Gu Yu, Zhu Wenyong, Zhang Zhihui, Shu Huiling, Huang Hao, Sun Xiao
State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
College of Acupuncture-Moxibustion and Tuina, Nanjing University of Chinese Medicine, Nanjing 210023, China.
Genes (Basel). 2025 Jul 12;16(7):817. doi: 10.3390/genes16070817.
: Tumor-associated macrophages (TAMs) are critical regulators of the hepatocellular carcinoma (HCC) microenvironment, yet their epigenetic heterogeneity and regulatory programs remain poorly defined. : We performed integrative analysis on single-cell RNA-seq and ATAC-seq profiling of HCC patients to dissect TAM subtypes at high resolution. By correlating chromatin accessibility with gene expression, we identified cell-type-specific candidate -regulatory elements (CREs). TAM subsets with prognostic significance were determined through integration with HCC clinical cohorts. Pseudotime and multi-regional analyses were used to uncover regulatory trajectories underlying macrophage phenotypic transitions. The identification framework of a super-enhancer (SE) was constructed, and potential therapeutic targets were prioritized using drug-gene interaction data. : We delineated the regulatory landscape of TAMs in HCC, revealing cell-type-specific chromatin accessibility patterns underlying TAM heterogeneity. The 65,342 CREs linked to gene expression were identified, with distal CREs contributing most to cell-type-specific regulation. Notably, SPP1 TAMs were found to be enriched in tumor cores and associated with poor prognosis in HCC. Liver-resident Kupffer cells showed progressive loss of the core transcription factors SPIC and MAFB, suggesting a potential transition into SPP1 TAMs under tumor pressure. We identified 133 SPP1 TAM-specific SEs and constructed a TF-SE-target gene regulatory network. Notably, 13 target genes showed higher drug-gene interaction effects, highlighting their therapeutic potential. : This study provides the chromatin accessibility map of TAMs in HCC and reveals how distal CRE-driven transcriptional programs shape TAM states. Our findings lay the foundation for understanding the epigenetic regulation of TAM heterogeneity and nominate potential targets for TAM-directed immunotherapy in HCC.
肿瘤相关巨噬细胞（TAMs）是肝细胞癌（HCC）微环境的关键调节因子，但其表观遗传异质性和调控程序仍不清楚。我们对HCC患者的单细胞RNA测序和ATAC测序图谱进行了综合分析，以高分辨率剖析TAM亚型。通过将染色质可及性与基因表达相关联，我们鉴定了细胞类型特异性候选调控元件（CREs）。通过与HCC临床队列整合，确定了具有预后意义的TAM亚群。使用伪时间和多区域分析来揭示巨噬细胞表型转变背后的调控轨迹。构建了超级增强子（SE）的鉴定框架，并使用药物-基因相互作用数据对潜在治疗靶点进行了优先排序。我们描绘了HCC中TAMs的调控图谱，揭示了TAM异质性背后的细胞类型特异性染色质可及性模式。鉴定出与基因表达相关的65342个CREs，其中远端CREs对细胞类型特异性调控贡献最大。值得注意的是，发现SPP1 TAMs在肿瘤核心中富集，并与HCC的不良预后相关。肝脏驻留的库普弗细胞显示核心转录因子SPIC和MAFB逐渐丧失，表明在肿瘤压力下可能转变为SPP1 TAMs。我们鉴定了133个SPP1 TAM特异性SEs，并构建了一个转录因子-SE-靶基因调控网络。值得注意的是，13个靶基因显示出更高的药物-基因相互作用效应，突出了它们的治疗潜力。这项研究提供了HCC中TAMs的染色质可及性图谱，并揭示了远端CRE驱动的转录程序如何塑造TAM状态。我们的发现为理解TAM异质性的表观遗传调控奠定了基础，并为HCC中针对TAM的免疫治疗提名了潜在靶点。
