中国组织工程研究 ›› 2026, Vol. 30 ›› Issue (24): 6421-6432.doi: 10.12307/2026.242

• 组织工程相关大数据分析 Big data analysis in tissue engineering • 上一篇    

阿尔茨海默病中m6A相关铁死亡基因表达与免疫浸润:机器学习和分子生物学验证

徐东方1,赵  堃2,卢长柱2,王玉阁2,白连杰3,孟凡谋2,王  洋2,4,姚宏波5   

  1. 1齐齐哈尔医学院,黑龙江省齐齐哈尔市   161000;齐齐哈尔医学院基础医学院,2生理教研室,5组胚教研室,黑龙江省齐齐哈尔市   161000;3齐齐哈尔医学院附属第二医院超声科,黑龙江省齐齐哈尔市   161000;4黑龙江省药食同源资源与代谢性疾病防治重点实验室,黑龙江省齐齐哈尔市   161000
  • 收稿日期:2025-10-15 修回日期:2025-11-14 出版日期:2026-08-28 发布日期:2026-02-05
  • 通讯作者: 王洋,博士,硕士生导师,齐齐哈尔医学院基础医学院生理教研室,黑龙江省齐齐哈尔市 161000;黑龙江省药食同源资源与代谢性疾病防治重点实验室,黑龙江省齐齐哈尔市 161000 并列通讯作者:姚宏波,博士,硕士生导师,齐齐哈尔医学院基础医学院组胚教研室,黑龙江省齐齐哈尔市 161000
  • 作者简介:徐东方,女,2004年生,河南省鹤壁市人,汉族,主要从事中医药防治神经退行性疾病方面的研究。
  • 基金资助:
    黑龙江省自然科学基金项目(LH2021H122),项目负责人:姚宏波;黑龙江省博士后资助项目(LBH-Z23294),项目负责人:王洋;齐齐哈尔市科技计划联合引导项目(LSFGG-2023035),项目负责人:王洋;齐齐哈尔医学科学院项目(QMSI2021M-11),项目负责人:王洋

m6A-related ferroptosis gene expression and its association with immune infiltration in Alzheimer’s disease: machine learning and molecular biology validation

Xu Dongfang1, Zhao Kun2, Lu Changzhu2, Wang Yuge2, Bai Lianjie3, Meng Fanmou2, Wang Yang2, 4, Yao Hongbo5   

  1. 1Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China; 2Department of Physiology, 5Department of Histology and Embryology, School of Basic Medicine, Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China; 3Department of Ultrasound, the Second Affiliated Hospital of Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China; 4Heilongjiang Provincial Key Laboratory of Food & Medicine Homology and Metabolic Disease Prevention, Qiqihar 161000, Heilongjiang Province, China
  • Received:2025-10-15 Revised:2025-11-14 Online:2026-08-28 Published:2026-02-05
  • Contact: Wang Yang, PhD, Master's supervisor, Department of Physiology, School of Basic Medicine, Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China; Heilongjiang Provincial Key Laboratory of Food & Medicine Homology and Metabolic Disease Prevention, Qiqihar 161000, Heilongjiang Province, China Co-corresponding author: Yao Hongbo, PhD, Master's supervisor, Department of Histology and Embryology, School of Basic Medicine, Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China
  • About author:Xu Dongfang, Qiqihar Medical University, Qiqihar 161000, Heilongjiang Province, China
  • Supported by:
    Heilongjiang Natural Science Foundation of China, No. LH2021H122 (to YHB); Heilongjiang Postdoctoral Funding Project, No. LBH-Z23294 (to WY); Qiqihar Science and Technology Plan Joint Guidance Project, No. LSFGG-2023035 (to WY); Qiqihar Academy of Medical Sciences Project, No. QMSI2021M-11 (to WY)

摘要:



文题释义:
阿尔茨海默病:是一种神经退行性疾病,以进行性认知功能障碍和神经元退化为核心特征,其病理机制涉及β-淀粉样蛋白沉积、Tau蛋白异常磷酸化以及氧化应激和神经炎症等多重因素。随着全球老龄化加剧,阿尔茨海默病的发病率正逐年攀升,深入研究其发病机制并开发有效干预策略已成为当前神经科学领域极具价值的课题。
铁死亡:是一种依赖铁离子代谢失调的程序性细胞死亡形式,以细胞内铁过载引发脂质过氧化积累为特征,受铁离子代谢、线粒体功能、氧化还原平衡及多种病理信号通路协同调控,在癌症、神经退行性疾病等多种疾病中发挥关键作用,是探索新型治疗靶点的重要方向。
N6-甲基腺嘌呤(m6A):是哺乳动物mRNA中最常见的转录后修饰,发生于腺嘌呤第6位氮原子上,其动态调控依赖于甲基转移酶、去甲基化酶和特异性识别蛋白。该修饰通过影响mRNA稳定性、剪接、翻译及定位等过程,在细胞分化、胚胎发育和疾病发生中起关键作用。

背景:阿尔茨海默病是一种神经退行性病变,尽管β-淀粉样蛋白和Tau蛋白是阿尔茨海默病诊断的核心生物标志物,但由于其异质性及诊断局限性,探索新型生物标志物对疾病诊断与治疗仍具有重要意义。
目的:通过机器学习、生物信息学分析以及实验验证,分析阿尔茨海默病中N6-甲基腺嘌呤表观转录组修饰与铁死亡基因的互作关系,鉴定阿尔茨海默病发病的特征基因,并揭示其通过免疫微环境的调控关联,为阿尔茨海默病早期诊断及精准治疗提供新型生物标志物。
方法:整合GEO数据库中GSE5281、GSE48350(训练集)及GSE33000(验证集)人脑海马组织基因组数据;筛选训练集中阿尔茨海默病差异表达的N6-甲基腺嘌呤调控因子,评估N6-甲基腺嘌呤与铁死亡基因的相关性,识别与N6-甲基腺嘌呤关联的铁死亡差异基因;采用支持向量机递归特征消除算法联合Boruta特征选择模型,确定阿尔茨海默病特征基因;通过基因集富集分析解析特征基因功能模块;构建逻辑回归模型联合受试者工作特征曲线,在验证集中评估特征基因诊断效能;应用单样本基因集富集分析量化免疫细胞浸润水平,并分析其与特征基因的调控关联;基于ENCORI数据库、miRWalk 3.0数据库联合NetworkAnalyst预测转录因子/miRNA-mRNA调控网络;通过CTD数据库筛选潜在治疗化合物;利用qRT-PCR以及Western Blotting实验,对APP/PS1双转基因小鼠海马组织进行特征基因实验验证。
结果与结论:①鉴定出2个显著差异表达的N6-甲基腺嘌呤调控因子,即威尔姆丝瘤1相关蛋白(WTAP)、甲基转移酶样蛋白14 (METTL14),与其关联的铁死亡相关基因共16个;②机器学习方法筛选出5个核心特征基因,即延胡索酸水合酶、天冬氨酸转氨酶、HRas蛋白、金属硫蛋白3、组蛋白赖氨酸N-甲基转移酶SETD1B基因;③特征基因功能富集在氧化磷酸化信号通路、亨廷顿病、帕金森病、脂肪酸降解及代谢通路、蛋白酶体信号通路;④逻辑回归诊断模型在训练集和验证集曲线下面积值分别达0.873和0.904,显示特征基因的优异诊断效能;⑤免疫微环境分析显示,HRas蛋白基因与趋化因子受体趋化因子受体家族及浆细胞样树突状细胞浸润水平显著相关;⑥构建包含5个mRNA-37个miRNA-142个转录因子的调控网络,预测出71种靶向治疗药物;⑦实验验证显示APP/PS1小鼠海马中天冬氨酸转氨酶、HRas蛋白、组蛋白赖氨酸N-甲基转移酶SETD1B的mRNA以及蛋白表达具有显著差异(P < 0.05或P < 0.01),与生物信息学分析结果一致;⑧结果揭示延胡索酸水合酶、天冬氨酸转氨酶、HRas蛋白、金属硫蛋白3、组蛋白赖氨酸N-甲基转移酶SETD1B可作为阿尔茨海默病的特征基因;免疫浸润细胞关联分析提示,HRas蛋白可能具备阿尔茨海默病免疫治疗标志物的价值,可为疾病早期诊断及靶向治疗提供理论依据。

https://orcid.org/0009-0004-3722-2050 (徐东方) 


中国组织工程研究杂志出版内容重点:干细胞;骨髓干细胞;造血干细胞;脂肪干细胞;肿瘤干细胞;胚胎干细胞;脐带脐血干细胞;干细胞诱导;干细胞分化;组织工程

关键词: 阿尔茨海默病, N6-甲基腺嘌呤, 铁死亡, 机器学习, 免疫浸润, 基因集富集分析, APP/PS1双转基因小鼠, 实验验证

Abstract: BACKGROUND: Alzheimer's disease is a neurodegenerative disorder. Although amyloid-beta and tau proteins are core biomarkers for the diagnosis of Alzheimer's disease, exploring new biomarkers for disease diagnosis and treatment is still of great significance due to their heterogeneity and diagnostic limitations.
OBJECTIVE: To analyze the interplay between N6-methyladenosine epitranscriptomic modifications and ferroptosis-related genes in Alzheimer’s disease, and identify characteristic genes associated with Alzheimer’s disease pathogenesis through machine learning, bioinformatics analysis, and experimental validation, and to reveal their regulatory associations through the immune microenvironment, providing novel biomarkers for the early diagnosis and precise treatment of Alzheimer’s disease.
METHODS: The tissue transcriptomic data from GSE5281, GSE48350 (training sets) and GSE33000 (validation set) in the GEO database were integrated. N6-methyladenine regulatory factors with differential expression in Alzheimer’s disease from the training set were screened. The correlation between N6-methyladenine and ferroptosis genes was evaluated. Ferroptosis-related differential genes associated with N6-methyladenine were identified. Support vector machine recursive feature elimination algorithm combined with the Boruta feature selection model was used to determine the characteristic genes of Alzheimer’s disease. The functional modules of these characteristic genes were deciphered via gene set enrichment analysis. A logistic regression model integrated with the receiver operating characteristic curve were evaluated the diagnostic efficacy of the characteristic genes in the validation set. The single-sample gene set enrichment analysis was quantified immune cell infiltration levels and their regulatory associations of these cells with the characteristic genes were analyzed. Based on the ENCORI database, miRWalk 3.0 database, and NetworkAnalyst, the transcription factor/miRNA–mRNA regulatory network was constructed. Potential therapeutic compounds were further screened using the CTD database. The experimental validation in the hippocampal tissue of APP/PS1 double-transgenic mice was conducted using quantitative reverse transcription polymerase chain reaction and Western blotting.
RESULTS AND CONCLUSION: (1) Two significantly differentially expressed N6-methyladenosine regulatory factors were identified, namely Wilms’ tumor 1-associating protein (WTAP) and methyltransferase-like protein 14 (METTL14), along with a total of 16 ferroptosis-related genes associated with them. (2) Five hub characteristic genes were screened using machine learning, including fumarate hydratase, aspartate aminotransferase, GTPase HRas, metallothionein-3, histone-lysine n-methyltransferase SETD1B. (3) The functions of characteristic genes were enriched in the oxidative phosphorylation signaling pathway, Huntington's disease, Parkinson's disease, fatty acid degradation and metabolic pathway, and proteasome signaling pathway. (4) The area under the curve values of the constructed logistic regression diagnostic model in the training set and the validation set were 0.873 and 0.904, respectively, indicating excellent diagnostic efficiency of the feature genes. (5) Immune microenvironment analysis revealed that the GTPase HRas gene is significantly correlated with the levels of CC chemokine receptor family members and plasmacytoid dendritic cell infiltration. (6) The regulatory network containing 5 mRNA-37 miRNA-142 transcription factors was constructed, predicting 71 targeted therapeutic drugs. (7) Experimental verification showed that the mRNA and protein expression levels of aspartate aminotransferase, GTPase HRas and histone-lysine N-methyltransferase SETD1B in the hippocampus of APP/PS1 mice were significantly different (P < 0.05 or P < 0.01), which was consistent with the bioinformatics results. (8) These results reveal that fumarate hydratase, aspartate aminotransferase, GTPase HRas, metallothionein-3 and histone-lysine N-methyltransferase SETD1B as characteristic genes associated with the pathogenesis of Alzheimer's disease. Immune infiltration cell association analysis suggests that GTPase HRas may have the value of immunotherapy markers for Alzheimer's disease, providing a theoretical basis for early diagnosis and targeted therapy of the disease.

Key words: Alzheimer’s disease, N6-methyladenosine, ferroptosis, machine learning, immune infiltration, gene enrichment analysis, APP/PS1 transgenic mice, experimental validation

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