Integrating microarray-based spatial transcriptomics and single-cell RNA-sequencing reveals tissue architecture in esophageal squamous cell carcinoma

EBioMedicine. 2022 Oct;84:104281. doi: 10.1016/j.ebiom.2022.104281. Epub 2022 Sep 23.


Background: The tumor microenvironment (TME) serves as an important factor in tumorigenesis and metastasis. Although distinct cell subsets can be identified via single-cell RNA sequencing (scRNA-seq), the spatial composition of cells within the TME is difficult to characterise.

Methods: Tissue samples were collected from three patients with esophageal squamous cell carcinoma (ESCC), and scRNA-seq was performed to identify distinct cell subsets. In addition, a microarray-based spatial transcriptomics (ST) method was used to characterise the spatial landscape of expression data via an array of spots. Using multimodal intersection analysis (MIA) to integrate scRNA-seq and ST, the exact cellular components of the tumor and stromal regions were annotated.

Findings: The subpopulations of seven stromal cells were identified within the TME of ESCC, and the architecture of scRNA-seq-determined subsets was mapped in cancer and stromal regions. The distribution of various stromal cells and their subpopulations was heterogeneous. Compared with immune cells, non-immune stromal cells were significantly enriched in the TME. Most subsets of epithelial cells were enriched in the cancer regions, whereas inflammatory cancer-associated fibroblasts were correlated with the stromal regions. Furthermore, TME features were different between metastatic and non-metastatic samples and between the primary and metastatic sites of the metastatic sample.

Interpretation: This study revealed the spatial landscape of various cell subsets within the TME and the potential cross-talk among diverse cells, which provides novel insights into cancer intervention.

Funding: A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.

Keywords: ESCC; Spatial transcriptomics; Tumor microenvironment; scRNA-seq.

MeSH terms

  • Esophageal Neoplasms* / genetics
  • Esophageal Neoplasms* / pathology
  • Esophageal Squamous Cell Carcinoma* / genetics
  • Humans
  • RNA
  • Transcriptome
  • Tumor Microenvironment / genetics


  • RNA