本研究旨在利用生物信息学方法构建经铜诱导的ATP7B基因敲除HepG2细胞系的转录调控网络。探讨关键转录因子在肝豆状核变性发生、发展中的潜在作用机制。收集公共基因表达数据库(gene expression omnibus,GEO)中包含野生型、ATP7B基因敲...本研究旨在利用生物信息学方法构建经铜诱导的ATP7B基因敲除HepG2细胞系的转录调控网络。探讨关键转录因子在肝豆状核变性发生、发展中的潜在作用机制。收集公共基因表达数据库(gene expression omnibus,GEO)中包含野生型、ATP7B基因敲除型、铜诱导的野生型和铜诱导的ATP7B基因敲除型HepG2细胞系数据。筛选由铜诱导产生的差异表达基因(differentially expressed genes,DEGs)后进行基因本体论(gene ontology,GO)、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)富集分析。基于蛋白相互作用网络,识别疾病关键基因和功能模块,并对关键功能模块中的基因进行富集分析。最后,构建转录调控网络,筛选核心转录因子。共筛选出1034个差异表达基因,其中上调525个,下调509个。上、下调关键功能模块分别包括了3785个和3931个基因。关键功能模块中的基因主要定位于细胞-基质连接、染色体、剪接复合体、核糖体等区域,共同参与了mRNA加工、组蛋白修饰、RNA剪切、DNA代谢调节、蛋白磷酸化等生物学过程,且与转录共调控活性、DNA转录因子结合、泛素样蛋白连接酶结合等分子功能相关。KEGG分析表明功能模块中的基因显著富集的通路包括乙型肝炎、有丝分裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信号通路、细胞衰老和凋亡、神经营养信号通路和神经变性途径等。肝豆状核变性转录调控网络包括11个差异表达转录因子和96个差异表达基因,其中U2AF1、NFRKB、FUS、MAX、SRSF1、CEBPA和RXRA为核心差异表达转录因子。该研究为肝豆状核变性转录调控相关分子的生物学功能研究提供了重要的参考依据。展开更多
OBJECTIVE:To screen for m RNAs associated with blood stasis syndrome and to explore the genetic mechanisms of blood stasis syndrome in hypertension.METHODS:This study involved groups of patients with hypertension and ...OBJECTIVE:To screen for m RNAs associated with blood stasis syndrome and to explore the genetic mechanisms of blood stasis syndrome in hypertension.METHODS:This study involved groups of patients with hypertension and blood stasis,including those with Qi deficiency,Qi stagnation,cold retention and heat retention;as well as hypertensive patients without blood stasis and healthy individuals.Human umbilical vein endothelial cells were co-cultured with the sera of these healthy individuals and patients with blood stasis syndrome.Total RNA was extracted from these cells and assessed by a high-throughput sequencing method(Solexa)and digital gene expression.Differentially expressed genes among these six groups were compared using whole genome sequences,and m RNAs associated with blood stasis syndrome identified.Differences in gene use and gene ontology function were an-alyzed.Genes enriched significantly and their pathways were determined,as were network interactions,and encoded proteins.Gene identities were confirmed by real-time polymerase chain reactions.RESULTS:Compared with cells cultured in sera of the blood stasis groups,those culture in sera of healthy individuals and of the non-blood stasis group showed 11 and 301 differences,respectively in stasis-related genes.Genes identified as differing between the blood stasis and healthy groups included activating transcription factor 4,activating transcription factor 3,DNA-damage inducible transcription factor 3,Tribbles homolog 3,CCAAT/enhancer binding protein-β,and Jun proto-oncogene(JUN).Pathway and protein interaction network analyses showed that these genes were associated with endoplasmic reticulum stress.Cells cultured in sera of patients with blood stasis and Qi deficiency,Qi stagnation,heat retention,and cold retention were compared with cells cultured in sera of patients with the other types blood stasis syndrome.The comparison showed differences in expression of 28,28,34,and 32 specific genes,respectively.CONCLUSION:The pathogenesis of blood stasis syndrome in hypertension is related to endoplasmic reticulum stress and involves the differential expression of the activating transcription factor 4,activating transcription factor 3,DNA-damage inducible transcription factor 3,Tribbles homolog 3,CCAAT/enhancer binding protein-β,and JUN genes.展开更多
文摘本研究旨在利用生物信息学方法构建经铜诱导的ATP7B基因敲除HepG2细胞系的转录调控网络。探讨关键转录因子在肝豆状核变性发生、发展中的潜在作用机制。收集公共基因表达数据库(gene expression omnibus,GEO)中包含野生型、ATP7B基因敲除型、铜诱导的野生型和铜诱导的ATP7B基因敲除型HepG2细胞系数据。筛选由铜诱导产生的差异表达基因(differentially expressed genes,DEGs)后进行基因本体论(gene ontology,GO)、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)富集分析。基于蛋白相互作用网络,识别疾病关键基因和功能模块,并对关键功能模块中的基因进行富集分析。最后,构建转录调控网络,筛选核心转录因子。共筛选出1034个差异表达基因,其中上调525个,下调509个。上、下调关键功能模块分别包括了3785个和3931个基因。关键功能模块中的基因主要定位于细胞-基质连接、染色体、剪接复合体、核糖体等区域,共同参与了mRNA加工、组蛋白修饰、RNA剪切、DNA代谢调节、蛋白磷酸化等生物学过程,且与转录共调控活性、DNA转录因子结合、泛素样蛋白连接酶结合等分子功能相关。KEGG分析表明功能模块中的基因显著富集的通路包括乙型肝炎、有丝分裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信号通路、细胞衰老和凋亡、神经营养信号通路和神经变性途径等。肝豆状核变性转录调控网络包括11个差异表达转录因子和96个差异表达基因,其中U2AF1、NFRKB、FUS、MAX、SRSF1、CEBPA和RXRA为核心差异表达转录因子。该研究为肝豆状核变性转录调控相关分子的生物学功能研究提供了重要的参考依据。
基金Supported by National Scientific Fund(Assessing Micro RNA-mediated Endothelial Cell Injury in Blood Stasis,No.81173157)Guangdong Scientific Fund(Assessing Micro RNA-mediated Endothelial Cell Injury in Blood Stasis,No.10151063201000045)
文摘OBJECTIVE:To screen for m RNAs associated with blood stasis syndrome and to explore the genetic mechanisms of blood stasis syndrome in hypertension.METHODS:This study involved groups of patients with hypertension and blood stasis,including those with Qi deficiency,Qi stagnation,cold retention and heat retention;as well as hypertensive patients without blood stasis and healthy individuals.Human umbilical vein endothelial cells were co-cultured with the sera of these healthy individuals and patients with blood stasis syndrome.Total RNA was extracted from these cells and assessed by a high-throughput sequencing method(Solexa)and digital gene expression.Differentially expressed genes among these six groups were compared using whole genome sequences,and m RNAs associated with blood stasis syndrome identified.Differences in gene use and gene ontology function were an-alyzed.Genes enriched significantly and their pathways were determined,as were network interactions,and encoded proteins.Gene identities were confirmed by real-time polymerase chain reactions.RESULTS:Compared with cells cultured in sera of the blood stasis groups,those culture in sera of healthy individuals and of the non-blood stasis group showed 11 and 301 differences,respectively in stasis-related genes.Genes identified as differing between the blood stasis and healthy groups included activating transcription factor 4,activating transcription factor 3,DNA-damage inducible transcription factor 3,Tribbles homolog 3,CCAAT/enhancer binding protein-β,and Jun proto-oncogene(JUN).Pathway and protein interaction network analyses showed that these genes were associated with endoplasmic reticulum stress.Cells cultured in sera of patients with blood stasis and Qi deficiency,Qi stagnation,heat retention,and cold retention were compared with cells cultured in sera of patients with the other types blood stasis syndrome.The comparison showed differences in expression of 28,28,34,and 32 specific genes,respectively.CONCLUSION:The pathogenesis of blood stasis syndrome in hypertension is related to endoplasmic reticulum stress and involves the differential expression of the activating transcription factor 4,activating transcription factor 3,DNA-damage inducible transcription factor 3,Tribbles homolog 3,CCAAT/enhancer binding protein-β,and JUN genes.
