Abstract
In this study, single-cell RNA-seq data were collected to analyze the characteristics of Histone deacetylation factor (HDF). The tumor microenvironment (TME) cell clusters related to prognosis and immune response were identified by using CRC tissue transcriptome and immunotherapy cohorts from public repository. We explored the expression characteristics of HDF in stromal cells, macrophages, T lymphocytes, and B lymphocytes of the CRC single-cell dataset TME and further identified 4 to 6 cell subclusters using the expression profiles of HDF-associated genes, respectively. The regulatory role of HDF-associated genes on the CRC tumor microenvironment was explored by using single-cell trajectory analysis, and the cellular subtypes identified by biologically characterized genes were compared with those identified by HDF-associated genes. The interaction of HDF-associated gene-mediated microenvironmental cell subtypes and tumor epithelial cells were explored by using intercellular communication analysis, revealing the molecular regulatory mechanism of tumor epithelial cell heterogeneity. Based on the expression of feature genes mediated by HDF-related genes in the microenvironment T-cell subtypes, enrichment scoring was performed on the feature gene expression in the CRC tumor tissue transcriptome dataset. It was found that the feature gene scoring of microenvironment T-cell subtypes (HDF-TME score) has a certain predictive ability for the prognosis and immunotherapy benefits of CRC tumor patients, providing data support for precise immunotherapy in CRC tumors.
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Availability of Data and Materials
All data are available in a public, open-access repository. The datasets used and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) and The Cancer Genome Atlas (TCGA) network (https://cancergenome.nih.gov/). R and other custom scripts for analyzing data are available upon reasonable request.
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ZZ—Conceptualization, data curation, writing (original draft). YW—Investigation, software, visualization. XG–Formal analysis, methodology, validation. CY–Formal analysis, methodology, validation. GY—Conceptualization, methodology, writing (review & editing).
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Zhao, Z., Wu, Y., Geng, X. et al. Single-Cell Analysis Reveals Histone Deacetylation Factor Guide Intercellular Communication of Tumor Microenvironment that Contribute to Colorectal Cancer Progression and Immunotherapy. Biochem Genet (2024). https://doi.org/10.1007/s10528-024-10730-8
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DOI: https://doi.org/10.1007/s10528-024-10730-8