Analysis of differentially expressed genes in human rectal carcinoma using suppression subtractive hybridization

The existence and treatment of rectal cancer are important for the function of defecation and the quality of life. However, the precise mechanisms of rectal carcinogenesis remain unclear. To screen the overexpressed gene in rectal carcinoma, we performed suppressive subtractive hybridization (SSH) on rectal carcinoma cells and the corresponding normal rectal cells. A total of 64 recombinant clones were subjected to DNA sequencing analysis, and 9 known genes were found to overexpressed in the tumors compared with those of the normal tissues. The genes are ST3 beta-galactoside alpha-2,3-sialyltransferase (ST3GAL5), interferon-induced transmembrane protein 3 (IFITM3), platelet-derived growth factor A–associated protein 1 (PDAP1), AlkB alkylating repair homolog 3 (ALKBH3), nucleoside diphosphate linked moiety X (Nudix)-type motif 14 (NUDT14), calponin 2 (CNN2), mitogen-activated protein kinase 14 (MAPK14), aconitase 1 (ACO1), and selenophosphate synthetase 1 (SEPHS1). The expression profiles of the genes were further confirmed in rectal carcinoma cells and the corresponding normal rectal cells of 12 patients by quantitative real-time RT–PCR. Our results revealed that ST3GAL5, IFITM3, PDAP1, ALKBH3, NUDT14, CNN2, MAPK14, ACO1, and SEPHS1 may be involved in rectal carcinogenesis.     

Improved subtractive suppression hybridization combined with high density cDNA array screening identifies differentially expressed viral and cellular genes

Suppression subtractive hybridization (SSH) combines normalization and suppression PCR effect step in a single cycle to isolate differentially expressed genes in two cDNA samples. The PCR suppression effect is mediated by long inverted terminal repeats. The efficiency of the restriction enzyme digestion and the adapter ligation are crucial in the success of the SSH. We modified the original SSH protocol in order to improve the efficiency of the subtraction. A magnetic bead based separation step has been included after the ligation step, to purify the successfully ligated fraction of the tester. EBV(NEO) infected Akata(-) Burkitt's lymphoma cell line was compared with the EBV(-) Akata(-) cell line to isolate differentially expressed genes with the improved SSH protocol. Some 44 cDNA clones that showed the greatest differences in expression have been sequenced. Of them, 20 showed more than 3-fold difference in expression. Seven of the 20 genes were EBV genes. To quantitate the expression levels, high density nylon cDNA array hybridization was optimized. Statistical analysis of the data revealed that the spotting of the arrayer is exceptionally reproducible, which makes the comparison of the hybridization of parallel filters possible.     

应用抑制消减杂交技术构建结核分枝杆菌差异表达基因消减cDNA文库

目的:构建结核分枝杆菌H37Rv与H37Ra的差异表达基因消减文库,分离结核分枝杆菌差异表达cDNA片段.方法:利用抑制性消减杂交技术分析结核分枝杆菌强毒株H37Rv和弱毒株H37Ra的基因组mRNA的表达差异,并进行两轮消减杂交和两次PCR,将第二次PCR产物与pGEM-T载体相连,电击转化大肠杆菌E.coff DH5α进行文库扩增和蓝白斑筛选,RT-PCR承鉴定差异表达文库.结果:以结核分枝杆菌强毒株H37Rv的cDNA为检测子的正相杂交和以弱毒株H37Ra的cDNA为检测子的反相杂交各自高表达或特异性表达的片段都得到选择性扩增,成功构建了差异表达cDNA文库 A库和B库.所长出的菌落中90%为白色克隆,其中单一条带的克隆占75%和80%,片段大小集中在100～800 bp之间.结论:利用SSH技术成功构建了结核分枝杆菌强毒株H37Rv和弱毒株H37Ra差异表达基因消减cDNA文库,该消减文库的建立为进一步筛选、克隆这两种菌株之间差异表达的新基因奠定了基础.     

Analysis of differentially expressed genes in the precocious line of Eimeria maxima and its parent strain using suppression subtractive hybridization and cDNA microarrays

The precocious line of Eimeria spp., obtained by repeated passages of oocysts initially collected from feces of previously infected chickens, has unique phenotypes and plays an important role in immunizing chickens against coccidiosis. However, the genetic basis of precocious phenotype in Eimeria is still poorly understood. To investigate gene expression changes in sporulated oocysts between the precocious line of E. maxima and its parent strain, subtractive cDNA libraries were constructed by suppression subtractive hybridization (SSH). A total of 3,164 cDNA fragments were selected from the SSH cDNA libraries to fabricate cDNA microarrays and further identify the differentially expressed genes. The credibility of the microarray data was verified by real-time PCR. A total of 360 valid expressed sequence tags (ESTs) were obtained, which represented 32 unique sequences. Twenty-one genes were validated as downregulated and 11 genes as upregulated in the precocious line. Homology searching of the public sequence database showed that six genes encoded proteins homologous with previously reported proteins, including rhomboid-like protein and transhydrogenase of E. tenella, serpin, and cation-transporting ATPase of E. acervulina, a heat-shock protein of E. maxima, and a conserved hypothetical protein of Toxoplasma gondii. Thus, the remaining 26 ESTs have not been previously reported. Further characterization of these differentially expressed genes will be useful in understanding the genetic basis for the precocious phenotype in Eimeria spp.     

抑制性消减杂交筛选不稳定性心绞痛相关基因

目的:筛选并鉴定不稳定性心绞痛淋巴细胞相关差异表达基因,探讨不稳定性心绞痛发病的分子机理。方法:应用抑制性消减杂交技术(SSH)和斑点杂交技术,筛选不稳定性心绞痛组和稳定性心绞痛组淋巴细胞差异表达基因,应用反向Northern杂交和RNA狭线杂交技术,鉴定并获得阳性序列表达标签(EST),将获得EST测序,并进行同源性比较。结果:在不稳定性心绞痛组获得3个阳性EST,在稳定性心绞痛组获得1个阳性EST,全部为已知基因的部分序列。结论:所筛选的EST与不稳定性心绞痛的患者动脉粥样硬化斑块不稳定有关。     

应用抑制性消减杂交技术研究哮喘发作外周血嗜酸细胞与细胞粘附及免疫调节相关基因的差异表达

目的：研究哮喘发作时外周血嗜酸细胞(EOS)与细胞粘附及免疫调节相关基因的差异表达。 方法:利用Percoll密度梯度离心分离哮喘患者发作时与治疗缓解外周血嗜酸性粒细胞，提取总RNA，并利用Super SMART cDNA Synthesis技术合成cDNA第1链及优化扩增第2链。按照SSH常规方法构建cDNA消减文库，筛选阳性克隆并加以鉴定以得到带有差异表达的基因克隆。 结果:成功构建具有高消减效率的哮喘发作患者外周血EOS　cDNA文库，筛选鉴定后确认15个差异表达基因，测序并同源性比对分别为夏科-莱登结晶蛋白（CLC protein, galectin-10）、假定mRNA前剪接调节子female-lethal(2D)［putative pre-mRNA splicing regulator female-lethal(2D)］、水通道蛋白9（AQP-9）、IL-8、slingshot磷酸酶(SSH-2L)、蛋白磷酸酶1催化亚基β亚型（PP1CB）、RNA解旋酶HELZ、β2-微球蛋白（β2-MG）及一个线粒体相关基因。 结论:这些基因的差异表达证明了EOS的趋化、迁移、粘附及免疫调节功能参与了哮喘病理生理调节，对这些途径的干预可能为未来哮喘靶向性治疗提供依据。     

应用抑制性消减杂交技术鉴定肿瘤转移抑制相关基因

目的 克隆与肿瘤转移抑制相关的基因，探讨成骨肉瘤转移的分子机理。方法 采用抑制性消减杂交技术构建了人成骨肉瘤低转移细胞株SOSP－9607的消减文库，对部分克隆进行了测序和同源性分析，用Northern杂交及后转录PCR技术证实了克隆的表达情况。结果 在低转移细胞株SOSP－9607中高表达的克隆中有2个克隆与人端粒结合因子2（telomeric repeat binding factor 2,TERF2)同源。Northern杂交及反转录PCR证实这个基因只在低转移细胞中表达，而在高转移人成骨肉瘤细胞株SOSP－M和裸鼠肺转移结节中均未表达。结论 TERF2可能在维持肿瘤细胞自身相对稳定、抑制骨肉瘤演进中起重要作用。     

Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization.

Suppression polymerase chain reaction-based subtractive hybridization was used to identify genes that are expressed during Xenopus laevis hindlimb regeneration. Subtractions were done by using RNAs extracted from the regeneration-competent stage (stage 53) and regeneration-incompetent stage (stage 59) of limb development. Forward and reverse subtractions were done between stage 53 7-day blastema and stage 53 contralateral limb (competent stage), stage 59 7-day pseudoblastema and stage 59 contralateral limb (incompetent stage), and stage 53 7-day blastema and stage 59 7-day pseudoblastema. Several thousand clones were analyzed from the various subtracted libraries, either by random selection and sequencing (1,920) or by screening subtracted cDNA clones (6,150), arrayed on nylon membranes, with tissue-specific probes. Several hundred clones were identified from the array screens whose expression levels were at least twofold higher in experimental tissue vs. control tissue (e.g., blastema vs. limb) and selected for sequencing. In addition, primers were designed to assay several of the randomly selected clones and used to assess the level of expression of these genes during regeneration and normal limb development. Approximately half of the selected clones were differentially expressed, as expected, including several that demonstrate blastema-specific enhancement of expression. Three distinct categories of expression were identified in our screens: (1) clones that are expressed in both regeneration-competent blastemas and -incompetent pseudoblastemas, (2) clones that are expressed at highest levels in regeneration-competent blastemas, and (3) clones that are expressed at highest levels in regeneration-incompetent pseudoblastemas. Characterizing the role of each of these three categories of genes will be important in furthering our understanding of the process of tissue regeneration.     

Identification of differentially expressed genes in the denervated rat hippocampus by cDNA arrays

To elucidate the molecular mechanism underlying the physiological responses to injury in the central nervous system, gene expression profiles in rodent hippocampus following perforant path transection were investigated using cDNA array hybridization. Of the 8000 arrayed clones, 47 exhibited differential expression by >3-fold difference in the denervated hippocampus from control, with 15 up-regulated and 22 down-regulated. They can be functionally assigned into several classes, among which the most prominent are those coding proteins involved in macromolecules synthesis and processing. Northern blot analysis verified the validation of the aforementioned array data. These results throw some new light on the physiological responses of the hippocampus to entorhinal deafferentation at molecular level.     

D-半乳糖导致小鼠海马基因表达谱变化

本实验采用cDNA芯片研究D-半乳糖皮下注射小鼠海马的基因表达变化。小鼠皮下注射D-半乳糖[50m∥(kg．d)]60d造模，Morris水迷宫测试小鼠行为，分别提取模型组和对照组海马组织总RNA，掺入荧光分子Cy3和Cy5，经逆转录合成cDNA荧光探针与4000点小鼠cDNA基因芯片杂交。结果显示，在4000条待研究的基因中，两组小鼠海马间存在2倍表达差异的有76条，其中上调26条，下调50条。经分析，模型组基因表达谱与老年性痴呆(AD)相关基因表达谱在氧应激、能量代谢相关基因等方面有相似之处。提示D-半乳糖小鼠模型有可能作为拟AD病理模型。     

放射治疗后宫颈癌组织内差异表达基因鉴定

目的 研究放射治疗对宫颈癌组织基因表达的影响,探讨差异表达基因对放射治疗敏感及在抗拒中的作用.方法 患者接受相同的放疗模式:全盆腔外照射总剂量45戈瑞(Gy),共25次(45 Gy/25 f),腔内近距离内照射每次剂量5～6 Gy,共治疗5～6次.分别在近距离放射治疗前、近距离放射治疗中、近距离放射治疗结束时留取标本....     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

目的 筛选新疆地区结核分枝杆菌临床分离株与国际标准株H37Rv之间的差异基因,初步分析这些基因的功能.方法 利用抑制性消减杂交技术,通过两轮两相杂交,驱赶相同基因富集差异基因.结果 正相抑制性消减杂交一共获得6条新疆地区临床分离株中存在的差异基因,虽然这些基因在H37Rv基因组中不存在,但与国际标准临床株CDC1551以及复合群国际标准株KMS中的对应基因高度同源,分别与编码多萜醇磷酸甘露糖基转移酶Ⅱ、单加氧酶黄素结合蛋白、酰基转移酶蛋白、染色体复制起始密码子、脂酰基载体蛋白以及5'-磷酸吡哆胺氧化酶的基因有关.结论 新疆地区结核分枝杆菌临床分离株与国际标准株H37Rv之间存在差异基因,这些差异基因的功能可能与已知同源基因的功能相似:增强细菌胞壁蛋白的吸附能力、抵抗氮氧合酶消化、提高乙酰基辅酶A的合成能力、调控复制起始密码子、合成胞壁脂酰基载脂蛋白和促进5'-磷酸吡哆胺氧化酶代谢.     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

Objective To screen differential Mycobacterium tuberculosis genes between Xinjiang clinical strains and H37Rv by suppression subtractive hybridization( SSH), and to analyze the function of these specifically pathopoiesis genes. Methods Both M. tuberculosis Xinjiang clinical strains and H37Rv as tester and driver each other, most identical genome was drived whereas some distinctive genes was re-mained and enriched by utilization SSH technique. Meanwhile through inserting differential genes to E. coli all of sequences that we have cloned were determined by BLAST in GenBank. The function of differential genes between M. tuberculosis H37Rv and Xinjiang clinical strains were analyzed. Results We cloned and analyzed six different DNA fragments that only existed in Xinjiang clinical strains. One is the fragment of a gene ceding monooxygenase, flavin-binding family identified by Glimmer2. One fragment belongs to acyl-transferase family protein. One for aminotransferase, class Ⅱ, acyl carrier protein. One fragment belongs to chromosomal replication initiator protein DNA and one for M. tuberculosis paralogous family 11-pyridoxamine 5'-phosphate oxidase-related. Meanwhile, we cloned ten DNA fragments only in H37Rv. Conclusion SSH technique can efficiently screen differential genes in M. tuberculosis in Xinjiang clinical strains. They are possible key genes that M. tuberculosis survive and fortify virulence in mal-environment as same as their ho-mogenic genes, such as enhanced adsorbability in wall-held protein, counteracted digestion by nitro-oxygen-ase, elevated composition capability in the acyhransferase, control chromosomal replication initiator protein, synthesized aminotransferase acyl cartier protein and pyridoxamine 5'-phosphate oxidase.     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

Objective To screen differential Mycobacterium tuberculosis genes between Xinjiang clinical strains and H37Rv by suppression subtractive hybridization( SSH), and to analyze the function of these specifically pathopoiesis genes. Methods Both M. tuberculosis Xinjiang clinical strains and H37Rv as tester and driver each other, most identical genome was drived whereas some distinctive genes was re-mained and enriched by utilization SSH technique. Meanwhile through inserting differential genes to E. coli all of sequences that we have cloned were determined by BLAST in GenBank. The function of differential genes between M. tuberculosis H37Rv and Xinjiang clinical strains were analyzed. Results We cloned and analyzed six different DNA fragments that only existed in Xinjiang clinical strains. One is the fragment of a gene ceding monooxygenase, flavin-binding family identified by Glimmer2. One fragment belongs to acyl-transferase family protein. One for aminotransferase, class Ⅱ, acyl carrier protein. One fragment belongs to chromosomal replication initiator protein DNA and one for M. tuberculosis paralogous family 11-pyridoxamine 5'-phosphate oxidase-related. Meanwhile, we cloned ten DNA fragments only in H37Rv. Conclusion SSH technique can efficiently screen differential genes in M. tuberculosis in Xinjiang clinical strains. They are possible key genes that M. tuberculosis survive and fortify virulence in mal-environment as same as their ho-mogenic genes, such as enhanced adsorbability in wall-held protein, counteracted digestion by nitro-oxygen-ase, elevated composition capability in the acyhransferase, control chromosomal replication initiator protein, synthesized aminotransferase acyl cartier protein and pyridoxamine 5'-phosphate oxidase.     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

Objective To screen differential Mycobacterium tuberculosis genes between Xinjiang clinical strains and H37Rv by suppression subtractive hybridization( SSH), and to analyze the function of these specifically pathopoiesis genes. Methods Both M. tuberculosis Xinjiang clinical strains and H37Rv as tester and driver each other, most identical genome was drived whereas some distinctive genes was re-mained and enriched by utilization SSH technique. Meanwhile through inserting differential genes to E. coli all of sequences that we have cloned were determined by BLAST in GenBank. The function of differential genes between M. tuberculosis H37Rv and Xinjiang clinical strains were analyzed. Results We cloned and analyzed six different DNA fragments that only existed in Xinjiang clinical strains. One is the fragment of a gene ceding monooxygenase, flavin-binding family identified by Glimmer2. One fragment belongs to acyl-transferase family protein. One for aminotransferase, class Ⅱ, acyl carrier protein. One fragment belongs to chromosomal replication initiator protein DNA and one for M. tuberculosis paralogous family 11-pyridoxamine 5'-phosphate oxidase-related. Meanwhile, we cloned ten DNA fragments only in H37Rv. Conclusion SSH technique can efficiently screen differential genes in M. tuberculosis in Xinjiang clinical strains. They are possible key genes that M. tuberculosis survive and fortify virulence in mal-environment as same as their ho-mogenic genes, such as enhanced adsorbability in wall-held protein, counteracted digestion by nitro-oxygen-ase, elevated composition capability in the acyhransferase, control chromosomal replication initiator protein, synthesized aminotransferase acyl cartier protein and pyridoxamine 5'-phosphate oxidase.     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

Objective To screen differential Mycobacterium tuberculosis genes between Xinjiang clinical strains and H37Rv by suppression subtractive hybridization( SSH), and to analyze the function of these specifically pathopoiesis genes. Methods Both M. tuberculosis Xinjiang clinical strains and H37Rv as tester and driver each other, most identical genome was drived whereas some distinctive genes was re-mained and enriched by utilization SSH technique. Meanwhile through inserting differential genes to E. coli all of sequences that we have cloned were determined by BLAST in GenBank. The function of differential genes between M. tuberculosis H37Rv and Xinjiang clinical strains were analyzed. Results We cloned and analyzed six different DNA fragments that only existed in Xinjiang clinical strains. One is the fragment of a gene ceding monooxygenase, flavin-binding family identified by Glimmer2. One fragment belongs to acyl-transferase family protein. One for aminotransferase, class Ⅱ, acyl carrier protein. One fragment belongs to chromosomal replication initiator protein DNA and one for M. tuberculosis paralogous family 11-pyridoxamine 5'-phosphate oxidase-related. Meanwhile, we cloned ten DNA fragments only in H37Rv. Conclusion SSH technique can efficiently screen differential genes in M. tuberculosis in Xinjiang clinical strains. They are possible key genes that M. tuberculosis survive and fortify virulence in mal-environment as same as their ho-mogenic genes, such as enhanced adsorbability in wall-held protein, counteracted digestion by nitro-oxygen-ase, elevated composition capability in the acyhransferase, control chromosomal replication initiator protein, synthesized aminotransferase acyl cartier protein and pyridoxamine 5'-phosphate oxidase.