• Title, Summary, Keyword: gene copy number

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Bioinformatic identification of prognostic signature defined by copy number alteration and expression of CCNE1 in non-muscle invasive bladder cancer

  • Song, Bic-Na;Kim, Seon-Kyu;Chu, In-Sun
    • Experimental and Molecular Medicine
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    • v.49 no.1
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    • pp.4.1-4.7
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    • 2017
  • Non-muscle invasive bladder cancer (NMIBC) patients frequently fail to respond to treatment and experience disease progression because of their clinical and biological diversity. In this study, we identify a prognostic molecular signature for predicting the heterogeneity of NMIBC by using an integrative analysis of copy number and gene expression data. We analyzed the copy number and gene expression profiles of 404 patients with bladder cancer obtained from The Cancer Genome Atlas (TCGA) consortium. Of the 14 molecules with significant copy number alterations that were previously reported, 13 were significantly correlated with copy number and expression changes. Prognostic gene sets based on the 13 genes were developed, and their prognostic values were verified in three independent patient cohorts (n = 501). Among them, a signature of CCNE1 and its coexpressed genes was significantly associated with disease progression and validated in the independent cohorts. The CCNE1 signature was an independent risk factor based on the result of a multivariate analysis (hazard ratio = 6.849, 95% confidence interval = 1.613-29.092, P = 0.009). Finally, gene network and upstream regulator analyses revealed that NMIBC progression is potentially mediated by CCND1-CCNE1-SP1 pathways. The prognostic molecular signature defined by copy number and expression changes of CCNE1 suggests a novel diagnostic tool for predicting the likelihood of NMIBC progression.

Evaluation of Methane Oxidation and the Production Potential of Soils in an Urban School (도심 학교 토양의 메탄 산화 및 생성 잠재력 평가)

  • Lee, Yun-Yeong;Kim, Tae Gwan;Ryu, Hee Wook;Cho, Kyung-Suk
    • Microbiology and Biotechnology Letters
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    • v.42 no.1
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    • pp.32-40
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    • 2014
  • Methane oxidation and the production potentials of ground soil (soil A) and garden soil (soil B, C, & D) in an urban school were evaluated, and the methanotrophic and methanogen communities in the soil samples were quantified using quantitative realtime PCR. The methanotrophic community in the raw soil A sample possessed a $6.1{\times}10^3$ gene copy number/g dry weight soil, whereas those in the raw soils B~D samples were $1.6-1.9{\times}10^5$ gene copy numbers/g dry weight soil. Serum bottles added with the soil samples were enriched with methane gas, and then evaluated for their methane oxidation potential. The soil A sample had a longer induction phase for methane oxidation than the other soils. However, soil A showed a similar methane oxidation potential with soils B~D after the induction phase. The methanotrophic community in the enriched soil A sample was increased by up to $2.3{\times}10^7$ gene copy numbers/g dry weight soil, which had no significantly difference compared with those in soils B~D ($1.2-2.8{\times}10^8$ gene copy numbers/g dry weight soil). Methane production showed a similar tendency to methane oxidation. The methanogens community in raw soil A ($1.7{\times}10^5$ gene copy number/g dry weight soil) was much less than those in raw soils B~D ($1.3-3.4{\times}10^7$ gene copy numbers/g dry weight soil). However, after methane gas was produced by adding starch to the soils, soil samples A~D showed $10^7$ gene copy numbers/g dry weight soil in methanogens communities. The results indicate that methanotrophic and methanogenic bacteria have coexisted in this urban school's soils. Moreover, under appropriate conditions for methane oxidation and production, methanotrophic bacteria and methanogens are increased and they have the potential for methane oxidation and production.

Low Level of TERC Gene Amplification between Chronic Myeloid Leukaemia Patients Resistant and Respond to Imatinib Mesylate Treatment

  • Mohamad Ashari, Zaidatul Shakila;Sulong, Sarina;Hassan, Rosline;Husin, Azlan;Sim, Goh Ai;Wahid, S. Fadilah Abdul
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.4
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    • pp.1863-1869
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    • 2014
  • The amplification of telomerase component (TERC) gene could play an important role in generation and treatment of haematological malignancies. This present study was aimed to investigate copy number amplification status of TERC gene in chronic myeloid leukaemia (CML) patients who were being treated with imatinib mesylate (IM). Genomic DNA was extracted from peripheral blood of CML-IM Resistant (n=63), CML-IM Respond (n=63) and healthy individuals (n=30). TERC gene copy number predicted (CNP) and copy number calculated (CNC) were determined based on $Taqman^{(R)}$ Copy Number Assay. Fluorescence in situ hybridization (FISH) analysis was performed to confirm the normal signal pattern in C4 (calibrator) for TERC gene. Nine of CML patients showed TERC gene amplification (CNP=3), others had 2 CNP. A total of 17 CML patients expressed CNC>2.31 and the rest had 2.31>CNC>1.5. TERC gene CNP value in healthy individuals was 2 and their CNC value showed in range 1.59-2.31. The average CNC TERC gene copy number was 2.07, 1.99 and 1.94 in CML-IM Resistant patients, CML-IM Respond and healthy groups, respectively. No significant difference of TERC gene amplification observed between CML-IM Resistant and CML-IM Respond patients. Low levels of TERC gene amplification might not have a huge impact in haematological disorders especially in terms of resistance towards IM treatment.

Direct Evaluation of the Effect of Gene Dosage on Secretion of Protein from Yeast Pichia pastoris by Expressing EGFP

  • Liu, Hailong;Qin, Yufeng;Huang, Yuankai;Chen, Yaosheng;Cong, Peiqing;He, Zuyong
    • Journal of Microbiology and Biotechnology
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    • v.24 no.2
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    • pp.144-151
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    • 2014
  • Increasing the gene copy number has been commonly used to enhance the protein expression level in the yeast Pichia pastoris. However, this method has been shown to be effective up to a certain gene copy number, and a further increase of gene dosage can result in a decrease of expression level. Evidences indicate the gene dosage effect is product-dependent, which needs to be determined when expressing a new protein. Here, we describe a direct detection of the gene dosage effect on protein secretion through expressing the enhanced green fluorescent protein (EGFP) gene under the direction of the ${\alpha}$-factor preprosequence in a panel of yeast clones carrying increasing copies of the EGFP gene (from one to six copies). Directly examined under fluorescence microscopy, we found relatively lower levels of EGFP were secreted into the culture medium at one copy and two copies, substantial improvement of secretion appeared at three copies, plateau happened at four and five copies, and an apparent decrease of secretion happened at six copies. The secretion of EGFP being limiting at four and five copies was due to abundant intracellular accumulation of proteins, observed from the fluorescence image of yeast and confirmed by western blotting, which significantly activated the unfolded protein response indicated by the up-regulation of the BiP (the KAR2 gene product) and the protein disulfide isomerase. This study implies that tagging a reporter like GFP to a specific protein would facilitate a direct and rapid determination of the optimal gene copy number for high-yield expression.

Functional Effects of Increased Copy Number of the Gene Encoding Proclavaminate Amidino Hydrolase on Clavulanic Acid Production in Streptomyces clavuligerus ATCC 27064

  • Song, Ju-Yeon;Kim, Eun-Sook;Kim, Dae-Wi;Jesen, Susan E.;Lee, Kye-Joon
    • Journal of Microbiology and Biotechnology
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    • v.18 no.3
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    • pp.417-426
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    • 2008
  • The effect of increasing levels of proclavaminate amidino hydrolase (Pah) on the rate of clavulanic acid production in Streptomyces clavuligerus ATCC 27064 was evaluated by increasing dosoge of a gene (pah2) encoding Pah. A strain (SMF5703) harboring a multicopy plasmid containing the pah2 gene showed significantly retarded cell growth and reduced clavulanic acid production, possibly attributable to the deleterious effects of the multicopy plasmid. In contrast, a strain (SMF5704) carrying a single additional copy of pah2 introduced into chromosome via an integrative plasmid showed enhanced production of clavulanic acid and increased levels of pah2 transcripts. Analysis of transcripts of other genes involved in the clavulanic acid biosynthetic pathway revealed a pattern similar to that seen in the parent. From these results, it appears that clavulanic acid production can be enhanced by duplication of pah2 through integration of a second copy of the gene into chromosome. However, increasing the copy number of only one gene, such as pah2, does not affect the expression of other pathway genes, and so only modest improvements in clavulanic acid production can be expected. Flux controlled by Pah did increase when the copy number of pah2 was doubled, suggesting that under these growth conditions, Pah levels may be a limiting factor regulating the rate of clavulanic acid biosynthesis in S. clavuligerus.

Role of GSTM1 Copy Number Variant in the Prognosis of Thai Colorectal Cancer Patients Treated with 5-FU-based Chemotherapy

  • Pongtheerat, Tanett;Saelee, Pensri
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.10
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    • pp.4719-4722
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    • 2016
  • Background: Glutathione S-transferase M1 (GSTM1) is involved in the detoxification of carcinogenic agents. DNA copy number variants of GSTM1 may be associated with cancer progression and may result in reduced survival time of various cancers. Determination of DNA copy number variants was here used to assess the association between GSTM1 copy number variant and pathological status and survival time of colorectal-cancer patients treated with 5-fluorouracil-based chemotherapy. Methods: One hundred thirteen Thai colorectal-cancer patients were investigated for GSTM1 copy number variant by real-time PCR. Relationships between gene copy number variants and clinico-pathological parameters were determined. Result: Associations were evident between GSTM1 copy number and stage of tumor (P = 0.026) and metastasis at diagnosis (P = 0.049), with odds ratio values of 0.2 and 0.3 respectively. Conclusions: GSTM1 copy number variant was here not related with reduced overall survival for the colorectal-cancer patients receiving 5-FU-based chemotherapy.

Plasmid Propagation and Heterologous Gene Expression in Recombinant Yeast (효모균에서의 Plasmid 번식체계와 혼성유전자 발현)

  • 홍억기
    • KSBB Journal
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    • v.8 no.2
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    • pp.133-142
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    • 1993
  • The effects of genetic and environmental factors on productivity of a cloned protein were studied in recombinant Saccharomyces cerevisiae. Plasmid stability and copy level were very high for a $REP^+$ system(at ca. 10 generations, stability: 65-90%, plasmid copy number per cell: 40-200), whereas these were very low for a yep- system(at ca. 10 generations, stability: 30%, plasmid copy number per cell 20). In plasmids containing the $2{\mu}m$ circle genome, a $[cir^o]$ strain was a preferred host cell since the plasmid stability and the copy number in a $[cir^o]$ strain were higher than in a $[cir^+]$strain. Cloned gene expression was dependent on plasmid copy number and stability. The inducer (galactose) level played a very important role in cloned lacZ gene expression, showing that a galactose concentration of 0.8% was sufficient for induction of gene expression. Induction rate was very fast in the case of plasmids exhibiting high stability and copy number by a factor of 4 to 25. The time to reach the peak value of gene expression was longer when galactose was added at the start of fermentation (ca. 26 hours) than at the mid-exponential phase (ca. 6 hours). Glucose repression was reduced by a factor of 2 to 5 as the relative inducer level increased.

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No Association between Copy Number Variation of the TCRB Gene and the Risk of Autism Spectrum Disorder in the Korean Population

  • Yang, So-Young;Yim, Seon-Hee;Hu, Hae-Jin;Kim, Soon-Ae;Yoo, Hee-Jeong;Chung, Yeun-Jun
    • Genomics & Informatics
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    • v.8 no.2
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    • pp.76-80
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    • 2010
  • Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.

Studies on KEM1 Gene Controlling Mitotic Cell Division in Yeast: Molecular Cloning of a High Copy Suppressor (ROK1) of kem1 (효모에서 세포분열을 조절하는 KEM1 유전자에 관한 연구: kemi의 High Copy Suppressor (ROK1) 클로닝)

  • Kim, Sang Hyeon;Kim, Jin Mi
    • Korean Journal of Microbiology
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    • v.30 no.1
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    • pp.37-41
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    • 1992
  • The KEM1 gene is known to affect microtubule and spindle pole body function during the cell division cycle in Saccharomjyces cerevisiae. To identify new genes with functions similar or related to those of KEM1, we isolated a high copy suppressor gene (ROK1) that suppresses the kem1 mutation when cloned on a high copy number plasmid but not on a low copy number plasmid. Two clones which suppress both the benomyl hypersensitivity and the $Kar^{-}$ enhancing phenotype of kem1 null mutation were isolated and were shown to have a 9.0 kb identical insert by restriction endonuclease analysis. The restriction map constructed indicates that this suppressor gene, ROK1 is not KEM1. Subcloning experiments suggest that the functional region of ROK1 is at least 3.0kb in size.

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Development of Simultaneous YAC Manipulation-Amplification (SYMA) system by Chromosome Splitting Technique Harboring Copy Number Amplification System (복제수 증폭시스템과 염색체 분단기술을 이용한 Simultaneous YAC Manipulation-Amplification (SYMA) 시스템의 개발)

  • Kim, Yeon-Hee;Nam, Soo-Wan
    • Journal of Life Science
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    • v.20 no.5
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    • pp.789-793
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    • 2010
  • Artificial chromosome manipulation and amplification of single-copy yeast artificial chromosome (YAC) are usually required in order to use YACs for applications such as physical mapping and functional analysis in eukaryotes. We designed and implemented a Simultaneous YAC Manipulation-Amplification (SYMA) system that combines the copy number amplification system of YAC with a convenient YAC manipulation system. To achieve the desired split and to amplify a YAC clone-harboring plant chromosome, a pBGTK plasmid containing a conditional centromere and thymidine kinase (TK) gene was constructed as a template to amplify the splitting fragment via PCR. By splitting, new 490-kb and 100-kb split YACs containing the elements for copy number amplification were simultaneously generated from a 590-kb YAC clone. The 100-kb split YAC was then successfully amplified 14.4-fold by adding 3 mg/ml sulfanilamide and $50\;{\mu}g/ml$ methotrexate (S3/M50) as inducing substances.