Molecular and clinical characterization of PTPN2 expression from RNA-seq data of 996 brain gliomas

Journal of Neuroinflammation
Peng-Fei WangChang-Xiang Yan

Abstract

Immune checkpoint inhibitors have been shown to promote antitumor immunity and achieve durable tumor remissions. However, certain tumors are refractory to current immunotherapy. These negative results encouraged us to uncover other therapeutic targets and strategies. PTPN2 (protein tyrosine phosphatase, non-receptor type 2) has been newly identified as an immunotherapy target. Loss of PTPN2 sensitizes the tumor to immunotherapy via IFNγ signaling. Here, we investigated the relationship between PTPN2 mRNA levels and clinical characteristics in gliomas. RNA-seq data of a cohort of 325 patients with glioma were available from the Chinese Glioma Genome Atlas and 671 from The Cancer Genome Atlas. R language, GraphPad Prism 5, and SPSS 22.0 were used to analyze data and draw figures. PTPN2 transcript levels increased significantly with higher grades of glioma and in isocitrate dehydrogenase (IDH) wild-type and mesenchymal subtype gliomas. A comprehensive biological analysis was conducted, which indicated a crucial role of PTPN2 in the immune and inflammation responses in gliomas. Specifically, PTPN2 was positively associated with HCK, LCK, MHC II, and STAT1 but negatively related to IgG and interferon. Moreover, canonical correlation...Continue Reading

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Citations

Jun 27, 2019·Journal of Cellular Biochemistry·Liquan WuZhibiao Chen

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Methods Mentioned

BETA
RNA-seq
RNAseq

Software Mentioned

R
GSVA
SPSS
GraphPad Prism
Cluster
AmiGO
DAVID
gene set variation analysis ( GSVA )

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