Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China.
Department of Pathogen Biology, School of Basic Medicine Southwest Medical University, China.
Dis Markers. 2022 Aug 19;2022:1354005. doi: 10.1155/2022/1354005. eCollection 2022.
Using human gene chip expression profiling technology to screen out downstream genes related to TrkB regulation in laryngeal cancer cells.
Using the Hep-2 TrkB shRNA cell line, divide it into an experimental group (shNTRK2) and a control group (PLKO1), and use the human gene expression microarray to screen out the differential genes. Then, select 10 upregulated genes and 10 downregulated genes from the differential genes, and use RT-PCR to verify whether the screening results of human gene expression microarray profiles are reliable. Use GO, KEGG, and miRNA enrichment analyses, PPI network diagram, etc., to analyze the differential genes and further screen out the key genes.
A total of 318 differential genes (87 upregulated genes and 231 downregulated genes) were screened in laryngeal cancer cells. Use RT-PCR for the 10 upregulated differential genes (DMKN, FHL1, FOXN4, GGNBP1, HOXB9, ABCB1, TNFAI, RGS2, LINC01133, and FGG) and 10 downregulated differential genes (CHI3L1, FMOD, IGFBP1, IRF5, SPARC, NPAS4, TRPS1, TRAP, COL8A1, and DNER), and the results are consistent with the chip results, confirming the accuracy of the chip results; GO analysis results show that the downstream differential genes (DEGs) regulated by TrkB are mainly involved in biological processes such as retinol metabolic process, diterpenoid metabolic process, and regulation of cell-substrate adhesion. DEGs mainly affect cytoskeletal protein binding, serotonin-activated cation-selective channel activity, and sphingosine molecular functions. DEGs are mainly enriched in the cell periphery, secretory granule, cytoplasmic membrane-bounded vesicle lumen, blood microparticle, and other molecular components. The results of disease enrichment analysis show that the downstream differential genes regulated by TrkB are mainly involved in atypical hemolytic uremic syndrome, hematologic disease, meningococcal disease, lung cancer, susceptibility, asthma, and other diseases. The PPI network diagram results showed 7 hub genes, and then, we used GO analysis and KEGG enrichment analysis to see the biological process, cell component, molecular functions, and biological pathways.
Gene chip technology was used to screen out the differential genes of TrkB epigenetic modification in the Hep-2 cell line, and seven key genes (ALDH1A1, SDR16C5, PIK3R1, PLCG2, IL2RG, PIK3CD, and SPARC) were further screened using bioinformatics technology.
利用人类基因芯片表达谱技术筛选出与喉癌细胞中 TrkB 调节相关的下游基因。
使用 Hep-2 TrkB shRNA 细胞系，将其分为实验组（shNTRK2）和对照组（PLKO1），并使用人类基因表达微阵列筛选差异基因。然后，从差异基因中选择 10 个上调基因和 10 个下调基因，使用 RT-PCR 验证人类基因表达微阵列图谱筛选结果的可靠性。使用 GO、KEGG、miRNA 富集分析、PPI 网络图等方法分析差异基因，并进一步筛选关键基因。
在喉癌细胞中筛选出 318 个差异基因（87 个上调基因和 231 个下调基因）。使用 RT-PCR 对 10 个上调差异基因（DMKN、FHL1、FOXN4、GGNBP1、HOXB9、ABCB1、TNFAI、RGS2、LINC01133 和 FGG）和 10 个下调差异基因（CHI3L1、FMOD、IGFBP1、IRF5、SPARC、NPAS4、TRPS1、TRAP、COL8A1 和 DNER）进行验证，结果与芯片结果一致，证实了芯片结果的准确性；GO 分析结果表明，TrkB 调节的下游差异基因（DEGs）主要参与视黄醇代谢过程、二萜代谢过程和细胞-基质粘附调节等生物学过程。DEGs 主要影响细胞骨架蛋白结合、血清素激活的阳离子选择性通道活性和神经鞘氨醇分子功能。DEGs 主要富集在细胞外周、分泌颗粒、细胞质膜结合囊泡腔、血液微粒体等分子成分中。疾病富集分析结果表明，TrkB 调节的下游差异基因主要涉及非典型溶血性尿毒症综合征、血液疾病、脑膜炎球菌病、肺癌、易感性、哮喘等疾病。PPI 网络图结果显示 7 个枢纽基因，然后我们使用 GO 分析和 KEGG 富集分析来观察生物过程、细胞成分、分子功能和生物途径。
利用基因芯片技术筛选出 Hep-2 细胞系中 TrkB 表观遗传修饰的差异基因，然后利用生物信息学技术进一步筛选出 7 个关键基因（ALDH1A1、SDR16C5、PIK3R1、PLCG2、IL2RG、PIK3CD 和 SPARC）。
