Identification and Validation of Autophagy-Related Genes in Necrotizing Enterocolitis.
Identification and Validation of Autophagy-Related Genes in Necrotizing Enterocolitis.
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坏死性小肠结肠炎自噬相关基因的鉴定和验证
DOI：
10.3389/fped.2022.839110
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发表时间：
2022
影响因子：
2.6
通讯作者：
中科院分区：
文献类型：
--
作者：
自噬在坏死性小肠结肠炎（NEC）的发生、发展过程中起重要作用。本研究拟通过生物信息学方法和实验研究对NEC中可能与自噬相关的基因进行鉴定和验证。通过分析实验新生小鼠模型和数据集GSE 46619的RNA测序数据，鉴定NEC的自噬相关差异表达基因（arDEG）。蛋白质-蛋白质相互作用（PPI）、基因本体（GO）富集分析和京都基因和基因组百科全书（KEGG）途径富集分析用于arDEG。然后，在实验NEC中，通过Venn分析鉴定两个数据集中共表达的自噬相关基因，并通过qRT-PCR验证。自噬在实验NEC中增加，并且通过RNA测序在实验NEC中鉴定出47个arDEG。PPI结果表明这些基因相互作用。arDEG的GO和KEGG富集结果报告了与自噬和巨自噬相关的某些富集途径。此外，从数据集GSE 46619中在人NEC中鉴定了22个arDEG。这些基因的GO和KEGG富集分析显示与实验NEC结果相似的富集项。最后，通过Venn分析，在来自数据集GSE 46619和实验NEC的人NEC中，HIF-1a、VEGFA、ITGA 3、ITGA 6、ITGB 4和NAMPT被鉴定为共表达的自噬相关基因。实时定量PCR（qRT-PCR）结果显示，实验性NEC中HIF-1a和ITGA 3表达上调，VEGFA和ITGB 4表达下调。我们通过生物信息学分析在实验NEC中鉴定了47个arDEG，在人NEC中鉴定了22个arDEG。HIF-1a、ITGA 3、VEGFA和ITGB 4可能通过调节自噬而影响NEC的进展。
Autophagy plays an essential role in the occurrence and progression of necrotizing enterocolitis (NEC). We intend to carry out the identification and validation of the probable autophagy-related genes of NEC via bioinformatics methods and experiment trials. The autophagy-related differentially expressed genes (arDEGs) of NEC were identified by analyzing the RNA sequencing data of the experiment neonatal mouse model and dataset GSE46619. Protein–protein interactions (PPIs), Gene Ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used for the arDEGs. Then, co-expressed autophagy-related genes in two datasets were identified by Venn analysis and verified by qRT-PCR in experimental NEC. Autophagy increased in experimental NEC and 47 arDEGs were identified in experimental NEC by RNA-sequencing. The PPI results proclaimed those genes interplayed with each other. The GO and KEGG enrichment results of arDEGs reported certain enriched pathways related to autophagy and macroautophagy. Furthermore, 22 arDEGs were identified in human NEC from dataset GSE46619. The GO and KEGG enrichment analysis of these genes showed similar enriched terms with the results of experimental NEC. Finally, HIF-1a, VEGFA, ITGA3, ITGA6, ITGB4, and NAMPT were identified as co-expressed autophagy-related genes by Venn analysis in human NEC from dataset GSE46619 and experimental NEC. The result of quantified real-time PCR (qRT-PCR) revealed that the expression levels of HIF-1a and ITGA3 were upregulated, while VEGFA and ITGB4 were downregulated in experimental NEC. We identified 47 arDEGs in experimental NEC and 22 arDEGs in human NEC via bioinformatics analysis. HIF-1a, ITGA3, VEGFA, and ITGB4 may have effects on the progression of NEC through modulating autophagy.
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影响因子：
4.4
作者：
Ren, Ziying;Zhang, Long;Hu, Xuegang
通讯作者：
Hu, Xuegang
影响因子：
16.6
作者：
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通讯作者：
Hackam DJ
DOI：
10.1038/nri.2016.100
发表时间：
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期刊：
Nature reviews. Immunology
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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DOI：
10.1038/s41568-021-00344-2
发表时间：
2021-05
期刊：
Nature reviews. Cancer
影响因子：
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作者：
Xia H;Green DR;Zou W
通讯作者：
Zou W