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Hephzibah Cathryn R, Udhaya Kumar S, Younes S, Zayed H, George Priya Doss C. A review of bioinformatics tools and web servers in different microarray platforms used in cancer research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:85-164. [PMID: 35871897 DOI: 10.1016/bs.apcsb.2022.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.
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Affiliation(s)
- R Hephzibah Cathryn
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
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Zhang LX, Yan H, Liu Y, Xu J, Song J, Yu DJ. Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. J Chem Inf Model 2022; 62:1794-1807. [PMID: 35353532 DOI: 10.1021/acs.jcim.1c01403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Characteristic gene selection and tumor classification of gene expression data play major roles in genomic research. Due to the characteristics of a small sample size and high dimensionality of gene expression data, it is a common practice to perform dimensionality reduction prior to the use of machine learning-based methods to analyze the expression data. In this context, classical principal component analysis (PCA) and its improved versions have been widely used. Recently, methods based on supervised discriminative sparse PCA have been developed to improve the performance of data dimensionality reduction. However, such methods still have limitations: most of them have not taken into consideration the improvement of robustness to outliers and noise, label information, sparsity, as well as capturing intrinsic geometrical structures in one objective function. To address this drawback, in this study, we propose a novel PCA-based method, known as the robust Laplacian supervised discriminative sparse PCA, termed RLSDSPCA, which enforces the L2,1 norm on the error function and incorporates the graph Laplacian into supervised discriminative sparse PCA. To evaluate the efficacy of the proposed RLSDSPCA, we applied it to the problems of characteristic gene selection and tumor classification problems using gene expression data. The results demonstrate that the proposed RLSDSPCA method, when used in combination with other related methods, can effectively identify new pathogenic genes associated with diseases. In addition, RLSDSPCA has also achieved the best performance compared with the state-of-the-art methods on tumor classification in terms of major performance metrics. The codes and data sets used in the study are freely available at http://csbio.njust.edu.cn/bioinf/rlsdspca/.
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Affiliation(s)
- Lu-Xing Zhang
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - He Yan
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Yan Liu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Jian Xu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
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3
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Jurischka C, Dinter F, Efimova A, Weiss R, Schiebel J, Schulz C, Fayziev B, Schierack P, Fischer T, Rödiger S. An explorative study of polymers for 3D printing of bioanalytical test systems. Clin Hemorheol Microcirc 2020; 75:57-84. [PMID: 31929149 DOI: 10.3233/ch-190713] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The 3D printing is relevant as a manufacturing technology of functional models for forensic, pharmaceutical and bioanalytical applications such as drug delivery systems, sample preparation and point-of-care tests. OBJECTIVE Melting behavior and autofluorescence of materials are decisive for optimal printing and applicability of the product which are influenced by varying unknown additives. METHODS We have produced devices for bioanalytical applications from commercially available thermoplastic polymers using a melt-layer process. We characterized them by differential scanning calorimetry, fluorescence spectroscopy and functional assays (DNA capture assay, model for cell adhesion, bacterial adhesion and biofilm formation test). RESULTS From 14 tested colored, transparent and black materials we found only deep black acrylonitrile-butadiene-styrene (ABS) and some black polylactic acid (PLA) useable for fluorescence-based assays, with low autofluorescence only in the short-wave range of 300-400 nm. PLA was suitable for standard bioanalytical purposes due to a glass transition temperature of approximately 60°C, resistance to common laboratory chemicals and easy print processing. For temperature-critical methods, such as hybridization reactions up to 90°C, ABS was better suited. CONCLUSIONS Autofluorescence was not a disadvantage per se but can also be used as a reference signal in assays. The rapid development of individual protocols for sample processing and analysis required the availability of a material with consistent quality over time. For fluorescence-based assays, the use of commercial standard materials did not seem to meet this requirement.
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Affiliation(s)
- Christoph Jurischka
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Anastasia Efimova
- Chair of Inorganic Chemistry, BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Romano Weiss
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Juliane Schiebel
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Schulz
- Project Group Pz-Syn, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Potsdam, Germany Located at the BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Bekzodjon Fayziev
- Chair of Mathematical Modeling, Samarkand State University, Samarkand, Uzbekistan
| | - Peter Schierack
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany
| | - Thomas Fischer
- Zentrales Analytisches Labor, BTU Cottbus - Senftenberg, Cottbus, Germany.,Study Program Forensic Sciences and Engineering, BTU Cottbus - Senftenberg, Cottbus, Germany
| | - Stefan Rödiger
- Chair of Multiparametric Diagnostics, BTU Cottbus - Senftenberg, Senftenberg, Germany.,Study Program Forensic Sciences and Engineering, BTU Cottbus - Senftenberg, Cottbus, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Senftenberg, Germany
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Abstract
RNA sequencing (RNA-seq) is a recently developed approach to perform transcriptome profiling using next-generation sequencing (NGS) technologies. Studies have shown that RNA-seq provides accurate measurement of transcript levels as well as their isoforms, which is useful to address complex transcriptomes. In addition, the increasing publicly available sequencing datasets and decreasing sequencing cost promote the use of RNA-seq for hypothesis-generating studies. In this chapter, we demonstrate how to analyze RNA-seq data and generate interpretable results using CLC genomic workbench software and perform the downstream pathway analysis using ingenuity pathway analysis (IPA).
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Affiliation(s)
- Chia-Hsin Liu
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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6
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Cauley AN, Wilson JN. Functionalized lignin biomaterials for enhancing optical properties and cellular interactions of dyes. Biomater Sci 2018; 5:2114-2121. [PMID: 28831468 DOI: 10.1039/c7bm00518k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report a library of functionalized lignins and demonstrate their utility as nanocontainers for organic dyes in biologically relevant applications. Kraft lignin was modified via SN2 reaction at the phenolic -OH group utilizing a mild base, potassium carbonate, and various alkyl halides, several bearing additional functionalities, with dimethylsulfoxide as solvent. The resulting phenoxy ethers were characterized by 1H-NMR and IR spectroscopy, as well as DLS and SEM to evaluate their morphology and supramolecular organization. Lignin modified with long-chain hydrocarbon tails was found to effectively encapsulate DiD, a cyanine dye, decrease aggregation, enhance optical transitions and exert a photoprotective effect. The dye-lignin assemblies were also examined as imaging agents, via confocal microscopy, and found to accumulate intracellularly with no leaching of the dye to hydrophobic subcellular components observed. Lignin functionalized with short chain carboxylic acids interacts with ligands directed at the norepinephrine transporter (NET), suggesting applications in sequestration of neuroactive compounds.
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Affiliation(s)
- Anthony N Cauley
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33124, USA.
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7
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A landscape of bioinformatics patents - Garnering of IPR in the field of bioinformatics. WORLD PATENT INFORMATION 2017. [DOI: 10.1016/j.wpi.2017.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Wechalekar MD, Smith MD. Arthroscopic guided synovial biopsy in rheumatology: current perspectives. Int J Rheum Dis 2016; 20:141-144. [DOI: 10.1111/1756-185x.13020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mihir D. Wechalekar
- Rheumatology Unit; Repatriation General Hospital; Adelaide South Australia Australia
- Flinders University of South Australia; Adelaide South Australia Australia
| | - Malcolm D. Smith
- Flinders University of South Australia; Adelaide South Australia Australia
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9
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Cho SS, Kim Y, Yoon J, Seo M, Shin SK, Kwon EY, Kim SE, Bae YJ, Lee S, Sung MK, Choi MS, Park T. A Model-Based Joint Identification of Differentially Expressed Genes and Phenotype-Associated Genes. PLoS One 2016; 11:e0149086. [PMID: 26964035 PMCID: PMC4786130 DOI: 10.1371/journal.pone.0149086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last decade, many analytical methods and tools have been developed for microarray data. The detection of differentially expressed genes (DEGs) among different treatment groups is often a primary purpose of microarray data analysis. In addition, association studies investigating the relationship between genes and a phenotype of interest such as survival time are also popular in microarray data analysis. Phenotype association analysis provides a list of phenotype-associated genes (PAGs). However, it is sometimes necessary to identify genes that are both DEGs and PAGs. We consider the joint identification of DEGs and PAGs in microarray data analyses. The first approach we used was a naïve approach that detects DEGs and PAGs separately and then identifies the genes in an intersection of the list of PAGs and DEGs. The second approach we considered was a hierarchical approach that detects DEGs first and then chooses PAGs from among the DEGs or vice versa. In this study, we propose a new model-based approach for the joint identification of DEGs and PAGs. Unlike the previous two-step approaches, the proposed method identifies genes simultaneously that are DEGs and PAGs. This method uses standard regression models but adopts different null hypothesis from ordinary regression models, which allows us to perform joint identification in one-step. The proposed model-based methods were evaluated using experimental data and simulation studies. The proposed methods were used to analyze a microarray experiment in which the main interest lies in detecting genes that are both DEGs and PAGs, where DEGs are identified between two diet groups and PAGs are associated with four phenotypes reflecting the expression of leptin, adiponectin, insulin-like growth factor 1, and insulin. Model-based approaches provided a larger number of genes, which are both DEGs and PAGs, than other methods. Simulation studies showed that they have more power than other methods. Through analysis of data from experimental microarrays and simulation studies, the proposed model-based approach was shown to provide a more powerful result than the naïve approach and the hierarchical approach. Since our approach is model-based, it is very flexible and can easily handle different types of covariates.
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Affiliation(s)
- Samuel Sunghwan Cho
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
| | - Joon Yoon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
| | - Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
| | - Su-kyung Shin
- Center for Food and Nutritional Genomics Research, Department of Food Science and Nutrition, Kyungpook National University, Daegu, Korea
| | - Eun-Young Kwon
- Center for Food and Nutritional Genomics Research, Department of Food Science and Nutrition, Kyungpook National University, Daegu, Korea
| | - Sung-Eun Kim
- Department of Food and Nutrition, Sookmyung Women’s University, Seoul, Korea
| | - Yun-Jung Bae
- Division of Food Science and Culinary Arts, Shinhan University, Gyeonggi, Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Seoul, Korea
| | - Mi-Kyung Sung
- Department of Food and Nutrition, Sookmyung Women’s University, Seoul, Korea
| | - Myung-Sook Choi
- Center for Food and Nutritional Genomics Research, Department of Food Science and Nutrition, Kyungpook National University, Daegu, Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
- Department of Statistics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, Korea
- * E-mail:
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10
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Surface plasmon resonance imaging (SPRi) for analysis of DNA aptamer:β-conglutin interactions. Methods 2015; 97:20-6. [PMID: 26515644 DOI: 10.1016/j.ymeth.2015.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 12/22/2022] Open
Abstract
Surface plasmon resonance imaging (SPRi) is a label-free detection method that offers a suitable and reliable platform for the real time monitoring of biomolecular interactions. In the work reported here, SPRi was used to evaluate the affinity and specificity of three different aptamers selected against the Lup an 1 anaphylactic allergen β-conglutin (β-conglutin binding aptamers I and II (β-CBA I and β-CBA II)), as well as an 11-mer truncated version of β-CBA I. Thiol modified aptamers were immobilised on a gold substrate through a self-assembling process and the use of different blocking strategies to prevent non-specific binding were evaluated. Dissociation constants of 20, 13 and 1 nM were determined for β-CBA I, β-CBA II and the 11-mer truncated aptamer, respectively. The three aptamers were then studied in various different sandwich formats and the β-CBA I/11-mer and β-CBA II were observed to bind to different aptatopes on the target protein. Each of the aptamers were then used either as surface immobilised aptamer, or as reporter aptamer, and added with the protein target β-conglutin in either a sequential of simultaneous manner, and the changes in SPR signal monitored. The preferred approach for formation of a sandwich aptacomplex was with immobilised β-CBA II, followed by addition of pre-incubated β-conglutin and 11-mer, whilst addition of the 11-mer following addition of the β-conglutin, resulted in displacement of the bound target. The ability to provide parallel qualitative and quantitative detection establishes SPRi as a powerful tool for the study of immobilised aptamer-target interactions.
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Li J, Hou R, Niu X, Liu R, Wang Q, Wang C, Li X, Hao Z, Yin G, Zhang K. Comparison of microarray and RNA-Seq analysis of mRNA expression in dermal mesenchymal stem cells. Biotechnol Lett 2015; 38:33-41. [DOI: 10.1007/s10529-015-1963-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/22/2015] [Indexed: 12/28/2022]
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12
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Giannopoulou EG, Elemento O, Ivashkiv LB. Use of RNA sequencing to evaluate rheumatic disease patients. Arthritis Res Ther 2015; 17:167. [PMID: 26126608 PMCID: PMC4488125 DOI: 10.1186/s13075-015-0677-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the detection of non-coding transcripts and alternative splicing events. In this review, we describe how RNA sequencing enables unbiased interrogation of the abundance and complexity of the transcriptome, and present a typical experimental workflow and bioinformatics tools that are often used for RNA sequencing analysis. We also discuss different uses of this next-generation sequencing technology to evaluate rheumatic disease patients and investigate the pathogenesis of rheumatic diseases such as rheumatoid arthritis, systemic lupus erythematosus, juvenile idiopathic arthritis and Sjögren’s syndrome.
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Affiliation(s)
- Eugenia G Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, 11201, USA. .,Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
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13
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Fumagalli D, Blanchet-Cohen A, Brown D, Desmedt C, Gacquer D, Michiels S, Rothé F, Majjaj S, Salgado R, Larsimont D, Ignatiadis M, Maetens M, Piccart M, Detours V, Sotiriou C, Haibe-Kains B. Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology. BMC Genomics 2014; 15:1008. [PMID: 25412710 PMCID: PMC4289354 DOI: 10.1186/1471-2164-15-1008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/10/2014] [Indexed: 01/02/2023] Open
Abstract
Background Microarrays have revolutionized breast cancer (BC) research by enabling studies of gene expression on a transcriptome-wide scale. Recently, RNA-Sequencing (RNA-Seq) has emerged as an alternative for precise readouts of the transcriptome. To date, no study has compared the ability of the two technologies to quantify clinically relevant individual genes and microarray-derived gene expression signatures (GES) in a set of BC samples encompassing the known molecular BC’s subtypes. To accomplish this, the RNA from 57 BCs representing the four main molecular subtypes (triple negative, HER2 positive, luminal A, luminal B), was profiled with Affymetrix HG-U133 Plus 2.0 chips and sequenced using the Illumina HiSeq 2000 platform. The correlations of three clinically relevant BC genes, six molecular subtype classifiers, and a selection of 21 GES were evaluated. Results 16,097 genes common to the two platforms were retained for downstream analysis. Gene-wise comparison of microarray and RNA-Seq data revealed that 52% had a Spearman’s correlation coefficient greater than 0.7 with highly correlated genes displaying significantly higher expression levels. We found excellent correlation between microarray and RNA-Seq for the estrogen receptor (ER; rs = 0.973; 95% CI: 0.971-0.975), progesterone receptor (PgR; rs = 0.95; 0.947-0.954), and human epidermal growth factor receptor 2 (HER2; rs = 0.918; 0.912-0.923), while a few discordances between ER and PgR quantified by immunohistochemistry and RNA-Seq/microarray were observed. All the subtype classifiers evaluated agreed well (Cohen’s kappa coefficients >0.8) and all the proliferation-based GES showed excellent Spearman correlations between microarray and RNA-Seq (all rs >0.965). Immune-, stroma- and pathway-based GES showed a lower correlation relative to prognostic signatures (all rs >0.6). Conclusions To our knowledge, this is the first study to report a systematic comparison of RNA-Seq to microarray for the evaluation of single genes and GES clinically relevant to BC. According to our results, the vast majority of single gene biomarkers and well-established GES can be reliably evaluated using the RNA-Seq technology. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1008) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory (BCTL), Institut Jules Bordet, Brussels, Belgium.
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Gene Expression Profiling of Tumors From Heavily Pretreated Patients With Metastatic Cancer for the Selection of Therapy: A Pilot Study. Am J Clin Oncol 2014; 40:140-145. [PMID: 25144266 DOI: 10.1097/coc.0000000000000116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Recently, it has been shown that it is possible to identify tumor profiles of sensitivity for potentially useful drugs, both conventional and experimental, based on whole oligonucleotide microarray gene expression studies in heavily pretreated patients with metastatic solid tumors. METHODS Fresh-frozen tumor biopsies for molecular profiling (MP) were obtained from patients with advanced and refractory cancer. Total tumor and control tissue RNA was hybridized to a whole human genome oligonucleotide microarray. Differentially expressed genes interacting with potential therapeutic targets were identified. Results were complemented with DNA sequencing of selected driver genes and with immunohistochemistry and fluorescent "in situ" hybridization. The results were used to guide experimental treatment. RESULTS MP assays led to a potentially active available drug in 91.2% of the patients. The median number of available active drugs per tumor was 5 (range, 1 to 9). Nine treated patients were not evaluable for response. Partial response was observed in 18 patients (33%), stable disease in 22 patients (40%) (clinical benefit rate of 73%), and progression in 15 (27%). Overall median progression-free survival and overall survival were 8 and 13 months, respectively. CONCLUSION MP-guided therapy is feasible and seems to improve the clinical outcome of extensively pretreated patients but prospective and confirmatory trials are needed.
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15
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Hong SH, Goh SH, Lee SJ, Hwang JA, Lee J, Choi IJ, Seo H, Park JH, Suzuki H, Yamamoto E, Kim IH, Jeong JS, Ju MH, Lee DH, Lee YS. Upregulation of adenylate cyclase 3 (ADCY3) increases the tumorigenic potential of cells by activating the CREB pathway. Oncotarget 2014; 4:1791-803. [PMID: 24113161 PMCID: PMC3858564 DOI: 10.18632/oncotarget.1324] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Adenylate cyclase 3 (ADCY3) is a widely expressed membrane-associated protein in human tissues, which catalyzes the formation of cyclic adenosine-3′,5′-monophosphate (cAMP). However, our transcriptome analysis of gastric cancer tissue samples (NCBI GEO GSE30727) revealed that ADCY3 expression was specifically altered in cancer samples. Here we investigated the tumor-promoting effects of ADCY3 overexpression and confirmed a significant correlation between the upregulation of ADCY3 and Lauren's intestinal-type gastric cancers. ADCY3 overexpression increased cell migration, invasion, proliferation, and clonogenicity in HEK293 cells; conversely, silencing ADCY3 expression in SNU-216 cells reduced these phenotypes. Interestingly, ADCY3 overexpression increased both the mRNA level and activity of matrix metalloproteinase 2 (MMP2) and MMP9 by increasing the levels of cAMP and phosphorylated cAMP-responsive element-binding protein (CREB). Consistent with these findings, treatment with a protein kinase A (PKA) inhibitor decreased MMP2 and MMP9 expression levels in ADCY3-overexpressing cells. Knockdown of ADCY3 expression by stable shRNA in human gastric cancer cells suppressed tumor growth in a tumor xenograft model. Thus, ADCY3 overexpression may exert its tumor-promoting effects via the cAMP/PKA/CREB pathway. Additionally, bisulfite sequencing of the ADCY3 promoter region revealed that gene expression was reduced by hypermethylation of CpG sites, and increased by 5-Aza-2′-deoxycytidine (5-Aza-dC)-induced demethylation. Our study is the first to report an association of ADCY3 with gastric cancer as well as its tumorigenic potentials. In addition, we demonstrate that the expression of ADCY3 is regulated through an epigenetic mechanism. Further study on the mechanism of ADCY3 in tumorigenesis will provide the basis as a new molecular target of gastric cancer.
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Affiliation(s)
- Seung-Hyun Hong
- Cancer Genomics Branch, Research Institute, National Cancer Center, Republic of Korea
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Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet 2014; 46:588-94. [PMID: 24793136 DOI: 10.1038/ng.2981] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/11/2014] [Indexed: 12/15/2022]
Abstract
Coordinate control of different classes of cyclins is fundamentally important for cell cycle regulation and tumor suppression, yet the underlying mechanisms are incompletely understood. Here we show that the PARK2 tumor suppressor mediates this coordination. The PARK2 E3 ubiquitin ligase coordinately controls the stability of both cyclin D and cyclin E. Analysis of approximately 5,000 tumor genomes shows that PARK2 is a very frequently deleted gene in human cancer and uncovers a striking pattern of mutual exclusivity between PARK2 deletion and amplification of CCND1, CCNE1 or CDK4-implicating these genes in a common pathway. Inactivation of PARK2 results in the accumulation of cyclin D and acceleration of cell cycle progression. Furthermore, PARK2 is a component of a new class of cullin-RING-containing ubiquitin ligases targeting both cyclin D and cyclin E for degradation. Thus, PARK2 regulates cyclin-CDK complexes, as does the CDK inhibitor p16, but acts as a master regulator of the stability of G1/S cyclins.
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Chang J, Oikawa S, Iwahashi H, Kitagawa E, Takeuchi I, Yuda M, Aoki C, Yamada Y, Ichihara G, Kato M, Ichihara S. Expression of proteins associated with adipocyte lipolysis was significantly changed in the adipose tissues of the obese spontaneously hypertensive/NDmcr-cp rat. Diabetol Metab Syndr 2014; 6:8. [PMID: 24468282 PMCID: PMC3937142 DOI: 10.1186/1758-5996-6-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 01/09/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The etiology of the metabolic syndrome is complex, and is determined by the interplay of both genetic and environmental factors. The present study was designed to identify genes and proteins in the adipose tissues with altered expression in the spontaneously hypertensive/NIH -corpulent rat, SHR/NDmcr-cp (CP) and to find possible molecular targets associated with the pathogenesis or progression of obesity related to the metabolic syndrome. METHODS We extracted RNAs and proteins from the epididymal adipose tissues in CP, SHR/Lean (Lean), and Wistar Kyoto (WKY) rats and performed microarray analysis and two-dimensional difference in gel electrophoresis (2D-DIGE) linked to a matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS). RESULTS The results showed different mRNA and protein expression levels in the adipose tissue: oligo DNA microarray identified 33 genes that were significantly (P < 0.01) up-regulated and 17 genes significantly down-regulated in CP compared with WKY and Lean rats at both 6 and 25 weeks of age. The affected genes-proteins were associated with lipolytic enzymes stimulated by peroxisome proliferator-activated receptor (PPAR) signaling. Further analysis using the 2D-DIGE connected with MALDI-TOF/TOF analysis, the expression of monoglyceride lipase (MGLL) was significantly up-regulated and that of carboxylesterase 3 (CES3) was significantly down-regulated in 6- and 25-week-old CP compared with age-matched control (WKY and Lean rats). CONCLUSIONS Our results suggest the possible involvement of proteins associated with adipocyte lipolysis in obesity related to the metabolic syndrome.
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Affiliation(s)
- Jie Chang
- Graduate School of Regional Innovation Studies, Mie University, 1577 Kurimamachiya-cho, Tsu 514-8507, Japan
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinji Oikawa
- Department of Molecular and Environmental Medicine, Mie University Graduate School of Medicine, Tsu, Japan
| | - Hitoshi Iwahashi
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Present address: Graduate School of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Emiko Kitagawa
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Present address: Applied Science, Roche Diagnostics, Tokyo, Japan
| | - Ichiro Takeuchi
- Department of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Masao Yuda
- Department of Medical Zoology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Chieko Aoki
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan
| | - Yoshiji Yamada
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan
| | - Gaku Ichihara
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Kato
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sahoko Ichihara
- Graduate School of Regional Innovation Studies, Mie University, 1577 Kurimamachiya-cho, Tsu 514-8507, Japan
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan
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Poirel L, Bonnin RA, Nordmann P. Rapid identification of antibiotic-resistant bacteria: how could new diagnostic tests halt potential endemics? Expert Rev Mol Diagn 2013; 13:409-11. [PMID: 23782246 DOI: 10.1586/erm.13.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zhou WJ, Halpern AR, Seefeld TH, Corn RM. Near infrared surface plasmon resonance phase imaging and nanoparticle-enhanced surface plasmon resonance phase imaging for ultrasensitive protein and DNA biosensing with oligonucleotide and aptamer microarrays. Anal Chem 2011; 84:440-5. [PMID: 22126812 DOI: 10.1021/ac202863k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The techniques of surface plasmon resonance-phase imaging (SPR-PI) and nanoparticle-enhanced SPR-PI have been implemented for the multiplexed bioaffinity detection of proteins and nucleic acids. The SPR-PI experiments utilized a near-infrared 860 nm light emitting diode (LED) light source and a wedge depolarizer to create a phase grating on a four-element single-stranded DNA (ssDNA) microarray; bioaffinity adsorption onto the various microarray elements was detected via multiplexed real time phase shift measurements. In a first set of demonstration experiments, an ssDNA aptamer microarray was used to directly detect thrombin at concentrations down to 100 pM with SPR-PI. Two different ssDNA aptamers were used in these experiments with two different Langmuir adsorption coefficients, K(A1) = 4.4 × 10(8) M(-1) and K(A2) = 1.2 × 10(8) M(-1). At concentrations below 1 nM, the equilibrium phase shifts observed upon thrombin adsorption vary linearly with concentration with a slope that is proportional to the appropriate Langmuir adsorption coefficient. The observed detection limit of 100 pM is approximately 20 times more sensitive than that observed previously with SPRI. In a second set of experiments, two short ssDNA oligonucleotides (38mers) were simultaneously detected at concentrations down to 25 fM using a three-sequence hybridization format that employed 120 nm DNA-modified silica nanoparticles to enhance the SPR-PI signal. In this first demonstration of nanoparticle-enhanced SPR-PI, the adsorbed silica nanoparticles provided a greatly enhanced phase shift upon bioaffinity adsorption due to a large increase in the real component of the interfacial refractive index from the adsorbed nanoparticle. As in the case of SPR-PI, the detection limit of 25 fM for nanoparticle-enhanced SPR-PI is approximately 20 times more sensitive than that observed previously with nanoparticle-enhanced SPRI.
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Affiliation(s)
- Wen-Juan Zhou
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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Khan S, Elshaer A, Rahman AS, Hanson P, Perrie Y, Mohammed AR. Systems biology approach to study permeability of paracetamol and its solid dispersion. Int J Pharm 2010; 417:272-9. [PMID: 21187133 DOI: 10.1016/j.ijpharm.2010.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 12/17/2010] [Accepted: 12/18/2010] [Indexed: 10/18/2022]
Abstract
Physiological changes that take place at cellular level are usually reflective of their level of gene expression. Different formulation excipients have an impact on physiological behavior of the exposed cells and in turn affect transporter genes, enterocyte-mediated metabolism and toxicity biomarkers. The aim of this study was to prepare solid dispersion of paracetamol and evaluate genetic changes that occur in Caco-2 cell lines during the permeability of paracetamol alone and paracetamol solid dispersion formulations. Paracetamol-PEG 8000 solid dispersion was prepared by melt fusion method and the formulation was characterised using differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). Formulation of solid dispersion resulted in the conversion of crystalline drug into an amorphous form. Permeability studies showed that paracetamol absorption was higher from the solid dispersion formulation. DNA microarrays analysis was carried out in order to investigate the involvement of any efflux/uptake transporters in paracetamol or its solid dispersion permeability. Neither transporter carriers nor efflux proteins were found to be involved in the absorption of paracetamol or its PEG solid dispersion. Gene expression analysis established that paracetamol toxicity was potentially reduced upon formulation into solid dispersion when ATP binding cassette (ABC) and solute carrier transporter (SLC) genes were analyzed.
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Affiliation(s)
- Sheraz Khan
- Aston Pharmacy School, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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Theron J, Eugene Cloete T, de Kwaadsteniet M. Current molecular and emerging nanobiotechnology approaches for the detection of microbial pathogens. Crit Rev Microbiol 2010; 36:318-39. [DOI: 10.3109/1040841x.2010.489892] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Liu Z, Ma S, Ji Y, Liu L, Hu Z, Guo J, Ma H, He Y. Quasi-Confocal, Multichannel Parallel Scan Hyperspectral Fluorescence Imaging Method Optimized for Analysis of Multicolor Microarrays. Anal Chem 2010; 82:7752-7. [DOI: 10.1021/ac101629x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zhiyi Liu
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Suihua Ma
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Yanhong Ji
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Le Liu
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Zhaoxu Hu
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Jihua Guo
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Hui Ma
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
| | - Yonghong He
- Laboratory of Optical Imaging and Sensing, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, P. R. China, and MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, Guangzhou, 510631, P. R. China
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Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med 2010; 12:85-92. [PMID: 20084009 DOI: 10.1097/gim.0b013e3181cc75d0] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To determine the sensitivity of whole-genome oligonucleotide array comparative genomic hybridization for the detection of mosaic cytogenetic abnormalities. METHODS Mosaicism sensitivity was evaluated by testing artificially derived whole chromosome and segmental aneuploidies ranging from 0% to 100% abnormal and additional naturally occurring mosaic specimens. RESULTS Using combined dye-reversed replicates and an unfiltered analysis, oligonucleotide array comparative genomic hybridization detected as low as 10% and 20-30% mosaicism from whole chromosome and segmental aneuploidies, respectively. To investigate discrepancies between cultured and uncultured specimens, array comparative genomic hybridization was performed on DNA from additional direct product of conception specimens with abnormal karyotypes in culture. Interestingly, 5 of 10 product of conception specimens with double trisomies on cultured cell analysis had only a single trisomy by array comparative genomic hybridization and quantitative polymerase chain reaction on DNA from the uncultured direct specimen, and all harbored the more commonly observed trisomy. Thus, oligonucleotide array comparative genomic hybridization revealed previously unidentified placental mosaicism in half of the products of conception with double-aneuploid conventional karyotypes. CONCLUSION Oligonucleotide array comparative genomic hybridization can detect low-level mosaicism for whole chromosome ( approximately 10%) and segmental ( approximately 20-30%) aneuploidies when using specific detection criteria. In addition, careful interpretation is required when performing array comparative genomic hybridization on DNA isolated from direct specimens as the results may differ from the cultured chromosome analysis.
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Metabolic profiling of transgenic rice with cryIAc and sck genes: An evaluation of unintended effects at metabolic level by using GC-FID and GC–MS. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:725-32. [DOI: 10.1016/j.jchromb.2009.01.040] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 01/29/2009] [Accepted: 01/29/2009] [Indexed: 11/17/2022]
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Baserga A, Viganò M, Casari CS, Turri S, Li Bassi A, Levi M, Bottani CE. Au-Ag template stripped pattern for scanning probe investigations of DNA arrays produced by dip pen nanolithography. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13212-13217. [PMID: 18950214 DOI: 10.1021/la801903u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report on DNA arrays produced by dip pen nanolithography (DPN) on a novel Au-Ag micropatterned template stripped surface. DNA arrays have been investigated by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) showing that the patterned template stripped substrate enables easy retrieval of the DPN-functionalized zone with a standard optical microscope permitting multi-instrument and multitechnique local detection and analysis. Moreover the smooth surface of the Au squares ( approximately 5-10 A roughness) allows AFM/STM to be sensitive to the hybridization of the oligonucleotide array with label-free target DNA. Our Au-Ag substrates, combining the retrieving capabilities of the patterned surface with the smoothness of the template stripped technique, are candidates for the investigation of DPN nanostructures and for the development of label-free detection methods for DNA nanoarrays based on the use of scanning probes.
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Affiliation(s)
- Andrea Baserga
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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Progress in fabricating arrays of soft spherical vessels on mesoscale with spatial control. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0485-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sagarzazu G, Bedu M, Martinelli L, Pelletier N, Safarov VI, Weisbuch C, Gacoin T, Benisty H. Quantitative analysis of enhanced light irradiance in waveguide-based fluorescent microarrays. Biosens Bioelectron 2008; 24:2281-4. [PMID: 19110414 DOI: 10.1016/j.bios.2008.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 10/30/2008] [Accepted: 11/05/2008] [Indexed: 10/21/2022]
Abstract
Probing microarray assays in the presence of a hybridization mix retrieves precious information on hybridization kinetics. However, in common detection schemes, useful surface signals compete with the high supernatant background from labelled targets in the mix. A known solution consists in exciting specifically the microarray surface with evanescent fields. Configurations using planar optical waveguides to produce such fields are shown here to present also a dramatic excitation irradiance enhancement at the guide/surrounding matter interface. We compare theoretically and experimentally a guided excitation with a classical external excitation. A full electromagnetic analysis predicts an irradiance increase higher than 10(4) for adequately tailored waveguides. We deposited high-index TiO(2) sol-gel waveguides on glass substrates according to best simulations. Quantitative enhancement analysis exploiting actual biological fluorescent spots perfectly confirms the irradiance amplification effect of a thin waveguide. The impact of amplification on the design of biochip readers is discussed since it leaves ample margin for simple and low-cost light couplers, advantageous in affordable readers and sensor systems.
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Novel developments for improved detection of specific mRNAs by DNA chips. Appl Microbiol Biotechnol 2008; 80:953-63. [PMID: 18784921 DOI: 10.1007/s00253-008-1680-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/20/2008] [Accepted: 08/21/2008] [Indexed: 10/21/2022]
Abstract
Microarrays have revolutionized gene expression analysis as they allow for highly parallel monitoring of mRNA levels of thousands of genes in a single experiment. Since their introduction some 15 years ago, substantial progress has been achieved with regard to, e.g., faster or more sensitive analyses. In this review, interesting new approaches for a more sensitive detection of specific mRNAs will be highlighted. Particularly, the potential of electrical DNA chip formats that allow for faster mRNA analyses will be discussed.
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Jin ZL, Zhang YK, Sun HY, Lin Z, Bi YC, Duan YZ, Ding Y. Osteogenic-related gene expression profiles of human dental follicle cells induced by dexamethasone. Acta Pharmacol Sin 2008; 29:1013-20. [PMID: 18718169 DOI: 10.1111/j.1745-7254.2008.00834.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM Human dental follicle cells (hDFC) have the ability to differentiate into mineralized tissue-forming cells during root and periodontal development or osteogenic induction in vitro. The present study aimed to validate the osteogenic induction of hDFC by dexamethasone (DEX) and to explore the changes of related genes responsible for the osteogenic differentiation process. METHODS Passage-cultured hDFC were induced by DEX and analyzed for mineralization activity by morphological observation, alkaline phosphatase (ALP) activity, and alizarin red S staining. GEArray Q series human osteogenesis gene array was used to describe large-scale gene expression in treated hDFC compared to the control group. Quantitative real-time RT-PCR was performed to confirm the microarray data by analyzing the expression of 7 critical transcripts. RESULTS Osteogenic differentiation of hDFC was confirmed by morphological change, elevated ALP activity and calcified nodules. In 96 genes investigated through the microarray analysis, 20 genes were upregulated and 8 genes were downregulated more than 2-fold. The results of the real-time RT-PCR correlated with the microarray analysis. The expression of the transforming growth factor-beta superfamily showed varying degrees of increase, and fibroblast growth factors exhibited a differential changing trend of expression. The expression of most types of collagen genes representative of extracellular matrixes increased under DEX treatment while small mothers against decapentaplegic 6 and 7 expressions significantly decreased. CONCLUSION Our results demonstrated that hDFC displayed osteoblastic features in both phenotypic and genotypic traits induced by DEX in vitro.
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Affiliation(s)
- Zuo-lin Jin
- Department of Orthodontics, School of Stomatology, Fourth Military Medical University, Xi'an 710032, China.
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Kaushik DK, Sehgal D. Developing Antibacterial Vaccines in Genomics and Proteomics Era. Scand J Immunol 2008; 67:544-52. [DOI: 10.1111/j.1365-3083.2008.02107.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rodenburg W, Keijer J, Kramer E, Vink C, van der Meer R, Bovee-Oudenhoven IMJ. Impaired barrier function by dietary fructo-oligosaccharides (FOS) in rats is accompanied by increased colonic mitochondrial gene expression. BMC Genomics 2008; 9:144. [PMID: 18371188 PMCID: PMC2311291 DOI: 10.1186/1471-2164-9-144] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 03/27/2008] [Indexed: 12/31/2022] Open
Abstract
Background Dietary non-digestible carbohydrates stimulate the gut microflora and are therefore presumed to improve host resistance to intestinal infections. However, several strictly controlled rat infection studies showed that non-digestible fructo-oligosaccharides (FOS) increase, rather than decrease, translocation of Salmonella towards extra-intestinal sites. In addition, it was shown that FOS increases intestinal permeability already before infection. The mechanism responsible for this adverse effect of FOS is unclear. Possible explanations are altered mucosal integrity due to changes in tight junctions or changes in expression of defense molecules such as antimicrobials and mucins. To examine the mechanisms underlying weakening of the intestinal barrier by FOS, a controlled dietary intervention study was performed. Two groups of 12 rats were adapted to a diet with or without FOS. mRNA was collected from colonic mucosa and changes in gene expression were assessed for each individual rat using Agilent rat whole genome microarrays. Results Among the 997 FOS induced genes we observed less mucosal integrity related genes than expected with the clear permeability changes. FOS did not induce changes in tight junction genes and only 8 genes related to mucosal defense were induced by FOS. These small effects are unlikely the cause for the clear increase in intestinal permeability that is observed. FOS significantly increased expression of 177 mitochondria-related genes. More specifically, induced expression of genes involved in all five OXPHOS complexes and the TCA cycle was observed. These results indicate that dietary FOS influences intestinal mucosal energy metabolism. Furthermore, increased expression of 113 genes related to protein turnover, including proteasome genes, ribosomal genes and protein maturation related genes, was seen. FOS upregulated expression of the peptide hormone proglucagon gene, in agreement with previous studies, as well as three other peptide hormone genes; peptide YY, pancreatic polypeptide and cholecystokinin. Conclusion We conclude that altered energy metabolism may underly colonic barrier function disruption due to FOS feeding in rats.
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Wu YT, Liao JD, Lin JI, Lu CC. Determination of the optimized conditions for coupling oligonucleotides with 16-mercaptohexadecanoic acid chemically adsorbed upon Au. Bioconjug Chem 2007; 18:1897-904. [PMID: 17970584 DOI: 10.1021/bc700217n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A specific 5'-modified amino group oligonucleotide (Primer 1), 15-mers in length, is selectively coupled with the carboxyl terminated 16-mercaptohexadecanoic acid (MHDA) chemically adsorbed on Au and subsequently hybridized with Antisense Primer. The amide-coupling process is of significance to create an intermediate structure for the purpose of adding Primer 1, while the hybridization reaction is relevant to various diagnostic purposes to determine the presence in nucleic acids for a target sequence. In this work, the coupling setting was particularly emphasized by varying commonly used temperatures and pH values with a definite concentration of coupling agents (i.e., 10 mM). The recombination with analogous hybridization treatment was investigated using high resolution X-ray photoelectron spectroscopy and a 75 degrees grazing angle Fourier transform infrared spectrometer. On the basis of the spectroscopic studies, the optimized conditions for the coupling process that is also correlated with the molecular density of subsequent hybridization process on MHDA/Au have been proposed at 37 degrees C and a pH value of 4.5. Therefore, it is pertinent to intensify the joining of short-chain DNA strands by complementary base pairing in diagnostic applications such as the identification of single nucleotide polymorphisms.
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Affiliation(s)
- Yi-Te Wu
- Department of Materials Science and Engineering, Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan, Taiwan
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Singh S, Kumar P, Gupta KC, Singh RK. Synthesis and biophysical studies on fluorescently labeled oligodeoxyribonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:521-31. [PMID: 17578747 DOI: 10.1080/15257770701426294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Two highly fluorescent compounds, viz. 6-(6-isobutyrylamino-1,3-dioxo-1 H,3H-benzo[de]isoquinolin-2-yl)-hexanoic acid and 6-(6-dimethylamino-1,3-dioxo-1 H,3H-benzo[de]isoqu-inolin-2-yl)-hexanoic acid have been synthesized, characterized, and attached to 12-mer oligodeoxyribonucleotides at their 5'-end using suitable linker molecule. These labeled oligodeoxyribonucleotides have shown appreciable fluorescence even at 0.0019 microM concentrations. Thermal denaturation studies have shown comparatively higher Tm values when oligodeoxyribonucleotides are labeled. These labeled oligodeoxyribonucleotides have been purified on RP-HPLC utilizing their hydrophobicity and on polyacrylamide gel because of their easy detection due to fluorescence.
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Affiliation(s)
- Shipra Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
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Rodenburg W, Keijer J, Kramer E, Roosing S, Vink C, Katan MB, van der Meer R, Bovee-Oudenhoven IMJ. Salmonella induces prominent gene expression in the rat colon. BMC Microbiol 2007; 7:84. [PMID: 17850650 PMCID: PMC2048963 DOI: 10.1186/1471-2180-7-84] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Accepted: 09/12/2007] [Indexed: 11/25/2022] Open
Abstract
Background Salmonella enteritidis is suggested to translocate in the small intestine. In vivo it induces gene expression changes in the ileal mucosa and Peyer's patches. Stimulation of Salmonella translocation by dietary prebiotics fermented in colon suggests involvement of the colon as well. However, effects of Salmonella on colonic gene expression in vivo are largely unknown. We aimed to characterize time dependent Salmonella-induced changes of colonic mucosal gene expression in rats using whole genome microarrays. For this, rats were orally infected with Salmonella enteritidis to mimic a foodborne infection and colonic gene expression was determined at days 1, 3 and 6 post-infection (n = 8 rats per time-point). As fructo-oligosaccharides (FOS) affect colonic physiology, we analyzed colonic mucosal gene expression of FOS-fed versus cellulose-fed rats infected with Salmonella in a separate experiment. Colonic mucosal samples were isolated at day 2 post-infection. Results Salmonella affected transport (e.g. Chloride channel calcium activated 6, H+/K+ transporting Atp-ase), antimicrobial defense (e.g. Lipopolysaccharide binding protein, Defensin 5 and phospholipase A2), inflammation (e.g. calprotectin), oxidative stress related genes (e.g. Dual oxidase 2 and Glutathione peroxidase 2) and Proteolysis (e.g. Ubiquitin D and Proteosome subunit beta type 9). Furthermore, Salmonella translocation increased serum IFNγ and many interferon-related genes in colonic mucosa. The gene most strongly induced by Salmonella infection was Pancreatitis Associated Protein (Pap), showing >100-fold induction at day 6 after oral infection. Results were confirmed by Q-PCR in individual rats. Stimulation of Salmonella translocation by dietary FOS was accompanied by enhancement of the Salmonella-induced mucosal processes, not by induction of other processes. Conclusion We conclude that the colon is a target tissue for Salmonella, considering the abundant changes in mucosal gene expression.
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MESH Headings
- Administration, Oral
- Animals
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Gene Expression
- Intestine, Small/metabolism
- Intestine, Small/microbiology
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Oligonucleotide Array Sequence Analysis
- Pancreatitis-Associated Proteins
- Rats
- Salmonella Infections, Animal/microbiology
- Salmonella enteritidis/chemistry
- Salmonella enteritidis/genetics
- Salmonella enteritidis/immunology
- Salmonella enteritidis/physiology
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Affiliation(s)
- Wendy Rodenburg
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands
- NIZO Food Research, PO Box 20, 6710 BA, Ede, The Netherlands
| | - Jaap Keijer
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Evelien Kramer
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Susanne Roosing
- RIKILT Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Carolien Vink
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- NIZO Food Research, PO Box 20, 6710 BA, Ede, The Netherlands
| | - Martijn B Katan
- Vrije Universiteit, Institute of Health Sciences, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Roelof van der Meer
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- NIZO Food Research, PO Box 20, 6710 BA, Ede, The Netherlands
- Nutrigenomics Consortium, TIFN, PO Box 557, 6700 AN, Wageningen, The Netherlands
| | - Ingeborg MJ Bovee-Oudenhoven
- TI Food and Nutrition, PO Box 557, 6700 AN, Wageningen, The Netherlands
- NIZO Food Research, PO Box 20, 6710 BA, Ede, The Netherlands
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Iida K, Nishimura I. Gene expression profiling by DNA microarray technology. CRITICAL REVIEWS IN ORAL BIOLOGY AND MEDICINE : AN OFFICIAL PUBLICATION OF THE AMERICAN ASSOCIATION OF ORAL BIOLOGISTS 2007; 13:35-50. [PMID: 12097236 DOI: 10.1177/154411130201300105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Methods in molecular and genetic biology have provided important clues to elucidate the complex mechanisms of oral and craniofacial development and pathogenesis of diseases. It has become increasingly clear that a biological phenotype is a result of multiple factors involving a large number of regulatory genes, while a single nucleotide mutation can cause various degrees of oral and craniofacial abnormalities. These oral and craniofacial problems often present a challenge to the molecular screening process. Recent advances in microarray-based technologies allow for large-scale gene expression analysis in a single experiment, which have been applied to genome-wide assays, mutational analysis, drug discovery, developmental biology, and molecular analysis of various diseases. This review introduces the basic principle and some modifications of techniques and materials used in microarray technology, as well as currently available microarray data analysis strategies. Microarray technology can be applied to the soon-to-be-available human genome database and will be a powerful research tool for those inquiring into specific problems associated with oral and craniofacial biology.
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Affiliation(s)
- Keisuke Iida
- The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, Division of Advanced Prosthodontics, Biomaterials and Hospital Dentistry, UCLA School of Dentistry, Los Angeles, California 90095-1668, USA
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Dupl'áková N, Reňák D, Hovanec P, Honysová B, Twell D, Honys D. Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. BMC PLANT BIOLOGY 2007; 7:39. [PMID: 17645793 PMCID: PMC1963329 DOI: 10.1186/1471-2229-7-39] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 07/23/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND Microarray technologies now belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. The number of experiments exploiting microarray technology has markedly increased in recent years. In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips. RESULTS The Arabidopsis GFP database has been designed as an easy-to-use tool for users needing an easily accessible resource for expression data of single genes, pre-defined gene families or custom gene sets, with the further possibility of keyword search. Arabidopsis Gene Family Profiler presents a user-friendly web interface using both graphic and text output. Data are stored at the MySQL server and individual queries are created in PHP script. The most distinguishable features of Arabidopsis Gene Family Profiler database are: 1) the presentation of normalized datasets (Affymetrix MAS algorithm and calculation of model-based gene-expression values based on the Perfect Match-only model); 2) the choice between two different normalization algorithms (Affymetrix MAS4 or MAS5 algorithms); 3) an intuitive interface; 4) an interactive "virtual plant" visualizing the spatial and developmental expression profiles of both gene families and individual genes. CONCLUSION Arabidopsis GFP gives users the possibility to analyze current Arabidopsis developmental transcriptomic data starting with simple global queries that can be expanded and further refined to visualize comparative and highly selective gene expression profiles.
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Affiliation(s)
- Nikoleta Dupl'áková
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic
- Department of Plant Physiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
| | - David Reňák
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic
- Department of Plant Physiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
- Department of Plant Physiology and Anatomy, Faculty of Biological Sciences, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | | | - Barbora Honysová
- Laboratory of Cell Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic
| | - David Twell
- Department of Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR v.v.i., Rozvojová 263, 165 00 Prague 6, Czech Republic
- Department of Plant Physiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
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Tyshko NV, Aksyuk IN, Tutelyan VA. Safety assessment of genetically modified organisms of plant origin in the Russian Federation. Biotechnol J 2007; 2:826-32. [PMID: 17526054 DOI: 10.1002/biot.200700020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The beginning of the 21st century is characterized by growing interest in the problems of biosafety, which are determined, on the one hand, by the wide use of novel biotechnologies and the necessity to develop the adequate precautionary measures, and, on the other hand, by the objective threat of bioterrorism. Therefore, improvement of the estimation system for genetically modified (GM) sources of food and strengthening the control of their circulation are the urgent problems of modern biology and medicine. Russia is one of the countries where the estimation system of food products obtained from the GM sources is rather efficient. The key features of this system are the complex toxicological and epidemiological examinations. One of the main parts of GM food safety assessment is based upon detection of their potentially toxic properties, which could provoke unintended effects of the genetic modification.
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Affiliation(s)
- Nadezhda V Tyshko
- Institute of Nutrition, Russian Academy of Medical Sciences, Moscow, Russian Federation
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Viganò M, Levi M, Turri S, Chiari M, Damin F. New copolymers of N,N-dimethylacrylamide with blocked isocyanates for oligonucleotide immobilization in DNA microarray technology. POLYMER 2007. [DOI: 10.1016/j.polymer.2007.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Baião AMT, Wowk PF, Sandrin-Garcia P, Junta CM, Fachin AL, Mello SS, Sakamoto-Hojo ET, Donadi EA, Passos GAS. cDNA microarray analysis of cyclosporin A (CsA)-treated human peripheral blood mononuclear cells reveal modulation of genes associated with apoptosis, cell-cycle regulation and DNA repair. Mol Cell Biochem 2007; 304:235-41. [PMID: 17534698 DOI: 10.1007/s11010-007-9505-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 05/03/2007] [Indexed: 11/25/2022]
Abstract
Cyclosporin A (CsA) is a potent immunosuppressant that has been extensively used to attenuate patient immune response following organ transplantation. The molecular biological mechanism of CsA has been extensively investigated in human T cells, and it has been shown to involve modulation of the intracellular calcineurin pathway. However, it is plausible that this chemical immunosuppressant certainly up- or down-regulate many other biochemical pathways of immune cells. In the present study, we used the cDNA microarray method to characterize the gene expression profile of human peripheral blood mononuclear cells (PBMC) treated in vitro with CsA and controls. The CsA treated PBMC displayed statistically significant induction of genes involved in the control of cell-cycle regulation (TRRAP), apoptosis/DNA repair (PRKDC, MAEA, TIA1), DNA metabolism/response to DNA damage stimulus (PRKDC, FEN1), transcription (NR4A2, THRA) and cell proliferation (FEN1, BIN1), whose data have permitted identification of target genes involved in CsA immunosuppression.
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Affiliation(s)
- Ana Maria T Baião
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), Sao Carlos, SP 13565-905, Brazil
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Rodenburg W, Bovee-Oudenhoven IMJ, Kramer E, van der Meer R, Keijer J. Gene expression response of the rat small intestine following oral Salmonella infection. Physiol Genomics 2007; 30:123-33. [PMID: 17374845 DOI: 10.1152/physiolgenomics.00190.2006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Data on the molecular response of the intestine to the food-borne pathogen Salmonella are derived from in vitro studies, whereas in vivo data are lacking. We performed an oral S. enteritidis infection study in Wistar rats to obtain insight in the in vivo response in time. Expression profiles of ileal mucosa (IM) and Peyer's patches (PP) were generated using DNA microarrays at days 1, 3, and 6 postinfection. An overview of Salmonella-regulated processes was obtained and confirmed by quantitative real-time PCR on pooled and individual samples. Salmonella-induced gene expression responses in vivo are fewer and smaller than observed in vitro, and the response develops over a longer period of time. Few effects are seen at day 1 and mainly occur in IM, suggesting the mucosa as the primary site of invasion. Later, a bigger response is observed, especially in PP. Decreased expression of anti-microbial peptides genes (in IM at day 1) suggests inhibition of this process by Salmonella. Newly identified target processes are carbohydrate transport (increased expression in IM at day 1) and phase I and phase II detoxification (decreased expression at days 3 and 6). Increase of cytokine and chemokine expression occurs at later time points, both in PP and IM. Pancreatitis-associated protein, lipocalin 2, and calprotectin, potential inflammatory marker proteins, showed induced expression from day 3 onward. We conclude that the in vivo gene expression response of the ileum to Salmonella differs to a large extent from the response seen in vitro.
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Pognan F. Toxicogenomics applied to predictive and exploratory toxicology for the safety assessment of new chemical entities: a long road with deep potholes. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:217, 219-38. [PMID: 17195477 DOI: 10.1007/978-3-7643-7567-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Toxicology is the perturbation of metabolism by external factors such as xenobiotics, environmental factors or drugs. As such, toxicology covers a broad range of fields from studies of the whole organism responses to minute biochemical events. Mechanistic toxicogenomics is an attempt to harness genomic tools to understand the physiological basis for a toxic event based on an analysis of transcriptional, translational or metabolomic profiles. These studies are complicated by non-toxic adaptive responses in transcript, protein or metabolite expression levels that have to be distinguished from those that are proximally related to the toxic event. Substantial progress has been made on the identification of biomarkers and the establishment of screens derived from such toxicogenomics studies. The ultimate goal, of course, is predictive toxicogenomics, which is an attempt to infer the likelihood of occurrence of a toxic event with exposure to a new agent based upon comparative responses with large databases of gene, protein or metabolite expression data. Gene expression databases are currently limited by the fact that measurable toxic phenotypes generally precede or at best coincide with the earliest observable changes in transcriptional profiles. Unfortunately, predictive protein databases have been limited by technical difficulties. Metabonomics-based databases, which would probably have the highest predictive value, are limited in turn by the inability to perform high dose studies in humans. This chapter will conclude by reviewing those elements of toxicogenomics that apply specifically to the development of anti-infectives and the potential for accurately modelling the toxicity of future drugs.
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Affiliation(s)
- François Pognan
- AstraZeneca Pharmaceuticals, Safety Assessment, Macclesfield, Cheshire, UK.
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42
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Ward NE, Pellis NR, Risin SA, Risin D. Gene expression alterations in activated human T-cells induced by modeled microgravity. J Cell Biochem 2006; 99:1187-202. [PMID: 16795038 DOI: 10.1002/jcb.20988] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Studies conducted in real Space and in ground-based microgravity analog systems (MAS) have demonstrated changes in numerous lymphocyte functions. In this investigation we explored whether the observed functional changes in lymphocytes in MAS are associated with changes in gene expression. NASA-developed Rotating Wall Vessel (RWV) bioreactor was utilized as a MAS. Activated T lymphocytes were obtained by adding 100 ng/ml of anti-CD3 and 100 U/ml of IL-2 in RPMI medium to blood donor mononuclear cells for 4 days. After that the cells were washed and additionally cultured for up to 2 weeks with media (RPMI, 10% FBS and 100 U/ml IL-2) replacement every 3-4 days. Flow cytometry analysis had proven that activated T lymphocytes were the only cells remaining in culture by that time. They were split into two portions, cultured for additional 24 h in either static or simulated microgravity conditions, and used for RNA extraction. The gene expression was assessed by Affymetrix GeneChip Human U133A array allowing screening for expression of 18,400 genes. About 4-8% of tested genes responded to MG by more than a 1.5-fold change in expression; however, reproducible changes were observed only in 89 genes. Ten of these genes were upregulated and 79 were downregulated. These genes were categorized by associated pathways and viewed graphically through histogram analysis. Separate histograms of each pathway were then constructed representing individual gene expression fold changes. Possible functional consequences of the identified reproducible gene expression changes are discussed.
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Wang H, Li H, Wang Q, Wang Y, Han H, Shi H. Microarray analysis of adipose tissue gene expression profiles between two chicken breeds. J Biosci 2006; 31:565-73. [PMID: 17301494 DOI: 10.1007/bf02708408] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The chicken is an important model organism that bridges the evolutionary gap between mammals and other vertebrates and provides a major protein source from meat and eggs throughout the world. Excessive accumulation of lipids in the adipose tissue is one of the main problems faced by the broiler industry nowadays. In order to visualize the mechanisms involved in the gene expression and regulation of lipid metabolism in adipose tissue, cDNA microarray containing 9024 cDNA was used to construct gene expression profile and screen differentially expressed genes in adipose tissue between broilers and layers of 10 wk of age. Sixty-seven differentially expressed sequences were screened out, and 42 genes were found when blasted with the GenBank database. These genes are mainly related to lipid metabolism, energy metabolism, transcription and splicing factor, protein synthesis and degradation. The remained 25 sequences had no annotation available in the GenBank database. Furthermore, Northern blot and semi-quantitative RT-PCR were developed to confirm 4 differentially expressed genes screened by cDNA microarray, and it showed great consistency between the microarray data and Northern blot results or semi-quantitative RT-PCR results. The present study will be helpful for clarifying the molecular mechanism of obesity in chickens.
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Affiliation(s)
- Hongbao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
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Jaumot J, Tauler R, Gargallo R. Exploratory data analysis of DNA microarrays by multivariate curve resolution. Anal Biochem 2006; 358:76-89. [PMID: 16962983 DOI: 10.1016/j.ab.2006.07.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 07/27/2006] [Accepted: 07/27/2006] [Indexed: 11/18/2022]
Abstract
In this work, the application of a multivariate curve resolution procedure based on alternating least squares optimization (MCR-ALS) for the analysis of data from DNA microarrays is proposed. For this purpose, simulated and publicly available experimental data sets have been analyzed. Application of MCR-ALS, a method that operates without the use of any training set, has enabled the resolution of the relevant information about different cancer lines classification using a set of few components; each of these defined by a sample and a pure gene expression profile. From resolved sample profiles, a classification of samples according to their origin is proposed. From the resolved pure gene expression profiles, a set of over- or underexpressed genes that could be related to the development of cancer diseases has been selected. Advantages of the MCR-ALS procedure in relation to other previously proposed procedures such as principal component analysis are discussed.
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Affiliation(s)
- Joaquim Jaumot
- Department of Analytical Chemistry, Universitat de Barcelona, Diagonal 647, E-08028 Barcelona, Spain
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Abstract
Genomics, proteomics and metabolomics, which can be also summarized as 'omics', have become increasingly inter-related with imaging. Gene expression profiling may be assessed using high-density microarrays for the detection of overexpression patterns, followed by the development of histochemical assays. Next, antibodies to the gene-corresponding proteins (for example, receptors) can be produced, leading to serum immunoassays for follow-up, as well as antibody-guided in vivo imaging or therapy. In vivo imaging for cancer detection and/or therapy can be performed by applying nonlabeled antibodies, by using radiolabeled antibodies for detection using single-photon tomography or positron emission tomography (PET), or by other tracers, for example, for magnetic resonance imaging tomography (MRI, MRT). Protein profiles from protein chips can be derived from mass maps obtained through mass spectrometry (MS). Electrophoretic separation of proteins has also been combined with MS to produce a two-dimensional assignment of proteins within a complex mixture. Overexpression of tumor-related proteins can be used for the development of antibodies to develop noninvasive assays that can be used in the screening of risk groups as a basis for further investigation by invasive imaging methods. Metabolomic profiling by nuclear magnetic resonance spectroscopy can be applied for the detection of biomarkers of the metabolome. Metabolite profiles in cells, tissues, and organisms can be generated with nuclear magnetic resonance spectroscopy and MS. Metabolic information provided by magnetic resonance spectroscopic imaging (MRSI) combined with the anatomical information provided by MRI can significantly improve the assessment of cancer location and extent, and cancer aggressiveness. Biomarkers found by MRSI can lead to new PET tracers. This article provides examples and discusses some of the recent achievements to bring forward novel strategies for the diagnosis and therapy of cancer.
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Affiliation(s)
- Peter Oehr
- University of Bonn, Bio-Med-Pharma Consulting, Am Buechel 53a, 53173 Bonn, Germany.
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Dhiman N, Ovsyannikova IG, Oberg AL, Grill DE, Jacobson RM, Poland GA. Immune activation at effector and gene expression levels after measles vaccination in healthy individuals: a pilot study. Hum Immunol 2006; 66:1125-36. [PMID: 16571413 DOI: 10.1016/j.humimm.2005.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 09/29/2005] [Indexed: 11/29/2022]
Abstract
Cellular immunity to measles vaccination is not fully understood at the effector response and gene expression levels. We enrolled 15 healthy individuals (15-25 years old) previously vaccinated with two doses of measles-mumps-rubella-II vaccine to characterize their cellular immunity. We detected a spectrum of lymphoproliferative response (median stimulation indices of 3.4), low precursor frequencies of interferon-gamma (median 0.11%) and interleukin-4 (median 0.05%) by Elispot, and cosecretion of Th1 and Th2 cytokines after measles virus stimulation. Further, global gene expression was examined in five subjects from this cohort after vaccination with an additional dose of measles vaccine (Attenuax, Merck) to identify the genes involved in measles immunity. Linear mixed effect models were used to identify genes significantly up or downregulated in vivo between baseline and Days 7 and 14 after measles vaccination. Measles vaccination induced upregulation of a set of 80 genes, which play a role in measles immunity, signal transduction, apoptosis, cell proliferation, and metabolic pathways. Among the 34 genes that were downregulated, only interferon-alpha is known to have a direct role in measles immunity. This study suggests that measles vaccination leads to activation of multiple cellular mechanisms that can override the immunosuppressant effects of the measles virus and induce immunity.
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Affiliation(s)
- Neelam Dhiman
- Mayo Vaccine Research Group, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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47
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Bally M, Halter M, Vörös J, Grandin HM. Optical microarray biosensing techniques. SURF INTERFACE ANAL 2006. [DOI: 10.1002/sia.2375] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Meltola NJ, Vaarno J, Soini AE. Dipyrrylmetheneboron difluorides as labels in two-photon excited fluorometry. Part II--Nucleic acid hybridization assays. J Fluoresc 2005; 15:233-42. [PMID: 15986150 DOI: 10.1007/s10895-005-2623-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 01/04/2005] [Indexed: 11/24/2022]
Abstract
Five two-photon excitable dipyrrylmetheneboron difluoride labels (dipyrrylmethene-BF(2) labels) with fluorescence emission maximum between 530 and 590 nm, and a frequently used rhodamine label, TAMRA, were conjugated to aminomodified oligonucleotides. The performance of the labeled oligonucleotides was studied in a separation-free nucleic acid hybridization assay using ArcDia TPX bioaffinity assay technology. The results show that oligonucleotide conjugates of dipyrrylmethene-BF(2) labels provide higher two-photon excited fluorescence yield and better assay sensitivity than corresponding TAMRA conjugate. The effect of conjugation on photophysical properties of the labels and performance of the labeled oligonucleotides in separation-free hybridization assay is discussed.
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Affiliation(s)
- Niko J Meltola
- Laboratory of Biophysics, Institute of Biomedicine, University of Turku, PO Box 123, 20521 Turku, Finland.
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Staal YCM, van Herwijnen MHM, van Schooten FJ, van Delft JHM. Application of four dyes in gene expression analyses by microarrays. BMC Genomics 2005; 6:101. [PMID: 16042794 PMCID: PMC1198227 DOI: 10.1186/1471-2164-6-101] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 07/25/2005] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes. RESULTS Following tests for cross-talk of fluorescence signals, Alexa 488, Alexa 594, Cyanine 3 and Cyanine 5 were selected for hybridizations. For self-hybridizations, a single RNA sample was labelled with all dyes and hybridized on commercial cDNA arrays or on in-house spotted oligonucleotide arrays. Correlation coefficients for all combinations of dyes were above 0.9 on the cDNA array. On the oligonucleotide array they were above 0.8, except combinations with Alexa 488, which were approximately 0.5. Standard deviation of expression differences for replicate spots were similar on the cDNA array for all dye combinations, but on the oligonucleotide array combinations with Alexa 488 showed a higher variation. CONCLUSION In conclusion, the four dyes can be used simultaneously for gene expression experiments on the tested cDNA array, but only three dyes can be used on the tested oligonucleotide array. This was confirmed by hybridizations of control with test samples, as all combinations returned similar numbers of differentially expressed genes with comparable effects on gene expression.
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Affiliation(s)
- Yvonne CM Staal
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. box 616, 6200 MD Maastricht, The Netherlands
| | - Marcel HM van Herwijnen
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. box 616, 6200 MD Maastricht, The Netherlands
| | - Frederik J van Schooten
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. box 616, 6200 MD Maastricht, The Netherlands
| | - Joost HM van Delft
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. box 616, 6200 MD Maastricht, The Netherlands
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Alldinger I, Dittert D, Peiper M, Fusco A, Chiappetta G, Staub E, Lohr M, Jesnowski R, Baretton G, Ockert D, Saeger HD, Grützmann R, Pilarsky C. Gene expression analysis of pancreatic cell lines reveals genes overexpressed in pancreatic cancer. Pancreatology 2005; 5:370-9. [PMID: 15983444 DOI: 10.1159/000086537] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 09/16/2004] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pancreatic cancer is one of the leading causes of cancer-related death. Using DNA gene expression analysis based on a custom made Affymetrix cancer array, we investigated the expression pattern of both primary and established pancreatic carcinoma cell lines. METHODS We analyzed the gene expression of 5 established pancreatic cancer cell lines (AsPC-1, BxPC-3, Capan-1, Capan-2 and HPAF II) and 5 primary isolates, 1 of them derived from benign pancreatic duct cells. RESULTS Out of 1,540 genes which were expressed in at least 3 experiments, we found 122 genes upregulated and 18 downregulated in tumor cell lines compared to benign cells with a fold change >3. Several of the upregulated genes (like Prefoldin 5, ADAM9 and E-cadherin) have been associated with pancreatic cancer before. The other differentially regulated genes, however, play a so far unknown role in the course of human pancreatic carcinoma. By means of immunohistochemistry we could show that thymosin beta-10 (TMSB10), upregulated in tumor cell lines, is expressed in human pancreatic carcinoma, but not in non-neoplastic pancreatic tissue, suggesting a role for TMSB10 in the carcinogenesis of pancreatic carcinoma. CONCLUSION Using gene expression profiling of pancreatic cell lines we were able to identify genes differentially expressed in pancreatic adenocarcinoma, which might contribute to pancreatic cancer development.
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Affiliation(s)
- Ingo Alldinger
- Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany
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