中药新药与临床药理2026，Vol.37Issue(3)：468-479,12.DOI:10.19378/j.issn.1003-9783.2026.03.009
基于加权基因共表达网络探索胃"炎-癌"转化的关键基因、生物学过程及靶向中药预测
Identification of Key Genes,Biological Processes,and Prediction of Targeted Chinese Medicines for Gastric"Inflammation-Cancer"Transformation via Weighted Gene Co-expression Network Analysis
摘要
Abstract
Objective To investigate the key molecular biological mechanisms underlying gastric"inflammation-cancer"transformation using Weighted Gene Co-expression Network Analysis(WGCNA)combined with RT-qPCR experimental validation,and to predict potential Chinese medicines for treating this transformation.Methods(1)The gene microarray dataset GSE2669 was downloaded from the GEO database.WGCNA was used to identify gene set modules associated with gastric"inflammation-cancer"transformation,and expression trends of the relevant modules were plotted.Genes within each module were subjected to enrichment analysis using the Reactome database as background to explore their biological functions.A protein-protein interaction(PPI)network for the gene set modules related to gastric"inflammation-cancer"transformation was constructed using the STRING website.The maximal clique centrality(MCC)algorithm was used to screen the top three highest-scoring genes in each module as key(Hub)genes.(2)Three gastric mucosal tissue samples each from patients with chronic gastritis(CG),intestinal metaplasia(IM),and gastric cancer(GC),diagnosed by histopathological biopsy under gastroscopy at the First Affiliated Hospital of Guangzhou University of Chinese Medicine from January to June 2024,were selected.The expression levels of the Hub genes in the gastric mucosal tissues were detected by RT-qPCR.(3)Potential Chinese medicines targeting the Hub genes were predicted using the Coremine Medical database.Results(1)Gene set modules related to gastric"inflammation-cancer"transformation were obtained,including the red,sky blue,pink,brown,and yellow modules(P＜0.001).The expression levels of the red and sky blue modules were significantly downregulated in the late stage of the transformation(P＜0.05,P＜0.000 1),while the pink,brown,and yellow modules were significantly upregulated in the late stage(P＜0.000 1).The red module was mainly enriched in biological oxidation and synthesis pathways such as the synthesis of specialized pro-resolving mediators(SPMs),ethanol oxidation,and bile acid and bile salt synthesis.The sky blue module was mainly enriched in metabolic pathways including the tricarboxylic acid(TCA)cycle,TP53-regulated metabolism,and respiratory electron transport.The pink module was primarily enriched in immune regulation-related signaling pathways such as neutrophil degranulation,interferon signaling,and FcγR-mediated phagocytosis.The brown module was mainly enriched in cell proliferation-related pathways including cell cycle and Polo-like kinase signaling.The yellow module was primarily enriched in epithelial-mesenchymal transition(EMT)-related pathways such as extracellular matrix(ECM)degradation,collagen formation,and PDGF signaling.(2)The Hub genes included ALDH3A1,AKR1C3,and AKR1C1 from the red module;UQCRFS1,COX5B,and NDUFV1 from the sky blue module;CCR1,FCGR3B,and ITGAX from the pink module;CCNA2,AURKB,and PLK1 from the brown module;and COL1A2,COL3A1,and BGN from the yellow module.RT-qPCR validation results showed that the mRNA expression levels of ALDH3A1,AKR1C3,UQCRFS1,COX5B,and NDUFV1 were significantly decreased in the late stage of the transformation(P＜0.05,P＜0.01,P＜0.001).The mRNA expression levels of CCR1,FCGR3B,ITGAX,CCNA2,AURKB,PLK1,COL1A2,COL3A1,and BGN were significantly increased in the late stage(P＜0.05,P＜0.01,P＜0.001).The mRNA expression level of AKR1C1 showed a decreasing trend,but the difference was not statistically significant(P＞0.05).The expression trends of the Hub genes from each module in gastric mucosal tissues at different pathological stages were largely consistent with the expression trends of the corresponding WGCNA modules.(3)Chinese medicinals predicted from the red module(e.g.,Ginseng Radix et Rhizoma Rubra,Cistanches Herba)primarily have effects of replenishing qi and warming yang.Chinese medicinals from the sky blue module(e.g.,Ginseng Radix et Rhizoma,Salviae Miltiorrhizae Radix et Rhizoma,Arnebiae Radix,Chuanxiong Rhizoma)mainly function to promote qi flow and strengthen the spleen,clear heat and activate blood circulation.Chinese medicinals from the pink module(e.g.,Acanthopanacis Senticosi Radix et Rhizoma seu Caulis,Poria,Polyporus)primarily fortify the spleen to replenish qi,promote diuresis and drain dampness.Chinese medicinals from the brown module(e.g.,Scutellariae Barbatae Herba,Rabdosiae Rubescentis Herba)mainly clear heat and remove toxins,activate blood circulation to dissipate masses and remove blood stasis.Chinese medicinals from the yellow module(e.g.,Ranunculi Ternati Radix,Paeoniae Radix Rubra)primarily resolve phlegm to disperse nodules,activate blood circulation to resolve stasis.Conclusion Gastric"inflammation-cancer"transformation involves biological processes such as biological oxidation and synthesis,body metabolism,immune regulation,cell proliferation,and epithelial-mesenchymal transition.Chinese medicinals with effects of replenishing qi,activating blood circulation,clearing heat,and resolving phlegm have potential intervention effects on these biological processes.关键词
胃"炎-癌"转化/加权基因共表达网络/关键基因/生物学过程/中药预测/生物信息学Key words
gastric"inflammation-cancer"transformation/weighted gene co-expression network analysis(WGCNA)/key genes/biological processes/prediction of Chinese medicinals/bioinformatics分类
医药卫生引用本文复制引用
陈璟铭,李培武,江晓涛,方欣悦,庄昆海,武安洲,文艺,姚思梦,黄远程,刘凤斌..基于加权基因共表达网络探索胃"炎-癌"转化的关键基因、生物学过程及靶向中药预测[J].中药新药与临床药理,2026,37(3):468-479,12.基金项目
国家重点研发计划"中医药现代化"重点专项课题(2023YFC3503602) （2023YFC3503602）
国家自然科学基金项目(82474404,82474408) （82474404,82474408）
广东省自然科学基金面上项目(2023A1515011019,2024A1515012532) （2023A1515011019,2024A1515012532）
广东省医学科学技术研究基金项目(2024111819485438) （2024111819485438）
国家中医药传承创新中心优势病种(慢性萎缩性胃炎)项目. （慢性萎缩性胃炎）
