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DJ-1 Enhances Cell Survival through the Binding of Cezanne, a Negative Regulator of NF-κB

JOURNAL OF BIOLOGICAL CHEMISTRY 2011年第6期286卷 4098-4106页

作者： Mcnally, R. Sean Davis, Beckley K. Clements, Casey M. Accavitti-Loper, Mary Ann Mak, Tak W. Ting, Jenny P. -Y. Univ N Carolina Lineberger Comprehens Canc Ctr Dept Microbiol Immunol Chapel Hill NC 27599 USA Univ Alabama Birmingham Dept Med Birmingham AL 35294 USA Univ Hlth Network Campbell Family Inst Breast Canc Res Toronto ON M5G 2C1 Canada

Heightened DJ-1 (Park7) expression is associated with a reduction in chemotherapeutic-induced cell death and poor prognosis in several cancers, whereas the loss of DJ-1 function is found in a subgroup of Parkinson disease associated with neuronal death. This study describes a novel pathway by which DJ-1 modulates cell survival. Mass spectrometry shows that DJ-1 interacts with BBS1, CLCF1, MTREF, and Cezanne/OTUD7B/Za20d1. Among these, Cezanne is a known deubiquitination enzyme that inhibits NF-kappa B activity. DJ-1/Cezanne interaction is confirmed by co-immunoprecipitation of over-expressed and endogenous proteins, maps to the amino-terminal 70 residues of DJ-1, and leads to the inhibition of the deubiquitinating activity of Cezanne. microarray profiling of shRNA-transduced cells shows that DJ-1 and Cezanne regulate IL-8 and ICAM-1 expression in opposing directions. Similarly, DJ-1 enhances NF-kappa B nuclear translocation and cell survival, whereas Cezanne reduces these outcomes. Analysis of mouse Park7(-/-) primary cells confirms the regulation of ICAM-1 by DJ-1 and Cezanne. As NF-kappa B is important in cellular survival and transformation, IL-8 functions as an angiogenic factor and pro-survival signal, and ICAM-1 has been implicated in tumor progression, invasion, and metastasis;these data provide an additional modality by which DJ-1 controls cell survival and possibly tumor progression via interaction with Cezanne.

关键词： CELL death CANCER -- Prognosis PARKINSON'S disease MASS spectrometry microarray technology MICE as laboratory animals

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Global Genome Transcription Profiling of Bifidobacterium bifidum PRL2010 under In Vitro Conditions and Identification of Reference Genes for Quantitative Real-Time PCR

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2011年第24期77卷 8578-8587页

作者： Turroni, Francesca Foroni, Elena Montanini, Barbara Viappiani, Alice Strati, Francesco Duranti, Sabrina Ferrarini, Alberto Delledonne, Massimo van Sinderen, Douwe Ventura, Marco Univ Parma Lab Probiogen Dept Genet Biol Microorganisms Anthropol & Evolut I-43100 Parma Italy Univ Parma Dept Biochem & Mol Biol I-43100 Parma Italy Natl Univ Ireland Alimentary Pharmabiot Ctr Cork Ireland Natl Univ Ireland Dept Microbiol Biosci Inst Cork Ireland Univ Verona Dipartimento Biotecnol I-37100 Verona Italy

Bifidobacteria have attracted significant scientific attention due to their perceived role as health-promoting microorganisms, although the genetics of the bacterial group is still underexplored. In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by microarray technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1,644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., the lag, exponential, and stationary phases. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes that are expressed in all phases. A proportion of these genes were further investigated as potential reference genes by quantitative real-time reverse transcription-PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, which included cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic, and osmotic), and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria.

关键词： BIFIDOBACTERIUM bifidum POLYMERASE chain reaction BIFIDOBACTERIUM GENE expression in microorganisms ENVIRONMENTAL engineering microarray technology

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Knockdown of RARB2 Identifies a Dual Role in Cancer

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GENES CHROMOSOMES & CANCER 2011年第9期50卷 700-714页

作者： Pappas, Jane J. Toulouse, Andre Basik, Mark Levesque, Luc Bradley, W. E. C. McGill Univ Dept Pharmacol & Therapeut Div Expt Med Montreal PQ H3G 1Y6 Canada McGill Univ Dept Med Ctr Rech CHUM Montreal PQ H3G 1Y6 Canada Natl Univ Ireland Univ Coll Cork Dept Anat & Neurosci Cork Ireland Sir Mortimer B Davis Jewish Hosp Lady Davis Inst Ctr Translat Res Canc Montreal PQ Canada

Two chemoprevention trials have shown that retinoic acid (RA) may be harmful in patients at risk for lung cancer, and RA administration to this high-risk group results in RARB2 reactivation. Although RARB2 is thought to possess tumor suppressive activity, its expression has recently been correlated with poorer prognosis in patients with nonsmall cell lung cancer. We hypothesized that RARB2 expression is necessary for the growth and maintenance of the oncogenic phenotype in lung cancer cells in which RARB2 has not been inactivated. We tested various antisense oligodeoxynucleotides (ASO) against RARB2 in multiple lung cancer cell lines and used microarray technology to compare the patterns of gene expression following ASO treatment versus RA treatment in the A-549 lung cancer cell line. We show that ASO treatment reduces proliferation and causes apoptosis in 3 RARB2-expressing lung cancer cell lines but has no apparent effect in at least two other lung cancer cells lines having lost RARB2 expression or one normal lung RARB2-expressing cell line;we demonstrate a correlation between resulting RARB2 expression levels and cell growth;and identify transcriptional effects related to both RA and RARB2 signaling. In particular, five genes known to contribute to carcinogenesis or chemotherapeutic resistance are down-regulated following ASO treatment: three of these are up-regulated following RA treatment. This work demonstrates a dual role for RARB2 (tumor suppression and tumor promotion) and identifies a challenge with respect to using RARB2 as a target for treatment or prevention strategies. (C) 2011 Wiley-Liss, Inc.

关键词： microarray technology Non-Small-Cell Lung Carcinoma Population at Risk Lung Cancer Cell Line Tumor Promotion lung cancer cell line Antistreptolysin O

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Differential miRNA expression in the mouse jejunum during garlic treatment of Eimeria papillata infections

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PARASITOLOGY RESEARCH 2011年第2期109卷 387-394页

作者： Al-Quraishy, Saleh Delic, Denis Sies, Helmult Wunderlich, Frank Abdel-Baki, Abdel Azeem S. Dkhil, Mohamed Abdel King Saud Univ Dept Zool Coll Sci Riyadh 11451 Saudi Arabia Univ Dusseldorf Dept Mol Parasitol D-40225 Dusseldorf Germany Univ Dusseldorf Dept Biochem & Mol Biol 1 D-40225 Dusseldorf Germany Beni Suef Univ Dept Zool Fac Sci Bani Suwayf Egypt Helwan Univ Dept Zool & Entomol Fac Sci Helwan Egypt

Accumulating evidence indicates a critical role of microRNAs (miRNAs) in the outcome of diseases. Here, we investigate the effect of garlic on the intestinal miRNA signature of male Balb/c mice during infections with Eimeria papillata. Garlic decreases the intracellular development as evidenced by a lowered fecal output of E. papillata oocysts from 3,150 +/- 410 to approximately 1,750 +/- 390 oocysts per gram feces on day 4 postinoculation. This anti-coccidial activity of garlic is associated with an inhibition of the E. papillata-induced increases of interferon gamma, inducible nitric oxide synthase, nitrite/nitrate, and malondialdehyde and decrease in glutathione. Moreover, garlic downregulates the E. papillata-induced increases in the expression of the miRNAs miR-1959, miR-203, and miR-21, and it upregulates the expression of the 11 miRNA species miR-142-5P, miR-15A, miR-10A, miR-29B, miR-1902, miR-125A-5P, let-7E, miR-148A, miR-130A, miR-10B, and miR-93, respectively, as revealed by miRXplore microarray technology. Real-time PCR confirms these effects of garlic in the jejunum of E. papillata-infected mice. Our data indicate that the anti-coccidial activity of garlic is associated with specific changes in the miRNA signature of the mouse jejunum, the target site of E. papillata. These changes may reflect an involvement of miRNAs in garlic-activated pathways to reduce and/or to repair E. papillata-induced tissue injuries.

关键词： GARLIC -- Therapeutic use MICE -- Diseases NITRIC oxide MALONDIALDEHYDE microarray technology EIMERIA TREATMENT

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Plasmonic-Based Imaging of Local Square Wave Voltammetry

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ANALYTICAL CHEMISTRY 2011年第19期83卷 7394-7399页

作者： Shan, Xiaonan Wang, Shaopeng Wang, Wei Tao, Nongjian Arizona State Univ Ctr Bioelect & Biosensors Biodesign Inst Tempe AZ 85287 USA Arizona State Univ Dept Elect Engn Tempe AZ 85287 USA

Square wave voltammetry (SWV) is widely used in electrochemical analysis and sensors because of its high sensitivity and efficient rejection of background current, but SWV by the conventional electrochemical detection method does not provide spatial resolution. We report here a plasmonic method to image local SWV, which opens the door for analyzing heterogeneous electrochemical reactions and for high-throughput detections of microarrays. We describe the basic principle, validate the principle by comparing the plasmonic-based SWV with those obtained with the conventional method, and demonstrate imaging capability for local electrochemical analysis.

关键词： VOLTAMMETRY ELECTROCHEMICAL analysis ELECTROCHEMICAL sensors microarray technology NEUROTRANSMITTERS SCANNING electron microscopy

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Long non-coding RNAs and chromatin regulation

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CURRENT OPINION IN PLANT BIOLOGY 2011年第2期14卷 168-173页

作者： De Lucia, Filomena Dean, Caroline John Innes Ctr Plant Sci Res Dept Cell & Dev Biol Norwich NR4 7UH Norfolk England

microarray analysis and new sequencing technologies have revealed that the majority of the genome is transcribed in many eukaryotes. Much of the RNA appears to be non-coding and an ongoing debate is how much of a functional role it has. Different mechanisms by which ncRNA can be regulatory have been described: direct ncRNA effects on transcription;recruitment of chromatin modifiers;formation of silent nuclear compartments. These have been documented chiefly in yeasts and mammals but examples are now appearing in plants. To date RNA-mediated transcriptional silencing studies in plants have focused on siRNAs, but data now show longer ncRNAs are also involved in this silencing. Roles for long ncRNAs in the phenotypic plasticity of plants are also suggested by whole genome analysis showing widespread effects of different external cues on ncRNA expression.

关键词： NON-coding RNA CHROMATIN microarray technology PLANT genomes PHENOTYPIC plasticity NUCLEOTIDE sequence PLANT gene silencing GENETIC regulation in plants

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Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections

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LANCET ONCOLOGY 2011年第3期12卷 273-285页

作者： Marchini, Sergio Cavalieri, Duccio Fruscio, Robert Calura, Enrica Garavaglia, Daniela Nerini, Ilaria Fuso Mangioni, Costantino Cattoretti, Giorgio Clivio, Luca Beltrame, Luca Katsaros, Dionyssios Scarampi, Luca Menato, Guido Perego, Patrizia Chiorino, Giovanna Buda, Alessandro Romualdi, Chiara D'Incalci, Maurizio Mario Negri Inst Pharmacol Res Dept Oncol I-20145 Milan Italy Univ Milano Bicocca San Gerardo Hosp Dept Obstet & Gynecol Monza Italy Univ Milano Bicocca San Gerardo Hosp Unit Anatomopathol Monza Italy Univ Florence Dept Pharmacol Florence Italy Univ Padua Dept Biol Padua Italy Univ Torino Dept Gynecol Oncol Azienda Osped OIRM S Anna Turin Italy Edo Tempia Fdn Canc Genom Lab Biella Italy MaNGO Grp Milan Italy

Background International Federation of Gynecology and Obstetrics stage I epithelial ovarian cancer (EOC) has a significantly better prognosis than stage III/IV EOC, with about 80% of patients surviving at 5 years (compared with about 20% of those with stage III/IV EOC). However, 20% of patients with stage I EOC relapse within 5 years. It is therefore crucial that the biological properties of stage I EOCs are further elucidated. MicroRNAs (miRNAs) have shown diagnostic and prognostic potential in stage III and IV EOCs, but the small number of patients diagnosed with stage I EOC has so far prevented an investigation of its molecular features. We profiled miRNA expression in stage I EOC tumours to assess whether there is a miRNA signature associated with overall and progression-free survival (PFS) in stage I EOC. Methods We analysed tumour samples from 144 patients (29 of whom relapsed) with stage I EOC gathered from two independent tumour tissue collections (A and B), both with a median follow-up of 9 years. 89 samples from tumour tissue collection A were stratified into a training set (51 samples, 15 of which were from patients who relapsed) for miRNA signature generation, and into a validation set (38 samples, seven of which were from patients who relapsed) for signature validation. Tumour tissue collection B (55 samples, seven of which were from patients who relapsed) was used as an independent test set. The Cox proportional hazards model and the log-rank test were used to assess the correlation of quantitative reverse transcription PCR (qRT-PCR)-validated miRNAs with overall survival and PFS. Findings A signature of 34 miRNAs associated with survival was generated by microarray analysis in the training set. In both the training set and validation set, qRT-PCR analysis confirmed that 11 miRNAs (miR-214, miR-199a-3p, miR-199a-5p, miR-145, miR-200b, miR-30a, miR-30a*, miR-30d, miR-200c, miR-20a, and miR-143) were expressed differently in relapsers compared with non-r

关键词： OVARIAN cancer CANCER invasiveness RNA CANCER relapse microarray technology LONGEVITY RETROSPECTIVE studies MOLECULAR biology CANCER -- Prognosis NON-coding RNA

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Increased Synovial Expression of Nuclear Receptors Correlates With Protection in Pristane-Induced Arthritis A Possible Novel Genetically Regulated Homeostatic Mechanism

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ARTHRITIS AND RHEUMATISM 2011年第10期63卷 2918-2929页

作者： Brenner, Max Linge, Carl P. Li, Wentian Gulko, Percio S. Feinstein Inst Med Res Ctr Genom & Human Genet Lab Expt Rheumatol Manhasset NY 11030 USA Elmezzi Grad Sch Mol Med Manhasset NY USA

Objective. To use microarray analyses of gene expression to characterize the synovial molecular pathways regulated by the arthritis regulatory locus Cia25 and to determine how it operates to control disease severity and joint damage. Methods. Synovial tissues from DA rats and DA. ACI(Cia25) rats obtained 21 days after induction of pristane-induced arthritis were used for RNA extraction and hybridization to Illumina RatRef-12 Expression BeadChips (22,228 genes). Genes with a P value <= 0.01 and a fold difference in expression >= 1.5 between DA rats and DA. ACI(Cia25) rats were considered significant. Results. Interleukin-1 beta (IL-1 beta) (7.4-fold), IL-6 (67-fold), Ccl2, Cxcl10, Mmp3, Mmp14, and innate immunity genes were expressed at increased levels in DA rats and at significantly lower levels in DA. ACI( Cia25) congenic rats. DA. ACI(Cia25) rats had increased expression of 10 nuclear receptor (NR) genes, including those known to interfere with NF-kappa B activity and cytokine expression, such as Lxra, Pparg, and Rxrg. DA. ACI(Cia25) rats also had increased expression of NR targets, suggesting increased NR activity. While Vdr was not differentially expressed, a Vdr expression signature was detected in congenic rats, along with up-regulation of mediators of vitamin D synthesis. Conclusion. This is the first description of the association between increased synovial levels of NRs and arthritis protection. The expression of NRs was inversely correlated with the expression of key mediators of arthritis, suggesting reciprocally opposing effects either via NF-kappa B or at the genomic level in the synovial tissue. We consider that the NR signature may have an important role in maintaining synovial homeostasis and an inflammation-free tissue. These processes are regulated by the Cia25 gene and suggest a new function for this gene.

关键词： GENETICS of rheumatoid arthritis ANIMAL experimentation BIOLOGICAL models CHEMOKINES CHI-squared test GENETIC polymorphisms POLYMERASE chain reaction RATS FINANCING of research RHEUMATOID arthritis SYNOVIAL membranes T-test (Statistics) U-statistics EQUIPMENT & supplies SEVERITY of illness index REVERSE transcriptase polymerase chain reaction DATA analysis software microarray technology

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miR-10a overexpression is associated with NPM1 mutations and MDM4 downregulation in intermediate-risk acute myeloid leukemia

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EXPERIMENTAL HEMATOLOGY 2011年第10期39卷 1030-1042页

作者： Ovcharenko, Dmitriy Stoelzel, Friedrich Poitz, David Fierro, Fernando Schaich, Markus Neubauer, Andreas Kelnar, Kevin Davison, Timothy Mueller-Tidow, Carsten Thiede, Christian Bornhaeuser, Martin Ehninger, Gerhard Brown, David Illmer, Thomas Tech Univ Dresden Med Klin & Poliklin 1 D-8027 Dresden Germany Asuragen Inc Austin TX USA Altogen Labs Austin TX USA Tech Univ Dresden Kardiol Klin D-8027 Dresden Germany Univ Munster Klin Innere Med Hamatol & Onkol D-4400 Munster Germany Univ Marburg Marburg Germany Univ Hosp Klin Innere Med Hamatol Onkol & Immunol Giessen Germany Univ Hosp Klin Innere Med Hamatol Onkol & Immunol Marburg Germany

Objective. The study investigated differential microRNA (miRNA) expression patterns in acute myeloid leukemia (AML) patients with intermediate-risk (IR) characteristics. After characterization and validation of miR-10a, which was specifically upregulated in nucleophosmin 1 (NPM1) mutant AML samples, functional consequences of miR-10a overexpression were further delineated in vitro. Materials and Methods. microarray analysis of miRNAs in bone marrow samples from AML (IR) patients with NPM1 mutations and healthy donors was performed to detect differential expression patterns. After validation of miRNA expression specific for NPM1 mutation in AML patients by quantitative reverse transcription polymerase chain reaction, a functional target gene search was conducted using complementary DNA microarray data from samples transfected with miR-10a. Potential target gene validation was done using transient transfection of K562 cells followed by Western blotting and luciferase reporter assay. Results. In comparison with wild-type samples, NPM1 mutant AML samples were shown to markedly overexpress miR-10a. Subsequent in vitro miR-10a overexpression induced differential gene expression as determined by microarray analysis. Here the murine double minute 4 (MDM4) gene turned out as a candidate gene for miR-10a. Validation of MDM4 in leukemic cells revealed a robust negative relationship between miR-10a overexpression and MDM4 downregulation. Furthermore, we determined an inverse association between miR-10a and MDM4 expression in AML (IR) samples with respect to their NPM1 mutational status. Conclusions. miR-10a expression is highly characteristic for AML (IR) patients with NPM1 mutations and may influence its biological properties in AML by interfering with the p53 machinery partly regulated by MDM4. (C) 2011 ISEH - Society for Hematology and Stem Cells. Published by Elsevier Inc.

关键词： ACUTE myeloid leukemia GENE expression MUTATION (Biology) GENETIC regulation REVERSE transcriptase polymerase chain reaction microarray technology WESTERN immunoblotting LUCIFERASES

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Overexpression of SPACIA1/SAAL1, a newly identified gene that is involved in synoviocyte proliferation, accelerates the progression of synovitis in mice and humans

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ARTHRITIS AND RHEUMATISM 2011年第12期63卷 3833-3842页

作者： Sato, Tomoo Fujii, Ryoji Konomi, Koji Yagishita, Naoko Aratani, Satoko Araya, Natsumi Aono, Hiroyuki Yudoh, Kazuo Suzuki, Noboru Beppu, Moroe Yamano, Yoshihisa Nishioka, Kusuki Nakajima, Toshihiro St Marianna Univ Sch Med Inst Med Sci Miyamae Ku Kawasaki Kanagawa 2168512 Japan Santen Pharmaceut Co Ltd Osaka Japan Tokyo Med Univ Tokyo Japan Misato Marine Hosp Kochi Japan

Objective To identify novel genes associated with dysregulated proliferation of activated synovial fibroblasts, which are involved in arthritic joint destruction. Methods. We performed transcriptome analysis to identify genes that were up-regulated in the foot joints of mice with collagen-induced arthritis (CIA). The effect of candidate genes on proliferation of synovial fibroblasts was screened using antisense oligodeoxynucleotides and small interfering RNAs (siRNAs). We characterized the expression and function of a novel gene, synoviocyte proliferation-associated in collagen-induced arthritis 1 (SPACIA1)/serum amyloid A-like 1 (SAAL1) using antibodies and siRNA and established transgenic mice to examine the effect of SPACIA1/ SAAL1 overexpression in CIA. Results. Human and mouse SPACIA1/SAAL1 encoded 474 amino acid proteins that shared 80% homology. SPACIA1/SAAL1 was primarily expressed in the nucleus of rheumatoid arthritis (RA) synovial fibroblasts and was highly expressed in the hyperplastic lining of inflamed synovium. In addition, its expression level in RA-or osteoarthritis (OA)-affected synovial tissue was positively correlated with the thickness of the synovial lining. Furthermore, SPACIA1/SAAL1 siRNA inhibited the proliferation of synovial fibroblasts, especially tumor necrosis factor alpha-induced synovial fibroblasts, by blocking entry into the S phase without inducing apoptosis. Finally, transgenic mice overexpressing SPACIA1/SAAL1 exhibited early onset and rapid progression of CIA. Conclusion. These results suggest that SPACIA1/ SAAL1 is necessary for abnormal proliferation of synovial fibroblasts and its overexpression is associated with the progression of synovitis in mice and humans. Thus, therapy targeting SPACIA1/SAAL1 might have potential as an inhibitor of synovial proliferation in RA and/or OA.

关键词： SYNOVITIS ANALYSIS of variance ANIMAL experimentation BIOLOGICAL models CHI-squared test FISHER exact test IMMUNOHISTOCHEMISTRY KNEE MICE OSTEOARTHRITIS FINANCING of research RHEUMATOID arthritis STATISTICS T-test (Statistics) U-statistics WESTERN immunoblotting DATA analysis EQUIPMENT & supplies microarray technology GENETIC aspects

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