Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis
Abstract Periodontitis is a chronic inflammatory disease that mainly occurs in the dental supporting tissues. Endoplasmic reticulum autophagy (ER-phagy) is a new type of selective autophagy. The main function of ER-phagy is to degrade excess ER membranes or toxic protein aggregates, control the volu...
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Nature Portfolio
2025-07-01
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| author | Ruyue Wang Jinyue Hu Qing Sun Shuixiang Guo Gege Zhang Ao Lu Shuo Liu Xue Yang Lina Wang |
| author_facet | Ruyue Wang Jinyue Hu Qing Sun Shuixiang Guo Gege Zhang Ao Lu Shuo Liu Xue Yang Lina Wang |
| author_sort | Ruyue Wang |
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| description | Abstract Periodontitis is a chronic inflammatory disease that mainly occurs in the dental supporting tissues. Endoplasmic reticulum autophagy (ER-phagy) is a new type of selective autophagy. The main function of ER-phagy is to degrade excess ER membranes or toxic protein aggregates, control the volume of ER, and maintain cell homeostasis. This study utilized bioinformatics to identify and validate potential ER-phagy-related biomarkers for periodontitis. The relationship between immune cell infiltration and periodontitis as well as potential biomarkers was analyzed, to identify new targets for the diagnosis and treatment of periodontitis. Data from GeneCards and Gene Expression Omnibus (GEO) databases were utilized to identify differentially-expressed ER-phagy-related genes, and to conduct functional enrichment and pathway analyses. Random forest, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature removal (SVM-RFE) algorithms were used to identify hub genes. Receiver operating characteristic (ROC) curves and areas under the curve (AUCs) were calculated to assess diagnostic performance and identify potential biomarkers for periodontitis. The CIBERSORT deconvolution algorithm was used to study the link between potential biomarkers and distinct types of immune cells. In addition, clinical samples were examined using Real-time quantitative polymerase chain reaction (RT-qPCR) to verify the expression of genes related to ER-phagy in periodontitis and identify a signature which may better predict this disease. Bioinformatics analysis identified 88 differentially-expressed ER-phagy-related genes (DE-ERGs). 6 hub genes were found using LASSO, SVM-RFE and Random forest, namely ATP1A1, CD69, DNAJB11, GANAB, IL7, and PSME2. ATP1A1 and GANAB exhibited robust diagnostic efficacy in both the training set and validation set. The results of immune cell infiltration analysis revealed a significantly greater abundance of plasma cells in periodontitis tissue samples compared to healthy periodontal tissue samples (P < 0.05). Correlation analysis between potential biomarkers and immune cells demonstrated that the expression levels of ATP1A1 and GANAB were correlated with plasma cells and resting dendritic cells. Clinical samples examined by RT-qPCR verified that these ER-phagy-related signature genes in periodontitis may better predict the development of periodontitis.ER-phagy is closely related to the pathological process of periodontitis. The infiltration of immune cells differs between tissues affected by periodontitis and healthy periodontal tissues, and a variety of immune cell subsets are significantly correlated with ATP1A1 and GANAB, thus ATP1A1 and GANAB have good diagnostic efficiency for periodontitis and can be used as potential biomarkers for early diagnosis. |
| format | Article |
| id | doaj-art-ab5955fefe5d49ac990be83fd473345d |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
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| spelling | doaj-art-ab5955fefe5d49ac990be83fd473345d2025-08-20T03:04:25ZengNature PortfolioScientific Reports2045-23222025-07-0115111410.1038/s41598-025-08180-2Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitisRuyue Wang0Jinyue Hu1Qing Sun2Shuixiang Guo3Gege Zhang4Ao Lu5Shuo Liu6Xue Yang7Lina Wang8Department of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityDepartment of Endodontics and Periodontics, School of Stomatology, Dalian Medical UniversityAbstract Periodontitis is a chronic inflammatory disease that mainly occurs in the dental supporting tissues. Endoplasmic reticulum autophagy (ER-phagy) is a new type of selective autophagy. The main function of ER-phagy is to degrade excess ER membranes or toxic protein aggregates, control the volume of ER, and maintain cell homeostasis. This study utilized bioinformatics to identify and validate potential ER-phagy-related biomarkers for periodontitis. The relationship between immune cell infiltration and periodontitis as well as potential biomarkers was analyzed, to identify new targets for the diagnosis and treatment of periodontitis. Data from GeneCards and Gene Expression Omnibus (GEO) databases were utilized to identify differentially-expressed ER-phagy-related genes, and to conduct functional enrichment and pathway analyses. Random forest, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature removal (SVM-RFE) algorithms were used to identify hub genes. Receiver operating characteristic (ROC) curves and areas under the curve (AUCs) were calculated to assess diagnostic performance and identify potential biomarkers for periodontitis. The CIBERSORT deconvolution algorithm was used to study the link between potential biomarkers and distinct types of immune cells. In addition, clinical samples were examined using Real-time quantitative polymerase chain reaction (RT-qPCR) to verify the expression of genes related to ER-phagy in periodontitis and identify a signature which may better predict this disease. Bioinformatics analysis identified 88 differentially-expressed ER-phagy-related genes (DE-ERGs). 6 hub genes were found using LASSO, SVM-RFE and Random forest, namely ATP1A1, CD69, DNAJB11, GANAB, IL7, and PSME2. ATP1A1 and GANAB exhibited robust diagnostic efficacy in both the training set and validation set. The results of immune cell infiltration analysis revealed a significantly greater abundance of plasma cells in periodontitis tissue samples compared to healthy periodontal tissue samples (P < 0.05). Correlation analysis between potential biomarkers and immune cells demonstrated that the expression levels of ATP1A1 and GANAB were correlated with plasma cells and resting dendritic cells. Clinical samples examined by RT-qPCR verified that these ER-phagy-related signature genes in periodontitis may better predict the development of periodontitis.ER-phagy is closely related to the pathological process of periodontitis. The infiltration of immune cells differs between tissues affected by periodontitis and healthy periodontal tissues, and a variety of immune cell subsets are significantly correlated with ATP1A1 and GANAB, thus ATP1A1 and GANAB have good diagnostic efficiency for periodontitis and can be used as potential biomarkers for early diagnosis.https://doi.org/10.1038/s41598-025-08180-2PeriodontitisER-phagyBioinformaticsBiomarkersImmune |
| spellingShingle | Ruyue Wang Jinyue Hu Qing Sun Shuixiang Guo Gege Zhang Ao Lu Shuo Liu Xue Yang Lina Wang Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis Scientific Reports Periodontitis ER-phagy Bioinformatics Biomarkers Immune |
| title | Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis |
| title_full | Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis |
| title_fullStr | Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis |
| title_full_unstemmed | Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis |
| title_short | Identification and validation of endoplasmic reticulum autophagy-related potential biomarkers in periodontitis |
| title_sort | identification and validation of endoplasmic reticulum autophagy related potential biomarkers in periodontitis |
| topic | Periodontitis ER-phagy Bioinformatics Biomarkers Immune |
| url | https://doi.org/10.1038/s41598-025-08180-2 |
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