纳米金增强复杂体系中PCR扩增低拷贝基因的反应特异性初步研究

目的：利用纳米金颗粒提高复杂体系基因组低拷贝基因PCR扩增的反应特异性。方法：首先,模拟复杂基因组扩增模式体系,以接近单拷贝的λDNA为模板,在PCR过程中加入纳米金颗粒,设计优化实验,以便模拟建立复杂基因组低拷贝目的基因PCR扩增的模式体系。随后,扩增人类基因组的疾病相关的低拷贝基因模板（如人基因组肿瘤坏死因子基因外显子1的380bp）,以检验纳米金优化增强PCR反应特异性的实际效果。结果：在复杂体系基因组的低拷贝基因PCR扩增中,纳米金颗粒能够较好地增强其PCR反应的特异性。结论：初步表明基于纳米金的纳米粒子PCR方法可以对复杂的实际基因组体系低拷贝基因的PCR扩增起到优化作用,这对于PCR反应优化方法的改进、推广具有重要的参考价值。     

乳腺癌中EGFR蛋白表达和基因扩增的检测结果比较

目的:比较免疫组织化学技术检测乳腺癌中EGFR蛋白表达和荧光原位杂交检测EGFR基因扩增的结果的符合率,为EGFR靶向治疗病例的选择提供依据。方法:随机选取2005年1月到2011年12月冷水江市人民医院和湖南省肿瘤医院病理科的147例乳腺癌档案病例,采用免疫组织化学技术检测乳腺癌组织中EGFR蛋白表达,荧光原位杂交检测EGFR的基因扩增,比较两种方法阳性结果的符合率。结果:免疫组化染色结果显示EGFR在原发性和转移性乳腺癌中的阳性表达率分别为85%(105/123)和79%1(9/24),两组比较无显著差异(P0.05)。FISH检测结果显示原发性和转移性乳腺癌中分别有12%(15/123)和8%(2/24)存在EGFR基因扩增,两组比较结果无显著差异(P0.05)。所有存在EGFR基因扩增的原发性和转移性乳腺癌的EGFR免疫组织化学结果均为阳性。在原发性和转移性乳腺癌中,免疫组化阳性和基因扩增程度间呈显著正相关(P0.05),但免疫组化结果预测基因扩增的特异性较低。结论:免疫组织化学检测EGFR只能作为EGFR靶向治疗病例选择的初步筛选,进一步进行荧光原位杂交检测EGFR基因扩增是必须的。     

乳腺癌中EGFR蛋白表达和基因扩增的检测结果比较

目的：比较免疫组织化学技术检测乳腺癌中EGFR蛋白表达和荧光原位杂交检测EGFR基因扩增的结果的符合率,为EGFR靶向治疗病例的选择提供依据。方法：随机选取2005年1月到2011年12月冷水江市人民医院和湖南省肿瘤医院病理科的147例乳腺癌档案病例,采用免疫组织化学技术检测乳腺癌组织中EGFR蛋白表达,荧光原位杂交检测EGFR的基因扩增,比较两种方法阳性结果的符合率。结果：免疫组化染色结果显示EGFR在原发性和转移性乳腺癌中的阳性表达率分别为85%（105/123）和79%1（9/24）,两组比较无显著差异（P〉0.05）。FISH检测结果显示原发性和转移性乳腺癌中分别有12%（15/123）和8%（2/24）存在EGFR基因扩增,两组比较结果无显著差异（P〉0.05）。所有存在EGFR基因扩增的原发性和转移性乳腺癌的EGFR免疫组织化学结果均为阳性。在原发性和转移性乳腺癌中,免疫组化阳性和基因扩增程度间呈显著正相关（P〈0.05）,但免疫组化结果预测基因扩增的特异性较低。结论：免疫组织化学检测EGFR只能作为EGFR靶向治疗病例选择的初步筛选,进一步进行荧光原位杂交检测EGFR基因扩增是必须的。     

Enhanced gene amplification in human cells knocked down for DNA-PKcs

Gene amplification, a key mechanism for oncogene activation and drug resistance in tumour cells, involves the generation and joining of DNA double-strand breaks. Amplified DNA can be carried either on intra-chromosomal arrays or on extra-chromosomal elements (double minutes). We previously showed that, in rodent cells deficient in DNA-PKcs, intra-chromosomal amplification is significantly enhanced. In the present work, we studied gene amplification in human HeLa cell lines in which the expression of the DNA-PKcs gene was constitutively inhibited by shRNAs. These cell lines showed an increased sensitivity to ionizing radiations, an enhanced frequency of chromosomal aberrations and an increased rate of occurrence of methotrexate resistant colonies compared to the control cell lines (6-18 times). The main mechanism of resistance to methotrexate was extra-chromosomal amplification of the dihydrofolate reductase gene. These results indicate that, in human cells, inhibition of DNA-PKcs gene expression favours gene amplification occurring via the production of double minutes. In addition, they show that cell lines constitutively expressing shRNAs are good model systems to study the role of specific functions in gene amplification.     

Gamma-ray and hydrogen peroxide induction of gene amplification in hamster cells deficient in DNA double strand break repair

To investigate the role of DNA double strand breaks (DSBs) and of their repair in gene amplification, we analyzed this process in the V3 Chinese hamster cell line and in the parental line AA8, after exposure to gamma-rays and to hydrogen peroxide (H2O2). V3 is defective in DSB repair because of a mutation in the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) gene, a gene involved in the non-homologous end-joining pathway. As a measure of gene amplification we used the frequency of colonies resistant to N-(phosphonacetyl)-L-aspartate (PALA), since in rodent cells PALA resistance is mainly achieved through the amplification of the CAD (carbamyl-P-synthetase, aspartate transcarbamylase, dihydro-orotase) gene. After treatment with different doses of gamma-rays and of H2O2, we found a dose related increase in the frequency of gene amplification and of chromosome aberrations. When the same doses of damaging agents were used, these increments were higher in V3 than in AA8. These results indicate that DSBs that are not efficiently repaired can be responsible for the induction of gene amplification. H2O2 stimulates gene amplification as well as gamma-rays, however, at similar levels of amplification induction, chromosome damage was about 50% lower. This suggests that gene amplification can be induced by H2O2 through pathways alternative to a direct DNA damage. Stimulation of gene amplification by H2O2, which is one of the products of the aerobic metabolism, supports the hypothesis that cellular metabolic products themselves can be a source of genome instability.     

生长因子受体类癌基因的扩增与胃癌癌变的关系

用Ｓｏｕｔｈｅｒｎ杂交技术检查了３２例胃癌组织和４株胃癌细胞系中原癌基因ｍｅｔ、ｅｒｂＢ２、ＥＧＦＲ、ＡＫＴ－２、Ｒａｓ和ｍｙｃ的扩增,发现ｍｅｔ基因扩增６例,ＥＧＦＲ扩增１例、缺失２例,ＡＫＴ－２扩增２例,没有发现Ｒａｓ基因和ｍｙｃ基因的扩增．有癌基因异常的病例多为低分化、临床分期为Ⅲ、Ⅳ期的个体,提示癌基因扩增是肿瘤发展的晚期事件。     

Mechanisms of DNA sequence amplification and their evolutionary consequences

DNA sequence amplification is a phenomenon that occurs predictably at defined stages during normal development in some organisms and has been shown to occur spontaneously, but sporadically, in a variety of cells, including mammalian cells, selected for overproduction of a gene product. Developmentally programmed gene amplification includes rDNA amplification during o?genesis in amphibia, chorion protein gene amplification in Drosophila and the chromosomal changes accompanying macronuclear formation in ciliates. Selected gene amplification is illustrated by mutant mammalian cells which have been selected in vitro or in vivo for the overproduction of a gene product. In these cells the unit of DNA that is amplified is much larger than the gene under selection, and appears to be formed by multiple recombination events, which bring together sequences not normally adjacent to each other. Often the product of amplification can be seen microscopically as aberrant chromosome forms. The vast majority of DNA amplification events occur in somatic nuclei, and thus would not have any direct effect on the evolution of a genome. However, the ability to amplify DNA in somatic cells does have consequences for the composition of the genomes of the organisms in which it can occur, and should DNA amplification occur, even sporadically, in germ-line cells the potential effect on evolution would be great.     

The amplification and evolution of orthologous 22-kDa α-prolamin tandemly arrayed genes in <Emphasis Type="Italic">coix</Emphasis>, sorghum and maize genomes

Tandemly arrayed genes (TAGs) account for about one-third of the duplicated genes in eukaryotic genomes. They provide raw genetic material for biological evolution, and play important roles in genome evolution. The 22-kDa prolamin genes in cereal genomes represent typical TAG organization, and provide the good material to investigate gene amplification of TAGs in closely related grass genomes. Here, we isolated and sequenced the Coix 22-kDa prolamin (coixin) gene cluster (283 kb), and carried out a comparative analysis with orthologous 22-kDa prolamin gene clusters from maize and sorghum. The 22-kDa prolamin gene clusters descended from orthologous ancestor genes, but underwent independent gene amplification paths after the separation of these species, therefore varied dramatically in sequence and organization. Our analysis indicated that the gene amplification model of 22-kDa prolamin gene clusters can be divided into three major stages. In the first stage, rare gene duplications occurred from the ancestor gene copy accidentally. In the second stage, rounds of gene amplification occurred by unequal crossing over to form tandem gene array(s). In the third stage, gene array was further diverged by other genomic activities, such as transposon insertions, segmental rearrangements, etc. Unlike their highly conserved sequences, the amplified 22-kDa prolamin genes diverged rapidly at their expression capacities and expression levels. Such processes had no apparent correlation to age or order of amplified genes within TAG cluster, suggesting a fast evolving nature of TAGs after gene amplification. These results provided insights into the amplification and evolution of TAG families in grasses.     

Estrogen receptor gene amplification is found in some estrogen receptor-positive human breast tumors

The genomic organization of the estrogen receptor (ER) gene has been analyzed in 21 primary human breast cancers and 1 axillary metastasis. No evidence of rearrangements of the ER gene was found in the analyzed tumors. In 6/14 ER-positive tumors a certain degree of amplification of the ER gene, ranging from 1.6 to 3-fold, was detected. No correlation was observed between the level of gene amplification and the amount of ER in the tumors. In the 8 ER-negative tumors analyzed no amplification could be detected. It is concluded that ER gene amplification may be one of the mechanisms underlying the increased ER expression in some breast tumors.     

APPLICATION OF GENE AMPLIFICATION IN CONJUNCTION WITH A HYBRIDIZATION SENSOR FOR RAPID DETECTION OF SALMONELLA SPP. AND FECAL CONTAMINATION INDICATORS IN ANIMAL FEEDS

The rapid detection of pathogenic microbial species in feed is of paramount importance considering its implications for animal production and food safety. To demonstrate the feasibility of rapidly detecting Salmonella spp. and fecal pollution microbial indicators in feed using gene amplification protocols, commercial and mixed feed samples were inoculated with two levels of a marker strain of S. typhimurium. Liquid extracts of the feed samples were used as templates in gene amplification reactions to amplify sequences associated with fecal contamination indicators. The sequence specificity of the amplification products (amplicons) were confirmed using biotin and fluorescein labeled probes in a navel dual probe based hybridization sensor. Using the combination of gene amplification and the hybridization sensor, the presence of sequences associated with fecal contamination were detected in 15 different feed matrices without employing preenrichment steps. Using this detection methodology, fecal pollution can be confirmed in feed at naturally occurring concentrations. The study demonstrates that it is possible to rapidly detect and confirm the presence of pathogenic bacterial genera in feed matrices by combining robust gene amplification reactions with appropriate post amplification detection systems.     

转水稻粗缩病毒运动蛋白缺陷型基因玉米的二重PCR检测研究

本研究以外源基因（RDV MP-）和玉米内源基因Zein作为PCR扩增对象,旨在建立一种简便有效的转基因玉米及其产品的二重PCR检测技术。转外源基因（RDV MP-）材料的常规PCR检测结果证明外源基因在转基因材料中可稳定遗传;对常规PCR检测的阴性结果材料进行二重PCR检测,扩增结果除进一步证实常规PCR检测的阴性结果结论外,还证明提取的植物总DNA质量符合试验要求,进而从二重PCR检测结果还得出常规PCR检测的阴性结果出错率为1.4%。此方法简单,实用,结果可靠,可适用于转基因植物及产品的检测。     

The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks

DNA palindromes often colocalize in cancer cells with chromosomal regions that are predisposed to gene amplification. The molecular mechanisms by which palindromes can cause gene amplification are largely unknown. Using yeast as a model system, we found that hairpin-capped double-strand breaks (DSBs) occurring at the location of human Alu-quasipalindromes lead to the formation of intrachromosomal amplicons with large inverted repeats (equivalent to homogeneously staining regions in mammalian chromosomes) or extrachromosomal palindromic molecules (equivalent to double minutes [DM] in mammalian cells). We demonstrate that the specific outcomes of gene amplification depend on the applied selection, the nature of the break, and the chromosomal location of the amplified gene relative to the site of the hairpin-capped DSB. The rules for the palindrome-dependent pathway of gene amplification defined in yeast may operate during the formation of amplicons in human tumors.     

Relationship between EGFR overexpression and gene amplification status in central nervous system gliomas

OBJECTIVE: To correlate epidermal growth factor receptor (EGFR) protein overexpression, as assessed by immunohistochemistry, with EGFR gene amplification determined by fluorescence in situ hybridization in a series of gliomas. STUDY DESIGN: Forty-seven central nervous system gliomas, including 34 cases of glioblastoma multiforme, 3 oligodendrogliomas, 4 juvenile pilocytic astrocytomas and 5 low grade astrocytomas, were obtained from the files of the University of Utah Pathology Department. In each case a representative paraffin block was selected, and EGFR protein expression was quantified using immunohistochemistry. EGFR gene amplification status was determined by fluorescence in situ hybridization. RESULTS: EGFR protein overexpression was detected in 9 cases of glioblastoma multiforme. EGFR gene amplification was present in 7 of these cases. Both nonamplified glioblastomas demonstrated only 2+ overexpression of EGFR protein. None of the low grade, pilocytic or anaplastic astrocytomas demonstrated either EGFR protein overexpression or gene amplification. CONCLUSION: EGFR protein overexpression is closely associated with gene amplification. Seventy-eight percent of cases showing protein overexpression demonstrated gene amplification. All cases of central nervous system neoplasms showing protein overexpression but lacking gene amplification were associated with only 2+ protein overexpression. All central nervous system neoplasms demonstrating gene amplification and/or overexpression were high grade neoplasms.     

From amplification to function: the case of the MDR1 gene.

This review describes the features of gene amplification associated with the selection of multidrug-resistant cell lines. Some of these lines carry multiple copies of the MDR1 gene that encodes P-glycoprotein, a broad specificity efflux pump. The MDR1 gene was initially identified as the common component of the amplicons found in multidrug-resistant cell lines selected with different drugs. Subsequent studies have established that increased MDR1 expression is sufficient for the multidrug-resistant phenotype. MDR1-containing amplicons may include a number of additional transcribed genes that do not appear to contribute to multidrug resistance. MDR1 amplification is associated with specific chromosomal changes and apparently non-random recombinational events. Increased expression of the MDR1 gene, however, does not necessarily require gene amplification. Although amplification of the MDR1 gene has not been found in clinical tumor samples, increased expression of this gene is commonly observed in different types of cancer and appears to be a significant marker of clinical drug resistance.     

Cyclin D1 gene amplification in proliferating haemangioma

Cyclin D1 gene amplification has been reported to promote abnormal endothelial cell proliferation and angiogenesis; these findings constantly present in proliferating haemangiomas. The present study was conducted to evaluate cyclin D1 gene amplification by fluorescence in situ hybridization analysis in tissue biopsies of 22 proliferating haemangiomas from 20 infants. Two significant correlations of cyclin D1 gene amplification with the early onset and the duplication of proliferating haemangiomas have been observed. Moreover, a significant correlation (P≤0.05) has been found between the treatment parameters of proliferating haemangiomas with the amplified versus the normal cyclin D1 gene. Proliferating haemangiomas with the amplified cyclin D1 gene required more frequent flashlamp pulsed dye laser treatment sessions at the maximum dosimetry and more frequent intralesional steroid injections at the maximum dose/injection but treatment outcomes were limited. The more frequent post-treatment complications among proliferating haemangiomas with cyclin D1 gene amplification might be attributable not only to the associated more aggressive natural course, but also to the higher treatment parameters needed for effective treatment. Within the limitations of the present study, cyclin D1 gene amplification was seen for the first time in proliferating haemangiomas. We have found that the amplification of the cyclin D1 gene can predict the more aggressive natural course of proliferating haemangiomas and the limited outcome and higher incidence of complications after non–excision treatment modalities. The present findings reflect the possible usefulness of antisense cyclin D1 to improve the therapeutic outcome of proliferating haemangiomas.     

Effect of gene amplification on mercuric ion reduction activity of Escherichia coli.

The mercury resistance (mer) operon of plasmid R100 was cloned onto various plasmid vectors to study the effect of mer gene amplification on the rate of Hg2+ reduction by Escherichia coli cells. The plasmids were maintained at copy numbers ranging from 3 to 140 copies per cell. The overall Hg2+ reduction rate of intact cells increased only 2.4-fold for the 47-fold gene amplification. In contrast, the rate of the cytoplasmic reduction reaction, measured in permeabilized cells, increased linearly with increasing gene copy number, resulting in a 6.8-fold overall amplification. RNA hybridizations indicated that mRNA of the cytoplasmic mercuric reductase (merA gene product) increased 11-fold with the 47-fold gene amplification, while mRNA of the transport protein (merT gene product) increased only 5.4-fold. Radiolabeled proteins produced in maxicells were used to correlate the expression levels of the mer polypeptides with the measured reduction rates. The results indicated that, with increasing gene copy number, there was an approximately 5-fold increase in the merA gene product compared with a 2.5-fold increase in the merT gene product. These data demonstrate a parallel increase of Hg2+ reduction activity and transport protein expression in intact cells with plasmids with different copy numbers. In contrast, the expression level of the mercuric reductase gene underwent higher amplification than that of the transport genes at both the RNA and protein levels as plasmid copy number increased.     

Effect of gene amplification on mercuric ion reduction activity of Escherichia coli.

The mercury resistance (mer) operon of plasmid R100 was cloned onto various plasmid vectors to study the effect of mer gene amplification on the rate of Hg2+ reduction by Escherichia coli cells. The plasmids were maintained at copy numbers ranging from 3 to 140 copies per cell. The overall Hg2+ reduction rate of intact cells increased only 2.4-fold for the 47-fold gene amplification. In contrast, the rate of the cytoplasmic reduction reaction, measured in permeabilized cells, increased linearly with increasing gene copy number, resulting in a 6.8-fold overall amplification. RNA hybridizations indicated that mRNA of the cytoplasmic mercuric reductase (merA gene product) increased 11-fold with the 47-fold gene amplification, while mRNA of the transport protein (merT gene product) increased only 5.4-fold. Radiolabeled proteins produced in maxicells were used to correlate the expression levels of the mer polypeptides with the measured reduction rates. The results indicated that, with increasing gene copy number, there was an approximately 5-fold increase in the merA gene product compared with a 2.5-fold increase in the merT gene product. These data demonstrate a parallel increase of Hg2+ reduction activity and transport protein expression in intact cells with plasmids with different copy numbers. In contrast, the expression level of the mercuric reductase gene underwent higher amplification than that of the transport genes at both the RNA and protein levels as plasmid copy number increased.