Related Experiment Video
Updated: Aug 27, 2025
Development of Compendium for Esophageal Squamous Cell Carcinoma
Published on: April 12, 2024
Integrating microarray-based spatial transcriptomics and single-cell RNA-sequencing reveals tissue architecture in
Wei Guo1, Bolun Zhou2, Zhenlin Yang2
1Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China.
This study maps cell subsets within the tumor microenvironment (TME) of esophageal squamous cell carcinoma (ESCC) using spatial transcriptomics. Findings reveal TME heterogeneity and differences between metastatic and non-metastatic samples, offering insights for cancer intervention.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- The tumor microenvironment (TME) is crucial for cancer development and spread.
- Single-cell RNA sequencing (scRNA-seq) identifies cell types, but TME spatial organization remains challenging.
- Understanding TME cellular composition is vital for effective cancer therapies.
Purpose of the Study:
- To spatially map distinct cell subsets within the TME of esophageal squamous cell carcinoma (ESCC).
- To integrate scRNA-seq and spatial transcriptomics (ST) for detailed cellular annotation.
- To investigate TME heterogeneity and its relation to metastasis.
Main Methods:
- Collected ESCC tissue samples from three patients.
- Performed scRNA-seq to identify cell subpopulations.
- Utilized microarray-based ST and multimodal intersection analysis (MIA) to map spatial expression and annotate cell types.
Main Results:
- Identified seven stromal cell subpopulations within the ESCC TME.
- Mapped the spatial distribution of scRNA-seq subsets in cancer and stromal regions, noting heterogeneity.
- Found non-immune stromal cells were enriched, epithelial cells in cancer regions, and inflammatory fibroblasts in stromal regions.
- Observed distinct TME features in metastatic versus non-metastatic samples.
Conclusions:
- Revealed the spatial landscape of diverse cell subsets within the TME.
- Provided insights into potential cellular cross-talk.
- Offered novel perspectives for developing targeted cancer interventions.
