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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2022, Vol. 42 Issue (5): 18-26    DOI: 10.13523/j.cb.2112014
研究报告     
基于单细胞转录组的基因富集方法分析星形胶质细胞与阿尔茨海默病的关系*
乔隆1,廖亚金2,潘瑞远2,袁增强1,2,**()
1 安徽医科大学基础医学院 合肥 230032
2 军事科学院军事医学研究院军事认知与脑科学研究所 北京 100850
Study of the Relationship Between Astrocytes and Alzheimer’s Disease by Gene Set Enrichment Analysis Based on Single-cell RNA Sequence
QIAO Long1,LIAO Ya-jin2,PAN Rui-yuan2,YUAN Zeng-qiang1,2,**()
1 School of Basic Medicine, Anhui Medical University, Hefei 230032,China
2 Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
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摘要：

目的:通过生物信息学方法分析阿尔茨海默病(Alzheimer disease, AD)中与星形胶质细胞相关的糖代谢通路,为揭示AD患者的星形胶质细胞在大脑中的糖代谢过程提供理论基础。方法:首先根据细胞特异性表达基因将AD患者和健康人脑组织单细胞转录组学测序结果进行降维分析,再根据星形胶质细胞不同亚型的基因表达特征进行细胞分群,对星形胶质细胞差异表达基因进行基因注释(Gene Ontology. GO)、信号通路分析(Kyoto Encyclopedia of Genes and Genomes, KEGG)以及基因集富集分析(Gene Set Enrichment Analysis, GSEA),采用转录调控网络分析与AD的星形胶质细胞相关的转录辅助因子。结果:所有细胞降维分析结果显示AD患者脑内星形胶质细胞和兴奋性神经元数量显著减少;星形胶质细胞降维分析结果显示其可以被进一步分为6个亚群,其中在AD患者中减少的星形胶质细胞主要为RASGEF1B+SLC26A3+亚群和NRGN+CALM1+亚群;GO分析结果显示AD患者与健康对照星形胶质细胞差异表达基因主要与轴突发生、神经元的迁移、胶质细胞分化、体内锌离子稳态、突触传递的正调控、血管运输有关。KEGG结果显示,上述差异基因主要与PI3K-Akt信号通路、AMPK信号通路、钙信号通路有关。GSEA分析结果显示,AD患者差异基因在糖酵解/糖异生通路中得到富集,其中丙酮酸激酶PKM、PFKL、ACSS1、乳酸脱氢酶LDHB在AD患者星形胶质细胞中下调。转录调控网络分析结果显示,星形胶质细胞中差异表达转录辅助因子有5个,其中PKM、SOX2、SOX9在AD患者星形胶质细胞中下调。SREBF1和BCL6在AD患者星形胶质细胞中上调。结论:AD患者脑内兴奋性神经元和星形胶质细胞数量降低,以及星形胶质细胞糖酵解相关基因下调。结合星形胶质细胞作为神经元的主要乳酸供应细胞,其数量减少和糖酵解能力减低提示星形胶质细胞供能不足可能是AD发生的机制之一。
关键词： 丙酮酸激酶;  阿尔茨海默病;  星形胶质细胞;  糖酵解    
Abstract:

Objective: To analyze the glucose metabolism pathway associated with astrocytes in Alzheimer’s disease (AD) by the bioinformatics method, and to provide a theoretical basis for revealing the glycolysis metabolism of astrocytes in the brains of AD patients. Methods: Firstly, the single-cell transcriptome data from AD patients and healthy persons were analyzed with t-distributed stochastic neighbor embedding (t-SNE); secondly, the genes differently expressed in astrocytes from AD patients and healthy persons were analyzed by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Set Enrichment Analysis (GSEA); lastly, the transcription cofactors related to AD were analyzed by the transcriptional regulatory network. Results: The t-SNE analysis indicated that the ratio of excitatory neurons and astrocytes was decreased in the brains of AD patients. In addition, the decreased astrocytes were characterized with RASGEF1B+SLC26A3+ or NRGN+CALM1+; GO analysis showed that differentially expressed genes were mainly related to axongenesis, neuronal migration, glial cell differentiation, zinc homeostasis, positive regulation of synaptic transmission and vascular transport. KEGG analysis showed that the differentially expressed genes were mainly related to PI3K-Akt signaling pathway, AMPK signaling pathway and calcium signaling pathway. GSEA analysis results showed that the differentially regulated genes in AD patients were enriched in glycolysis and gluconeogenesis pathway. In addition, PKM, PFKL, ACSS1 and LDHB were down-regulated in astrocytes from AD patients.Transcriptional regulatory network analysis showed that PKM,SOX2 and SOX9 were down-regulated in astrocytes from AD patients. SREBF1 and BCL6 were up-regulated in astrocytes of AD patients. Conclusion: The reduction of excitatory neurons and astrocytes in the brains of AD patients, as well as the down-regulation of the glycolysis pathway in astrocytes from the brains of AD patients, suggest that the impaired glycolysis in astrocytes could be one of the mechanisms underlying the development of AD.
Key words: PKM    Alzheimer’s disease(AD)    Astrocyte    Glycolysis
收稿日期: 2021-12-07 出版日期: 2022-06-17
ZTFLH:  Q811.4  
基金资助: *国家自然科学基金(81930029)
通讯作者: 袁增强     E-mail: zyuan620@yahoo.com
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乔隆
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引用本文:

乔隆,廖亚金,潘瑞远,袁增强. 基于单细胞转录组的基因富集方法分析星形胶质细胞与阿尔茨海默病的关系*[J]. 中国生物工程杂志, 2022, 42(5): 18-26.

QIAO Long,LIAO Ya-jin,PAN Rui-yuan,YUAN Zeng-qiang. Study of the Relationship Between Astrocytes and Alzheimer’s Disease by Gene Set Enrichment Analysis Based on Single-cell RNA Sequence. China Biotechnology, 2022, 42(5): 18-26.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2112014    或    https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I5/18

图1  细胞类型鉴定、各种细胞类型的分布情况以及细胞标记基因的热图
图2  各种细胞类型的分布情况及细胞的比例
Expression Astro Endo Mic Excit Inhibit Oligo
Up 208 59 79 87 93 257
Down 287 35 267 129 101 308
Total 495 94 346 216 194 565
表1  各种细胞类型的差异基因表达情况
图3  星形胶质细胞差异基因的通路富集信息
图4  星形胶质细胞的转录辅助因子及其表达水平
[1] Cai Z Y, Wan C Q, Liu Z. Astrocyte and Alzheimer’s disease. Journal of Neurology, 2017, 264(10): 2068-2074.
doi: 10.1007/s00415-017-8593-x
[2] Wakabayashi K, Miki Y. Deposition and clearance of β-amyloid in the brain. Brain and Nerve, 2013, 65(12): 1433-1444.
[3] Choi S S, Lee S R, Lee H J. Neurorestorative role of stem cells in Alzheimer’s disease: astrocyte involvement. Current Alzheimer Research, 2016, 13(4): 419-427.
doi: 10.2174/156720501304160314162812
[4] Tarczyluk M A, Nagel D A, Rhein Parri H, et al. Amyloid β 1-42 induces hypometabolism in human stem cell-derived neuron and astrocyte networks. Journal of Cerebral Blood Flow and Metabolism, 2015, 35(8): 1348-1357.
doi: 10.1038/jcbfm.2015.58 pmid: 25853906
[5] Stipursky J, Romão L, Tortelli V, et al. Neuron-Glia signaling: implications for astrocyte differentiation and synapse formation. Life Sciences, 2011, 89(15-16): 524-531.
doi: 10.1016/j.lfs.2011.04.005 pmid: 21569780
[6] Carter S F, Herholz K, Rosa-Neto P, et al. Astrocyte biomarkers in Alzheimer’s disease. Trends in Molecular Medicine, 2019, 25(2): 77-95.
doi: 10.1016/j.molmed.2018.11.006
[7] Mathys H, Davila-Velderrain J, Peng Z, et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature, 2019, 570 (7761): 332-337.
doi: 10.1038/s41586-019-1195-2
[8] Zhou Y, Song W M, Andhey P S, et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease. Nature Medicine, 2020, 26 (1): 131-142.
doi: 10.1038/s41591-019-0695-9
[9] Zhang X X, Lan Y J, Xu J Y, et al. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Research, 2018, 47(D1): D721-D728.
doi: 10.1093/nar/gky900
[10] Weise C M, Chen K W, Chen Y H, et al. Left lateralized cerebral glucose metabolism declines in amyloid-β positive persons with mild cognitive impairment. NeuroImage: Clinical, 2018, 20: 286-296.
doi: 10.1016/j.nicl.2018.07.016
[11] Croteau E, Castellano C A, Fortier M, et al. A cross-sectional comparison of brain glucose and ketone metabolism in cognitively healthy older adults, mild cognitive impairment and early Alzheimer’s disease. Experimental Gerontology, 2018, 107: 18-26.
doi: S0531-5565(17)30228-0 pmid: 28709938
[12] Arnold S E, Arvanitakis Z, Macauley-Rambach S L, et al. Brain insulin resistance in type 2 diabetes and Alzheimer disease: concepts and conundrums. Nature Reviews Neurology, 2018, 14(3): 168-181.
doi: 10.1038/nrneurol.2017.185
[13] Butterfield D A, di Domenico F, Barone E. Elevated risk of type 2 diabetes for development of Alzheimer disease: a key role for oxidative stress in brain. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2014, 1842(9): 1693-1706.
doi: 10.1016/j.bbadis.2014.06.010
[14] Neth B J, Craft S. Insulin resistance and Alzheimer’s disease: bioenergetic linkages. Frontiers in Aging Neuroscience, 2017, 9: 345.
doi: 10.3389/fnagi.2017.00345
[15] Haughey N J, Mattson M P. Alzheimer’s amyloid beta-peptide enhances ATP/gap junction-mediated calcium-wave propagation in astrocytes. Neuromolecular Medicine, 2003, 3(3): 173-180.
pmid: 12835512
[16] Siracusa R, Fusco R, Cuzzocrea S. Astrocytes: role and functions in brain pathologies. Frontiers in Pharmacology, 2019, 10: 1114.
doi: 10.3389/fphar.2019.01114 pmid: 31611796
[17] Siino V, Jensen P, James P, et al. Obesogenic diets cause alterations on proteins and theirs post-translational modifications in mouse brains. Nutrition and Metabolic Insights, 2021, 14: 11786388211012405.
[18] Sultana R, Boyd-Kimball D, Cai J, et al. Proteomics analysis of the Alzheimer’s disease hippocampal proteome. Journal of Alzheimer’s Disease: JAD, 2007, 11(2): 153-164.
[19] Meier-Ruge W, Iwangoff P, Reichlmeier K. Neurochemical enzyme changes in Alzheimer’s and Pick’s disease. Archives of Gerontology and Geriatrics, 1984, 3(2): 161-165.
pmid: 6089677
[20] Kim J, Han J, Jang Y, et al. High-capacity glycolytic and mitochondrial oxidative metabolisms mediate the growth ability of glioblastoma. International Journal of Oncology, 2015, 47(3): 1009-1016.
doi: 10.3892/ijo.2015.3101
[21] Wang F, Xu C S, Chen W H, et al. Identification of blood-based glycolysis gene associated with Alzheimer’s disease by integrated bioinformatics analysis. Journal of Alzheimer’s Disease: JAD, 2021, 83(1): 163-178.
[22] Shindyapina A V, Komarova T V, Sheshukova E V, et al. The antioxidant cofactor alpha-lipoic acid may control endogenous formaldehyde metabolism in mammals. Frontiers in Neuroscience, 2017, 11: 651.
doi: 10.3389/fnins.2017.00651 pmid: 29249928
[23] Sathe G, Na C H, Renuse S, et al. Quantitative proteomic profiling of cerebrospinal fluid to identify candidate biomarkers for Alzheimer’s disease. PROTEOMICS - Clinical Applications, 2019, 13(4): 1800105.
doi: 10.1002/prca.201800105
[24] El Kadmiri N, Slassi I, El Moutawakil B, et al. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Alzheimer’s disease. Pathologie-biologie, 2014, 62(6): 333-336.
doi: 10.1016/j.patbio.2014.08.002
[25] Rahman M R, Islam T, Shahjaman M, et al. Discovering biomarkers and pathways shared by Alzheimer’s disease and ischemic stroke to identify novel therapeutic targets. Medicina (Kaunas, Lithuania), 2019, 55(5): 191.
[26] Shen L M, Chen C, Yang A C, et al. Redox proteomics identification of specifically carbonylated proteins in the hippocampi of triple transgenic Alzheimer’s disease mice at its earliest pathological stage. Journal of Proteomics, 2015, 123: 101-113.
doi: 10.1016/j.jprot.2015.04.005
[27] Butterfield D A, Halliwell B. Oxidative stress, dysfunctional glucose metabolism and Alzheimer disease. Nature Reviews Neuroscience, 2019, 20 (3): 148-160.
doi: 10.1038/s41583-019-0132-6 pmid: 30737462
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