Immunological heterogeneity in esophageal squamous cell carcinoma (ESCC) poses a significant challenge to the efficacy and response to immunotherapy. In this study, we used single-cell RNA sequencing to uncover substantial heterogeneity in the tumor microenvironments (TMEs) among patients received PD-1 inhibitor with partial response (PR), stable disease (SD), and that who underwent surgery without prior therapy. Notably, tumors classified as SD demonstrated an immunosuppressive environment, characterized by a higher prevalence of M2-like macrophages and lower frequencies of T and B cells, especially PD1highCD8+ T cells. These PD1highCD8+ T cells were found to frequently engage with macrophages within the TMEs. Focusing on macrophages, we observed elevated expression of the Iron-Sulfur Cluster Assembly Enzyme (ISCU) in macrophages infiltrating SD tumors. ISCU was identified as a promoter of M2 macrophage polarization in a p53-dependent manner. Mechanistically, ISCU sequestrates p53 in the cytoplasm, reducing its nuclear location and relieving transcriptional repression of xCT and Arg1. Consequently, the increased expression of xCT and Arg1 modulates macrophage sensitivity to ferroptosis and the arginine metabolic pathway, thus affecting macrophage differentiation and inflammatory responses. Furthermore, inhibition of ISCU expression was found to repolarize macrophages, enhance CD8+ T cell cytotoxicity, and boost the efficacy of anti-PD-1 antibody. Collectively, our findings highlight the complex interplay within ESCC TMEs and suggest that targeting ISCU might be a novel strategy to reprogram the immunosuppressive TME, potentially improving immunotherapy outcomes in ESCC patients. Schematic illustration of the mechanism by which ISCU facilitates M2 macrophage polarization. ISCU interacted with p53, promoting its retention in the cytoplasm during M2 macrophage polarization. This nuclear reduction of p53 results in the upregulation of xCT and Arg1, as both are negatively regulated at the transcriptional level by p53. The increased expression of xCT and Arg1 modulates macrophage sensitivity to ferroptosis and the arginine metabolic pathway, respectively, thus affecting macrophage differentiation and inflammatory responses. The graphical abstract was created with BioRender.com.
© 2025. The Author(s).

High-throughput single-cell RNA sequencing (scRNA-seq) has become a frequently used tool to assess immune cell heterogeneity. Recently, the combined measurement of RNA and protein expression was developed, commonly known as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcripts but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets. Here, we describe a targeted transcriptomics approach that combines an analysis of over 400 genes with simultaneous measurement of over 40 proteins on 2 × 104 cells in a single experiment. This targeted approach requires only about one-tenth of the read depth compared to a whole-transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic datasets, we adapted one-dimensional soli expression by nonlinear stochastic embedding (One-SENSE) for intuitive visualization of protein-transcript relationships on a single-cell level.
Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.