目的筛选肝细胞癌中N6-甲基腺苷(m6A)相关免疫基因构建预后模型,并探讨其关键基因DDX1在肝癌细胞中的作用。方法本研究选取癌症基因组图谱(TCGA)数据库中368例肝癌样本数据作为训练数据集,基因表达综合数据库(GEO)GSE 14520数据集中242...目的筛选肝细胞癌中N6-甲基腺苷(m6A)相关免疫基因构建预后模型,并探讨其关键基因DDX1在肝癌细胞中的作用。方法本研究选取癌症基因组图谱(TCGA)数据库中368例肝癌样本数据作为训练数据集,基因表达综合数据库(GEO)GSE 14520数据集中242例肝癌样本数据作为验证数据集,并基于表达相关性进行m6A相关的免疫基因筛选。通过LASSO Cox回归模型筛选与预后相关的m6A免疫基因,并构建风险评分(RS)模型。根据RS中位数值,分别将训练集和验证集中所有样本分为高与低风险组,Kaplan-Meier法评估高低风险组的生存预后差异。使用实时荧光定量PCR(RT-qPCR)检测肝癌细胞系(HuH-7、SK-HEP-1、PLC/PRF/5和SNU-449)以及人正常肝细胞系THLE-2中筛选的关键基因表达水平;挑选表达变化较显著的基因,运用功能加强和缺失实验对其功能进行细胞验证。one-way ANOVA法比较多组间统计学差异,其中两两比较采用Tukey法。结果基于共表达分析共获得130个m6A相关免疫基因,最终筛选了5个基因(DDX1、HDAC1、HDAC2、NRAS和PLK1)用于RS模型构建。构建的模型显示,与低风险组比较,高风险组的生存率较低,在TCGA(P<0.001)和GSE 14520数据集(P=0.003)中,差异有统计学意义。与其他基因相比,DDX1在肝癌细胞中高表达。CCK-8实验结果显示,过表达DDX1可促进PLC/PRF/5和SNU-449细胞增殖,差异有统计学意义,P<0.05。Transwell结果显示,与阴性对照组相比,DDX1过表达可促进PLC/PRF/5和SNU-449细胞的迁移(105.00±12.53 vs 173.67±12.22;100.00±10.15 vs 147.33±12.10)和侵袭(83.00±10.81 vs 131.00±13.23;85.33±10.01 vs 135.00±12.49)。DDX1过表达可升高细胞丙二醛(1.01±0.10 vs 1.73±0.13)和活性氧(17.54±1.30 vs 25.97±2.24)水平,但降低超氧化物歧化酶(1.03±0.12 vs 0.52±0.12)的水平。DDX1敲除得到了相反的结果。结论本研究基于5个m6A相关免疫基因构建的预后模型可以有效预测肝癌患者的预后以及对免疫治疗的反应。其中DDX1可促进肝癌进展。展开更多
Foot-and-mouth disease virus(FMDV)can infect domestic and wild cloven-hoofed animals.The non-structural protein 3D plays an important role in FMDV replication and pathogenesis.However,the interaction partners of 3D,an...Foot-and-mouth disease virus(FMDV)can infect domestic and wild cloven-hoofed animals.The non-structural protein 3D plays an important role in FMDV replication and pathogenesis.However,the interaction partners of 3D,and the effects of those interactions on FMDV replication,remain incompletely elucidated.In the present study,using the yeast two-hybrid system,we identified a porcine cell protein,DEAD-box RNA helicase 1(DDX1),which interacted with FMDV 3D.The DDX1-3D interaction was further confirmed by co-immunoprecipitation experiments and an indirect immunofluorescence assay(IFA)in porcine kidney 15(PK-15)cells.DDX1 was reported to either inhibit or facilitate viral replication and regulate host innate immune responses.However,the roles of DDX1 during FMDV infection remain unclear.Our results revealed that DDX1 inhibited FMDV replication in an ATPase/helicase activity-dependent manner.In addition,DDX1 stimulated IFN-p activation in FMDV-infected cells.Together,our results expand the body of knowledge regarding the role of DDX1 in FMDV infection.展开更多
The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism...The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism,tumo-rigenesis,and tumor development.However,how DDX1 functions in various cancers remains unclear.Here,we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)databases.DDX1 is highly expressed in breast cancer(BRCA),cholangiocarcinoma(CHOL),and colon adenocarcinoma(COAD),but it is lowly expressed in renal cancers,including kidney renal clear cell carcinoma(KIRC),kidney chromophobe(KICH),and kidney renal papillary cell carcinoma(KIRP).Low expression of DDX1 in KIRC is cor-related with a good prognosis of overall survival(OS)and disease-free survival(DFS).Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma(ACC),bladder urothelial carcinoma(BLCA),KICH,and liver hepatocellular carcinoma(LIHC).Also,the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer(OV)but decreased in KIRC.Immune infiltration analysis exhibited that DDX1 expression affected CD8+T cells,and it was significantly associated with MSI(microsatellite instability),TMB(tumor mutational burden),and ICT(immune checkpoint blockade therapy)in tumors.In addition,the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines.DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database.Thus,our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer.展开更多
Nullbasic is a mutant form of HIV-1 Tat that has strong ability to protect cells from HIV-1 replication by inhibiting three different steps of viral replication: reverse transcription, Rev export of viral m RNA from t...Nullbasic is a mutant form of HIV-1 Tat that has strong ability to protect cells from HIV-1 replication by inhibiting three different steps of viral replication: reverse transcription, Rev export of viral m RNA from the nucleus to the cytoplasm and transcription of viral m RNA by RNA polymerase II. We previously showed that Nullbasic inhibits transduction of human cells including T cells by HIV-1-based lentiviral vectors. Here we investigated whether the Nullbasic antagonists huTat2(a Tat targeting intrabody), HIV-1 Tat or Rev proteins or cellular DDX1 protein could improve transduction by a HIV-1 lentiviral vector conveying Nullbasic-Zs Green1 to human T cells. We show that overexpression of huTat2, Tat-FLAG and DDX1-HA in virus-like particle(VLP) producer cells significantly improved transduction efficiency of VLPs that convey Nullbasic in Jurkat cells. Specifically, co-expression of Tat-FLAG and DDX1-HA in the VLP producer cell improved transduction efficiency better than if used individually. Transduction efficiencies could be further improved by including a spinoculation step. However, the same optimised protocol and using the same VLPs failed to transduce primary human CD4^+T cells. The results imply that the effects of Nullbasic on VLPs on early HIV-1 replication are robust in human CD4^+T cells. Given this significant block to lentiviral vector transduction by Nullbasic in primary CD4^+T cells, our data indicate that gammaretroviral, but not lentiviral, vectors are suitable for delivering Nullbasic to primary human T cells.展开更多
文摘目的筛选肝细胞癌中N6-甲基腺苷(m6A)相关免疫基因构建预后模型,并探讨其关键基因DDX1在肝癌细胞中的作用。方法本研究选取癌症基因组图谱(TCGA)数据库中368例肝癌样本数据作为训练数据集,基因表达综合数据库(GEO)GSE 14520数据集中242例肝癌样本数据作为验证数据集,并基于表达相关性进行m6A相关的免疫基因筛选。通过LASSO Cox回归模型筛选与预后相关的m6A免疫基因,并构建风险评分(RS)模型。根据RS中位数值,分别将训练集和验证集中所有样本分为高与低风险组,Kaplan-Meier法评估高低风险组的生存预后差异。使用实时荧光定量PCR(RT-qPCR)检测肝癌细胞系(HuH-7、SK-HEP-1、PLC/PRF/5和SNU-449)以及人正常肝细胞系THLE-2中筛选的关键基因表达水平;挑选表达变化较显著的基因,运用功能加强和缺失实验对其功能进行细胞验证。one-way ANOVA法比较多组间统计学差异,其中两两比较采用Tukey法。结果基于共表达分析共获得130个m6A相关免疫基因,最终筛选了5个基因(DDX1、HDAC1、HDAC2、NRAS和PLK1)用于RS模型构建。构建的模型显示,与低风险组比较,高风险组的生存率较低,在TCGA(P<0.001)和GSE 14520数据集(P=0.003)中,差异有统计学意义。与其他基因相比,DDX1在肝癌细胞中高表达。CCK-8实验结果显示,过表达DDX1可促进PLC/PRF/5和SNU-449细胞增殖,差异有统计学意义,P<0.05。Transwell结果显示,与阴性对照组相比,DDX1过表达可促进PLC/PRF/5和SNU-449细胞的迁移(105.00±12.53 vs 173.67±12.22;100.00±10.15 vs 147.33±12.10)和侵袭(83.00±10.81 vs 131.00±13.23;85.33±10.01 vs 135.00±12.49)。DDX1过表达可升高细胞丙二醛(1.01±0.10 vs 1.73±0.13)和活性氧(17.54±1.30 vs 25.97±2.24)水平,但降低超氧化物歧化酶(1.03±0.12 vs 0.52±0.12)的水平。DDX1敲除得到了相反的结果。结论本研究基于5个m6A相关免疫基因构建的预后模型可以有效预测肝癌患者的预后以及对免疫治疗的反应。其中DDX1可促进肝癌进展。
基金supported by grants from the National Natural Science Foundation of China (Nos. 31302106, 31260616, and 31602035)the National Key Research and Development Program of China (Nos. 2016YFD0500901 and 2017YFD0500903)
文摘Foot-and-mouth disease virus(FMDV)can infect domestic and wild cloven-hoofed animals.The non-structural protein 3D plays an important role in FMDV replication and pathogenesis.However,the interaction partners of 3D,and the effects of those interactions on FMDV replication,remain incompletely elucidated.In the present study,using the yeast two-hybrid system,we identified a porcine cell protein,DEAD-box RNA helicase 1(DDX1),which interacted with FMDV 3D.The DDX1-3D interaction was further confirmed by co-immunoprecipitation experiments and an indirect immunofluorescence assay(IFA)in porcine kidney 15(PK-15)cells.DDX1 was reported to either inhibit or facilitate viral replication and regulate host innate immune responses.However,the roles of DDX1 during FMDV infection remain unclear.Our results revealed that DDX1 inhibited FMDV replication in an ATPase/helicase activity-dependent manner.In addition,DDX1 stimulated IFN-p activation in FMDV-infected cells.Together,our results expand the body of knowledge regarding the role of DDX1 in FMDV infection.
基金supported by grants from the National Natural Science Foundation of China(82071782)the Shanghai Committee of Science and Technology(20XD1400800)to JL.
文摘The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism,tumo-rigenesis,and tumor development.However,how DDX1 functions in various cancers remains unclear.Here,we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)databases.DDX1 is highly expressed in breast cancer(BRCA),cholangiocarcinoma(CHOL),and colon adenocarcinoma(COAD),but it is lowly expressed in renal cancers,including kidney renal clear cell carcinoma(KIRC),kidney chromophobe(KICH),and kidney renal papillary cell carcinoma(KIRP).Low expression of DDX1 in KIRC is cor-related with a good prognosis of overall survival(OS)and disease-free survival(DFS).Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma(ACC),bladder urothelial carcinoma(BLCA),KICH,and liver hepatocellular carcinoma(LIHC).Also,the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer(OV)but decreased in KIRC.Immune infiltration analysis exhibited that DDX1 expression affected CD8+T cells,and it was significantly associated with MSI(microsatellite instability),TMB(tumor mutational burden),and ICT(immune checkpoint blockade therapy)in tumors.In addition,the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines.DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database.Thus,our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer.
基金supported by the National Health and Medical Research Council Project Grant (1085359)supported by Prime Minister’s Australia Asia Endeavour Postgraduate (Ph.D.) Award funded by the Australian Government,epartment of Education and Training,UQ international scholarship (UQI) and UQ Centenial scholarship (UQCent)
文摘Nullbasic is a mutant form of HIV-1 Tat that has strong ability to protect cells from HIV-1 replication by inhibiting three different steps of viral replication: reverse transcription, Rev export of viral m RNA from the nucleus to the cytoplasm and transcription of viral m RNA by RNA polymerase II. We previously showed that Nullbasic inhibits transduction of human cells including T cells by HIV-1-based lentiviral vectors. Here we investigated whether the Nullbasic antagonists huTat2(a Tat targeting intrabody), HIV-1 Tat or Rev proteins or cellular DDX1 protein could improve transduction by a HIV-1 lentiviral vector conveying Nullbasic-Zs Green1 to human T cells. We show that overexpression of huTat2, Tat-FLAG and DDX1-HA in virus-like particle(VLP) producer cells significantly improved transduction efficiency of VLPs that convey Nullbasic in Jurkat cells. Specifically, co-expression of Tat-FLAG and DDX1-HA in the VLP producer cell improved transduction efficiency better than if used individually. Transduction efficiencies could be further improved by including a spinoculation step. However, the same optimised protocol and using the same VLPs failed to transduce primary human CD4^+T cells. The results imply that the effects of Nullbasic on VLPs on early HIV-1 replication are robust in human CD4^+T cells. Given this significant block to lentiviral vector transduction by Nullbasic in primary CD4^+T cells, our data indicate that gammaretroviral, but not lentiviral, vectors are suitable for delivering Nullbasic to primary human T cells.
