Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis
IntroductionPeriodontitis is an inflammatory disease and its molecular mechanisms is not clear. A recently discovered cell death pathway called cuproptosis, may related to the disease.MethodsThe datasets GSE10334 of human periodontitis and control were retrieved from the Gene Expression Omnibus data...
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1164667/full |
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| author | Shuying Liu Jiaying Ge Yiting Chu Shuangyu Cai Aixiu Gong Jun Wu Jinghan Zhang |
| author_facet | Shuying Liu Jiaying Ge Yiting Chu Shuangyu Cai Aixiu Gong Jun Wu Jinghan Zhang |
| author_sort | Shuying Liu |
| collection | DOAJ |
| description | IntroductionPeriodontitis is an inflammatory disease and its molecular mechanisms is not clear. A recently discovered cell death pathway called cuproptosis, may related to the disease.MethodsThe datasets GSE10334 of human periodontitis and control were retrieved from the Gene Expression Omnibus database (GEO) for analysis.Following the use of two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature removal (SVM-RFE) were used to find CRG-based signature. Then the Receiver operating characteristic (ROC) curves was used to evaluate the gene signature's discriminatory ability. The CIBERSORT deconvolution algorithm was used to study the link between hub genes and distinct types of immune cells. Next, the association of the CRGs with immune cells in periodontitis and relevant clusters of cuproptosis were found. The link between various clusters was ascertained by the GSVA and CIBERSORT deconvolution algorithm. Finally, An external dataset (GSE16134) was used to confirm the diagnosis capacity of the identified biomarkers. In addition, clinical samples were examined using qRT-PCR and immunohistochemistry to verifiy the expression of genes related to cuprotosis in periodontitis and the signature may better predict the periodontitis. Results15 periodontitis-related DE-CRGs were found,then 11-CRG-based signature was found by using of LASSO and SVM-RFE. ROC curves also supported the value of signature. CIBERSORT results of immune cell signature in periodontitis showed that signature genes is a crucial component of the immune response.The relevant clusters of cuproptosis found that the NFE2L2, SLC31A1, FDX1,LIAS, DLD, DLAT, and DBT showed a highest expression levels in Cluster2 ,while the NLRP3, MTF1, and DLST displayed the lowest level in Cluster 2 but the highest level in Cluster1. The GSVA results also showed that the 11 cuproptosis diagnostic gene may regulate the periodontitis by affecting immune cells. The external dataset (GSE16134) confirm the diagnosis capacity of the identified biomarkers, and clinical samples examined by qRT-PCR and immunohistochemistry also verified that these cuprotosis related signiture genes in periodontitis may better predict the periodontitis. ConclusionThese findings have important implications for the cuproptosis and periodontitis, and highlight further research is needed to better understand the mechanisms underlying this relationship between the cuproptosis and periodontitis. |
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| last_indexed | 2024-03-11T20:20:22Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-5c460bad741c4bb2a1fe711d4e284eb72023-10-03T04:54:18ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-05-011410.3389/fimmu.2023.11646671164667Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitisShuying Liu0Jiaying Ge1Yiting Chu2Shuangyu Cai3Aixiu Gong4Jun Wu5Jinghan Zhang6Department of Stomatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Anatomy, Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Stomatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Anatomy, Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Stomatology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Anatomy, Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, ChinaDepartment of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, ChinaIntroductionPeriodontitis is an inflammatory disease and its molecular mechanisms is not clear. A recently discovered cell death pathway called cuproptosis, may related to the disease.MethodsThe datasets GSE10334 of human periodontitis and control were retrieved from the Gene Expression Omnibus database (GEO) for analysis.Following the use of two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature removal (SVM-RFE) were used to find CRG-based signature. Then the Receiver operating characteristic (ROC) curves was used to evaluate the gene signature's discriminatory ability. The CIBERSORT deconvolution algorithm was used to study the link between hub genes and distinct types of immune cells. Next, the association of the CRGs with immune cells in periodontitis and relevant clusters of cuproptosis were found. The link between various clusters was ascertained by the GSVA and CIBERSORT deconvolution algorithm. Finally, An external dataset (GSE16134) was used to confirm the diagnosis capacity of the identified biomarkers. In addition, clinical samples were examined using qRT-PCR and immunohistochemistry to verifiy the expression of genes related to cuprotosis in periodontitis and the signature may better predict the periodontitis. Results15 periodontitis-related DE-CRGs were found,then 11-CRG-based signature was found by using of LASSO and SVM-RFE. ROC curves also supported the value of signature. CIBERSORT results of immune cell signature in periodontitis showed that signature genes is a crucial component of the immune response.The relevant clusters of cuproptosis found that the NFE2L2, SLC31A1, FDX1,LIAS, DLD, DLAT, and DBT showed a highest expression levels in Cluster2 ,while the NLRP3, MTF1, and DLST displayed the lowest level in Cluster 2 but the highest level in Cluster1. The GSVA results also showed that the 11 cuproptosis diagnostic gene may regulate the periodontitis by affecting immune cells. The external dataset (GSE16134) confirm the diagnosis capacity of the identified biomarkers, and clinical samples examined by qRT-PCR and immunohistochemistry also verified that these cuprotosis related signiture genes in periodontitis may better predict the periodontitis. ConclusionThese findings have important implications for the cuproptosis and periodontitis, and highlight further research is needed to better understand the mechanisms underlying this relationship between the cuproptosis and periodontitis.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1164667/fullcuproptosishubimmuneinfiltrationperiodontitis |
| spellingShingle | Shuying Liu Jiaying Ge Yiting Chu Shuangyu Cai Aixiu Gong Jun Wu Jinghan Zhang Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis Frontiers in Immunology cuproptosis hub immune infiltration periodontitis |
| title | Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| title_full | Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| title_fullStr | Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| title_full_unstemmed | Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| title_short | Identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| title_sort | identification of hub cuproptosis related genes and immune cell infiltration characteristics in periodontitis |
| topic | cuproptosis hub immune infiltration periodontitis |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1164667/full |
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