应用高通量测序研究人参皂苷Rh1对乳腺癌SKBR3细胞基因表达的影响

Effects of Ginsenoside Rh1 on Gene Expression of Breast Cancer SKBR3 Cells by High Throughput Sequencing

目的观察人参皂苷Rh1对乳腺癌SKBR3细胞基因表达的影响,筛查人参皂苷Rh1干预下乳腺癌SKBR3细胞中差异表达的基因。方法对乳腺癌SKBR3细胞进行样本准备,获得去rRNA链特异性转录组;测序获得原始图像文件经碱基识别后转化为原始序列文件;通过质量分析评估测序数据是否适合进行生物信息学分析,应用剪切转录产物比对软件(STAR)对测序数据与参考基因组进行比对;基于美国国家生物技术信息中心(NCBI)数据库,对人参皂苷Rh1干预下乳腺癌SKBR3细胞基因的表达及差异基因的表达进行分析。结果高通量测序共筛查出基因26978个,其中根据NCBI数据库注释为m RNA的基因19229个,注释为lncRNA的基因4385个,高通量测序结果表明差异表达基因6580个,以Fold change>1为上调,<-1为下调,上调差异基因3403个,其中差异表达显著基因为小整合膜蛋白11A(SMIM11A)、嘌呤能受体P2X1(P2RX1)、碳酸酐酶9(CA9)、磷脂酰肌醇-3激酶催化亚基δ核糖核酸2(PIK3CD-AS2)、血管活性肠肽受体2(VIPR2)、非特征LOC100506314(LOC100506314)、长基因间非蛋白编码核糖核酸1389(LINC01389)、表皮生长因子受体激酶底物8-样蛋白3(EPS8L3)、视网膜筋膜基因2(FSCN2)、肠壁碱性磷酸酶(ALPI);下调差异表达基因3177个,其中差异表达显著基因为溶质载体家族1成员3(SLC1A3)、羟基类固醇17-β脱氢酶1(HSD17B1)、碳水化合物磺基转移酶11(CHST11)、溶质载体家族25成员51(SLC25A51)、β-1,3-半乳糖基转移酶6(B3GALT6)、非特征LOC101929882(LOC101929882)、δ连环蛋白家族成员(ARVCF)、蛋白磷酸酶2A催化亚基α(PPP2CA)、星形胶质细胞上调基因-1(AEG1)、磷脂酰肌醇-4-激酶B(PI4KB)。结论应用高通量测序技术可筛查出人参皂苷Rh1对乳腺癌SKBR3细胞增殖相关的差异性表达基因,并对筛选出的重要基因进行总结和分类。

Objective To determine the effects of ginsenoside Rh1 on gene expression of breast cancer SKBR3 cells;To screen the differentially expressed genes in breast cancer SKBR3 cells under the intervention of ginsenoside Rh1.Methods Samples of breast cancer SKBR3 cells were prepared to obtain rRNA chain-removed specific transcriptome.The original image file obtained by sequencing was transformed into the original sequence file after base recognition.After quality analysis,the sequencing data were evaluated whether suitable for bioinformatics analysis and the sequencing data were compared with the reference genome by using STAR software.Based on the NCBI database,the gene expression level and differential gene expression of SKBR3 cells under the intervention of ginsenoside Rh1 were screened and annotated.Results Through high throughput sequencing technology,a total of 26978 genes were screened,of which 19229 genes were annotated to m RNA and 4385 genes were annotated to lncRNA according to the NCBI database.High throughput sequencing showed 6580 differentially expressed genes.Fold change value greater than 1 was used as up-regulation,less than-1 as down-regulation.There were 3403 differentially expressed genes up-regulated,including SMIM11 A(small integral membrane protein 11 A),P2 RX1(purinergic receptor P2 X1),CA9(carbonic anhydrase 9),PIK3 CD-AS2(PIK3 CD antisense RNA 2),VIPR2(vasoactive intestinal peptide receptor 2),LOC100506314(uncharacterized LOC100506314),LINC01389(long intergenic non-protein coding RNA 1389),EPS8 L3(epidermal growth factor receptor kinase substrate 8-like protein 3),FSCN2(fascin gene 2),ALPI(alkaline phosphatase,intestinal).There were 3177 down-regulated genes,including SLC1 A3(solute carrier family 1 member 3),HSD17B1(hydroxysteroid 17-beta dehydrogenase 1),CHST11(carbohydrate sulfotransferase 11),SLC25 A51(solute carrier family 25 member 51),B3GALT6(beta-1,3-galactosyltransferase 6),LOC101929882(uncharacterized LOC101929882),ARVCF(delta catenin family member),PPP2CA(protein phosphatase 2 catalytic subunit alpha),AEG1(astrocyte elevated gene-1 protein),and PI4KB(phosphatidylinositol 4-kinase beta).Conclusion This study screens out the differentially expressed genes of ginsenoside Rh1 related to the proliferation of SKBR3 cells by high throughput sequencing technology,and summarizes and classifies the important genes.