基于转录组学、单细胞虚拟敲除和分子模拟提示CHST11在三阴性乳腺癌中的潜在调控作用

Transcriptomic, Single-Cell Virtual Knockout, and Molecular Simulation Analyses Suggest a Potential Regulatory Role of CHST11 in Triple-Negative Breast Cancer

摘要: 目的：本研究旨在系统解析三阴性乳腺癌(TNBC)的分子特征，并探讨CHST11在TNBC发生发展中的潜在作用。方法：基于GEO转录组数据，采用差异表达分析和WGCNA筛选TNBC相关候选基因，并通过LASSO回归和随机森林算法筛选核心候选基因。随后进行GO、KEGG、GSEA和Metascape功能富集分析。利用HPA数据库评估核心基因的蛋白表达，并结合CIBERSORT分析其与免疫浸润的关系。通过单细胞RNA测序评估核心基因在TNBC肿瘤微环境细胞亚群中的表达分布，并采用scTenifoldKnk进行核心基因虚拟敲除及扰动基因富集分析。最后，通过分子对接和分子动力学模拟评估槲皮素与核心基因编码蛋白的结合稳定性。结果：共筛选获得678个TNBC相关候选基因，并筛选CHST11为核心候选基因。功能富集结果显示，候选基因主要参与细胞增殖、迁移、上皮–间质转化、细胞外基质重塑及炎症反应，并显著富集于PI3K/AKT、IL-6/JAK-STAT3、TGF-β和NF-κB等通路。HPA验证显示CHST11在乳腺癌组织中表达上调。免疫浸润分析提示其与多类免疫细胞亚群密切相关。单细胞分析进一步显示，CHST11主要表达于巨噬细胞、单核细胞、成纤维细胞、B细胞、CD8⁺ T细胞、树突状细胞和内皮细胞。CHST11虚拟敲除后共有27个基因发生显著扰动，扰动基因主要富集于炎症信号、免疫调节、细胞黏附迁移、细胞外基质重塑及血管通透性调控等过程。分子对接和动力学模拟显示，槲皮素与CHST11蛋白具有稳定结合能力。结论：CHST11可能通过参与多信号通路调控促进TNBC发生发展，而槲皮素可能作为靶向CHST11的潜在治疗分子。

Abstract: Objective: This study aimed to systematically characterize the molecular features of triple-negative breast cancer (TNBC) and explore the potential role of CHST11 in TNBC development and progression. Methods: Based on GEO transcriptomic data, TNBC-related candidate genes were screened using differential expression analysis and weighted gene co-expression network analysis, and core genes were identified using LASSO regression and random forest algorithms. GO, KEGG, GSEA, and Metascape functional enrichment analyses were then performed. Protein expression of the core gene was assessed using the HPA database, and its association with immune infiltration was evaluated using CIBERSORT. Single-cell RNA sequencing was further used to evaluate the expression distribution of the core gene across different cell subsets in the TNBC tumor microenvironment. scTenifoldKnk was applied for virtual knockout of the core gene and enrichment analysis of perturbed genes. Finally, molecular docking and molecular dynamics simulation were performed to assess the binding stability between quercetin and the protein encoded by the core gene. Results: A total of 678 TNBC-related candidate genes were identified, and CHST11 was screened as a core candidate gene. Functional enrichment analysis showed that the candidate genes were mainly involved in cell proliferation, migration, epithelial-mesenchymal transition, extracellular matrix remodeling, and inflammatory responses, and were significantly enriched in the PI3K/AKT, IL-6/JAK-STAT3, TGF-β, and NF-κB pathways. HPA validation showed that CHST11 was upregulated in breast cancer tissues, and immune infiltration analysis indicated that CHST11 was closely associated with multiple immune cell subsets. Single-cell analysis further revealed that CHST11 was mainly expressed in macrophages, monocytes, fibroblasts, B cells, CD8⁺ T cells, dendritic cells, and endothelial cells. After CHST11 virtual knockout, 27 genes were significantly perturbed, and these perturbed genes were mainly enriched in inflammatory signaling, immune regulation, cell adhesion and migration, extracellular matrix remodeling, and vascular permeability regulation. Molecular docking and molecular dynamics simulation suggested that quercetin may stably bind to CHST11. Conclusion: CHST11 may promote TNBC development and progression by participating in multiple signaling pathways, while quercetin may serve as a potential therapeutic molecule targeting CHST11.