Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis

Quanwei Zhou; Xuejun Yan; Weidong Liu; Wen Yin; Hongjuan Xu; Damei Cheng; Xingjun Jiang; Caiping Ren

doi:10.3389/fonc.2020.586019

Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis

Front Oncol. 2020 Dec 23:10:586019. doi: 10.3389/fonc.2020.586019. eCollection 2020.

Authors

Quanwei Zhou¹, Xuejun Yan^{2

3}, Weidong Liu^{2

3}, Wen Yin¹, Hongjuan Xu^{2

3}, Damei Cheng^{2

3}, Xingjun Jiang¹, Caiping Ren^{1

2

3}

Affiliations

¹ Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
² Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.
³ The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.

Abstract

Diffuse glioma is one of the most prevalent malignancies of the brain, with high heterogeneity of tumor-infiltrating immune cells. However, immune-associated subtypes of diffuse glioma have not been determined, nor has the effect of different immune-associated subtypes on disease prognosis and immune infiltration of diffuse glioma patients. We retrieved the expression profiles of immune-related genes from The Cancer Genome Atlas (TCGA) (n = 672) and GSE16011 (n = 268) cohorts and used them to identify subtypes of diffuse glioma via Consensus Cluster Plus analysis. We used the limma, clusterProfiler, ESTIMATE, and survival packages of R for differential analysis, functional enrichment, immune and stromal score evaluation respectively in three subtypes, and performed log-rank tests in immune subtypes of diffuse glioma. The immune-associated features of diffuse glioma in the two cohorts were characterized via bioinformatic analyses of the mRNA expression data of immune-related genes. Three subtypes (C1-3) of diffuse glioma were identified from TCGA data, and were verified using the GSE16011 cohort. We then evaluated their immune characteristics and clinical features. Our mRNA profiling analyses indicated that the different subtypes of diffuse glioma presented differential expression profile of specific genes and signal pathways in the TCGA cohort. Patients with subtype C1, who were mostly diagnosed with grade IV glioma, had poorer outcomes than patients with subtype C2 or C3. Subtype C1 was characterized by a higher degree of immune cell infiltration as estimated by GSVA, and more frequent wildtype IDH1. By contrast, subtype C3 included more grade II and IDH1-mutated glioma, and was associated with more infiltration of CD4⁺T cells. Most subtype C2 had the features between subtypes C1 and C3. Meanwhile, immune checkpoints and their ligand molecules, including PD1/(PD-L1/PDL2), CTLA4/(CD80/CD86), and B7H3/TLT2, were significantly upregulated in subtype C1 and downregulated in subtype C3. In addition, patients with subtype C1 exhibited more frequent gene mutations. Univariate and multivariate Cox regression analyses revealed that diffuse glioma subtype was an effective, independent, and better prognostic factor. Therefore, we established a novel immune-related classification of diffuse glioma, which provides potential immunotherapy targets for diffuse glioma.

Keywords: Gene Expression Omnibus (GEO); The Cancer Genome Atlas (TCGA); bioinformatic analysis; diffuse glioma; immune checkpoint molecule; immune-associated subtype; tumor immune infiltration.