Identification of a prognostic signature consisting of three macrophage-related genes for glioblastoma based on bulk and single-cell transcriptomes analyses

Tumor-associated macrophages have been implicated in the progression and treatment resistance of glioblastoma (GBM). This study aimed to identify macrophage-related genes associated with prognosis and therapeutic response in GBM. Bulk RNA-seq data from 533 patients with GBM were downloaded from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Bioinformatic tools were used to detect the co-expression gene modules associated with the infiltration of immune cells, identify a prognostic macrophage-related gene signature, and explore their association with sensitivity to chemotherapeutic drugs and immune checkpoint blockade. Single-cell RNA-seq data and multiplexed immunofluorescence were used to validate ISG20 expression (a member of the identified gene signature) in macrophages. We detected gene modules associated with macrophages and identified a signature consisting of three macrophage-related genes (ISG20, PARP12 and IFIT5) in the discovery set (TCGA–GBM, <i>n</i> = 159), and validated its prognostic value in the validation set (CGGA–GBM, <i>n</i> = 374). This gene signature demonstrated favorable accuracy in predicting prognosis and resistance of immuno- and chemo-therapy. The co-expression of ISG20 and PD-1 in macrophages was verified by single-cell RNA-seq data and multiplex immunofluorescence. This study presents a macrophage-related gene signature to predict prognosis and therapeutic response in GBM. ISG20, PARP12 and IFIT5 are interferon-stimulated genes, and further investigations may provide new insights into the interplay between macrophages and interferon signaling in GBM.

肿瘤相关巨噬细胞（tumor-associated macrophages, TAMs）已被证实与胶质母细胞瘤（glioblastoma, GBM）的进展及治疗耐药密切相关。本研究旨在筛选与GBM患者预后及治疗应答相关的巨噬细胞相关基因。我们从癌症基因组图谱（TCGA）及中国胶质瘤基因组图谱（CGGA）数据库中下载了533例GBM患者的批量RNA测序（bulk RNA-seq）数据。借助生物信息学工具，本研究筛选出与免疫细胞浸润相关的共表达基因模块，构建了预后相关巨噬细胞基因特征，并探究其与化疗药物敏感性及免疫检查点阻断治疗应答的关联。此外，本研究采用单细胞RNA测序（single-cell RNA-seq）及多重免疫荧光技术，验证了所筛选基因特征中的成员ISG20在巨噬细胞中的表达情况。在发现队列（TCGA-GBM，n=159）中，我们筛选出与巨噬细胞相关的基因模块，并构建了由ISG20、PARP12及IFIT5这3个巨噬细胞相关基因组成的基因特征；随后在验证队列（CGGA-GBM，n=374）中验证了该特征的预后价值。该基因特征在预测GBM患者预后及免疫、化疗耐药性方面表现出良好的准确率。单细胞RNA测序及多重免疫荧光结果进一步验证了ISG20与PD-1在巨噬细胞中的共表达情况。本研究构建了一款可用于预测GBM患者预后及治疗应答的巨噬细胞相关基因特征。ISG20、PARP12及IFIT5均为干扰素刺激基因，后续研究可进一步探索巨噬细胞与干扰素信号通路在GBM中的相互作用，为该领域提供新的研究视角。