Pan-cancer single-cell and spatial transcriptome analysis reveals the tumor heterogeneity and metastasis-associated cellular neighborhood architecture

Abstract

Metastasis, the primary cause of cancer-related deaths, involves a highly intricate and underexplored tumor microenvironment (TME). The TME is a dynamic system comprising various tumor and non-tumor elements, with tumor-associated macrophages (TAMs) and cancer-associated fibroblasts (CAFs) playing pivotal roles in tumor growth, metastasis, immune evasion, and therapeutic response.

Initially, single-cell transcriptome sequencing was conducted on Esophageal Squamous Cell Carcinoma (ESCC) patients with lymph node metastases, revealing significant differences between primary tumors and lymph node metastatic microenvironments. A worse prognostic epithelia-immune dual expression program was identified, marked by the overexpression of immune cell signaling mediators (MHC Class II associated genes), indicating immune microenvironment remodeling by tumor cells. It was also determined that POSTN+ CAFs and APOC1+APOE+ TAMs are major components in the metastatic microenvironment of ESCC. Two models of potential intercellular interactions were proposed: one involving tumor cells supporting growth in primary tumors, and another involving APOC1+APOE+ TAMs mediating cell adhesion and distant metastasis in lymph nodes.

Subsequently, an integrative analysis of all published ESCC single-cell RNA-sequencing data focused on the secretions of CAFs, revealing that MFGE8 is specifically secreted by CAFs in ESCC and promotes tumor progression by activating the AKT pathways.

Finally, a pan-cancer analysis was performed on 97 samples across six solid cancer types to profile the TME at single-cell resolution, highlighting the commonalities and plasticity of heterogeneous TAMs. Notably, the enrichment of SPP1+MMP12+ TAMs in the metastatic TME was associated with worse prognosis across multiple cancer types, as supported by deconvolution analysis of primary (PanCancer-TCGA, 5,185 tumors) and metastatic (MET500, 681 tumors) cancers of shared origins. Spatial transcriptomics analysis of 51 tumors with liver and brain metastases (143,018 spots total) further revealed that SPP1+MMP12+ TAMs form a pro-metastatic cellular neighborhood characterized by increased levels of Hypoxia/MAPK/WNT/VEGF signaling, anti-apoptosis, cell proliferation, migration, focal adhesion, and glycolysis.

These findings offer valuable insights into the TME and may inform the development of innovative strategies targeting pro-metastatic non-tumor components (CAFs, TAMs) to inhibit tumor growth and prevent metastasis.