胃癌差异表达基因在染色体上的定位及其功能分析

利用标准化的Affymetrix公司生产的U133A基因芯片检测胃癌（T）与切缘正常胃黏膜（C）基因表达谱差异,并利用生物信息学方法对检测结果进行差异基因在染色体定位和功能分析。结果表明：胃癌与正常胃黏膜比较差异8倍以上共有270个基因,其中表达上调[信号比的对数值（SLR）≥3]有157个,表达下调（SLR≤-3）有113个。从表达差异的基因在染色体定位分析,发现除4个基因未知其定位外,其余所有差异表达基因散在分布和各条染色体上,但以1号染色体为最多,有26个（占9．8％）,其次是11和19号染色体上分别有24个（各占9．1％）。而差异表达的基因发生在染色体短臂（q）上有173个（占65％）。从表达差异的基因功能分类看,属于酶和酶调控子基因最多（67个,24．8占％）,其次是信号传导基因（43个,占15．9％）,第3类是核酸结合基因（17个,占6．3％）,第4类是转运子基因（15个,占5．5％）,第5类是蛋白结合基因（12个,占4．4％）,还有功能未知的基因有50个,占18．5％。以上5大类共占基因总数56．9％。胃癌差异表达基因散在分布在各条染色体上,但以1、11、19号染色体差异表达基因居多。这5大类（酶和酶调控子、信号传导、核酸结合、转运子、蛋白结合）相关基因异常是今后研究胃癌的重要基因。     

用基因芯片筛选高转移卵巢癌细胞系转移相关基因

用标准化的Affymetrix公司生产U133A基因芯片技术研究高(H)转移卵巢癌细胞株(HO-8910PM)和正常卵巢上皮(C)基因表达谱差异,筛选与卵巢癌转移相关的基因及其在染色体的定位和功能。结果发现高转移卵巢癌细胞株和正常卵巢上皮比较表达差异8倍以上共有1,237个基因,其中表达上调(信号比的对数值SLR≥3)有597个,表达下调(SLR≤-3)有640个。从表达差异的基因在染色体定位分析,发现除1个基因未知其定位外,其余所有差异表达基因散在分布在各条染色体上,但以1号染色体最多,有115个(9.3%)。其次是2号染色体有94个(7.6%),第三是12号染色体有88个(7.1%)。第四是11号染色体有76个(6.1%)。第五是X染色体有71个(5.7%)。第6是17号染色体有69个(5.6%)。而差异表达的基因发生在染色体短臂(q)上有805个(占65.1%),在13,14,15,21和22号仅发现在q上有差异表达基因。从表达差异的基因分子功能分类看,属于酶和酶调控子基因最多(306个,占24.7%),其次是核酸结合基因(144个,占11.6%)。第三类是信号传导基因(137个,占11.1%)。第四类是蛋白结合基因(116个,占9.4%)。以上4大类共占基因总数56.8%。还有功能未知的基因有207个,占16.7%。结论:高转移卵巢癌细胞株差异表达基因散在分布在各条染色体上,但以1、2、12、11、17和X染色体差异表达基因居多,肿瘤的转移是多基因共同作用的结果。4大类(酶和酶调控子活性、核酸结合活性、信号传导活性、蛋白结合活性)差异表达基因是我们今后研究卵巢癌转移相关的重要基因。     

高低转移卵巢癌细胞株差异表达基因在染色体定位及其功能

用基因芯片技术研究高（H）、低（L）转移卵巢癌细胞株（HO-8910PM和HO-8910）和正常卵巢上皮（C）基因表达谱差异,筛选与卵巢癌转移相关的基因,并利用生物信息学方法对检测结果进行差异基因在染色体定位和功能分析。结果：高、低转移卵巢癌细胞株比较表达差异2倍以上共有409个基因,其中表达上调（信号比的对数值[SLR]≥1）有271个,表达下调（SLR≤-1）有138个。从表达差异的基因在染色体定位分析,发现除1个基因未知其定位外,其余所有差异表达基因散在分布于各条染色体上,但以1号染色体最多有43个（占10．7％）。其次是6号染色体有39个（占9．6％）,第三是2号染色体有29个（占7．1％）。第四是17号染色体有28个（占6．9％）。第五是3号染色体有25个（占6．2％）。第6是5号和11号染色体各有24个（各占5．9％）。而差异表达的基因发生在染色体短臂（q）的有264个（占64．7％）,在13,14,15,21和22号仅发现在q都有异常表达。从表达差异基因的分子功能分类看,属于酶和酶调控子基因为最多（104个,占25．4％）,其次是信号传导基因（43个,占10．5％）。第3类是核酸结合基因（42个,占10．3％）。第4类是蛋白结合基因（34个,占8．3％）。以上4大类共占基因总数54．5％。还有功能未知的基因有76个,占18．6％。高、低转移卵巢癌细胞株差异表达基因散在分布在各条染色体上,但以1、6、2、17、3、5和11号染色体差异表达基因居多。肿瘤的转移是多基因共同作用的结果。4大类（酶和酶调控子、信号传导、核酸结合和蛋白结合）相关基因异常是我们今后研究卵巢癌转移的重要基因。     

Identification of Differentially Expressed Genes in the High and Low Metastatic Human Ovarian Cancer Cell Lines and Analyses of Their Chromosomal Localizations and Functions

Oligonucleotide microarrays were used to study the differences of gene expressions in high (H) and low (L) metastatic ovarian cancer cell lines and in normal ovarian tissues (C). Bioinformatics was used to identify novel genes and their functions as well as chromosomal localizations. A total of 409 genes were differentially expressed between the high and low metastatic ovarian cancer cell lines. Of them, 271 genes were up regulated (Signal Log Ratio[SLR] ≥1), and 138 genes were down regulated (SLR≤-1). Except one gene whose location was unknown, all these genes were localized randomly on all the chromosomes, with a majority of them localized to Chromosomes 1, 6, 2, 17, 3, 5 and 11. Chromosome 1 contained, 43 of them (10.7%), the most for a single chromosome. A total of 264 genes (64.7%) were localized on the short arm of the chromosome (q). Functional classification showed that the 104 (25.4%) genes coding for enzymes and enzyme regulators made up the largest functional group, followed by signal transduction activity genes (43, 10.5%), nucleic acid binding activity genes (42, 10.3%), and proteins binding activity genes (34, 8.3%). These four groups accounted for 54.5% of all the differentially expressed genes. In addition, the functions of 76 genes (18.6%) were unknown. Tumor metastasis is the result of a number of genes acting in concert. The four functional groups of genes classified among these genes and their abnormalities would be the focus of further studies on ovarian cancer metastasis.     

杨盘二孢菌诱导的杨树差异表达基因的功能分析和染色体定位

利用cDNA芯片技术从含有2,952个克隆的杨树芯片中筛选出1,160个受杨盘二孢菌诱导的基因。功能分析表明,该1,160个基因分别属于11个功能类别,除了功能未知基因外,参与新陈代谢、防御反应、信号传导及转录调控的基因最多,这4大类基因约占基因总数的42%。1,160个差异表达基因中有926个基因被定位于19条染色体上,其中被定位于第Ⅱ条染色体上的差异基因最多,共102个(11.0%),其次是第Ⅰ条染色体,共93个(10%),被定位到第ⅩⅦ条染色体上的差异基因最少,仅有11个,基因在染色体上的分布则表现为在部分染色体的末端区域存在大量的聚集,在中间区段则相对较少和排列稀疏,基因的这种分布情况与植物抗病的关系有待进一步研究。     

Identification of differentially expressed genes in normal and tumor human gastric tissue

The search for differentially expressed genes in gastric cancer may help define molecular alterations and molecular diagnosis of gastric cancer. Using the differential display PCR technique, we identified 18 genes that are differentially expressed between normal and tumor human gastric tissues. Their expressions were verified with reverse Northern blot analysis and Northern blot analysis. Oxidative phosphorylation-related genes, antizyme inhibitor of ornithine decarboxylase, protein phosphatase-1beta, 35-kDa peroxisomal membrane protein, and cystic fibrosis transmembrane conductance receptor were highly expressed in tumor tissue, whereas pepsinogen A, Na-K ATPase alpha subunit, nerve growth factor receptor, and alpha-tropomyosin were highly expressed in normal tissue. In addition, 3 unknown genes were found to be differentially expressed in paired gastric tissues. These differentially expressed genes may provide significant opportunities for further understanding of gastric carcinogenesis and the molecular diagnosis of gastric cancer.     

胃癌组织中肿瘤相关成纤维细胞与正常成纤维细胞之间转录组学研究及验证

胃癌组织中肿瘤相关成纤维细胞(carcinoma associated fibroblasts, CAFs)是胃癌微环境的重要成分,主要来源于正常成纤维细胞(normal fibroblasts, NFs)的活化,对胃癌的发生发展有重要作用,但是两者之间的基因表达差异并不完全清楚。本研究选取从人胃癌组织中分离获得的CAFs及NFs 各3组,进行转录组学研究,筛选出3组细胞中交集且差异倍数较大的基因12个,用Omicsbean在线工具对差异基因进行Gene Ontology (GO)功能及KEGG通路富集,构建蛋白质相互作用调控网络;最后用RT-qPCR验证CAFs和NFs中差异基因的表达。结果显示,筛选出的12个差异表达基因主要参与NF-κB信号、炎症、细胞黏附、细胞表面受体和细胞因子等功能,上述功能均与肿瘤的发生发展密切相关。RT-qPCR检测发现,与NFs相比,CAFs中BCL2A1、NKX3-2、CXCL12、TNFAIP3、FOS、CDH4及CLDN1表达上调;ATF3、CYFIP2、CCL11、KLF2及GDF15基因表达下调,差异均具有统计学意义(P＜0.05)。结果提示,胃癌CAFs与NFs中存在肿瘤相关的差异表达基因,这些差异基因可能在胃癌微环境中发挥重要作用。     

Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster

Chromosomal instability, which involves the deletion and duplication of chromosomes or chromosome parts, is a common feature of cancers, and deficiency screens are commonly used to detect genes involved in various biological pathways. However, despite their importance, the effects of deficiencies, duplications, and chromosome losses on the regulation of whole chromosomes and large chromosome domains are largely unknown. Therefore, to explore these effects, we examined expression patterns of genes in several Drosophila deficiency hemizygotes and a duplication hemizygote using microarrays. The results indicate that genes expressed in deficiency hemizygotes are significantly buffered, and that the buffering effect is general rather than being mainly mediated by feedback regulation of individual genes. In addition, differentially expressed genes in haploid condition appear to be generally more strongly buffered than ubiquitously expressed genes in haploid condition, but, among genes present in triploid condition, ubiquitously expressed genes are generally more strongly buffered than differentially expressed genes. Furthermore, we show that the 4^th chromosome is compensated in response to dose differences. Our results suggest general mechanisms have evolved that stimulate or repress gene expression of aneuploid regions as appropriate, and on the 4^th chromosome of Drosophila this compensation is mediated by Painting of Fourth (POF).     

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection.

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.     

Electrophoretic karyotype and linkage groups of the amoeboflagellate Naegleria gruberi

We have constructed a molecular karyotype for two strains of Naegleria gruberi using pulsed field gel electrophoresis. Each strain has about 23 chromosomes, considerably more than any previous estimate. These chromosomes range in size from 400 kilobasepairs to over 2,000 kilobasepairs. In Naegleria, construction of the DNA karyotype depends on assessment of the anomalous electrophoretic mobility of the circular ribosomal RNA genes. We have determined the chromosomal locations of an identified unique gene (flagellar calmodulin) and four identified multigene families (alpha- and beta-tubulin, actin, ubiquitin), as well as three differentially expressed genes of unknown functions. The ca. 12 actin genes are dispersed over at least seven chromosomes, whereas the majority of the more than eight alpha-tubulin genes are confined to a single chromosome. The ubiquitin genes are found on five chromosomes in one strain and seven in the other and the beta-tubulin genes are on three or four. Our observations provide a foundation for molecular genetic studies in this organism.     

Analysis of gene expression profiles of gastric normal and cancer tissues by SAGE

In an attempt to understand the molecular bases of gastric cancer progression, we have analyzed the differentially expressed genes in gastric cancer by SAGE. Four SAGE cDNA tag libraries were constructed from two sets of gastric cancer and normal tissues and 241,127 tags were obtained. By comparing the tags from cancer and normal tissues, 414 differentially expressed tags, representing 383 genes, were identified in cancer tissues (p 相似文献   

Electrophoretic Karyotype and Linkage Groups of the Amoeboflagellate Naegleria gruberi

ABSTRACT. We have constructed a molecular karyotype for two strains of Naegleria gruberi using pulsed field gel electrophoresis. Each strain has about 23 chromosomes, considerably more than any previous estimate. These chromosomes range in size from 400 kilobasepairs to over 2,000 kilobasepairs. In Naegleria , construction of the DNA karyotype depends on assessment of the anomalous electrophoretic mobility of the circular ribosomal RNA genes. We have determined the chromosomal locations of an identified unique gene (flagellar calmodulin) and four identified multigene families (α- and β-tubulin, actin, ubiquitin), as well as three differentially expressed genes of unknown functions. The ca. 12 actin genes are dispersed over at least seven chromosomes, whereas the majority of the more than eight α-tubulin genes are confined to a single chromosome. The ubiquitin genes are found on five chromosomes in one strain and seven in the other and the β-tubulin genes are on three or four. Our observations provide a foundation for molecular genetic studies in this organism.     

Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer

Background

Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level.

Principal Findings

We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis.

Conclusions

This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic targets.     

基于已知疾病基因构建共表达网络识别胃癌进展及预后相关非编码基因

本研究旨在总结整理已有胃癌研究的基础上,进一步挖掘出非编码基因在胃癌的进展及预后中起的关键作用。通过胃癌患者编码及非编码基因的表达数据,结合已知胃癌致病基因,进行编码基因与非编码基因的共表达计算,识别出由miRNA介导的并且与已知胃癌基因互作的lncRNA,挖掘出三者(mRNA-miRNA-lncRNA)相互作用的模块,进而对模块进行筛选,并对疾病相关的显著模块的基因进行生存分析。除已知的胃癌相关基因外,研究也使用了差异表达的胃癌基因,这些基因显著的富集在细胞增殖、细胞粘附、肌肉收缩、血管重塑、细胞分裂、染色体分离等生物过程,这些生物过程都与胃的基础功能及胃癌发生发展密切相关。分值最高的三元组模块内核心基因BGN在胃癌患者中显著高表达,而且和胃癌患者的预后显著相关;同时也发现该模块内的miRNA has-miRNA-153-5p和has-miRNA-5001-5p均为已证实的胃癌相关基因;模块内的mRNA和miRNA的表达异常可能是由于与他们显著相关的lncRNA的表达异常导致的。本研究为胃癌已知致病基因的表达异常研究找到了新突破口,潜在的胃癌相关的非编码基因的发现为胃癌预防与治疗提供了新的靶点,为未来的临床应用提供了依据。     

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.