Roles of the m6A Modification of RNA in the Glioblastoma Microenvironment as Revealed by Single-Cell Analyses

Feng Yuan; Xiangming Cai; Zixiang Cong; Yingshuai Wang; Yuanming Geng; Yiliyaer Aili; Chaonan Du; Junhao Zhu; Jin Yang; Chao Tang; Aifeng Zhang; Sheng Zhao; Chiyuan Ma

doi:10.3389/fimmu.2022.798583

Roles of the m⁶A Modification of RNA in the Glioblastoma Microenvironment as Revealed by Single-Cell Analyses

Front Immunol. 2022 Apr 26:13:798583. doi: 10.3389/fimmu.2022.798583. eCollection 2022.

Authors

Feng Yuan¹, Xiangming Cai², Zixiang Cong¹, Yingshuai Wang³, Yuanming Geng⁴, Yiliyaer Aili⁴, Chaonan Du¹, Junhao Zhu¹, Jin Yang⁵, Chao Tang⁵, Aifeng Zhang^{2

6}, Sheng Zhao^{2

7

8}, Chiyuan Ma^{1

2

4

5

9}

Affiliations

¹ Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
² School of Medicine, Southeast University, Nanjing, China.
³ Department of Internal Medicine III, University Hospital Munich, Ludwig Maximilians-University Munich, Munich, Germany.
⁴ Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China.
⁵ Department of Neurosurgery, Jinling Hospital, Nanjing, China.
⁶ Department of Pathology, School of Medicine, Southeast University, Nanjing, China.
⁷ Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, Nanjing, China.
⁸ The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, Nanjing, China.
⁹ Department of Neurosurgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China.

Abstract

Purpose: Glioblastoma multiforme (GBM) is a common and aggressive form of brain tumor. The N⁶-methyladenosine (m⁶A) mRNA modification plays multiple roles in many biological processes and disease states. However, the relationship between m⁶A modifications and the tumor microenvironment in GBM remains unclear, especially at the single-cell level.

Experimental design: Single-cell and bulk RNA-sequencing data were acquired from the GEO and TCGA databases, respectively. We used bioinformatics and statistical tools to analyze associations between m⁶A regulators and multiple factors.

Results: HNRNPA2B1 and HNRNPC were extensively expressed in the GBM microenvironment. m⁶A regulators promoted the stemness state in GBM cancer cells. Immune-related BP terms were enriched in modules of m⁶A-related genes. Cell communication analysis identified genes in the GALECTIN signaling network in GBM samples, and expression of these genes (LGALS9, CD44, CD45, and HAVCR2) correlated with that of m⁶A regulators. Validation experiments revealed that MDK in MK signaling network promoted migration and immunosuppressive polarization of macrophage. Expression of m⁶A regulators correlated with ICPs in GBM cancer cells, M2 macrophages and T/NK cells. Bulk RNA-seq analysis identified two expression patterns (low m⁶A/high ICP and high m⁶A/low ICP) with different predicted immune infiltration and responses to ICP inhibitors. A predictive nomogram model to distinguish these 2 clusters was constructed and validated with excellent performance.

Conclusion: At the single-cell level, m⁶A modification facilitates the stemness state in GBM cancer cells and promotes an immunosuppressive microenvironment through ICPs and the GALECTIN signaling pathway network. And we also identified two m⁶A-ICP expression patterns. These findings could lead to novel treatment strategies for GBM patients.

Keywords: cell communication; glioblastoma; immune microenvironment; m6A; single-cell analysis.

MeSH terms

Adenosine / analogs & derivatives*
Adenosine / genetics
Biomarkers, Tumor / genetics
Galectins / genetics
Gene Expression Regulation, Neoplastic
Glioblastoma*
Humans
Prognosis
RNA
Single-Cell Analysis
Tumor Microenvironment* / genetics

Substances

Biomarkers, Tumor
Galectins
RNA
N-methyladenosine
Adenosine