基于转录组测序对GULP1下游靶基因筛选及分析
收稿日期: 2024-08-02
修回日期: 2024-09-01
网络出版日期: 2024-09-02
基金资助
国家自然科学基金项目(82260162);新疆维吾尔自治区“天山英才”项目(2023TSYCCX0116);新疆维吾尔自治区“天山英才”项目(2023TSYCQNTJ0032);新疆生产建设兵团指导性科技计划项目(2022ZD001);新疆生产建设兵团指导性科技计划项目(2023ZD037)
Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing
Received date: 2024-08-02
Revised date: 2024-09-01
Online published: 2024-09-02
Supported by
National Natural Science Foundation of China Project(82260162);Xinjiang Uyghur Autonomous Region “Tianshan Talent” Project(2023TSYCCX0116);Xinjiang Uyghur Autonomous Region “Tianshan Talent” Project(2023TSYCQNTJ0032);Xinjiang Production and Construction Corps Guided Science and Technology Plan Project(2022ZD001);Xinjiang Production and Construction Corps Guided Science and Technology Plan Project(2023ZD037)
GULP1是一种含磷酸化酪氨酸结合(phosphotyrosine-binding，PTB)结构域的吞噬衔接蛋白，已有的研究表明它可促进脂肪细胞3T3-L1的糖摄取。为进一步挖掘GULP1下游关键的代谢相关差异基因，本研究对过表达GULP1的脂肪细胞和骨骼肌细胞进行转录组分析，然后对表达异常基因进行生物信息学分析，并通过实时荧光定量PCR (real-time fluorescent quantitative PCR，qRT-PCR)与转录组测序进行相互验证。 结果表明：以P<0.05和|Log2Foldchange|≥1为阈值筛选差异表达基因，发现与对照细胞相比，过表达GULP1的脂肪细胞中有278个上调基因和263个下调基因，与代谢相关的GO (Gene Ontology)条目包括胆固醇生物合成过程、胆固醇代谢过程、对脂多糖的反应、脂质代谢过程等，有52个代谢相关差异表达基因富集到10条KEGG(Kyoto Encyclopedia of Genes and Genomes)通路，其中脂质代谢被高度富集；过表达GULP1的骨骼肌细胞有280个上调基因和302个下调基因，与代谢相关的GO条目包括激素代谢过程、对脂多糖的反应、单碳代谢过程等，有86个代谢相关差异表达基因富集到10条KEGG通路，其中氨基酸代谢、脂质代谢、碳水化合物代谢被高度富集。GULP1的生物学功能涉及广泛，包括脂代谢、肿瘤等方面。本研究通过转录组学以及生物信息学分析，筛选出GULP1下游关键的代谢相关差异基因，获得了过表达GULP1后的代谢相关差异基因及信号通路，为今后GULP1下游靶基因的研究提供了重要的理论依据。
温馨, 梅锦, 钱美玉, 蒋一丹, 王娟, 许士博, 王翠喆, 张君 . 基于转录组测序对GULP1下游靶基因筛选及分析[J]. 遗传, 2024 , 46(10) : 860 -870 . DOI: 10.16288/j.yczz.24-221
GULP1 is an engulfment adaptor protein containing a phosphotyrosine-binding (PTB) domain, and existing studies have shown that it can promote glucose uptake in 3T3-L1 adipocytes. To further explore key metabolically related differential genes downstream of GULP1, this study conducted transcriptome analysis on adipocytes and skeletal muscle cells overexpressing GULP1. Subsequently, abnormally expressed genes were subjected to bioinformatic analysis, and real-time fluorescent quantitative PCR (qRT-PCR) was used for mutual validation with transcriptome sequencing. The results indicated that, with a threshold of P < 0.05 and |Log2FoldChange| ≥ 1 for screening differentially expressed genes, compared with control cells, there were 278 upregulated and 263 downregulated genes in adipocytes overexpressing GULP1. Metabolism-related GO (Gene Ontology) terms included cholesterol biosynthetic process, cholesterol metabolic process, response to lipopolysaccharide, lipid metabolic process, etc. A total of 52 metabolically related differentially expressed genes were enriched in 10 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, with lipid metabolism being highly enriched. In skeletal muscle cells overexpressing GULP1, there were 280 upregulated and 302 downregulated genes, with metabolism-related GO terms including hormone metabolic process, response to lipopolysaccharide, one-carbon metabolic process, etc. A total of 86 metabolically related differentially expressed genes were enriched in 10 KEGG pathways, with amino acid metabolism, lipid metabolism, and carbohydrate metabolism being highly enriched. GULP1's biological functions are extensive, including lipid metabolism and oncology. This study, through transcriptomics and bioinformatic analysis, identified key metabolically related differential genes downstream of GULP1, obtained metabolically related differential genes and signaling pathways after GULP1 overexpression, providing important theoretical basis for future research on GULP1 downstream target genes.
Key words： GULP1; transcriptome; differentially expressed gene; metabolism; bioinformatic
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