In silico identification of breast cancer genes by combined multiple high throughput analyses

Publicly available human genomic sequence data provide an unprecedented opportunity for researchers to decode the functionality of human genome. Such information is extremely valuable in cancer prevention diagnosis and treatment. Cancer Genome Anatomy Project (CGAP) and Gene Expression Omnibus (GEO) are two bioinformatic infrastructures for studying functional genomics. The goal of this study is to explore the feasibility of incorporating the Internet-available bioinformatic databases to discover human breast cancer-related genes. Several tools including the Gene Finder, Virtual Northern (vNorthern) and SAGE digital gene expression displayer (DGED) were used to analyze differential gene expression between benign and malignant breast tissues. A pilot study was performed using both EST and SAGE vNorthern to analyze the expression of a panel of known genes, including high abundance genes beta-actin and G3PDH, low abundance genes BRCA1 and p53, tissue-specific genes CEA and PSA and two breast cancer-related genes Her2/neu and MUC1. We found a high expression of beta-actin and G3PDH and a low expression of BRCA1 and p53 across different types of tissues as well as a tissue-specific expression of CEA in colon and PSA in prostate. A further analysis of 30 known breast cancer-related genes in breast cancer tissues by vNorthern demonstrated a high expression of oncogenes and low expression of tumor suppressor genes. An open-end analysis of two pools of breast cancer and benign breast tissue libraries by SAGE DGED produced 53 differentially expressed genes according to the screening criteria of a >five-fold difference and p<0.01. Further analysis by EST vNorthern and virtual microarray analysis reduced the candidate genes to six, with four down-regulated genes, ANXA1, CAV1, KRT5 and MMP7, and two up-regulated genes, ERBB2 and G1P3 in breast cancer. These findings were validated by a real-time RT-PCR analysis in eight paired human breast cancer tissue samples. We conclude that the combined multiple high throughput analyses is an effective data mining strategy in cancer gene identification. This approach may improve the usage of public available genomic data through strategic data mining of high throughput analysis.     

中药“神经再生素”促神经生长过程中基因差异性表达的初步研究

为了探索中药“神经再生素”促神经生长过程中基因水平的变化。本实验采用 dd-PCR方法 ,从体外培养背根神经节细胞加药组和不加药组中获得两者的差异表达片段 ,并经反杂交筛选、克隆测序、DNA序列检索分析、Northern验证。结果表明 ,差异显示共获得 8个差异条带 ,一个为下调基因 ,其余为上调基因 ,其中 2个 c DNA序列与 RRAJ5 16 1基因 (增殖相关基因 )、AF196 3 15基因 (锌指样蛋白 DDP2 ) 10 0 %同源 ,2个 c DNA序列与 AK0 0 175 7基因、STA5 SRR基因 (t RNA合成酶 )部分同源。结论是中药“神经再生素”在促神经生长过程中 ,对神经元基因的选择性表达起着重要的调控作用。     

胃癌高表达cDNA片段W41的克隆及组织表达谱分析

目的：从人胃癌组织中克隆新的相关易感基因。方法：利用cDNA末端快速扩增PCR技术得到了扩增片段，将其克隆、核苷酸序列分析，并将序列在GenBank进行同源性比较。利用Northern杂交、多组织Northern及基因表达系列分析了所得基因片段的组织表达谱。结果：获得1条533bp带有poly(A)尾的cDNA片段，可见加尾信号AATAAA，与GenBank基因数据库同源比较，该序列未见与任何已知基因同源，登录GenBank(登录号为AF325202）。该序列在胃癌组织的表达强度高于对应正常组织，多组织Northern及基因表达系列分析表明该序列在多种肿瘤组织中高表达，在正常组织中表达减弱。结论：得到了1条与胃癌可能相关的新的cDNA序列。     

Identification of testis development and spermatogenesis-related genes in human and mouse testes using cDNA arrays

We have constructed cDNA microarrays from the human testis large insert cDNA library, containing 9216 genes, together with several housekeeping genes. The cDNA microarrays were used to identify gene expression differences between human fetal and adult testes. Of >8700 hybridized clones, 731 exhibited significant differential expression characteristics. About 7500 genes were identified when the same cDNA microarrays were used for hybridization with cDNA probes from mouse testis, with 256 genes having significant differential expression between the age of 1-4 weeks. Among these genes, 101 were identified as critically related to testis development and possibly to spermatogenesis since they were found in both human and mouse testes, and expressed differentially at different stages of testis development. Of the 101 development-related genes, 59 full-length cDNAs have been sequenced previously, while the full-length cDNAs of the other 42 genes have not been published. We have obtained 11 full-length sequences of the 42 genes and deposited them in the GenBank. The conserved testis development-related genes found in both human and mouse testes may include genes that are likely to be involved in testicular functions, especially spermatogenesis, thus providing a basis for further functional characterization of the genes in mouse models.     

Genome‐wide association study of shared liability to anxiety disorders in Army STARRS

Anxiety disorders (ANX), namely generalized anxiety, panic disorder, and phobias, are common, etiologically complex syndromes that show increasing prevalence and comorbidity throughout adolescence and beyond. Few genome‐wide association studies (GWAS) examining ANX risk have been published and almost exclusively in individuals of European ancestry. In this study, we phenotyped participants from the Army Study To Assess Risk and Resilience in Servicemembers (STARRS) to approximate DSM‐based ANX diagnoses. We factor‐analyzed those to create a single dimensional anxiety score for each subject. GWAS were conducted using that score within each of three ancestral groups (EUR, AFR, LAT) and then meta‐analyzed across ancestries (N_Total = 16,510). We sought to (a) replicate prior ANX GWAS findings in ANGST; (b) determine whether results extended to other ancestry groups; and (c) meta‐analyze with ANGST for increased power to identify novel susceptibility loci. No reliable genome‐wide significant SNP associations were detected in STARRS. However, SNPs within the CAMKMT gene located in region 2p21 associated with shared ANX risk in ANGST were replicated in EUR soldiers but not other ancestry groups. Combining EUR STARRS and ANGST (N = 28,950) yielded a more robust 2p21 association signal (p = 9.08x10^?11). Gene‐based analyses supported three genes within 2p21 and LBX1 on chromosome 10. More powerful ANX genetic studies will be required to identify further loci.     

人B细胞活化相关基因BC-1514全长cDNA的克隆与原核表达

目的 克隆与B细胞活化相关的新基因及其原核表达。方法 采用差异显示反转录PCR（DDRT-PCR）技术对人扁桃体活化和静止B细胞mRNA的差异表达进行分析。差异显示的片段经过Northern杂交验证后,作为探针进行入活化B细胞cDNA文库的筛选,将所获得的阳性克隆的编码区经PCR扩增后克隆到原核表达载体pGEX-5X-1中,重组质粒经酶切,测序鉴定后转化大肠杆菌BL-21,以IPTG诱导表达融合蛋白。结果 以在活化B细胞高表达的EST32为探针,经3轮筛选人活化B细胞文库获得一个新的全长为1514bp的cDNA克隆（命名为BC-1514）,重组的BC-1514蛋白可在E.coli中以融合蛋白的形式有效表达,其表达量约占细菌总蛋白量的14.3%左右,BC-1514cDNA的GenBank的登录号为AF304442。结论 获得了1条新的与B细胞活化相关的cDNA克隆并在E.coliBL-21中得到了有效表达。     

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。     

慢性乙型肝炎患者外周血单个核细胞基因表达谱的研究

目的 分析慢性乙型肝炎患者外周血单个核细胞差异表达基因，探索慢性乙型肝炎形成的分子机制。方法 应用含14000条人体cDNA的微阵列芯片和来自外周血单个核细胞的标记cDNA，分析了10例慢性乙型肝炎患者和10例健康人基因表达谱。通过应用GenePix 4000B扫描仪和ImaGene3．0分析软件比较cy5标记的慢性乙型肝炎来源cDNA与Cy3标记的健康人来源cDNA的杂交结果，获得个体基因的相对表达比值。结果 在分析的14000条基因中，差异表达的基因有92条，占0．66％。其中51条基因表达水平显著上调，41条基因表达水平显著下调。这些差异表达的基因主要为细胞信号转导，细胞周期和代谢，凋亡及炎症相关类基因。结论 在乙型肝炎病毒致慢性乙型肝炎过程中，涉及到了众多基因的差异表达，为进一步阐明慢性乙型肝炎形成的分子机制提供基础。     

Epsin3在结直肠癌中的差异表达及生物信息学分析

目的 探讨介导内吞作用的衔接蛋白epsin 3（EPN3）在结直肠癌中的表达及意义,为深入研究EPN3的调控模式提供实验依据。 方法 分别运用GEPIA和GEDS数据库分析EPN3在结直肠癌组织和细胞中的表达情况,并通过SMART和cBioPortal数据库分析EPN3基因甲基化和拷贝数变异与其表达水平的关系;利用Metascape数据库对EPN3相关的共表达基因集进行GO富集和通路分析;运用BioPlex蛋白互作数据库分析EPN3在HCT116细胞中的蛋白作用网络。为了对EPN3进一步验证,我们收集13对结直肠癌癌旁组织和癌组织标本,用Real-time PCR检测EPN3 mRNA表达;并通过敲减EPN3观察其对肿瘤细胞增殖、集落形成和迁移能力的影响。 结果 GEPIA、GEDS、SMART和cBioPortal等数据库分析显示,EPN3在结直肠肿瘤组织中高表达(P<0.01)。其表达水平与甲基化和拷贝数变异相关。EPN3相关基因的富集结果显示主要与细胞黏附相关。EPN3与UBB、CCDC130、TNFAIP1、PHGDH、EPN2等构成的蛋白相对作用网络与蛋白泛素化有关。Real-time PCR结果显示,EPN3在癌组织中高表达(P<0.05)。通过沉默EPN3可以抑制HCT116和HT29细胞的增殖、集落形成和迁移能力。 结论 EPN3在结直肠癌组织中高表达,且与细胞黏附和蛋白泛素化等生物学过程有关,敲低EPN3可抑制结直肠癌细胞系HCT116和HT29的增殖、集落形成和迁移等过程。     

AAC-11 overexpression induces invasion and protects cervical cancer cells from apoptosis

To identify the genes involved in cervical carcinogenesis, we applied the mRNA differential display (DD) method to analyze normal cervical tissue, cervical cancer, metastatic lymph node, and cervical cancer cell line. We cloned a 491-bp cDNA fragment, CC231, which was present in metastatic tissue and cervical cancer cell line, but absent in normal cervical and cervical cancer tissues. The 491 bp cDNA fragment has 98% homology to the previously published sequence, AAC-11 (antiapoptosis clone 11). The levels of AAC-11 mRNA expressions in nine normal cervical and nine primary cervical cancer tissues were low. Its expression was higher in three metastatic tissues and five cervical cancer cell lines (HeLa, CaSki, SiHa, CUMC-3, and CUMC-6). Invasion of matrigel and adhesion to laminin by AAC-11 transfected CUMC-6 cells were increased by approximately 2-fold and 4-fold, respectively. Northern blot analysis showed that matrix metalloproteinase (MMP)-2 and membrane type 1 MMP (MT1-MMP) genes were found to be expressed in high levels in AAC-11-transfected cancer cells. But MMP-2 and MT1-MMP were not expressed in cells transfected with vector alone or wild-type cells. AAC-11-transfected cells expressed an elevated level of MMP-2 protein as assessed by immunoblotting. On the contrary, tissue inhibitor of MMP (TIMP-2) expression was detectable in cells transfected with vector alone or wild-type cells, respectively. Its expression was undetectable in AAC-11 transfected cells. In cervical cancer cells transfected with AAC-11, the expression of beta-catenin was up-regulated. These suggest that overexpressions of MMP-2 and MT1-MMP, loss of TIMP-2 expression, and up-regulation of beta-catenin by AAC-11 transfection may contribute to the development of cervical cancer invasion. AAC-11 gene transfection increased cervical cancer cell colonization. The effect of AAC-11 on cultured cervical cancer cells was associated with antiapoptotic process. Approximately 50% of the AAC-11 transfected cells in serum-free medium died after 2 weeks, compared to 1 week for vector alone or wild-type cells. These results suggest that AAC-11 may serve as a candidate metastasis-related and apoptosis-inhibiting gene in human cervical cancer.     

Age-related changes of gene expression in mouse kidney: fluorescence differential display--PCR analyses

We used a fluorescence differential display--PCR (FDD-PCR) technique to analyze the genes expressed in mouse kidneys collected at nine different developmental stages ranging from 3 days to 15 months after birth. We found ten genes that were age-dependent and differentially-expressed in the kidneys during our experimental period. We confirmed by comparative RT-PCR that of the ten cDNAs, seven showed reproducible age-dependent expression. Four of the nucleotide sequences of these cDNA clones, had high homology with known genes (fibronectin, soluble guanylyl cyclase alpha-1 subunit, cytosolic aldehyde dehydrogenase and mitochondrial DNA), and three with expressed sequence tags of unknown genes. The FDD-PCR method was very useful for detecting new age-related genes expressed differentially in the mouse kidney.     

The pattern of differentially expressed genes in biliary atresia

Biliary atresia is a progressive obliterative cholangiopathy, but the etiology of this disorder remains uncertain. Identifying genes specifically expressed in biliary atresia and analyzing the pattern of expression may lead to a better understanding of the pathogenesis. Liver tissues were taken from a recipient with biliary atresia and a normal donor during liver transplantation. Total RNA was extracted from each sample and reversely transcribed to cDNA. Then radiolabeled cDNA probe pools were made by random primed DNA labeling method and used for screening of differentially expressed genes by hybridizing with expressed sequence tags (EST) dot blot panel. Northern blot hybridization was done to confirm that these genes are also differentially expressed in other liver tissues. Among 1730 EST clones, 26 cDNA clones were significantly overexpressed in biliary cirrhosis, while 2 clones were significantly decreased in biliary atresia. By Northern blot hybridization, the results of tissue inhibitor of metalloproteinase (TIMP)-1 and IGFBP-2 were well correlated with differential EST screening (DES). This study identified the pattern of differentially expressed genes in the biliary cirrhosis due to biliary atresia using DES technique.     

SLE及IDDM患者外周血单个核细胞中基因表达差异的研究

目的 :了解系统性红斑狼疮 (Systemiclupuserythematosus,SLE)和胰岛素依赖型糖尿病 (insulindependentdiabetesmellitusdisease,IDDM)外周血单个核细胞 (PBMC)的基因表达概况 ,为探讨这些基因表达的差异与该 2种疾病的关系奠定基础。方法 :以分别来自SLE和IDDM患者的PBMCpolyA RNA为模板逆转录合成cDNA表达探针 ,与AtlascDNA表达阵列膜进行差异杂交。结果 :放射自显影结果显示在SLE疾病所分析的 1176种已知基因中 ,有表达差异的 376个 ,其中表达上调差异率大于 3的 8个 ,表达下调差异率大于 6的 6个 ;在IDDM疾病所分析的 1176种已知基因中 ,有表达差异的 5 5 8个 ,其中表达上调差异率大于 6的 13个 ,表达下调差异率大于 6的 3个。与细胞的分化增殖、粘附与信号转导、凋亡、转录与调控及DNA损伤修复等相关的基因表达水平发生了明显的改变。结论 :AtlascDNA表达阵列差异杂交分析为初步了解SLE及IDDN患者PBMC的基因表达概况 ,进而了解基因表达差异在疾病发生发展中的作用提供了一个较好的方法。     

Interferon-inducible gene expression in chimpanzee liver infected with hepatitis C virus.

The molecular host response to hepatitis C virus (HCV) infection was examined by isolation of HCV-induced genes from a cDNA library constructed from chimpanzee liver during the acute phase of hepatitis C. Two cDNA clones, 130-7 and 130-51, were obtained by differential hybridization with cDNA probes prepared from poly(A)+ RNAs of infected and uninfected livers. Northern blot analysis revealed that the 130-7 and 130-51 cDNAs were expressed as 1.5- and 1.0-kb products, respectively, in chimpanzee liver and that their induction rates of the two were 20 and 4, respectively. Nucleotide sequence analyses of these cDNA inserts showed that the sequence of cDNA 130-7 was that of a class I major histocompatibility antigen and that the sequence of cDNA 130-51 was 98% homologous with a human interferon-inducible mRNA. These results suggest that HCV infection may actively induce interferon, which in turn induces the expressions of these interferon-inducible genes. Furthermore, the high expression of HLA class I antigen in the acute phase of hepatitis C suggests that liver cell injury in HCV infection may be mediated by cytotoxic T cells that recognize viral antigen in association with HLA class I antigen.     

胃癌基因表达谱的cDNA微阵列与聚类分析

目的 分析胃癌与非肿瘤胃组织中基因表达特征，探讨其生物学意义。方法 提取18例进展期胃癌患者术前未行治疗的新鲜肿瘤和非肿瘤胃组织总RNA，逆转录标记cy5和cy3制备cDNA探针，与148个基因组成的cDNA微阵列杂交，应用平均联接等级聚类和微阵列数据显著差异分析(significance analysis of microarrays，SAM)方法分析146个符合入选条件基因的实验数据。结果 胃癌与非肿瘤胃组织各被聚为一类，胃癌和非肿瘤胃组织又分别聚为两个亚类。基因在两种组织表达有3个特征，明显基因表达差异表现在特征B和特征C．特征B基因在胃癌组织呈低表达或不表达，特征C基因在胃癌组织呈高表达。在特征A，T2-S2亚类与T1和T2-S1亚类的基因表达存在差异性，然而13例患者的配对胃癌与非肿瘤胃组织有相似基因表达。结合SAM分析，从特征B和特征C分别检出19个和12个在两种组织间呈差异性表达基因。结论 cDNA微阵列实验结果客观地反映了胃癌和非肿瘤胃组织的基因表达特征，可以将胃癌与非肿瘤胃组织各聚为一类．胃癌组织之间基因表达既有相似性，又有异质性，反映了胃癌基因表达变异的复杂性．应用cDNA微阵列技术研究胃癌基因差异性表达特征，有助于阐明胃癌发生、发展的分子基础，为胃癌早期诊断和预后评估的生物标记物研究提供科学依据．