PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma

Peng Li; Fanfan Chen; Chen Yao; Kezhou Zhu; Bei Zhang; Zelong Zheng

doi:10.3390/brainsci12060763

Brain Sciences (Jun 2022)

PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma

Peng Li,
Fanfan Chen,
Chen Yao,
Kezhou Zhu,
Bei Zhang,
Zelong Zheng

Affiliations

Peng Li: VCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
Fanfan Chen: Neurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
Chen Yao: Neurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
Kezhou Zhu: VCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
Bei Zhang: Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
Zelong Zheng: Department of Neurosurgery, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China

DOI: https://doi.org/10.3390/brainsci12060763
Journal volume & issue: Vol. 12, no. 6
p. 763

Abstract

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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.

Published in Brain Sciences

ISSN: 2076-3425 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry
Website: https://www.mdpi.com/journal/brainsci/

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