Single-cell spatial analysis of pediatric high-grade glioma reveals a novel population of SPP1+/GPNMB+ myeloid cells with immunosuppressive and tumor-promoting capabilities

This repository contains the raw data files of the NanoString CosMx spatial transcriptomic experiment used to generate the figures within the pre-print (doi: https://doi.org/10.1101/2025.03.18.643953).

The bulk RNA-sequencing data of patients is access-restricted and access can be requested at the European Genome-phenome Archive under the accession number EGAS00001008002. Published DMG single cell RNA-sequencing data were downloaded under accession code GSE184357. Published DMG Visium data were downloaded under accession code GSE194329. Published bulk RNA-sequencing data was downloaded from https://pedcbioportal.org/.

Pediatric-type diffuse high-grade gliomas (pHGG) are the leading cause of pediatric cancer-related deaths. Immunotherapy recently emerged as a promising novel treatment opportunity, but so far, clinical responses remain limited to only a small proportion of pHGG patients. Therefore, more insights into the pHGG’s tumor immune microenvironment, the target of immunotherapy, are urgently needed. As emerging evidence in other cancers points to the spatial architecture of the tumor immune microenvironment as a major determinant of therapeutic efficacy, we employed single-cell spatial analysis at the proteomic and transcriptomic level by combining cyclical immunofluorescence imaging and Spatial Molecular Imaging. We analyzed 32 patient-derived pHGG samples assembled into a tissue microarray and mapped their single-cell spatial landscapes. Our findings revealed that the tumor immune microenvironment is dominated by myeloid cells, including brain-resident microglia and monocyte-derived macrophages, with limited T cells. A large proportion of these myeloid cells express mesenchymal-like genes and were found to be positive for SPP1 and GPNMB. Spatial analysis uncovered that these cells are positioned close to mesenchymal-like tumor cells, and negatively correlated with the location of CD8+ T cells. SPP1+/GPNMB+ cells express genes related to immunosuppression and epithelial-to-mesenchymal transition, suggesting that these cells are an important component of the immunosuppressive tumor microenvironment of pHGG, and may serve as a potential novel immunotherapeutic target.

本仓库包含了用于生成该预印本（DOI：https://doi.org/10.1101/2025.03.18.643953）内所有图表的NanoString CosMx空间转录组实验原始数据文件。
患者的批量RNA测序（bulk RNA-sequencing）数据受访问权限管控，可通过欧洲基因组-表型组档案馆（European Genome-phenome Archive）提交申请获取，其登录编号为EGAS00001008002。已发表的DMG单细胞RNA测序（single cell RNA-sequencing）数据通过登录编号GSE184357下载获取。已发表的DMG Visium空间转录组数据通过登录编号GSE194329下载获取。已发表的批量RNA测序数据则从https://pedcbioportal.org/下载获得。

儿童型弥漫性高级别胶质瘤（Pediatric-type diffuse high-grade gliomas, pHGG）是儿童癌症相关死亡的首要诱因。免疫治疗近年来作为一种极具潜力的新型治疗手段崭露头角，但截至目前，临床应答仅局限于极少数pHGG患者。因此，亟需进一步解析作为免疫治疗靶标的pHGG肿瘤免疫微环境。随着其他癌症的研究证据表明，肿瘤免疫微环境的空间结构是治疗疗效的关键决定因素，我们结合循环免疫荧光成像与空间分子成像技术，在蛋白质组与转录组层面开展了单细胞空间分析。我们对32例患者来源的pHGG样本进行组织微阵列组装，并绘制了它们的单细胞空间图谱。研究结果显示，肿瘤免疫微环境以髓系细胞为主，包括脑常驻小胶质细胞与单核细胞来源的巨噬细胞，而T细胞浸润有限。其中大量髓系细胞表达间充质样基因，且呈SPP1与GPNMB阳性。空间分析揭示，这类细胞定位于间充质样肿瘤细胞附近，且与CD8+ T细胞的分布呈负相关。SPP1+/GPNMB+细胞表达与免疫抑制及上皮间质转化相关的基因，提示这类细胞是pHGG免疫抑制性肿瘤微环境的重要组成部分，有望成为潜在的新型免疫治疗靶点。