates on meta-analytic data on genetic variations in immune mediator genes related with oral cancer risk.</div></div><div><h3>Material and methods</h3><div>A systematic search was performed for meta-analyses in this field that were published before September 22, 2024. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio (OR) at a prior probability of 10<sup>−3</sup> and 10<sup>−6</sup>. A methodological evaluation by the Venice criteria was performed and <em>in silico</em> networks were designed.</div></div><div><h3>Results</h3><div>Ten meta-analyses on the <em>TNFA</em>/rs361625/rs1800629, <em>VEGF</em>/rs3025039, <em>IL4</em>/rs2070874, <em>IL6</em>/rs1800795, <em>IL8</em>/rs4073 and <em>IL10</em>/rs1800896 genes/polymorphisms and oral cancer have been included. 88 significant OR association values from the meta-analyses included allowed the performance of 336 calculations for FPRP and 176 for BFDP. We found 35 noteworthy values (10.42 %) for FPRP and 59 noteworthy values (33.52 %) for BFDP that demonstrated the variants in <em>VEGF</em> and <em>IL10</em> with noteworthiness association with oral cancer. The gene-gene and protein-protein networks evidenced the role of <em>VEGF, TNFA, IL4, IL6, IL8</em> and <em>IL10</em> genes in the physiopathology of the disease.</div></div><div><h3>Conclusions</h3><div>The Bayesian calculations and the <em>in-silico</em> analyses indicated the rs3025039 and rs1800896 polymorphisms in the <em>VEGF</em> and <em>IL10</em> genes, respectively, as noteworthy molecular biomarkers for oral cancer risk evaluation.</div></div>","PeriodicalId":94378,"journal":{"name":"Oral Oncology Reports","volume":"13 ","pages":"Article 100729"},"PeriodicalIF":0.0000,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genetic variants in immune mediators as potential molecular biomarkers for oral cancer evaluation: Insights from a systematic revaluation by computational analyses and Bayesian approaches\",\"authors\":\"Juliana Campos Botelho ,&nbsp;Samuel Arcebispo Brasileiro ,&nbsp;André Victor Oliveira Monteiro ,&nbsp;Alessandro Luiz Araújo Bentes Leal ,&nbsp;Naum Neves da Costa dos Santos ,&nbsp;Gabrielly Ribeiro Alves ,&nbsp;Reyce Santos Koga ,&nbsp;Haline Alves da Silva ,&nbsp;José Rogério Souza Monteiro ,&nbsp;Denis Vieira Gomes Ferreira ,&nbsp;Adenilson Leão Pereira ,&nbsp;Ana Carolina Alves de Oliveira ,&nbsp;Márcia Socorro Silva Lima Duarte ,&nbsp;Felipe Rodolfo Pereira da Silva\",\"doi\":\"10.1016/j.oor.2025.100729\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><div>Oral cancer is a complex disease in which genetic variations in immune mediator play a relevant role in its pathophysiology. This study aimed at assessing the level of false-positive rates on meta-analytic data on genetic variations in immune mediator genes related with oral cancer risk.</div></div><div><h3>Material and methods</h3><div>A systematic search was performed for meta-analyses in this field that were published before September 22, 2024. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio (OR) at a prior probability of 10<sup>−3</sup> and 10<sup>−6</sup>. A methodological evaluation by the Venice criteria was performed and <em>in silico</em> networks were designed.</div></div><div><h3>Results</h3><div>Ten meta-analyses on the <em>TNFA</em>/rs361625/rs1800629, <em>VEGF</em>/rs3025039, <em>IL4</em>/rs2070874, <em>IL6</em>/rs1800795, <em>IL8</em>/rs4073 and <em>IL10</em>/rs1800896 genes/polymorphisms and oral cancer have been included. 88 significant OR association values from the meta-analyses included allowed the performance of 336 calculations for FPRP and 176 for BFDP. We found 35 noteworthy values (10.42 %) for FPRP and 59 noteworthy values (33.52 %) for BFDP that demonstrated the variants in <em>VEGF</em> and <em>IL10</em> with noteworthiness association with oral cancer. The gene-gene and protein-protein networks evidenced the role of <em>VEGF, TNFA, IL4, IL6, IL8</em> and <em>IL10</em> genes in the physiopathology of the disease.</div></div><div><h3>Conclusions</h3><div>The Bayesian calculations and the <em>in-silico</em> analyses indicated the rs3025039 and rs1800896 polymorphisms in the <em>VEGF</em> and <em>IL10</em> genes, respectively, as noteworthy molecular biomarkers for oral cancer risk evaluation.</div></div>\",\"PeriodicalId\":94378,\"journal\":{\"name\":\"Oral Oncology Reports\",\"volume\":\"13 \",\"pages\":\"Article 100729\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-02-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Oral Oncology Reports\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2772906025000172\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Oral Oncology Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2772906025000172","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

摘要

背景:口腔癌是一种复杂的疾病,免疫介质的遗传变异在其病理生理中起着重要作用。本研究旨在评估与口腔癌风险相关的免疫中介基因遗传变异的荟萃分析数据的假阳性率水平。材料与方法系统检索该领域在2024年9月22日之前发表的meta分析。计算假阳性率概率(FPRP)和贝叶斯错误发现概率(BFDP),在先验概率为10−3和10−6的情况下,优势比(OR)的统计功率分别为1.2和1.5,以评估值得注意性。通过威尼斯标准进行方法学评估,并设计了计算机网络。结果对TNFA/rs361625/rs1800629、VEGF/rs3025039、IL4/rs2070874、IL6/rs1800795、IL8/rs4073和IL10/rs1800896基因多态性与口腔癌的关系进行meta分析。meta分析包括88个显著OR关联值,FPRP计算336个,BFDP计算176个。我们发现FPRP有35个值得注意的值(10.42%),BFDP有59个值得注意的值(33.52%),这些值表明VEGF和IL10的变异与口腔癌有显著的关联。基因-基因和蛋白-蛋白网络证实了VEGF、TNFA、IL4、IL6、IL8和IL10基因在该疾病的生理病理中的作用。结论贝叶斯计算和芯片分析提示VEGF基因rs3025039和il - 10基因rs1800896的多态性可作为口腔癌风险评估的重要分子生物标志物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Genetic variants in immune mediators as potential molecular biomarkers for oral cancer evaluation: Insights from a systematic revaluation by computational analyses and Bayesian approaches

Background

Oral cancer is a complex disease in which genetic variations in immune mediator play a relevant role in its pathophysiology. This study aimed at assessing the level of false-positive rates on meta-analytic data on genetic variations in immune mediator genes related with oral cancer risk.

Material and methods

A systematic search was performed for meta-analyses in this field that were published before September 22, 2024. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio (OR) at a prior probability of 10−3 and 10−6. A methodological evaluation by the Venice criteria was performed and in silico networks were designed.

Results

Ten meta-analyses on the TNFA/rs361625/rs1800629, VEGF/rs3025039, IL4/rs2070874, IL6/rs1800795, IL8/rs4073 and IL10/rs1800896 genes/polymorphisms and oral cancer have been included. 88 significant OR association values from the meta-analyses included allowed the performance of 336 calculations for FPRP and 176 for BFDP. We found 35 noteworthy values (10.42 %) for FPRP and 59 noteworthy values (33.52 %) for BFDP that demonstrated the variants in VEGF and IL10 with noteworthiness association with oral cancer. The gene-gene and protein-protein networks evidenced the role of VEGF, TNFA, IL4, IL6, IL8 and IL10 genes in the physiopathology of the disease.

Conclusions

The Bayesian calculations and the in-silico analyses indicated the rs3025039 and rs1800896 polymorphisms in the VEGF and IL10 genes, respectively, as noteworthy molecular biomarkers for oral cancer risk evaluation.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
0.20
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信