基于转录组测序对GULP1下游靶基因筛选及分析

doi:10.16288/j.yczz.24-221

遗传 ›› 2024, Vol. 46 ›› Issue (10): 860-870.doi: 10.16288/j.yczz.24-221

基于转录组测序对GULP1下游靶基因筛选及分析

温馨(), 梅锦, 钱美玉, 蒋一丹, 王娟, 许士博, 王翠喆, 张君()

石河子大学医学院新疆地方病与民族高发病教育部重点实验室，石河子 832000

收稿日期:2024-08-02 修回日期:2024-09-01 出版日期:2024-09-02 发布日期:2024-09-02
通讯作者: 张君，博士，教授，研究方向：肥胖、炎症及代谢相关疾病中关键信号转导分子的调控机制和干预方式基础研究工作。E-mail: zhangjunyc@.163.com
作者简介:温馨，硕士研究生，专业方向：基础医学生物化学与分子生物学。E-mail: 1391476108@qq.com
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

Xin Wen(), Jin Mei, Meiyu Qian, Yidan Jiang, Juan Wang, Shibo Xu, Cuizhe Wang, Jun Zhang()

Key laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine，Shihezi University, Shihezi 832000, China

Received:2024-08-02 Revised:2024-09-01 Published:2024-09-02 Online: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)

摘要/Abstract

摘要：

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。

关键词: GULP1, 转录组, 差异表达基因, 代谢, 生物信息学

Abstract:

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

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.

Xin Wen, Jin Mei, Meiyu Qian, Yidan Jiang, Juan Wang, Shibo Xu, Cuizhe Wang, Jun Zhang. Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing[J]. Hereditas(Beijing), 2024, 46(10): 860-870.

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样本	原始 reads 数目	原始测序量	过滤后的Reads数目	过滤后的测序量	有效碱基百分比	Q30(%)	GC(%)
3T3-NC1	48.75	7.18	47.51	7	97.45	95.13	51.88
3T3-NC2	48.84	7.18	47.45	6.97	97.15	95.18	52.55
3T3-NC3	47.86	7.06	46.7	6.89	97.57	95.11	52.56
3T3-OE1	47.87	7.06	46.71	6.89	97.56	95.19	52.25
3T3-OE2	49.11	7.2	47.63	6.99	96.99	95.08	51.98
3T3-OE3	48.65	7.18	47.49	7.01	97.6	95.34	52.52
C2C12-NC1	48.39	7.12	47.06	6.93	97.26	95.17	52.9
C2C12-NC2	48.7	7.2	47.52	7.02	97.56	95.1	52.87
C2C12-NC3	48.5	7.12	47.11	6.92	97.13	95.23	52.53
C2C12-OE1	48.42	7.1	46.95	6.89	96.96	95.08	52.42
C2C12-OE2	48.21	7.1	46.91	6.91	97.3	95.11	53.01
C2C12-OE3	48.32	7.14	47.25	6.99	97.79	95.05	52.3

基因	上游引物序列(5′→3′)	下游引物序列(5′→3′)
Abca1	GCTTGTTGGCCTCAGTTAAGG	GTAGCTCAGGCGTACAGAGAT
Ccl3	TTCTCTGTACCATGACACTCTGC	CGTGGAATCTTCCGGCTGTAG
Ccl5	GCTGCTTTGCCTACCTCTCC	TCGAGTGACAAACACGACTGC
Fos	CGGGTTTCAACGCCGACTA	TTGGCACTAGAGACGGACAGA
Il6	TAGTCCTTCCTACCCCAATTTCC	TTGGTCCTTAGCCACTCCTTC
Lbp	GATCACCGACAAGGGCCTG	GGCTATGAAACTCGTACTGCC
Map2k6	ATGTCTCAGTCGAAAGGCAAG	TTGGAGTCTAAATCCCGAGGC
Map3k8	ATGGAGTACATGAGCACTGGA	GGCTCTTCACTTGCATAAAGGTT
Tlr7	ATGTGGACACGGAAGAGACAA	GGTAAGGGTAAGATTGGTGGTG
Angpt4	CAGCCAGCTATGCTACTAGATGG	CCTCTGGAGGCTATTGGAGC
Gngt2	CAGGACCTCAGTGAGAAGGAG	CCTGCTTGGGCCTCTACATAAT
Il2rb	TGGAGCCTGTCCCTCTACG	TCCACATGCAAGAGACATTGG
Ret	TTTCTCAAGGGATGCTTACTGGG	CCCGTAGGGCATGGACATAGA
Adora2a	GCCATCCCATTCGCCATCA	GCAATAGCCAAGAGGCTGAAGA
Atp1b2	GGCAGGTGGTTGAGGAGTG	GGGGTATGGTCAGAGACGGT
Calml4	TCTTCTGGTGTCCATGAGGTG	GAAGTCCAGCTCTCCGTTCTT
Npr1	GCTTGTGCTCTATGCAGATCG	TCGACGAACTCCTGGTGATTTA
Npy1r	GCTTGTGCTCTATGCAGATCG	TCGACGAACTCCTGGTGATTTA

基于转录组测序对GULP1下游靶基因筛选及分析

Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing

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