The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma

• Published in: Cancer letters Vol. 593; p. 216951
• Main Authors: Wang, Zheyi, Zhao, Yue, Wo, Yang, Peng, Yizhou, Hu, Weilei, Wu, Zhigang, Liu, Pengcheng, Shang, Yan, Liu, Chunnan, Chen, Xiao, Huang, Kan, Chen, Yuting, Hong, Hui, Li, Fei, Sun, Yihua
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.07.2024
• Subjects: Aged; Antineoplastic Combined Chemotherapy Protocols - pharmacology; Antineoplastic Combined Chemotherapy Protocols - therapeutic use; Chemokine CXCL13 - genetics; Chemokine CXCL13 - metabolism; Esophageal Neoplasms - drug therapy; Esophageal Neoplasms - genetics; Esophageal Neoplasms - immunology; Esophageal Neoplasms - pathology; Esophageal Neoplasms - therapy; Esophageal Squamous Cell Carcinoma - drug therapy; Esophageal Squamous Cell Carcinoma - genetics; Esophageal Squamous Cell Carcinoma - immunology; Esophageal Squamous Cell Carcinoma - pathology; Esophageal Squamous Cell Carcinoma - therapy; Female; Humans; Immunotherapy - methods; Leukocyte Common Antigens - genetics; Leukocyte Common Antigens - metabolism; Male; Memory T Cells - immunology; Memory T Cells - metabolism; Middle Aged; Neoadjuvant Therapy - methods; Receptors, Antigen, B-Cell - genetics; Receptors, Antigen, B-Cell - immunology; Receptors, Antigen, B-Cell - metabolism; Receptors, CXCR5 - genetics; Receptors, CXCR5 - metabolism; Single-Cell Analysis - methods; T-Lymphocytes, Regulatory - drug effects; T-Lymphocytes, Regulatory - immunology; Tumor Microenvironment - immunology
• ISSN: 0304-3835; 1872-7980; 1872-7980
• DOI: 10.1016/j.canlet.2024.216951

Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC. •By integrating analysis of 87357 CD45+ cells, we defined CD8+ CXCL13+ exhausted T cells (Tex) were enriched and clonal expanded in the non-responsive patients and CD4+ LAIR2+Treg were in activated states and highly plastic with various clonal sharing, which pointed out an exhausted and immunosuppressive environment in non-responsive patient following PD-1 blockade treatment. While, GZMK + effector memory T cells (Tem) were relatively enriched in responders, which suggested a memory lasting anti-tumor process with the stem-like ab + and FCRL4+ memory B (Bmem) with more differentiated states and the BCR expansion phenomenon were observed in responders. The class-switch recombination (CSR) and somatic hypermutation (SHM) process were also enriched in TNFRSF13B + Bmem implying its mature state as antigen-presenting (APC) roles. Furthermore, T-B crosstalk process via CD28−CD86 co-stimulation pattern and CXCL13-CXCR5 chemokines axis was validated using cellphoneDB algorithm and multiplex immunofluorescence (mIF) method. We also extracted a TNFRSF13B signature to predict response and OS benefits to immune checkpoint blockade in different cohorts to underscore their clinical relevance.•And the heterogeneity of myeloid cells was quite complex. According to pan-cancer results, we also validated FOLR2+ tissue-resident macrophage in our cohort showed a correlation with increment of Tem clusters, suggesting its APC roles. On the contrary, CCL3L1+ Neutrophils tended to a pro-tumoral phenotype with immunosuppressive and neutrophil extracellular traps (NETs) features.•While the elevated S100A7 in our ESCC cohort revealed by bulk RNA-seq relating to an exhaustion and immunosuppressive TME in upstream pathway may explain the inherent ICB resistance mechanism.