目的探究基因甲基化改变在矽肺病及煤工尘肺(coal workers’pneumoconiosis,CWP)中的生物过程和调控机制。方法2023年10月至2024年3月招募矽肺患者5例,煤工尘肺患者16例,对照组56例,经问卷调查了解人口学信息、职业病、既往病史、生活...目的探究基因甲基化改变在矽肺病及煤工尘肺(coal workers’pneumoconiosis,CWP)中的生物过程和调控机制。方法2023年10月至2024年3月招募矽肺患者5例,煤工尘肺患者16例,对照组56例,经问卷调查了解人口学信息、职业病、既往病史、生活史等内容;采用DNA甲基化高通量基因芯片对矽肺、煤工尘肺患者和对照组血样进行检测,分析CpG点位甲基化差异DNA,采用R软件ggplot2包用于绘制差异甲基化基因(differentially methylated genes,DMGs)火山图,pheatmap包用于构建热图;使用sesame(SEnsible Step-wise Analysis of DNA MEthylation BeadChips)软件混合线性模型对每两组样本进行分析,获得检测的差异甲基化点位(differentially methylated CpG,DMC),再进行FDR校正,得到校正后P值,采用P<0.05和Δβ绝对值>0.05进行筛选;对甲基化差异基因进行GO(gene ontology)富集分析找到其主要参与的生物过程,使用KEGG(kyoto encyclopedia of genes and genomes)通路分析寻找参与的相关细胞通路,并根据Venn图的重叠和独特DMGs结果进一步鉴定潜在的生物标志物。结果矽肺患者组男性4人,女性1人,年龄(54.60±2.70)岁,接害工龄(12.80±8.01)年。煤工尘肺患者组男性15人,女性1人,年龄(74.80±8.14)岁,接害工龄(31.38±10.11)年。对照组男性49人,女性7人,年龄(64.91±12.29)岁。年龄(F=7.78,P<0.01)、工龄(t=4.67,P<0.01)、吸烟(χ^(2)=16.41,P<0.01)在不同组间的差异有统计学意义,性别(χ^(2)=0.88,P>0.05)在不同组间的差异无统计学意义。基因测序结果显示,矽肺组与对照组比较有1128个显著差异的DMGs(包括720个上调和408个下调的DMGs),CWP组共发现423个显著差异DMGs(139个上调和284个下调的DMGs)。矽肺组与CWP组相比发现711个显著差异DMGs(440个上调和271个下调的DMGs)。GO富集分析显示,矽肺与CWP差异基因涉及276种生物过程、45种细胞组分及64种分子功能。KEGG分析显示差异基因显著富集于30条信号通路。结论矽肺和CWP患者血样中的DMGs分布和其涉及的生物过程与调控机制存在差异。展开更多
Understanding abiotic stress responses is one of the most important issues in plant research nowadays.Abiotic stress,including excess light,can promote the onset of oxidative stress through the accumulation of reactiv...Understanding abiotic stress responses is one of the most important issues in plant research nowadays.Abiotic stress,including excess light,can promote the onset of oxidative stress through the accumulation of reactive oxygen species.Oxidative stress also arises when in vitro propagated plants are exposed to high light upon transfer to ex vitro.To determine whether the underlying pathways activated at the transfer of in vitro grapevine to ex vitro conditions reflect the processes occurring upon light stress,we used Vitis vinifera Affymetrix GeneChip(VvGA)and a custom array of genes responsive to light stress(LSCA)detected by real-time reverse transcriptase PCR(qRT-PCR).When gene-expression profiles were compared,'protein metabolism and modification','signaling',and'anti-oxidative"genes were more represented in LSCA,while,in VvGA,'cell wall metabolism'and'secondary metabolism'were the categories in which gene expression varied more significantly.The above functional categories confirm previous studies involving other types of abiotic stresses,enhancing the common attributes of abiotic stress defense pathways.The LSCA analysis of our experimental system detected strong response of heat shock genes,particularly the protein rescuing mechanism involving the cooperation of two ATP-dependent chaperone systems,Hsp100 and Hsp70,which showed an unusually late response during the recovery period,of extreme relevance to remove non-functional,potentially harmful polypeptides arising from misfolding,denaturation,or aggregation brought about by stress.The success of LSCA also proves the feasibility of a custommade qRT-PCR approach,particularly for species for which no GeneChip is available and for researchers dealing with a specific and focused problem.展开更多
目的:揭示肝癌诱发过程中肝组织基因表达谱的演变,为中医药防治原发性肝癌提供参考。方法:采用DEN诱发大鼠肝癌,分别于诱癌的第4周、8周、16周、20周(肝癌形成)切取肝(合肝癌)组织,常规提取RNA,Affymetrix Rat 230A GeneChip及技术检测...目的:揭示肝癌诱发过程中肝组织基因表达谱的演变,为中医药防治原发性肝癌提供参考。方法:采用DEN诱发大鼠肝癌,分别于诱癌的第4周、8周、16周、20周(肝癌形成)切取肝(合肝癌)组织,常规提取RNA,Affymetrix Rat 230A GeneChip及技术检测大鼠肝组织基因表达的差异和演变。结果:在芯片的15710个基因中,正常组有9225个基因表达,诱癌4周表达增至9396个,8周增至9872个,16周增至10496个,20周有10420个。在肝癌诱发过程中,存在大量基因表达的消长以及高表达基因数的增加,其中部分已知基因的结果。结论:DEN诱发大鼠肝癌过程中基因组变化是十分复杂的,而且文献追踪表明,国内外对在这些基因的功能及其与肝癌发生、发展的关系大多不明确。因此,如何逐一找到那些起着关键作用的基因,进一步阐释其在肝癌的发生、发展和转归中的作用,及其与中医证候演变和相应治法的关系,是今后中医基础理论实验研究的重要方向。展开更多
文摘目的探究基因甲基化改变在矽肺病及煤工尘肺(coal workers’pneumoconiosis,CWP)中的生物过程和调控机制。方法2023年10月至2024年3月招募矽肺患者5例,煤工尘肺患者16例,对照组56例,经问卷调查了解人口学信息、职业病、既往病史、生活史等内容;采用DNA甲基化高通量基因芯片对矽肺、煤工尘肺患者和对照组血样进行检测,分析CpG点位甲基化差异DNA,采用R软件ggplot2包用于绘制差异甲基化基因(differentially methylated genes,DMGs)火山图,pheatmap包用于构建热图;使用sesame(SEnsible Step-wise Analysis of DNA MEthylation BeadChips)软件混合线性模型对每两组样本进行分析,获得检测的差异甲基化点位(differentially methylated CpG,DMC),再进行FDR校正,得到校正后P值,采用P<0.05和Δβ绝对值>0.05进行筛选;对甲基化差异基因进行GO(gene ontology)富集分析找到其主要参与的生物过程,使用KEGG(kyoto encyclopedia of genes and genomes)通路分析寻找参与的相关细胞通路,并根据Venn图的重叠和独特DMGs结果进一步鉴定潜在的生物标志物。结果矽肺患者组男性4人,女性1人,年龄(54.60±2.70)岁,接害工龄(12.80±8.01)年。煤工尘肺患者组男性15人,女性1人,年龄(74.80±8.14)岁,接害工龄(31.38±10.11)年。对照组男性49人,女性7人,年龄(64.91±12.29)岁。年龄(F=7.78,P<0.01)、工龄(t=4.67,P<0.01)、吸烟(χ^(2)=16.41,P<0.01)在不同组间的差异有统计学意义,性别(χ^(2)=0.88,P>0.05)在不同组间的差异无统计学意义。基因测序结果显示,矽肺组与对照组比较有1128个显著差异的DMGs(包括720个上调和408个下调的DMGs),CWP组共发现423个显著差异DMGs(139个上调和284个下调的DMGs)。矽肺组与CWP组相比发现711个显著差异DMGs(440个上调和271个下调的DMGs)。GO富集分析显示,矽肺与CWP差异基因涉及276种生物过程、45种细胞组分及64种分子功能。KEGG分析显示差异基因显著富集于30条信号通路。结论矽肺和CWP患者血样中的DMGs分布和其涉及的生物过程与调控机制存在差异。
文摘Understanding abiotic stress responses is one of the most important issues in plant research nowadays.Abiotic stress,including excess light,can promote the onset of oxidative stress through the accumulation of reactive oxygen species.Oxidative stress also arises when in vitro propagated plants are exposed to high light upon transfer to ex vitro.To determine whether the underlying pathways activated at the transfer of in vitro grapevine to ex vitro conditions reflect the processes occurring upon light stress,we used Vitis vinifera Affymetrix GeneChip(VvGA)and a custom array of genes responsive to light stress(LSCA)detected by real-time reverse transcriptase PCR(qRT-PCR).When gene-expression profiles were compared,'protein metabolism and modification','signaling',and'anti-oxidative"genes were more represented in LSCA,while,in VvGA,'cell wall metabolism'and'secondary metabolism'were the categories in which gene expression varied more significantly.The above functional categories confirm previous studies involving other types of abiotic stresses,enhancing the common attributes of abiotic stress defense pathways.The LSCA analysis of our experimental system detected strong response of heat shock genes,particularly the protein rescuing mechanism involving the cooperation of two ATP-dependent chaperone systems,Hsp100 and Hsp70,which showed an unusually late response during the recovery period,of extreme relevance to remove non-functional,potentially harmful polypeptides arising from misfolding,denaturation,or aggregation brought about by stress.The success of LSCA also proves the feasibility of a custommade qRT-PCR approach,particularly for species for which no GeneChip is available and for researchers dealing with a specific and focused problem.
文摘目的:揭示肝癌诱发过程中肝组织基因表达谱的演变,为中医药防治原发性肝癌提供参考。方法:采用DEN诱发大鼠肝癌,分别于诱癌的第4周、8周、16周、20周(肝癌形成)切取肝(合肝癌)组织,常规提取RNA,Affymetrix Rat 230A GeneChip及技术检测大鼠肝组织基因表达的差异和演变。结果:在芯片的15710个基因中,正常组有9225个基因表达,诱癌4周表达增至9396个,8周增至9872个,16周增至10496个,20周有10420个。在肝癌诱发过程中,存在大量基因表达的消长以及高表达基因数的增加,其中部分已知基因的结果。结论:DEN诱发大鼠肝癌过程中基因组变化是十分复杂的,而且文献追踪表明,国内外对在这些基因的功能及其与肝癌发生、发展的关系大多不明确。因此,如何逐一找到那些起着关键作用的基因,进一步阐释其在肝癌的发生、发展和转归中的作用,及其与中医证候演变和相应治法的关系,是今后中医基础理论实验研究的重要方向。
