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本研究通过整合高通量基因表达数据库(gene expression omnibus, GEO)中临床胃组织基因芯片数据与大鼠(Rattus norregicus)多时段尿液代谢组学数据，筛选并验证肠上皮化生(intestinal metaplasia, IM)相关的尿液生物标志物。首先，采用R语言分析临床胃炎到IM的差异表达基因(differentially expressed genes, DEGs)并进行通路富集分析。其次，构建大鼠IM模型，通过大鼠胃组织病理切片和IM免疫组化指标进行模型评价，并分别于造模第2、第4、第8周收集两组大鼠的尿液样本，进行液相色谱-串联质谱技术(liquid chromatography-tandem mass spectrometry, LC-MS/MS)代谢组学分析。最后，通过双向正交偏最小二乘法(two-way orthogonal partial least squares, O2PLS)将DEGs与差异代谢物进行整合分析，筛选相关联的尿液生物标志物，并通过受试者工作特征曲线(receiver operating characteristic, ROC)进行验证。GEO芯片分析共筛选到93个DEGs,主要富集在糖酵解/糖异生等代谢通路中。动物实验结果表明，相较于空白对照组(control check, CK),造模后胃黏膜出现炎性细胞浸润及异型增生；且尾型同源盒转录因子2(caudal-related homeobox transcription factor 2, CDX2)和黏蛋白2(mucin 2, MUC2)表达显著升高；尿液代谢组学结果表明，第8周代谢变化程度最大，将第8周的CK与模型组(model group, MG)尿液代谢差异进行比较，筛选出27个差异代谢物，其主要富集于戊糖和葡萄糖醛酸相互转化通路；通过O2PLS分析筛选到5个与临床样本密切关联的代谢物(5-羟基-6-甲氧基吲哚葡萄糖醛酸苷、 α-酮戊二酸、N-甲基烟酸内盐、N-乙酰异亮氨酸和2-硫酸抗坏血酸酯),进一步结合ROC曲线分析代谢物在不同时段的含量变化，最终得到2个IM阶段最有潜力的尿液生物标志物——5-羟基-6-甲氧基吲哚葡萄糖醛酸苷和α-酮戊二酸。本研究初步揭示了IM过程中的糖代谢异常及相关的特征性代谢物变化，为后续进一步研究IM的病理机制提供参考。
Abstract：This study screens and validates urine biomarkers associated with intestinal metaplasia(IM) by integrating clinical gastric tissue gene chip data from the gene expression omnibus(GEO) database with multi-time point urine metabolomics data of rat(Rattus norregicus). Firstly, R language was used to analyze differentially expressed genes(DEGs) from clinical gastritis to IM stages and perform pathway enrichment analysis. Subsequently, the IM rat model was constructed and evaluated through pathological sections of rat stomach tissue and immunohistochemical indicators. Urine samples were collected from both control groups and model groups of rat at 2, 4, and 8 weeks for liquid chromatography-tandem mass spectrometry(LC-MS/MS) metabolomics analysis. Finally, bidirectional orthogonal partial least squares(O2PLS) was employed to identify associated urinary biomarkers. Receiver operating characteristic(ROC) curve analysis was used for validation. GEO analysis identified 93 DEGs, primarily enriched in the glycolysis/gluconeogenesis pathway. Animal experiments revealed inflammatory cell infiltration and dysplasia in gastric mucosal tissues post-modeling, with significantly elevated expression of caudal-related homeobox transcription factor 2(CDX2)and mucin 2(MUC2) compared to the control check(CK). Urine metabolomics results indicated the most pronounced metabolic changes at week 8. The differences in urine metabolism between the CK and the model group(MG) at week 8 were compared, and 27 differential metabolites were identified, which were mainly enriched in the pentose and glucuronate interconversions pathway. O2PLS analysis screened five metabolites(5-hydroxy-6-methoxyindole glucuronide, α-oxoglutaric acid, trigonelline, N-acetylisoleucine, and ascorbic acid 2-sulfate) closely associated with clinical samples. Further ROC curve validation demonstrated that 5-hydroxy-6-methoxyindole glucuronide and α-oxoglutaric acid were the most promising urinary biomarkers for the IM stage. This study preliminarily revealed the abnormal glucose metabolism and changes in typical metabolites during IM, providing a reference for further research on the pathological mechanism of IM.
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基本信息:
DOI：10.13417/j.gab.044.001025
中图分类号:R735.2
引用信息:
[1]任贤芳,王玥,于舒婷,等.整合基因芯片及动态尿液代谢组学筛选肠上皮化生的生物标志物[J].基因组学与应用生物学,2025,44(10):1025-1039.DOI:10.13417/j.gab.044.001025.
基金信息:
山西省基础研究计划青年科学研究项目(202203021222268); 山西省中医药管理局科研课题(2023ZYYC065); 山西中医药大学博士科研启动基金项目(2023BK08)及山西中医药大学优秀博士毕业生来晋工作奖励经费科研启动基金项目(2023BKS16)共同资助
2025-09-15
2025-09-15
2025-09-15