PO.CL05.07 · 临床研究
整合多组学与空间转录组学揭示肝细胞癌的新型免疫治疗靶点
Integrative multi-omics and spatial transcriptomics reveal novel immunotherapy targets in hepatocellular carcinoma
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：免疫治疗已改变了肝细胞癌（HCC）的管理，但多数患者未能获得持久应答。塑造免疫逃逸的单细胞水平基因调控机制仍知之甚少。为揭示此前未知的治疗弱点，我们在一个25例患者的HCC免疫治疗队列中整合了单细胞多组学分析与空间转录组学。
方法：肿瘤样本接受10x multiome测序，利用共享条形码从同一细胞中同时进行scATAC-seq和scRNA-seq。这实现了对染色质可及性、转录状态和基因调控关系的细胞分辨率图谱绘制。我们识别了与临床免疫治疗结局相关的差异可及区域和基因表达变化。为在原位背景下解读这些调控程序，进行了空间转录组学分析以绘制肿瘤微环境内靶基因表达和免疫细胞定位。
结果：scATAC-scRNA联合整合揭示了区分应答者与无应答者的此前未识别的调控环路，包括单一模态检测无法发现的染色质预激（chromatin-primed）功能失调CD8⁺T细胞和TREM2+巨噬细胞程序。多组学分析识别出新的候选免疫调控靶点，其由单细胞水平染色质可及性和转录激活的协调变化所定义。空间图谱显示这些靶点富集于离散的免疫排斥区域和肿瘤-髓系界面，揭示了新的空间协调的免疫抑制机制。若干配体-受体对和非经典转录调控因子成为高可信度的治疗干预靶点。
结论：通过将共享条形码单细胞多组学与空间转录组学相结合，我们提供了驱动HCC免疫治疗耐药的基因调控变化的全面机制视角。本研究揭示了新的、经空间验证的免疫调控靶点，并凸显了此前未知的细胞状态转变，这些可被利用以改善免疫治疗疗效。致谢 本研究由李嘉诚基金会和香港中文大学内部经费支持。我们感谢所有实验室成员的贡献。
查看英文原文 English abstract
Background: Immunotherapy has transformed the management of hepatocellular carcinoma (HCC), yet most patients fail to achieve durable responses. The underlying single-cell-level gene-regulatory mechanisms shaping immune evasion remain poorly understood. To uncover previously unknown therapeutic vulnerabilities, we integrated single-cell multiomic profiling with spatial transcriptomics in a 25-patient HCC immunotherapy cohort.
Methods: Tumor samples underwent 10x multiome sequencing, enabling simultaneous scATAC-seq and scRNA-seq from the same cells using shared barcodes. This allowed cell-resolved mapping of chromatin accessibility, transcriptional states, and gene-regulatory relationships. We identified differentially accessible regions and gene-expression changes associated with clinical immunotherapy outcomes. To contextualize these regulatory programs in situ, spatial transcriptomic profiling was performed to map target-gene expression and immune-cell localization within the tumor microenvironment.
Results: Joint scATAC-scRNA integration revealed previously unrecognized regulatory circuits distinguishing responders from non-responders, including chromatin-primed dysfunctional CD8⁺ T cells and TREM2+ macrophage programs not detectable by single-modality assays. Multiomic analysis identified novel candidate immune-regulatory targets, defined by coordinated shifts in chromatin accessibility and transcriptional activation at the single-cell level. Spatial mapping demonstrated that these targets are enriched in discrete immune-excluded regions and at tumor-myeloid interfaces, revealing new spatially orchestrated mechanisms of immune suppression. Several ligand-receptor pairs and non-canonical transcriptional regulators emerged as high-confidence targets for therapeutic intervention.
Conclusions: By combining shared-barcode single-cell multiomics with spatial transcriptomics, we provide a comprehensive, mechanistic view of gene-regulatory changes driving immunotherapy resistance in HCC. This study uncovers novel, spatially validated immune-regulatory targets and highlights previously unknown cell-state transitions that may be leveraged to improve immunotherapy efficacy. Acknowledgements This research was supported by Li Ka Shing Foundation and internal funding from The Chinese University of Hong Kong. We thank all lab members for their contributions.
利益披露 Disclosure
Z. Zhao, None.