Correlation of immune phenotype with IDH mutation in diffuse glioma

Abstract

Background: Tumor infiltrating lymphocytes (TILs) and programmed death ligand 1 (PD-L1) are targets of immune checkpoint inhibitors.

Methods: Forty-three World Health Organization (WHO) grade II/III gliomas (39 IDH-mutant [mut], 4 IDH-wildtype [wt]) and 14 IDH-mut glioblastomas (GBM) were analyzed for TIL (CD3+; PD1+) infiltration and PD-L1 expression. Results were compared with the data of a previously published series of 117 IDH-wt glioblastomas. PD-L1 gene expression levels were evaluated in 677 diffuse gliomas grades II-IV from The Cancer Genome Atlas (TCGA) database.

Results: TIL and PD-L1 expression were observed in approximately half of WHO grade II/III gliomas. IDH-wt status was associated with significantly higher TIL infiltration and PD-L1 expression among all (grades II-IV) cases (n = 174, P < 0.001) and within the cohort of glioblastomas (n = 131, P < 0.001). In low-grade glioma (LGG) and glioblastoma cohorts of TCGA, significantly higher PD-L1 gene expression levels were evident in IDH-wt compared with IDH-mut samples (LGG: N = 516; P = 1.933e-11, GBM: N = 161; P < 0.009). Lower PD-L1 gene expression was associated with increased promoter methylation (Spearman correlation coefficient -0.36; P < 0.01) in the LGG cohort of TCGA. IDH-mut gliomas had higher PD-L1 gene promoter methylation levels than IDH-wt gliomas (P < 0.01).

Conclusions: The immunological tumor microenvironment of diffuse gliomas differs in association with IDH mutation status. IDH-wt gliomas display a more prominent TIL infiltration and higher PD-L1 expression than IDH-mut cases. Mechanistically this may be at least in part due to differential PD-L1 gene promoter methylation levels. Our findings may be relevant for immune modulatory treatment strategies in glioma patients.

Keywords: IDH mutation; PD-L1; glioblastoma; immune microenvironment; low grade glioma; promoter methylation.

Fig. 1

Difference in TIL density and PD-L1 expression in IDH-wt and IDH-mut glioma. (A, C, E) IDH-wt glioma WHO grade III without immunohistochemical staining for IDH-R132H mutant and lack of IDH gene 1 or 2 mutations based on gene sequencing (magnification × 100; A; scale bar 250 μm), scattered infiltration with CD3+ TILs (magnification × 200; C; scale bar 100 μm), fibrillary expression of PD-L1 (magnification × 400; E). (B, D, F) IDH-mut WHO grade II glioma presenting with anti–IDH-R132H immunostaining (magnification × 100; B), absence of CD3+ TILs (magnification × 200; D; scale bar 100 μm), lack of PD-L1 expression (magnification × 200; F; scale bar 100 μm).

Fig. 2

Bar graphs illustrating the correlation of TIL infiltration and PD-L1 expression with IDH status in the overall Vienna cohort of WHO grades II–IV diffuse glioma (n = 174). (A) CD3+ TILs in IDH-mut and IDH-wt glioma. (B) Fibrillary/diffuse PD-L1 expression in IDH-mut and IDH-wt glioma. (C) Membranous PD-L1 expression in IDH-mut and IDH-wt glioma.

Fig. 3

PD-L1 gene expression and gene promoter methylation in diffuse glioma. (A) PD-L1 gene expression is significantly lower in IDH-mut WHO II/III glioma than in IDH-wt WHO II/III glioma of TCGA WHO LGG cohort, while IDH-wt WHO II/III gliomas are not different from the cohort of TCGA GBM (for which RNA-Seq data are available). (B) PD-L1 gene expression levels show a significant negative correlation with PD-L1 gene promoter methylation, illustrated for a representative functional CpG (probe cg15837913, −0.36 [Spearman], P < 0.01) in WHO II/III glioma of the dataset of TCGA LGG. Black lines in the plot show the fit of linear regression, in gray local regression using Lowess smoothing. Methylation of the PD-L1 promoter is significantly higher in IDH-mut WHO II/III glioma than IDH-wt WHO II/III glioma (beta-values, P < 0.01, 2-sided Student’s t-test).