Interrogation of the microenvironmental landscape in spinal ependymomas reveals dual functions of tumor-associated macrophages

Qianqian Zhang,Bo Wang,Youqiao Chen,Min Li,Mengdi Wang,Yuxin Ge,Xiaoqun Wang,Ren Cao,Zengqi Wen,Yaowu Zhang,Qian Wu,Sijin Cheng,Qiang Ma,Weihao Liu,Yongzhi Wang,Wenqing Jia,Yufeng Lu

doi:10.1038/s41467-021-27018-9

Abstract

Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown. Here, our single-cell RNA-sequencing analyses of three spinal ependymoma subtypes dissect the microenvironmental landscape of spinal ependymomas and reveal tumor-associated macrophage (TAM) subsets with distinct functional phenotypes. CCL2+ TAMs are related to the immune response and exhibit a high capacity for apoptosis, while CD44+ TAMs are associated with tumor angiogenesis. By combining these results with those of single-cell ATAC-sequencing data analysis, we reveal that TEAD1 and EGR3 play roles in regulating the functional diversity of TAMs. We further identify diverse characteristics of both malignant cells and TAMs that might underlie the different malignant degrees of each subtype. Finally, assessment of cell-cell interactions reveal that stromal cells act as extracellular factors that mediate TAM diversity. Overall, our results reveal dual functions of TAMs in tumor progression, providing valuable insights for TAM-targeting immunotherapy.

Highlights

Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown
To comprehensively catalog the cellular heterogeneity of spinal ependymomas, we performed droplet-based scRNA-seq (10× Genomics) on cells isolated from tumor tissues of 15 treatment-naive patients diagnosed with different subtypes of spinal ependymoma, including subependymoma (SE, three patients), ependymoma (EPN, 9 patients), and anaplastic ependymoma (AEP, three patients) (Fig. 1a, b and Supplementary Data 1)
We separated nonmalignant cells from malignant cells and identified 14 cell types according to the expression of canonical gene markers, including markers of CD8+ T cells, CD4+ T cells, B cells, mast cells, conventional dendritic cells, plasmacytoid dendritic cells, monocytes, tumor-associated macrophage (TAM), fibroblasts, endothelial cells, and pericytes (Fig. 1d, e, Supplementary Fig. 1d, and Supplementary Data 2)

Summary

Introduction

Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown. Our single-cell RNA-sequencing analyses of three spinal ependymoma subtypes dissect the microenvironmental landscape of spinal ependymomas and reveal tumor-associated macrophage (TAM) subsets with distinct functional phenotypes. CCL2+ TAMs are related to the immune response and exhibit a high capacity for apoptosis, while CD44+ TAMs are associated with tumor angiogenesis By combining these results with those of single-cell ATAC-sequencing data analysis, we reveal that TEAD1 and EGR3 play roles in regulating the functional diversity of TAMs. We further identify diverse characteristics of both malignant cells and TAMs that might underlie the different malignant degrees of each subtype. Two distinct TAM subsets with different ontogenies and dual functional phenotypes could play crucial roles in tumor growth and invasiveness, which may inform TAMtargeting immunotherapy strategies in human ependymomas and other cancers

Methods

Results

Discussion

Conclusion