Integrative analyses of single‐cell and bulk RNA sequencing reveal tumour microenvironment features associated with neoadjuvant immunochemotherapy response in oesophageal squamous cell carcinoma

Background Neoadjuvant chemotherapy combined with immunotherapy (NACI) has shown promise in oesophageal squamous cell carcinoma (ESCC). However, a significant proportion of patients exhibit resistance to NACI, and the underlying mechanisms remain unresolved. Methods We integrated single‐cell RNA sequencing data, including seven patients with ESCC treated with NACI and 69 patients with ESCC treated with surgery alone. Bulk RNA sequencing data were obtained from a public database. Immunohistochemistry and multiplexed immunofluorescence staining were performed to verify the role of important immune cells and molecules in clinical treatment outcomes. Results Here, we profiled the transcriptomes of 512 736 cells from 76 patients with ESCC, revealing that the nonresponder baseline tumour microenvironment exhibited a relative absence of major histocompatibility complex II molecules expressed on CD20 + B cells and a low expression of CXCL13 on CD4_Tfh and CD8_Tex cells. We also identified CD68 + CD163 + macrophages that highly expressed the immunosuppressive LGALS9 gene and preferentially accumulated in the nonresponders after NACI treatment. In addition, nonresponders had a higher baseline fraction of POSTN + fibroblasts, which is associated with higher infiltration of CD68 + CD163 + macrophages and lower infiltration of germinal centre B cells. Finally, we described the different characteristics of malignant epithelial cells from different pathological responses to tumours. Conclusions This study has unveiled a potential regulatory network among immune cells, stromal cells and malignant epithelial cells under different pathological response conditions and provides a valuable resource for discovering novel targeted therapies for ESCC.