Comparative N-Glycoproteomics Reveals Subtype-Specific N-Glycosylation Signatures and Immune Associations in Cholangiocarcinoma.

IF 5.5 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Molecular & Cellular Proteomics Pub Date : 2025-10-06 DOI:10.1016/j.mcpro.2025.101084

Zhili Xia, Li Gao, Meng Hu, Yingjie Li, Kexin Yu, Ningzu Jiang, Long Gao, Yu Liu, Ying Lu, Yanxian Ren, Chenjun Tian, Yawen Lu, Jindu Zhang, Haiying Yu, Ping Yue, Yanyan Lin, Rou Zhang, Yanqiu Gong, Wenbo Meng

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引用次数: 0

Abstract

Cholangiocarcinoma (CCA) comprises intrahepatic (iCCA) and extrahepatic (eCCA) subtypes, each exhibiting distinct molecular characteristics. Understanding these differences is critical for identifying subtype-specific therapeutic targets and advancing precision medicine. Protein glycosylation, a key post-translational modification, regulates immune evasion and metastasis, yet the glycoproteomic difference between iCCA and eCCA remains unexplored. Here we presented the first comprehensive N-glycoproteomic profile of eCCA and compared it with iCCA using a publicly available dataset. Our N-glycoproteomic analysis of paired eCCA tumors and normal adjacent tissues (NATs) identified 8,372 N-glycopeptides, 3,467 N-glycosites, and 2,627 N-glycoproteins. Comparative analysis revealed distinct N-glycosylation signature, with eCCA exhibiting higher fucosylated glycans and iCCA showing increased sialylation. Pathway enrichment analysis of N-glycoproteins revealed a more prominent lysosome-related enrichment in eCCA, whereas pathways related to immune modulation, cytoskeletal components, and the extracellular matrix were significantly enriched in both subtypes. Immune profiling revealed an immunosuppressive microenvironment in both eCCA and iCCA, characterized by reduced natural killer cell infiltration and subtype-specific fibroblast and endothelial cell remodeling. DPM1, a glycosylation enzyme highly expressed in eCCA, was associated with tumor-specific N-glycopeptides and reduced immune cell infiltration. Its knockdown impaired cell migration, and glycoproteomic analysis implicated DPM1 in regulating adhesion, proteostasis, and immune pathways, highlighting its potential as a therapeutic target in eCCA. Our findings provide insights into N-glycosylation alterations in CCA subtypes, underscoring N-glycosylation-related mechanisms as potential biomarkers and therapeutic targets, particularly in eCCA.

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比较n糖蛋白组学揭示了胆管癌亚型特异性n糖基化特征和免疫关联。

胆管癌（CCA）包括肝内（iCCA）和肝外（eCCA）亚型，每种亚型都表现出不同的分子特征。了解这些差异对于确定亚型特异性治疗靶点和推进精准医学至关重要。蛋白糖基化是一种关键的翻译后修饰，调节免疫逃避和转移，但iCCA和eCCA之间的糖蛋白组学差异仍未被发现。在这里，我们提出了eCCA的第一个全面的n -糖蛋白组学分析，并使用公开可用的数据集将其与iCCA进行了比较。我们对配对的eCCA肿瘤和正常邻近组织（NATs）进行n -糖蛋白组学分析，鉴定出8,372个n -糖肽，3,467个n -糖位点和2,627个n -糖蛋白。比较分析显示了明显的n -糖基化特征，iCCA表现出更高的集中聚糖，iCCA表现出更高的唾液基化。n -糖蛋白的途径富集分析显示，在eCCA中，溶酶体相关的途径富集更为显著，而与免疫调节、细胞骨架成分和细胞外基质相关的途径在两种亚型中都显著富集。免疫分析显示，eCCA和iCCA均存在免疫抑制微环境，其特征是自然杀伤细胞浸润减少，亚型特异性成纤维细胞和内皮细胞重塑。DPM1是一种在eCCA中高度表达的糖基化酶，与肿瘤特异性n -糖肽和免疫细胞浸润减少有关。它的敲除会损害细胞迁移，糖蛋白组学分析表明DPM1与调节粘附、蛋白质停滞和免疫途径有关，突出了它作为eCCA治疗靶点的潜力。我们的研究结果为CCA亚型的n-糖基化改变提供了见解，强调了n-糖基化相关机制作为潜在的生物标志物和治疗靶点，特别是在eCCA中。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Molecular & Cellular Proteomics 生物-生化研究方法

CiteScore

11.50

自引率

4.30%

发文量

131

审稿时长

84 days

期刊介绍： The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action. The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data. Scope: -Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights -Novel experimental and computational technologies -Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes -Pathway and network analyses of signaling that focus on the roles of post-translational modifications -Studies of proteome dynamics and quality controls, and their roles in disease -Studies of evolutionary processes effecting proteome dynamics, quality and regulation -Chemical proteomics, including mechanisms of drug action -Proteomics of the immune system and antigen presentation/recognition -Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease -Clinical and translational studies of human diseases -Metabolomics to understand functional connections between genes, proteins and phenotypes