| Autor: |
Si-Zhu, Li, Yi-Bin, Yao, Zhong-Yuan, Tang, Ze-Yan, Shi, Ze-Guang, Wu, Bin, Luo, Zhi-Gang, Peng |
| Rok vydání: |
2021 |
| Předmět: |
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| Zdroj: |
Zhongguo shi yan xue ye xue za zhi. 29(3) |
| ISSN: |
1009-2137 |
| Popis: |
To analyze gene expression profile of T cell lymphoma Jurkat cell line treated with paclitaxel by computational biology based on next generation sequencing and to explore the possible molecular mechanism of paclitaxel resistance to T cell lymphoma at gene level.IC50 of paclitaxel on Jurkat cell line was determined by CCK-8 assay. Gene expression profile of Jurkat cells treated with paclitaxel was acquired by next generation sequencing technology. Gene microarray data related to human T cell lymphoma were screened from Gene Expression Omnibus (GEO) database (including 720 cases of T cell lymphoma and 153 cases of normal tissues). Combined with the sequencing data, differential expression genes (DEGs) were intersected and screened. DAVID database was used for enrichment analysis of GO function and KEGG pathway to determine and visualize functional entries of DEGs, and protein-protein interactions network of DEGs was drawn. The levels of gene expression were detected and verified by RT-qPCR.CCK-8 results showed that the proliferation of Jurkat cells was inhibited by paclitaxel depended on the concentration apparently. Treated by paclitaxel for 48 h, P0.05 and |log2(FC)|≥1 were used as filter criteria on the results of RNA Sequencing (RNA-Seq) and GeoChip, 351 DEGs were found from Jurkat cells, including 323 up-regulated genes and 28 down-regulated genes. The GO functional annotation and KEGG pathway enrichment analysis showed that the role of paclitaxel was mainly concentrated in protein heterodimerization activity, nucleosome assembly and transcriptional dysregulation in cancer, etc. The results of RT-qPCR were consistent with those of the sequencing analysis, which verified the reliability of this sequencing.Paclitaxel can affect the proliferation and apoptosis of T-cell lymphoma by up-regulating JUN gene, orphan nuclear receptor NR4A family genes and histone family genes.基于高通量测序及公共数据库探索紫杉醇抑制T细胞淋巴瘤机制.通过二代测序技术对紫杉醇作用下T细胞淋巴瘤细胞株Jurkat基因表达谱进行计算生物学分析，以在基因层面探讨紫杉醇抗T细胞淋巴瘤的可能分子机制.采用CCK-8法确定紫杉醇作用于Jurkat细胞的IC50，应用二代测序技术获得紫杉醇作用Jurkat细胞后基因表达谱，同时从GEO数据库中筛出与人T细胞淋巴瘤相关的基因芯片数据（其中包括720例T细胞淋巴瘤和153例正常对照组织），结合测序数据结果二者取交集并筛选差异表达基因（DEG）；使用DAVID数据库进行GO功能和KEGG通路富集分析，确定和可视化DEG的功能条目，并绘制DEG的蛋白质相互作用网络图。使用RT-qPCR验证基因的表达水平.CCK-8结果显示紫杉醇对Jurkat细胞抑制率有明显的浓度依赖性；紫杉醇作用于Jurkat细胞48 h后进行转录组测序（RNA-seq），对RNA-seq和GEO芯片中的基因，以P0.05，|log2(FC)|≥1为DEG筛选标准，共发现351个DEG，其中包括323个上调基因，28个下调基因；GO功能注释及KEGG通路富集分析结果表明，紫杉醇抗T细胞淋巴瘤的作用主要富集在蛋白质异源二聚活动、核小体装配以及癌症中的转录失调信号通路等；RT-qPCR基因表达结果与测序结果一致，验证本次测序的可靠性.紫杉醇可以通过上调JUN基因和孤儿核受体NR4A家族基因以及组蛋白家族基因来影响T细胞淋巴瘤的增殖和凋亡. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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