Models for Predicting Response to Immunotherapy and Prognosis in Patients with Gastric Cancer: DNA Damage Response Genes

Objective. DNA damage response (DDR) is a complex system that maintains genetic integrity and the stable replication and transmission of genetic material. m6A modifies DDR-related gene expression and affects the balance of DNA damage response in tumor cells. In this study, a risk model based on m6A-...

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Veröffentlicht in:BioMed research international 2022-12, Vol.2022, p.4909544-21
Hauptverfasser: Dong, Rui, Chen, Shuran, Lu, Fei, Zheng, Ni, Peng, Guisen, Li, Yan, Yang, Pan, Wen, Hexin, Qiu, Quanwei, Wang, Yitong, Wu, Huazhang, Liu, Mulin
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container_issue
container_start_page 4909544
container_title BioMed research international
container_volume 2022
creator Dong, Rui
Chen, Shuran
Lu, Fei
Zheng, Ni
Peng, Guisen
Li, Yan
Yang, Pan
Wen, Hexin
Qiu, Quanwei
Wang, Yitong
Wu, Huazhang
Liu, Mulin
description Objective. DNA damage response (DDR) is a complex system that maintains genetic integrity and the stable replication and transmission of genetic material. m6A modifies DDR-related gene expression and affects the balance of DNA damage response in tumor cells. In this study, a risk model based on m6A-modified DDR-related gene was established to evaluate its role in patients with gastric cancer. Methods. We downloaded 639 DNA damage response genes from the Gene Set Enrichment Analysis (GSEA) database and constructed risk score models using typed differential genes. We used Kaplan-Meier curves and risk curves to verify the clinical relevance of the model, which was then validated with the univariate and multifactorial Cox analysis, ROC, C-index, and nomogram, and finally this model was used to evaluate the correlation of the risk score model with immune microenvironment, microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Results. In this study, 337 samples in The Cancer Genome Atlas (TCGA) database were used as training set to construct a DDR-related gene model, and GSE84437 was used as external data set for verification. We found that the prognosis and immunotherapy effect of gastric cancer patients in the low-risk group were significantly better than those in the high-risk group. Conclusion. We screened eight DDR-related genes (ZBTB7A, POLQ, CHEK1, NPDC1, RAMP1, AXIN2, SFRP2, and APOD) to establish a risk model, which can predict the prognosis of gastric cancer patients and guide the clinical implementation of immunotherapy.
doi_str_mv 10.1155/2022/4909544
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DNA damage response (DDR) is a complex system that maintains genetic integrity and the stable replication and transmission of genetic material. m6A modifies DDR-related gene expression and affects the balance of DNA damage response in tumor cells. In this study, a risk model based on m6A-modified DDR-related gene was established to evaluate its role in patients with gastric cancer. Methods. We downloaded 639 DNA damage response genes from the Gene Set Enrichment Analysis (GSEA) database and constructed risk score models using typed differential genes. We used Kaplan-Meier curves and risk curves to verify the clinical relevance of the model, which was then validated with the univariate and multifactorial Cox analysis, ROC, C-index, and nomogram, and finally this model was used to evaluate the correlation of the risk score model with immune microenvironment, microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Results. In this study, 337 samples in The Cancer Genome Atlas (TCGA) database were used as training set to construct a DDR-related gene model, and GSE84437 was used as external data set for verification. We found that the prognosis and immunotherapy effect of gastric cancer patients in the low-risk group were significantly better than those in the high-risk group. Conclusion. We screened eight DDR-related genes (ZBTB7A, POLQ, CHEK1, NPDC1, RAMP1, AXIN2, SFRP2, and APOD) to establish a risk model, which can predict the prognosis of gastric cancer patients and guide the clinical implementation of immunotherapy.</description><identifier>ISSN: 2314-6133</identifier><identifier>ISSN: 2314-6141</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2022/4909544</identifier><identifier>PMID: 36578802</identifier><language>eng</language><publisher>United States: Hindawi</publisher><subject>Algorithms ; Cancer ; Care and treatment ; Cell cycle ; Cell Line, Tumor ; Chemotherapy ; Complex systems ; Damage ; Deoxyribonucleic acid ; DNA ; DNA damage ; DNA Damage - genetics ; DNA methylation ; DNA repair ; DNA-Binding Proteins ; Drug therapy ; Gastric cancer ; Gene expression ; Gene set enrichment analysis ; Genes ; Genetic aspects ; Genomes ; Health aspects ; Humans ; Immune checkpoint ; Immunotherapy ; Medical prognosis ; Microenvironments ; Microsatellite instability ; Mutation ; N6-methyladenosine ; Nomograms ; Patients ; Prognosis ; Receptor activity modifying proteins ; Risk ; Risk groups ; Stomach cancer ; Stomach Neoplasms - genetics ; Stomach Neoplasms - therapy ; Survival analysis ; Transcription Factors ; Tumor cells ; Tumor Microenvironment ; Tumors</subject><ispartof>BioMed research international, 2022-12, Vol.2022, p.4909544-21</ispartof><rights>Copyright © 2022 Rui Dong et al.</rights><rights>COPYRIGHT 2022 John Wiley &amp; Sons, Inc.</rights><rights>Copyright © 2022 Rui Dong et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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DNA damage response (DDR) is a complex system that maintains genetic integrity and the stable replication and transmission of genetic material. m6A modifies DDR-related gene expression and affects the balance of DNA damage response in tumor cells. In this study, a risk model based on m6A-modified DDR-related gene was established to evaluate its role in patients with gastric cancer. Methods. We downloaded 639 DNA damage response genes from the Gene Set Enrichment Analysis (GSEA) database and constructed risk score models using typed differential genes. We used Kaplan-Meier curves and risk curves to verify the clinical relevance of the model, which was then validated with the univariate and multifactorial Cox analysis, ROC, C-index, and nomogram, and finally this model was used to evaluate the correlation of the risk score model with immune microenvironment, microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Results. In this study, 337 samples in The Cancer Genome Atlas (TCGA) database were used as training set to construct a DDR-related gene model, and GSE84437 was used as external data set for verification. We found that the prognosis and immunotherapy effect of gastric cancer patients in the low-risk group were significantly better than those in the high-risk group. Conclusion. We screened eight DDR-related genes (ZBTB7A, POLQ, CHEK1, NPDC1, RAMP1, AXIN2, SFRP2, and APOD) to establish a risk model, which can predict the prognosis of gastric cancer patients and guide the clinical implementation of immunotherapy.</description><subject>Algorithms</subject><subject>Cancer</subject><subject>Care and treatment</subject><subject>Cell cycle</subject><subject>Cell Line, Tumor</subject><subject>Chemotherapy</subject><subject>Complex systems</subject><subject>Damage</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA damage</subject><subject>DNA Damage - genetics</subject><subject>DNA methylation</subject><subject>DNA repair</subject><subject>DNA-Binding Proteins</subject><subject>Drug therapy</subject><subject>Gastric cancer</subject><subject>Gene expression</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Immune checkpoint</subject><subject>Immunotherapy</subject><subject>Medical prognosis</subject><subject>Microenvironments</subject><subject>Microsatellite instability</subject><subject>Mutation</subject><subject>N6-methyladenosine</subject><subject>Nomograms</subject><subject>Patients</subject><subject>Prognosis</subject><subject>Receptor activity modifying proteins</subject><subject>Risk</subject><subject>Risk groups</subject><subject>Stomach cancer</subject><subject>Stomach Neoplasms - genetics</subject><subject>Stomach Neoplasms - therapy</subject><subject>Survival analysis</subject><subject>Transcription Factors</subject><subject>Tumor cells</subject><subject>Tumor Microenvironment</subject><subject>Tumors</subject><issn>2314-6133</issn><issn>2314-6141</issn><issn>2314-6141</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>RHX</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc9rFDEYhgdRbKm9eZaAF0HX5ncmHoRlq2uhahE9h2zmm9mUmWSbzFj735t11616MJcEvocn38tbVU8Jfk2IEGcUU3rGNdaC8wfVMWWEzyTh5OHhzdhRdZrzNS6nJhJr-bg6YlKousb0uPrxMTbQZ9TGhK4SNN6NPnToC-RNDBnQGNHFMEwhjmtIdnOHbGgKGLsQs8_IB3RlRw9hzOjWj2u0tHlM3qGFDQ7SG3T-aY7O7WA7uHcuIUB-Uj1qbZ_hdH-fVN_ev_u6-DC7_Ly8WMwvZ44rOc6clJrUHLeYQd0Ki11rJSF4hQlQS6FZ1U5arqizjhDbrNoSsq1ZA1o3QnF2Ur3deTfTaoDGlVWT7c0m-cGmOxOtN39Pgl-bLn43WmlKmSqCF3tBijcT5NEMPjvoexsgTtlQJTSVQnNR0Of_oNdxSqHE-0XVCjOl7qnO9mB8aGP5122lZq4Y0QITvKVe7SiXYs4J2sPKBJtt92bbvdl3X_Bnf8Y8wL-bLsDLHbD2obG3_v-6n00QtjU</recordid><startdate>20221219</startdate><enddate>20221219</enddate><creator>Dong, Rui</creator><creator>Chen, Shuran</creator><creator>Lu, Fei</creator><creator>Zheng, Ni</creator><creator>Peng, Guisen</creator><creator>Li, Yan</creator><creator>Yang, Pan</creator><creator>Wen, Hexin</creator><creator>Qiu, Quanwei</creator><creator>Wang, Yitong</creator><creator>Wu, Huazhang</creator><creator>Liu, Mulin</creator><general>Hindawi</general><general>John Wiley &amp; 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DNA damage response (DDR) is a complex system that maintains genetic integrity and the stable replication and transmission of genetic material. m6A modifies DDR-related gene expression and affects the balance of DNA damage response in tumor cells. In this study, a risk model based on m6A-modified DDR-related gene was established to evaluate its role in patients with gastric cancer. Methods. We downloaded 639 DNA damage response genes from the Gene Set Enrichment Analysis (GSEA) database and constructed risk score models using typed differential genes. We used Kaplan-Meier curves and risk curves to verify the clinical relevance of the model, which was then validated with the univariate and multifactorial Cox analysis, ROC, C-index, and nomogram, and finally this model was used to evaluate the correlation of the risk score model with immune microenvironment, microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Results. In this study, 337 samples in The Cancer Genome Atlas (TCGA) database were used as training set to construct a DDR-related gene model, and GSE84437 was used as external data set for verification. We found that the prognosis and immunotherapy effect of gastric cancer patients in the low-risk group were significantly better than those in the high-risk group. Conclusion. We screened eight DDR-related genes (ZBTB7A, POLQ, CHEK1, NPDC1, RAMP1, AXIN2, SFRP2, and APOD) to establish a risk model, which can predict the prognosis of gastric cancer patients and guide the clinical implementation of immunotherapy.</abstract><cop>United States</cop><pub>Hindawi</pub><pmid>36578802</pmid><doi>10.1155/2022/4909544</doi><tpages>21</tpages><orcidid>https://orcid.org/0000-0002-8768-995X</orcidid><orcidid>https://orcid.org/0000-0001-6103-2573</orcidid><orcidid>https://orcid.org/0000-0003-1645-6427</orcidid><orcidid>https://orcid.org/0000-0002-9451-6678</orcidid><orcidid>https://orcid.org/0000-0002-5482-3761</orcidid><orcidid>https://orcid.org/0000-0002-6849-3775</orcidid><orcidid>https://orcid.org/0000-0003-0824-7633</orcidid><orcidid>https://orcid.org/0000-0002-1818-6021</orcidid><orcidid>https://orcid.org/0000-0002-2872-6714</orcidid><orcidid>https://orcid.org/0000-0002-3345-7141</orcidid><orcidid>https://orcid.org/0000-0002-7774-2411</orcidid><orcidid>https://orcid.org/0000-0002-6283-839X</orcidid><oa>free_for_read</oa></addata></record>
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subjects Algorithms
Cancer
Care and treatment
Cell cycle
Cell Line, Tumor
Chemotherapy
Complex systems
Damage
Deoxyribonucleic acid
DNA
DNA damage
DNA Damage - genetics
DNA methylation
DNA repair
DNA-Binding Proteins
Drug therapy
Gastric cancer
Gene expression
Gene set enrichment analysis
Genes
Genetic aspects
Genomes
Health aspects
Humans
Immune checkpoint
Immunotherapy
Medical prognosis
Microenvironments
Microsatellite instability
Mutation
N6-methyladenosine
Nomograms
Patients
Prognosis
Receptor activity modifying proteins
Risk
Risk groups
Stomach cancer
Stomach Neoplasms - genetics
Stomach Neoplasms - therapy
Survival analysis
Transcription Factors
Tumor cells
Tumor Microenvironment
Tumors
title Models for Predicting Response to Immunotherapy and Prognosis in Patients with Gastric Cancer: DNA Damage Response Genes
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