| 引用本文: | 曾惠琼,卢小平,颜真波,柳梅芬,叶志中.系统型硬化症尿液lncRNA-mRNA差异表达基因筛选及生物信息学分析[J].生物信息学,2023,21(1):68-76. |
| ZENG Huiqiong,LU Xiaoping,YAN Zhenbo,LIU Meifen,YE Zhizhong.Bioinformatics analysis of differentially expressed lncRNA-mRNA in urine of systemic sclerosis[J].Chinese Journal of Bioinformatics,2023,21(1):68-76. |
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| 摘要: |
| 为探讨系统性硬化症(SSc)患者尿液样本中的长链非编码RNA(lncRNA)、信使RNA(mRNA)的表达谱和生物学功能。选取6名SSc患者和3名健康对照者(HC),采集样本为中段晨尿,应用mRNA和lncRNA微阵列检测总RNA表达变异,SSc组与 HC 组相比。检测尿液lncRNA和mRNA 表达,Gene ontology (GO)分析Kyoto Encyclopedia of Genes and Genomes (KEGG) 信号通路分析差异表达的lncRNA 功能分布；STRING 在线网站和 Cytoscape 软件网络应用分析构建蛋白质相互作用网络(PPI)并筛选出核心基因(Hub Gene)。结果发现:与HC相比,SSc患者尿液中共有645个(上调546,下调99)mRNA 和1 888个(上调1 647,下调241)lncRNA 差异表达(Fold Change绝对值≥2,且P≤ 0.05)。KEGG通路结果显示富集TGF-β信号通路、氧化磷酸化、磷酸戊糖通路。SSc 的GO分析显示与转录调控、DNA去甲基化、白介素6反应等相关；PPI 网络分析表明主要富集在氧化磷酸化、细胞凋亡、自噬途径通路。通过采用lncRNA基因芯片分析SSc患者尿液样本,发现存在异常表达的lncRNA和mRNA,说明SSc尿液生物学特征与HC组存在差异改变；尿液lncRNA可能可以为该病提供生物标志物及治疗靶点研究方向和手段,尿液线粒体基因可能是SSc生物标记物。 |
| 关键词: 生物学分析 lncRNA-mRNA 系统性硬化症 |
| DOI：10.12113/202108011 |
| 分类号:Q52 |
| 文献标识码:A |
| 基金项目:深圳市医疗卫生三名工程项目 (No.SZSM2016020287)；深圳市科创委自由探索项目 (No.JCYJ20180302145033769)；白求恩医学科学研究基金资助项目 (No.TY114DS)；深圳市福田区卫生公益性科研项目(No. FTWS2019010)；2020年福田风湿病专科医院院级科研项目 (No.FTFS202007). |
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| Bioinformatics analysis of differentially expressed lncRNA-mRNA in urine of systemic sclerosis |
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ZENG Huiqiong, LU Xiaoping, YAN Zhenbo, LIU Meifen, YE Zhizhong
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(Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen 518040, Guangdong, China)
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| Abstract: |
| To explore the expression profile and biological functions of long non-coding RNA (lncRNA) and messenger RNA (mRNA) in urine samples of patients with systemic sclerosis (SSc),six SSc patients and three healthy controls (HC) were recruited, whose midstream morning urine was collected. A microarray of mRNA and lncRNA was applied to explore total RNA expression variation between SSc and HC groups. The mRNA and lncRNA expressions in urine were detected. GO analysis and KEGG signal pathway analysis of differentially expressed lncRNA function distribution were conducted. STRING online website and Cytoscape software network application analysis were used to construct a protein-protein interaction(PPI) network and screen out hub genes. Results showed that compared with HC, there were 645 (546 up-regulated, 99 down-regulated) mRNA and 1 888 (1 647 up-regulated, 241 down-regulated) lncRNA differential expressions in urine of SSc patients (fold change absolute value≥ 2, and P≤ 0.05). Results of KEGG pathway showed enrichment in TGF-β signaling pathway, oxidative phosphorylation, and pentose phosphate pathway. GO analysis of SSc showed that it was related to transcription regulation, DNA demethylation, interleukin-6 response, and so on. PPI network analysis showed that it was mainly enriched in pathways of oxidative phosphorylation, apoptosis, and autophagy. Through the use of lncRNA microarray to analyze the urine samples of SSc patients, abnormal expression of lncRNA and mRNA was found, indicating that the biological characteristics of SSc urine and HC group (HC) have different changes. Urine lncRNA may provide research directions and methods of biomarkers and therapeutic targets, and urine mitochondrial genes may be SSc biomarkers. |
| Key words: Bioinformatics analysis lncRNA-mRNA Systemic sclerosis |
