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 , 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","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 , 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\",\"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}
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.