Genome wide DNA methylation landscape reveals glioblastoma's influence on epigenetic changes in tumor infiltrating CD4+ T cells.

Marpe Bam,Adam T Leibold,Kaleigh Fetcko,Sreenivasulu Chintala,Seema Siraj,Yunlong Liu,Brooke Carmen Williamsen,Sheng Liu,Jun Wan,Mahua Dey,Xiaoling Xuei

doi:10.18632/oncotarget.27955

Abstract

CD4+ helper T (Th) cells play a critical role in shaping anti-tumor immunity by virtue of their ability to differentiate into multiple lineages in response to environmental cues. Various CD4+ lineages can orchestrate a broad range of effector activities during the initiation, expansion, and memory phase of endogenous anti-tumor immune response. In this clinical corelative study, we found that Glioblastoma (GBM) induces multi- and mixed-lineage immune response in the tumor microenvironment. Whole-genome bisulfite sequencing of tumor infiltrating and blood CD4+ T-cell from GBM patients showed 13571 differentially methylated regions and a distinct methylation pattern of methylation of tumor infiltrating CD4+ T-cells with significant inter-patient variability. The methylation changes also resulted in transcriptomic changes with 341 differentially expressed genes in CD4+ tumor infiltrating T-cells compared to blood. Analysis of specific genes involved in CD4+ differentiation and function revealed differential methylation status of TBX21, GATA3, RORC, FOXP3, IL10 and IFNG in tumor CD4+ T-cells. Analysis of lineage specific genes revealed differential methylation and gene expression in tumor CD4+ T-cells. Interestingly, we observed dysregulation of several ligands of T cell function genes in GBM tissue corresponding to the T-cell receptors that were dysregulated in tumor infiltrating CD4+ T-cells. Our results suggest that GBM might induce epigenetic alterations in tumor infiltrating CD4+ T-cells there by influencing anti-tumor immune response by manipulating differentiation and function of tumor infiltrating CD4+ T-cells. Thus, further research is warranted to understand the role of tumor induced epigenetic modification of tumor infiltrating T-cells to develop effective anti-GBM immunotherapy.

Highlights

Naïve CD4+ helper T cell population is known for its polyfunctionality and highly plastic characteristics [1, 2]
To investigate the role of tumor microenvironment (TME) in regulating CD4+ T-cell lineages, we performed whole-genome bisulfite sequencing (WGBS) to decipher the DNA methylome of CD4+ T cells isolated from tumor and blood from 5 newly diagnosed GBM patients (Figure 1A and 1B, Table 1)
Using strict definition of at least 60% difference in DNA methylation, we observed significant difference in the methylation pattern between GBM infiltrating CD4+ T-cells compared to the blood with ~75% of the differentially methylated regions (DMR) were hypomethylated and ~25% were hypermethylated in tumor CD4+ T cells (Figure 1C)

Summary

Introduction

Naïve CD4+ helper T cell population is known for its polyfunctionality and highly plastic characteristics [1, 2]. To mount an effective immune response naïve CD4+ T-cells are capable of differentiating into specific subpopulations with distinct effector functions such as Th1, Th2, Th17, Treg etc. Recent studies have shown that epigenetic changes in DNA methylation is involved in CD4+ T-cell polarization resulting in differential Th1 and Th2 cytokine secretion [11, 12]. In the tumor microenvironment (TME), lineage commitments of CD4+ T cells reflect initiation of new programs of gene expression within tumor infiltrating naïve T cells [13]. These gene expression changes in tumor infiltrating CD4+ T-cells may be mediated by epigenetic events such as DNA methylation

Methods

Results

Conclusion