Purpose: The stromal microenvironment surrounding tumors plays a critical role in tumor progression, invasion, and metastasis. For instance, cancer-associated fibroblasts remodel the extracellular matrix to modulate metastasis, tumor-associated endothelial cells (TECs) form new blood vessels to increase nutrient delivery, and tumor-associated mural cells (TMCs) secrete cytokines to enhance cancer cell proliferation. Despite the importance of the stromal tumor microenvironment on cancer biology, little is known about the functional and cellular heterogeneity of these stromal cell types, especially TECs and TMCs. This knowledge gap likely has contributed to the limited success in developing anti-angiogenic therapies for solid-organ cancers. To address this knowledge gap, we constructed the first-ever single-cell transcriptomic atlas of TECs and TMCs across thousands of human and mouse tumors to characterize the functional and clinical relevance of TEC and TMC subtypes.
Methods: We generated a comprehensive atlas of TECs and TMCs by integrating all single cell RNA sequencing (scRNA-seq) datasets of human and mouse tumors that are publicly available on the NIH GEO and EBI ArrayExpress databases.To integrate and analyze these datasets, we used Seurat, Harmony, scVI, and FastMNN.
Results: To construct our comprehensive TEC and TMC atlases, we integrated scRNA-seq data from over 10 million cells from 2180 human and 339 mouse tumor samples across 178 datasets. Using this integrated all-cells atlas, we computationally isolated over 250,000 TECs and 150,000 TMCs. Sub-clustering of the TECs and TMCs revealed that there are four subtypes of TECs: artery, capillary, lymphatic, and vein. Further, we show that there are three subtypes of TMCs: matrix-producing Timp1+ pericytes, cytokine-secreting Ccl2+ pericytes, and vascular smooth muscle cells. Surprisingly, we found conservation of these TEC and TMC subclusters across 32 solid-organ tumor types, which suggests that the local TEC and TMC response is independent of cancer of origin.
Conclusion: Our comprehensive atlas of TECs and TMCs in human and mouse tumors provides the first-ever comprehensive cross-cancer examination of TEC and TMC transcriptional heterogeneity. By examining TECs and TMCs in over two thousand tumors, we definitively characterize the TEC and TMC response to solid-organ tumors. Our findings broadly delineate four types of TECs and three types of TMCs, which collectively unify the TEC and TMC literature. These data will help inform develop of anti-tumor therapies that specifically target various TEC and TMC subpopulations.