Abstract 1359: Characterisation of heterogeneity of esophageal squamous cell carcinoma ecosystem by single-cell transcriptomics analysis
Authors: Wong Carissa Wing-Yan , Ko Josephine Mun-Yee , Ng Hoi Yan , Yu Valen Zhuoyou , Law Simon , Lung Maria Li 
Published: April 2023

Background: Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Asia. Despite ESCC prevalence, the underlying heterogeneity in the tumor microenvironment (TME) and the interaction between tumor with stromal and immune components are still unclear. Immunotherapy treatments, such as CTLA-4 or PD-1 blockade, showed responses in a subset of ESCC patients. One reason for this could be attributed to the heterogeneity of immune cell states shaped by the extracellular microenvironment from normal and tumor tissues. The integrative analysis of tumor-associated stromal cells such as tumor-associated fibroblasts, tumor-associated endothelial cells and tumor-infiltrating immune cells could unravel the complex immuno-suppressive ESCC microenvironment. Therefore, we aim to decipher the ESCC TME for better understanding of the underlying biology and identifying prognostic subtypes of stromal cells in ESCC that may influence treatment management.

Method: Blood, tumor and adjacent normal tissue samples were obtained from 47 ESCC patients. For each sample, single-cell RNA-sequencing (scRNA-seq) was performed, where the gene expression, T-cell receptor and B-cell receptor libraries were sequenced. Unsupervised clustering identified different cell clusters and marker genes were determined in each cluster. To identify malignant ESCC cells, inferred copy number variation was used. The T-cell receptor and B-cell receptor library were combined with scRNA-seq data to generate clonotype information. Additionally, trajectory analysis was applied for visualising the evolution of ESCC cell types. Subsequently, the cell types were correlated with patient’s survival data.

Results: We identified various cell types, including T-cells, B-cells, epithelial cells, fibroblasts, endothelial cells, myeloid cells and platelets. Each cell type was further re-clustered for identification of subtypes and marker genes. Malignant cells were identified from normal epithelial cells by inferring copy number changes. The gene expression signatures were identified from malignant ESCC cells and correlated with survival. Tumor-infiltrating immune cells and their cell states were compared between tumor and normal tissues or blood. Trajectory analysis is underway to unravel the biological progression of various cell types in the ESCC microenvironment.

Conclusion: Our findings identified potential prognostic tumor transcriptomic signature and broadened our understanding in ESCC tumorigenesis by revealing the complex heterogeneity of tumor ecosystem regarding non-immune and immune cell subtypes. Funding acknowledgement: Theme-based Research Scheme funding (T12-701/17R) grant to Professors Maria Li Lung and Simon Law from the Research Grants Council of Hong Kong Special Administrative Region of China.

Citation Format: Carissa Wing-Yan Wong, Josephine Mun-Yee Ko, Hoi Yan Ng, Valen Zhuoyou Yu, Simon Law, Maria Li Lung. Characterisation of heterogeneity of esophageal squamous cell carcinoma ecosystem by single-cell transcriptomics analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1359.