中国组织工程研究

中国组织工程研究 ›› 2025, Vol. 29 ›› Issue (32): 7028-7040.doi: 10.12307/2025.937

• 组织构建相关数据分析 Date analysis of organization construction • 上一篇    

克罗恩病胆汁酸代谢靶点基因筛选及在疾病诊断和治疗监测中的价值

陈  晖1，张  璐1，陈  婧1，王楠章1，王若淳1，陆翠华1，2，纪易斐1，2   

  1. 南通大学附属医院，1消化内科，2临床医学研究中心，江苏省南通市  226001
  • 收稿日期:2024-10-16 接受日期:2024-12-10 出版日期:2025-11-18 发布日期:2025-04-29
  • 通讯作者: 纪易斐，副主任医师，硕士生导师，南通大学附属医院，消化内科，临床医学研究中心，江苏省南通市 226001
  • 作者简介:陈晖，男，1998年生，江苏省南通市人，汉族，南通大学在读硕士，主要从事消化系统疾病的研究。
  • 基金资助:
    国家自然科学基金项目(82070624)，项目负责人：陆翠华；江苏省卫生健康委员会科研项目(H2019072)，项目参与人：纪易斐；江苏省科技项目(BE2019692)，项目参与人：纪易斐；南通市卫生健康委员会科研课题(MSZ2023004)，项目负责人：纪易斐

Screening of target genes for bile acid metabolism in Crohn’s disease and its value in disease diagnosis and therapeutic monitoring

Chen Hui1, Zhang Lu1, Chen Jing1, Wang Nanzhang1, Wang Ruochun1, Lu Cuihua1, 2, Ji Yifei1, 2   

  1. 1Department of Gastroenterology, 2Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
  • Received:2024-10-16 Accepted:2024-12-10 Online:2025-11-18 Published:2025-04-29
  • Contact: Ji Yifei, Associate chief physician, Master’s supervisor, Department of Gastroenterology, and Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
  • About author:Chen Hui, Master candidate, Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
  • Supported by:
    National Natural Science Foundation of China, No. 82070624 (to LCH); Jiangsu Provincial Health Commission Research Project, No. H2019072 (to JYF); Jiangsu Provincial Science and Technology Project, No. BE2019692 (to JYF); Nantong Municipal Health Commission Research Project, No. MSZ2023004 (to JYF)

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摘要：


文题释义：
克罗恩病：是一种慢性、复发性的炎症性肠道疾病，以非连续性、跳跃性、可贯穿肠壁全层的肠道炎症为特点。
胆汁酸代谢：是指体内胆汁酸合成、转化、循环和排泄的复杂生理过程，这个过程主要涉及肝脏、肠道和肠道微生物的协同作用。

背景：胆汁酸代谢在克罗恩病的发生发展中具有重要影响，生物制剂治疗后胆汁酸代谢的变化及关键靶点基因尚未有相应的研究。
目的：探讨胆汁酸代谢相关基因在克罗恩病患者中的表达特征，挖掘与生物制剂治疗响应相关的关键基因。
方法：通过GEO数据库获取转录组数据，分析对比炎症组与对照组、炎症组与治疗组的差异表达基因。利用GO、KEGG和GSEA富集分析评估生物制剂治疗对胆汁酸代谢的影响，使用蛋白质互作网络和WGCNA算法分析差异表达基因，筛选出与生物制剂治疗反应密切相关的模块，进而确定胆汁酸代谢相关的关键基因UGT2A3。在GSE186582数据集的炎症组中，根据UGT2A3的表达水平将样本分为高、低表达组，研究其与免疫浸润的关系，深入探讨UGT2A3与免疫微环境的相互作用；对比分析高、低表达组的临床特征和肠道表现，研究UGT2A3与临床指标(C-反应蛋白、血细胞沉降率、克罗恩病活动指数和克罗恩病内镜活动评分)的相关性。构建UGT2A3的竞争性内源RNA调控网络，对其上游miRNA进行功能富集分析，探索UGT2A3参与胆汁酸代谢的分子机制。利用GSE134809的高通量测序数据进行单细胞分析聚类，观察UGT2A3在不同样本和细胞群间的表达。收集未治疗与经生物制剂治疗后克罗恩病患者的结肠组织样本以及肠息肉患者的健康结肠组织样本，通过免疫组化、qRT-PCR、Western blot检测UGT2A3表达。收集克罗恩病患者与健康对照人群的新鲜粪便，检测胆汁酸水平，并分析UGT2A3与粪便胆汁酸水平的关系。
结果与结论：共筛选出11个胆汁酸代谢相关差异表达基因，经生物制剂治疗后这些基因的表达发生显著变化。GO和KEGG富集分析显示，治疗后患者的肠道营养物质吸收和物质代谢过程趋于正常，白细胞趋化和炎症反应通路的活性降低。GSEA分析揭示了胆汁酸代谢相关通路在治疗后显著富集。蛋白质互作网络构建和WGCNA分析确定UGT2A3为与治疗响应密切相关的关键基因。UGT2A3在克罗恩病患者炎症肠道组织中的表达显著降低，生物制剂治疗后其表达恢复正常，该结果在临床标本中得到验证。UGT2A3表达水平与C-反应蛋白、红细胞沉降率、克罗恩病活动指数和克罗恩病内镜活动评分呈显著负相关。受试者工作特征曲线分析显示UGT2A3具有良好的诊断价值(曲线下面积AUC=0.801 0)，并且能够有效反映治疗效果。免疫浸润分析显示，UGT2A3低表达样本中多种免疫细胞浸润显著增加，其表达水平与免疫评分、微环境评分和基质评分均呈负相关。与UGT2A3低表达组相比，高表达组患者粪隐血、穿透性炎症更少，肠道狭窄及一般情况的严重程度更轻。粪便胆汁酸分析发现UGT2A3表达与初级胆汁酸水平呈强负相关，与次级胆汁酸含量呈强正相关。

https://orcid.org/0009-0009-2298-637X(陈晖)

中国组织工程研究杂志出版内容重点：组织构建；骨细胞；软骨细胞；细胞培养；成纤维细胞；血管内皮细胞；骨质疏松；组织工程

关键词: 克罗恩病, 炎症性肠病, 生物制剂, 胆汁酸代谢, 生物信息学, 工程化组织构建

Abstract: BACKGROUND: Bile acid metabolism plays a crucial role in the development and progression of Crohn’s disease. There is no research on changes in bile acid metabolism and key target genes following treatment with biological agents.
OBJECTIVE: To investigate the expression characteristics of bile acid metabolism-related genes in patients with Crohn’s disease, identify key genes associated with response to biological agents.
METHODS: Transcriptome data were obtained through the GEO database to analyze differentially expressed genes between inflammation-control groups and inflammation-treatment groups. GO, KEGG, and GSEA enrichment analyses were used to evaluate the effects of biological agent therapy on bile acid metabolism. Protein-protein interaction network and WGCNA algorithm were employed to analyze differentially expressed genes, identifying modules closely related to biological agent treatment response, which led to the determination of UGT2A3 as a key gene in bile acid metabolism. In the inflammation group of the GSE186582 dataset, samples were divided into high and low expression groups based on UGT2A3 levels to study its relationship with immune infiltration and explore the interaction between UGT2A3 and the immune microenvironment. Clinical characteristics and intestinal manifestations were compared between high and low expression groups, and correlations between UGT2A3 and clinical indicators (C-reactive protein, erythrocyte sedimentation rate, Crohn’s disease activity index, and Crohn’s disease endoscopic activity score) were investigated. The competing endogenous RNA regulatory network of UGT2A3 was constructed, and its upstream miRNA was functionally enriched to explore the molecular mechanism of UGT2A3 in bile acid metabolism. Single-cell analysis and clustering were performed using high-throughput sequencing data of GSE134809 to observe the expression of UGT2A3 in different samples and cell populations. Colon tissue samples from untreated and biologic-treated Crohn’s disease patients and healthy colon tissue samples from patients with intestinal polyps were collected, and UGT2A3 expression was detected by immunohistochemistry, qRT-PCR, and western blot assay. Fresh feces from Crohn’s disease patients and healthy controls were collected to detect bile acid levels, and the relationship between UGT2A3 and fecal bile acid levels was analyzed.
RESULTS AND CONCLUSION: A total of 11 bile acid metabolism-related genes were screened, showing significant changes in gene expression after biological agent therapy. GO and KEGG enrichment analyses revealed that intestinal nutrient absorption and metabolic processes normalized after treatment, while leukocyte chemotaxis and inflammatory response pathway activity decreased. GSEA analysis revealed significant enrichment of bile acid metabolism-related pathways after treatment. Protein-protein interaction network construction and WGCNA analysis identified UGT2A3 as a key gene closely associated with treatment response. UGT2A3 expression was significantly decreased in inflamed tissues of Crohn’s disease patients and returned to normal levels after biological agent therapy. This result was confirmed in clinical specimens. UGT2A3 expression levels showed significant negative correlations with C-reactive protein, erythrocyte sedimentation rate, Crohn’s Disease Activity Index, and Crohn’s Disease Endoscopic Index of Severity. Receiver Operating Characteristic curve analysis demonstrated that UGT2A3 has good diagnostic value (Area Under Curve AUC=0.801 0) and effectively reflects treatment outcomes. Immune infiltration analysis showed significantly increased infiltration of various immune cells in samples with low UGT2A3 expression, and its expression levels negatively correlated with immune scores, microenvironment scores, and stromal scores. Compared with the low UGT2A3 expression group, patients with high expression showed less fecal occult blood and penetrating inflammation, with milder intestinal strictures and general condition severity. Fecal bile acid analysis revealed that UGT2A3 expression strongly negatively correlated with primary bile acid content and strongly positively correlated with secondary bile acid content.


Key words: Crohn’s disease, inflammatory bowel disease, biologics, bile acid metabolism, bioinformatics, engineered tissue construction

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