PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma
Background: Glioma is one of the most common malignant tumors of the central nervous system. Immune infiltration of tumor microenvironment was associated with overall survival in low grade glioma (LGG). However, effects of Tyrosine phosphatase receptor type N (PTPRN) on the progress of LGG and its c...
| Main Authors: | , , , , , |
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Brain Sciences |
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| Online Access: | https://www.mdpi.com/2076-3425/12/6/763 |
| _version_ | 1797489394679021568 |
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| author | Peng Li Fanfan Chen Chen Yao Kezhou Zhu Bei Zhang Zelong Zheng |
| author_facet | Peng Li Fanfan Chen Chen Yao Kezhou Zhu Bei Zhang Zelong Zheng |
| author_sort | Peng Li |
| collection | DOAJ |
| description | Background: Glioma is one of the most common malignant tumors of the central nervous system. Immune infiltration of tumor microenvironment was associated with overall survival in low grade glioma (LGG). However, effects of Tyrosine phosphatase receptor type N (PTPRN) on the progress of LGG and its correlation with tumor infiltration are unclear. Methods: Here, datasets of LGG were from The Cancer Genome Atlas (TCGA) and normal samples were from GTEx dataset. Gepia website and Human Protein Atlas (HPA) Database were used to analyze the mRNA and protein expression of PTPRN. We evaluated the influence of PTPRN on survival of LGG patients. MethSurv was used to explore the expression and prognostic patterns of single CpG methylation of PTPRN gene in LGG. The correlations between the clinical information and PTPRN expression were analyzed using logistic regression and Multivariate Cox regression. We also explored the correlation between PTPRN expression and cancer immune infiltration by TIMER. Gene set enrichment analysis (GSEA) was formed using TCGA RNA-seq datasets. Results: PTPRN mRNA and protein expression decreased in LGG compared to normal brain tissue in TCGA and HPA database. Kaplan-Meier analysis showed that the high expression level of PTPRN correlated with a good overall survival (OS) of patients with LGG. The Multivariate Cox analysis demonstrated that PTPRN expression and other clinical-pathological factors (age, WHO grade, IDH status, and primary therapy outcome) significantly correlated with OS of LGG patients. The DNA methylation pattern of PTPRN with significant prognostic value were confirmed, including cg00672332, cg06971096, cg01382864, cg03970036, cg10140638, cg16166796, cg03545227, and cg25569248. Interestingly, PTPRN expression level significantly negatively correlated with infiltrating level of B cell, CD4+ T cells, Macrophages, Neutrophils, and DCs in LGG. Finally, GSEA showed that signaling pathways, mainly associated with tumor microenvironment and immune cells, were significantly enriched in PTPRN high expression. Conclusion: PTPRN is a potential biomarker and correlates with tumor immune infiltration in LGG. |
| first_indexed | 2024-03-10T00:15:54Z |
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| institution | Directory Open Access Journal |
| issn | 2076-3425 |
| language | English |
| last_indexed | 2024-03-10T00:15:54Z |
| publishDate | 2022-06-01 |
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| spelling | doaj.art-59271995112e4a49a618c20a939f1efa2023-11-23T15:51:03ZengMDPI AGBrain Sciences2076-34252022-06-0112676310.3390/brainsci12060763PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade GliomaPeng Li0Fanfan Chen1Chen Yao2Kezhou Zhu3Bei Zhang4Zelong Zheng5VCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USANeurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, ChinaNeurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, ChinaVCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USADepartment of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USADepartment of Neurosurgery, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, ChinaBackground: Glioma is one of the most common malignant tumors of the central nervous system. Immune infiltration of tumor microenvironment was associated with overall survival in low grade glioma (LGG). However, effects of Tyrosine phosphatase receptor type N (PTPRN) on the progress of LGG and its correlation with tumor infiltration are unclear. Methods: Here, datasets of LGG were from The Cancer Genome Atlas (TCGA) and normal samples were from GTEx dataset. Gepia website and Human Protein Atlas (HPA) Database were used to analyze the mRNA and protein expression of PTPRN. We evaluated the influence of PTPRN on survival of LGG patients. MethSurv was used to explore the expression and prognostic patterns of single CpG methylation of PTPRN gene in LGG. The correlations between the clinical information and PTPRN expression were analyzed using logistic regression and Multivariate Cox regression. We also explored the correlation between PTPRN expression and cancer immune infiltration by TIMER. Gene set enrichment analysis (GSEA) was formed using TCGA RNA-seq datasets. Results: PTPRN mRNA and protein expression decreased in LGG compared to normal brain tissue in TCGA and HPA database. Kaplan-Meier analysis showed that the high expression level of PTPRN correlated with a good overall survival (OS) of patients with LGG. The Multivariate Cox analysis demonstrated that PTPRN expression and other clinical-pathological factors (age, WHO grade, IDH status, and primary therapy outcome) significantly correlated with OS of LGG patients. The DNA methylation pattern of PTPRN with significant prognostic value were confirmed, including cg00672332, cg06971096, cg01382864, cg03970036, cg10140638, cg16166796, cg03545227, and cg25569248. Interestingly, PTPRN expression level significantly negatively correlated with infiltrating level of B cell, CD4+ T cells, Macrophages, Neutrophils, and DCs in LGG. Finally, GSEA showed that signaling pathways, mainly associated with tumor microenvironment and immune cells, were significantly enriched in PTPRN high expression. Conclusion: PTPRN is a potential biomarker and correlates with tumor immune infiltration in LGG.https://www.mdpi.com/2076-3425/12/6/763PTPRNgliomaimmune infiltrationbiomarkertumor microenvironment |
| spellingShingle | Peng Li Fanfan Chen Chen Yao Kezhou Zhu Bei Zhang Zelong Zheng PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma Brain Sciences PTPRN glioma immune infiltration biomarker tumor microenvironment |
| title | PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma |
| title_full | PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma |
| title_fullStr | PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma |
| title_full_unstemmed | PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma |
| title_short | PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma |
| title_sort | ptprn serves as a prognostic biomarker and correlated with immune infiltrates in low grade glioma |
| topic | PTPRN glioma immune infiltration biomarker tumor microenvironment |
| url | https://www.mdpi.com/2076-3425/12/6/763 |
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