Profiling of differentially expressed genes in human gastric carcinoma by cDNA expression array

AIM: To investigate the expression of cancer related genes in gastric carcinoma (GC) through the use of Atlas Human Cancer Array membranes with 588 well-characterized human genes related to cancer and tumor biology.METHODS: Hybridization of cDNA blotting membrane was performed with (32)P-labeled cDNA probes synthesized from RNA isolated from gastric carcinoma and adjacent noncancerous gastric epithelial tissue. AtlasImage, which is a software specific to array, was used to analyze the result.RESULTS: The differentially expression cell cycle/growth regulator in GC showed a stronger tendency toward cell proliferation with 2.7-fold up-regulation of CK1. The promoter genes of apoptosis were down-regulated, including caspase-8 precursor, caspase-9 and caspase-10. Among the oncogene/tumor suppressor genes, ABL2 was down-regulated. In addition, some genes were up-regulated, including matrix metalloproteinse 2(MMP-2), MMP-16(MT3-MMP), SKY, CD9 and semaphorin V. A number of genes were down-regulated, including neuroendocrine-dlg (NE-dlg), retinoic acid receptor gamma and tumor suppressor DCC colorectal. In general, The expression of the cancer progression genes were up-regulated, while the expression of anti-cancer progression genes were down-regulated.CONCLUSION: Investigation of these genes should help to disclose the molecular mechanism of the onset, progression and prognosis of GC. Several genes are reported herein to be altered in GC for the first time. The quick and high-throughout method of profiling gene expression by cDNA array provides us with an overview of key factors that may involved in GC, and may aid the study of GC carcinogenesis and provide molecular targets for diagnosis and therapy. The precise relationship between the altered genes and gastric carcinogenesis is a matter for further investigation.     

Profiling of differentially expressed genes in human Gastric carcinoma by cDNA expression array

AIM: To investigate the expression of cancer relatedgenes in gastric carcinoma (GC) through the use of AtlasHuman Cancer Array membranes with 588 well-characterized human genes related to cancer and tumorbiology.METHODS: Hybridization of cDNA blotting membranewas performed with 32P-labeled cDNA probessynthesized from RNA isolated from gastric carcinomaand adjacent noncancerous gastric epithelial tissue.AtlasImage, which is a software specific to array, wasused to analyze the result.RESULTS: The differentially expression cell cycle/growth regulator in GC showed a stronger tendencytoward cell proliferation with 2.7-fold up-regulation ofCK1. The promoter genes of apoptosis were down-regulated, including caspase-8 precursor, caspase-9and caspase-10. Among the oncogene/tumorsuppressor genes, ABL2 was down-regulated. Inaddition, some genes were up-regulated, includingmatrix metalloproteinse 2(MMP-2), MMP-16(MT3-MMP), SKY, CD9 and semaphorin V. A number of geneswere down-regulated, including neuroendocrine-dlg(NE-dig), retinoic acid receptor gamma and tumorsuppressor DCC colorectal. In general, The expressionof the cancer progression genes were up-regulated,while the expression of anti-cancer progression geneswero down-regulated.CONCLUSION: Investigation of these genes should helpto disclose the molecular mechanism of the onset,progression and prognosis of GC. Several genes arereported herein to be altered in GC for the first time.The quick and high-throughout method of profiling geneexpression by cDNA array provides us with an overviewof key factors that may involved in GC, and may aid thestudy of GC carcinogenesis and provide moleculartargets for diagnosis and therapy. The preciserelationship between the altered genes and gastriccarcinogenesis is a matter for further investigation.     

基因表达谱芯片在胰腺癌组织差异表达相关基因筛选中的应用

目的：探讨基因表达谱芯片技术筛选胰腺癌组织和癌旁正常组织基因表达谱差异的可行性。方法应用Agilent公司生产的包含27958条DNA的基因芯片检测4例胰腺癌患者胰腺癌组织和癌旁正常组织的基因表达谱,筛选差异表达基因,并用半定量RT-PCR法检测差异基因CD151、S100A4、TIMP-3和NME3表达情况。结果共筛选出46条基因表达谱差异基因,其中26条表达上调、20条表达下调。差异基因CD151、S100A4、TIMP-3和NME3的表达情况与基因表达谱芯片检测结果一致。结论基因表达谱芯片技术可以筛选出胰腺癌组织差异表达相关基因,为胰腺癌分子标志物研究提供了可靠依据。     

应用基因芯片技术研究甲状腺乳头状癌的基因表达

目的　应用基因芯片技术研究甲状腺乳头状癌 (PTC)和正常成人甲状腺组织基因的差异表达。方法　分别用Cy5和Cy3两种不同的荧光染料通过逆转录反应将PTC组和对照组甲状腺组织的mRNA分别标记成探针 ,并与载有一组靶基因的基因表达谱芯片进行杂交。通过扫描荧光强度 ,计算机软件分析 ,寻找两组差异表达基因 ,并用RT PCR、免疫组化对其中两条基因进行验证。结果　共有 65条差异表达基因 ,其中表达增加的有 48条 (2 .0倍以上 ) ,表达降低的有 17条 (0 .5倍以下 )。RT PCR、免疫组化结果与芯片扫描结果一致。结论　基因芯片是筛选PTC与正常成人甲状腺组织差异表达基因的有效方法。通过筛选所得差异基因提示 ,PTC的发病涉及细胞外基质、细胞因子、受体信号转导等多个方面。     

A bioinformatics analysis of differentially expressed genes associated with liver cancer

正Objective To investigate differentially expressed genes associated with liver cancer using bioinformatics methods,and to screen out molecular markers for early diagnosis of liver cancer and potential molecular targets for immunotherapy.Methods The microarray data associated with liver cancer were downloaded from Gene Expression Omnibus.JMP software was used for correlation analysis of GSE datasets,Limma program in R language     

应用基因芯片技术筛选大鼠再生肝中差异表达基因

目的应用基因芯片技术筛选大鼠再生肝中差异表达基因,为探讨急性肝功能衰竭的发病机制提供基础。方法雄性SD大鼠行95％肝部分切除术,用含1176个基因的大鼠尼龙膜微阵列筛选大鼠再生肝组织中差异表达的基因。RT—PCR随机验证若干差异表达基因在微阵列中的表达。结果再生肝组织有138个基因明显较对照组织表达高,它们主要是生长因子基因、核受体基因、核糖体蛋白基因、应急反应蛋白基因、细胞周期调节基因、神经递质基因等;下调基因共50个,主要为代谢酶基因、激素受体基因及表面抗原基因等。结论cDNA微阵列技术有助于研究急性肝功能衰竭的发病机制,并提供诊断和治疗的潜在靶点。     

急性病毒性心肌炎小鼠相关基因差异表达的研究

目的应用基因表达谱芯片筛选急性病毒性心肌炎相关基因,并对这些基因的功能进行初步分析。方法将8 464条小鼠PCR产物按微聚阵排列点样于化学涂层的载玻片上,制成基因芯片;用柯萨奇B3 (CVB3)病毒感染BALBc小鼠,在感染后的第4、8、21天,分别将正常和病毒性心肌炎心肌中mRNA逆转录,合成荧光分子(cy3／cy5)掺入的cDNA链制备表达谱探针,芯片杂交和严格洗片后,用ScanArray3000荧光扫描芯片荧光信号图像,利用计算机分析病毒性心肌炎心肌与正常心肌中丝氨酸苏氨酸磷酸化酶基因(PIM-3)、血管形成因子基因(Ang)-1、组织相容性基因-2的表达,并对获得的基因进行生物信息学分析。结果小鼠在CVB3感染后的第4、8、21天,心肌中分别发现了1 684、284、98条差异表达基因:PIM-3、Ang-1、组织相容性基因-2的表达被持续抑制。结论应用基因表达谱芯片可筛选出差异表达基因,PIM-3、Ang-1、组织相容性基因-2的差异表达可能与病毒性心肌炎发生和发展有关。     

自身免疫性肝炎小鼠模型差异表达基因的筛查及柴胡皂苷D对部分差异表达基因表达的影响

目的对自身免疫性肝炎(AIH)小鼠模型的差异表达基因进行基因芯片筛查,并观察柴胡皂苷D(SS-d)对部分差异表达基因表达的影响,探讨AIH的发病机制及SS-d对该病的治疗作用机制。方法健康、雌性SPF级C57BL/6小鼠40只[体质量(20±2)g],分为基因芯片组(n=8)和SS-d治疗组(n=32)。基因芯片组小鼠又分为正常对照组(n=4)和模型组(n=4),正常对照组常规饲养,模型组小鼠按15 mg/kg剂量给予尾静脉注射刀豆蛋白A(Con A),12 h后处死并提取肝组织,按Agilent芯片说明书进行差异表达基因的筛选,采用荧光定量PCR技术对部分差异表达基因进行验证。SS-d治疗组小鼠随机分为正常组(常规饲养)、模型组(按15 mg/kg剂量给予尾静脉注射Con A)、SS-d低剂量组和SS-d高剂量组(分别按2.5 mg/kg和5.0 mg/kg剂量给予腹腔注射SS-d预处理,8 h后按15 mg/kg剂量给予尾静脉注射Con A)(每组8只)。12 h后收集各组小鼠静脉血,ELISA法检测血清ALT、AST。无菌条件下提取小鼠肝组织,部分多聚甲醛固定后切片,并进行HE染色;部分肝组织用于提取RNA,采用荧光定量PCR技术检测部分差异表达基因(IFNγ、IL-4、IL-5、IL-13和IL-17)的mRNA水平变化。多组间比较采用单因素方差分析,进一步两两比较采用LSD-t法检验;两组间比较采用t检验。结果基因芯片组小鼠共筛查差异表达基因11512个,其中上调5189个,下调6323个,显著富集于138条信号通路;荧光定量PCR验证结果显示,与正常对照组比较,模型组小鼠IFNγmRNA和IL-17 mRNA的表达升高(P值均<0.01),而IL-4 mRNA、IL-5 mRNA和IL-13 mRNA的表达下调(P值均<0.01),与芯片筛查结果一致。在SS-d治疗组中,与正常对照组比较,模型组小鼠血清ALT、AST水平均升高(P值均<0.01);肝组织内可见大量淋巴细胞浸润;IFNγmRNA和IL-17 mRNA的表达水平明显升高(P值均<0.05),而IL-4 mRNA、IL-5 mRNA和IL-13 mRNA的表达水平明显降低(P值均<0.05)。与模型组比较,SS-d低剂量组和SS-d高剂量组小鼠血清ALT、AST水平均降低(P值均<0.05),肝组织内淋巴细胞浸润程度减轻;IFNγmRNA和IL-17 mRNA的表达水平均降低(P值均<0.05),IL-4 mRNA、IL-5 mRNA和IL-13 mRNA的表达水平均升高(P值均<0.05),上述基因的含量变化差异在SS-d高剂量组与SS-d低剂量组之间具有统计学意义(P<0.05)。结论AIH的发生发展系大量基因异常表达的共同作用结果。其中IFNγ、IL-4、IL-5、IL-13、IL-17与AIH的发病密切相关,同时也是SS-d发挥免疫调节及肝损伤保护作用的生物学靶点。     

Isolation of cDNA clones for differentially expressed genes of the human parasite Schistosoma mansoni.

Little is known about the mechanisms that control transformations during the life cycle of Schistosoma mansoni. To enable isolation of DNA sequences encoding developmentally regulated antigens a cDNA expression library in the vector lambda gt11 amp3 was constructed from adult mRNA and immunologically screened with sera from infected individuals. We report here on the properties of three recombinant clones that derive from developmentally regulated genes. Clone 10-3 encoded a beta-galactosidase fusion protein present in high abundance in infected Escherichia coli. Clones 7-2 and 8-2 also produced immunologically recognized proteins; however, the peptides did not appear to be beta-galactosidase fusion proteins. The expression of mRNAs hybridizing to these cDNAs was examined in the different stages of the parasite life cycle. Messenger RNA corresponding to clone 10-3, approximately equal to 1000 bases in length, was present in higher abundance in male worms than in females but was not detected in schistosome eggs. A 900-base mRNA hybridizing to clone 7-2 was observed in adult worms and eggs. Both clone 10-3 and clone 7-2 hybridized to smaller mRNAs in cercariae and freshly transformed schistosomula than in adult worms. Clone 8-2 contained tandem cDNA inserts. One cDNA hybridized to a 1700-base mRNA present in all stages, while the second hybridized to an 800-base mRNA specific to adult female worms.     

Identification of genes differentially expressed in mouse fetuses from streptozotocin-induced diabetic pregnancy by cDNA subtraction

Epidemiological studies have shown that the risks of fetal malformation such as neural tube defects increase in diabetic pregnancy. To explore the mechanism of fetal malformation induced by diabetes, cDNA subtraction using mouse embryos (E9.5) of diabetic dams and those of controls was performed to identify differentially expressed genes. The expression level of genes identified by cDNA subtraction was further verified by quantitative RT-PCR using E8.5 embryos, and differential expression of 4 genes, Brcc3, Commd3, Ddx1, and SET was confirmed. We also analyzed the expression level of neural tube defect-related genes, and found that Folbp1, EphrinA5 and Sox10 were differentially expressed. Altered expression of these genes mostly persisted throughout the later stages of the development (E10.5-14.5). Hierarchical clustering analysis showed correlation between expression levels of these genes, suggesting that these genes cooperatively play a role in embryonic development. Our results suggest that an altered gene expression profile in embryos underlies the development of congenital malformation in diabetic pregnancies.     

A comparison of aorta and vena cava medial message expression by cDNA array analysis identifies a set of 68 consistently differentially expressed genes, all in aortic media

We performed a systematic analysis of gene expression in arteries and veins by comparing message profiles of macaque aorta and vena cava media using a cDNA array containing 4048 known human genes, approximately 35% of currently named human genes (approximately 11,000). The data show extensive differences in RNA expression in artery versus vein media. Sixty-eight genes had consistent elevation in message expression by the aorta, but none were elevated in the vena cava. The most differentially expressed gene was regulator of G-protein signaling (RGS) 5, at an expression ratio of 46.5+/-12.6 (mean+/-SEM). The data set also contained 2 genes already known to be expressed in the aorta, elastin at 5.0+/-1.4, and the aortic preferentially expressed gene 1 (APEG-1) at 2.3+/-0.6. We chose to analyze RGS5 expression further because of its high level of differential expression in the aorta. Levels of RGS5 mRNA were confirmed by Northern analysis and in situ hybridization. A human tissue RNA dot blot showed that RGS5 message is highest in aorta, followed by small intestine, stomach, and then heart. Northern analysis confirmed that RGS5 expression in human aorta is higher than in any region of the heart. RGS5 is a G-protein signaling regulator of unknown specificity most homologous to RGS4, an inhibitory regulator of pressure-induced cardiac hypertrophy. The expression pattern of the 68 differential genes as a whole is a start toward identifying the molecular phenotypes of arteries and veins on a systematic basis.