[1]曹 君,金婕妤,张 胜,等.生物信息学方法筛选IL-3和IL-3+SCF诱导的小鼠骨髓来源肥大细胞的差异表达基因及相关信号通路分析[J].现代检验医学杂志,2024,39(01):16-22.[doi:10.3969/j.issn.1671-7414.2024.01.004]
　CAO Jun,JIN Jieyu,ZHANG Sheng,et al.Screening of IL-3 and IL-3+SCF Induce Differentially Expressed Genes and Signaling Pathways in Bone Marrow-derived Mast Cells Based on Bioinformatics[J].Journal of Modern Laboratory Medicine,2024,39(01):16-22.[doi:10.3969/j.issn.1671-7414.2024.01.004]
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生物信息学方法筛选IL-3和IL-3+SCF诱导的小鼠骨髓来源肥大细胞的差异表达基因及相关信号通路分析()
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《现代检验医学杂志》[ISSN:/CN:]

卷:
第39卷
期数:
2024年01期
页码:
16-22
栏目:
论著
出版日期:
2024-01-15

文章信息/Info

Title:
Screening of IL-3 and IL-3+SCF Induce Differentially Expressed Genes and Signaling Pathways in Bone Marrow-derived Mast Cells Based on Bioinformatics
文章编号:
1671-7414（2024）01-016-07
作者:
曹 君1; 金婕妤1; 张 胜1; 乔龙威2; 梁玉婷1
（1. 苏州大学附属第一医院临床检测中心，江苏苏州 215006；2. 南京医科大学附属苏州市立医院生殖与遗传中心，江苏苏州 215000）
Author(s):
CAO Jun1;  JIN Jieyu1;  ZHANG Sheng1;  QIAO Longwei2;  LIANG Yuting1
（1. Clinical Laboratory Center, the First Affiliated Hospital of Soochow University, Jiangsu Suzhou 215006, China; 2. Center for Reproduction and Genetics, Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Jiangsu Suzhou 215000, China）
关键词:
肥大细胞; 干细胞因子; 差异表达基因; 生物信息学
分类号:
R-332
DOI:
10.3969/j.issn.1671-7414.2024.01.004
文献标志码:
A
摘要:
目的　通过生物信息学方法分析IL-3 和IL-3+ 干细胞因子（stem cell factor, SCF）诱导的小鼠骨髓来源肥大细胞（bone marrow-derived mast cells，BMMCs）的差异表达基因及相关信号通路，为肥大细胞（mast cell, MC）的体外培养和功能学研究提供基础。方法　从GEO 数据库下载IL-3 和IL-3+SCF 诱导的BMMCs 的基因表达数据集GSE35332，采用R 软件分析差异表达基因（differentially expressed genes，DEGs），使用在线工具DAVID 数据库对DEGs 进行基因本体论（geneontology，GO）和京都基因与基因组百科全书KEGG（Kyoto encyclopedia of genes and genomes，KEGG）功能富集分析。采用STRING 在线软件分析DEGs 的蛋白相互网络。通过Cytoscape 软件的MCODE 插件筛选枢纽基因。结果　通过R 软件分析数据集GSE35332，共筛选出1 339 个DEGs，其中上调基因723 个，下调基因616 个。通过Cytoscape 软件的MCODE插件共筛选出6 个枢纽基因，分别为Psmd8，Psmd6，Psmd14，Psmc4，Psma6 和Psma3。GO 和KEGG 分析显示枢纽基因主要集中在蛋白质水解、MHC I 类分子呈递的抗原提呈和加工、泛素依赖性蛋白质分解代谢过程及Epstein-Barr 病毒感染等相关通路。结论　本研究基于GEO 数据库通过生物信息学方法，发现两种模式下诱导的小鼠BMMCs 基因表达谱存在明显差异，同时发现6 个枢纽基因参与泛素依赖性蛋白分解过程，为更深入研究MC 体外培养和功能提供帮助。
Abstract:
Objective　To identify the differentially expressed genes and pathways of bone marrow-derived mast cells (BMMCs) of mice induced by IL-3 and IL-3+stem cell factor（SCF）using bioinformatics analysis, which may provide a foundation for in vitro culture and functional study of mast cells（MC）. Methods　The matrix data of GSE35332 dataset in IL-3 and IL-3+SCF induced BMMCs was downloaded from the GEO database, and the R software was applied to screen differentially expressed genes (DEGs). The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis of EDGs were performed based on the online tool DAVID database. The protein interaction network was constructed by STRING database and hub genes were screened through MCODE plugin of the Cytoscape software. Results　The GSE35332 data set was analyzed by R software, and 1 339 DEGs were screened, including 723 up-regulated genes and 616 down-regulated genes. A total of 6 hub genes were screened through the MCODE plugin of Cytoscape software, namely Psmd8, Psmd6, Psmd14, Psmc4, Psma6 and Psma3. GO and KEGG analysis showed that the hub genes were concentrated in proteolysis, antigen processing and presentation of exogenous peptide antigen via MHC class I, proteasome-mediated ubiquitin-dependent protein catabolism process, and Epstein-Barr virus infection. Conclusion　This study found that there were significant differences in BMMCs gene expression profiles in mice induced by two modes and 6 hub genes participated in ubiquitin-dependent protein decomposition process through bioinformatics based on the GEO database, providing help for further research on MC vitro culture and function.

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备注/Memo

备注/Memo:
基金项目： 国家自然科学基金（81901632）：Mc-Exo 通过DCN 胞间转移调控气道平滑肌细胞表型转化在哮喘中的作用及研究机制；（82001576）：基于孕妇cfDNA 特征分析在自发性早产启动中的作用及机制研究。
作者简介：曹君（1987-），女，硕士，主管技师，研究方向：免疫学，E-mail：caojun198729@163.com。
通讯作者：梁玉婷，女，博士，主治医师，研究方向：肥大细胞及过敏性疾病，E-mail：liangyuting666@126.com。
更新日期/Last Update: 2024-01-15