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Lang JE, Magbanua MJM, Scott JH, Makrigiorgos GM, Wang G, Federman S, Esserman LJ, Park JW, Haqq CM. A comparison of RNA amplification techniques at sub-nanogram input concentration. BMC Genomics 2009; 10:326. [PMID: 19619282 PMCID: PMC2724417 DOI: 10.1186/1471-2164-10-326] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 07/20/2009] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Gene expression profiling of small numbers of cells requires high-fidelity amplification of sub-nanogram amounts of RNA. Several methods for RNA amplification are available; however, there has been little consideration of the accuracy of these methods when working with very low-input quantities of RNA as is often required with rare clinical samples. Starting with 250 picograms-3.3 nanograms of total RNA, we compared two linear amplification methods 1) modified T7 and 2) Arcturus RiboAmp HS and a logarithmic amplification, 3) Balanced PCR. Microarray data from each amplification method were validated against quantitative real-time PCR (QPCR) for 37 genes. RESULTS For high intensity spots, mean Pearson correlations were quite acceptable for both total RNA and low-input quantities amplified with each of the 3 methods. Microarray filtering and data processing has an important effect on the correlation coefficient results generated by each method. Arrays derived from total RNA had higher Pearson's correlations than did arrays derived from amplified RNA when considering the entire unprocessed dataset, however, when considering a gene set of high signal intensity, the amplified arrays had superior correlation coefficients than did the total RNA arrays. CONCLUSION Gene expression arrays can be obtained with sub-nanogram input of total RNA. High intensity spots showed better correlation on array-array analysis than did unfiltered data, however, QPCR validated the accuracy of gene expression array profiling from low-input quantities of RNA with all 3 amplification techniques. RNA amplification and expression analysis at the sub-nanogram input level is both feasible and accurate if data processing is used to focus attention to high intensity genes for microarrays or if QPCR is used as a gold standard for validation.
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Affiliation(s)
- Julie E Lang
- Department of Surgery, UCSF Comprehensive Cancer Center, 1500 Divisadero Street, San Francisco, CA 94143, USA.
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Chambers D, Wilson LJ, Alfonsi F, Hunter E, Saxena U, Blanc E, Lumsden A. Rhombomere-specific analysis reveals the repertoire of genetic cues expressed across the developing hindbrain. Neural Dev 2009; 4:6. [PMID: 19208226 PMCID: PMC2649922 DOI: 10.1186/1749-8104-4-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 02/10/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The Hox family of homeodomain transcription factors comprises pivotal regulators of cell specification and identity during animal development. However, despite their well-defined roles in the establishment of anteroposterior pattern and considerable research into their mechanism of action, relatively few target genes have been identified in the downstream regulatory network. We have sought to investigate this issue, focussing on the developing hindbrain and the cranial motor neurons that arise from this region. The reiterated anteroposterior compartments of the developing hindbrain (rhombomeres (r)) are normally patterned by the combinatorial action of distinct Hox genes. Alteration in the normal pattern of Hox cues in this region results in a transformation of cellular identity to match the remaining Hox profile, similar to that observed in Drosophila homeotic transformations. RESULTS To define the repertoire of genes regulated in each rhombomere, we have analysed the transcriptome of each rhombomere from wild-type mouse embryos and not those where pattern is perturbed by gain or loss of Hox gene function. Using microarray and bioinformatic methodologies in conjunction with other confirmatory techniques, we report here a detailed and comprehensive set of potential Hox target genes in r2, r3, r4 and r5. We have demonstrated that the data produced are both fully reflective and predictive of rhombomere identity and, thus, may represent some the of Hox targets. These data have been interrogated to generate a list of candidate genes whose function may contribute to the generation of neuronal subtypes characteristic of each rhombomere. Interestingly, the data can also be classified into genetic motifs that are predicted by the specific combinations of Hox genes and other regulators of hindbrain anteroposterior identity. The sets of genes described in each or combinations of rhombomeres span a wide functional range and suggest that the Hox genes, as well as other regulatory inputs, exert their influence across the full spectrum of molecular machinery. CONCLUSION We have performed a systematic survey of the transcriptional status of individual segments of the developing mouse hindbrain and identified hundreds of previously undescribed genes expressed in this region. The functional range of the potential candidate effectors or upstream modulators of Hox activity suggest multiple unexplored mechanisms. In particular, we present evidence of a potential new retinoic acid signalling system in ventral r4 and propose a model for the refinement of identity in this region. Furthermore, the rhombomeres demonstrate a molecular relationship to each other that is consistent with known observations about neurogenesis in the hindbrain. These findings give the first genome-wide insight into the complexity of gene expression during patterning of the developing hindbrain.
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Affiliation(s)
- David Chambers
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Leigh Jane Wilson
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Fabienne Alfonsi
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Ewan Hunter
- Infogen Bioinformatics Ltd, 83 South Middleton, Uphall, West Lothian, EH52 5GA, UK
| | - Uma Saxena
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Eric Blanc
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Andrew Lumsden
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, SE1 1UL, UK
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3
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Caretti E, Devarajan K, Coudry R, Ross E, Clapper ML, Cooper HS, Bellacosa A. Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection. J Cell Biochem 2008; 103:556-63. [PMID: 17546586 DOI: 10.1002/jcb.21426] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Laser capture microdissection (LCM) permits isolation of pure cell populations from which RNA can be extracted, amplified, and subjected to microarray analysis, allowing information to be obtained on the gene expression profile of defined cell types. To avoid amplification artifacts and detect genes expressed at different levels, it is important to optimize the choice of both RNA amplification step and microarray platform. We captured by LCM the same colon cancer biopsy and conducted a cross comparison of distinct RNA amplification methods and different chip platforms. We tested two RNA amplification methods with different chemistry: the one-cycle Ovation system (NuGEN) and the two-cycle Ribo OA method (Arcturus). We also compared two different whole genome platforms, based on Affymetrix technology: the U133 plus 2.0 and the X3P array, with probe sets closer to the 3' end of transcripts. After RNA amplification, microarray analysis, and data normalization, we investigated reproducibility and correlation of different methods and arrays. Our results indicate that the Arcturus Ribo OA method is superior for both array choices, especially in combination with X3P arrays, showing the lowest variance and Spearman correlation of 0.986. The quicker NuGEN procedure, when coupled with X3P arrays, also yielded excellent results (correlation of 0.951). These observations will be useful for planning large-scale analyses of LCM-dissected clinical samples.
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Affiliation(s)
- Elena Caretti
- Human Genetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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4
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Identification of gene signatures for invasive colorectal tumor cells. ACTA ACUST UNITED AC 2008; 31:282-95. [PMID: 17936523 DOI: 10.1016/j.cdp.2007.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2007] [Indexed: 01/16/2023]
Abstract
BACKGROUND Gene signatures of sporadic colorectal carcinoma tissues and microdissected colorectal tumor cells were analyzed to identify stromal and tumor cell-specific markers, respectively. METHODS Serial sections of frozen colorectal tumors (n=29) were subjected to RNA isolation of (1) entire tissue sections with a various tumor cell content and of (2) microdissected invasive tumor cells. Three matching samples of microdissected normal colorectal epithelial and invasive tumor cells were similarly obtained. RNA samples were analyzed using the HG95A and HG95Av2 GeneChip microarrays (Affymetrix). The microarray data was evaluated by established methods and validated by Q-RT-PCR. RESULTS Unsupervised hierarchical cluster analysis of 18 sample pairs (training set) clearly distinguished tumors from microdissected tumor cells. A 149-gene signature was identified using statistical methods, which was then validated by a hierarchical clustering analysis of 11 independent sample pairs (test set). Genes specifically associated with microdissected invasive tumor cells were for example CKS2 and NME1. In contrast, genes associated with stromal cells were for example MMP2, SDF1 and FBLN2. Finally, a 65-gene signature distinguished normal colorectal epithelial cells and invasive tumor cells, including down-regulation of BMP2 and ANPEP mRNA expression as well as up-regulation of TKT, SPARC, MCM5 mRNA expression. CONCLUSIONS Our approach allowed precise evaluation of molecular signatures in morphologically defined cell populations and identified novel target genes related to stroma-tumor interactions in colorectal cancer. The approach enables further analysis of gene signatures in different tumor areas and cell types, such as within invasive margins to decipher molecular mechanisms of colorectal cancer invasion and metastasis.
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5
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Duftner N, Larkins-Ford J, Legendre M, Hofmann HA. Efficacy of RNA amplification is dependent on sequence characteristics: implications for gene expression profiling using a cDNA microarray. Genomics 2008; 91:108-17. [PMID: 18006269 PMCID: PMC2258226 DOI: 10.1016/j.ygeno.2007.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 09/05/2007] [Accepted: 09/07/2007] [Indexed: 12/15/2022]
Abstract
Minute tissue samples or single cells increasingly provide the starting material for gene expression profiling, which often requires RNA amplification. Although much effort has been put into optimizing amplification protocols, the relative abundance of RNA templates in the amplified product is frequently biased. We applied a T7 polymerase-based technique to amplify RNA from two tissues of a cichlid fish and compared expression levels of unamplified and amplified RNA on a cDNA microarray. Amplification bias was generally minor and comprised features that were lost (1.3%) or gained (2.5%) through amplification and features that were scored as regulated before but unregulated after amplification (4.2%) or vice versa (19.5%). We examined 10 sequence-specific properties and found that GC content, folding energy, hairpin length and number, and lengths of poly(A) and poly(T) stretches significantly affected RNA amplification. We conclude that, if RNA amplification is used in gene expression studies, preceding experiments controlling for amplification bias should be performed.
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Affiliation(s)
- Nina Duftner
- Section for Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonah Larkins-Ford
- Section for Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Matthieu Legendre
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hans A. Hofmann
- Section for Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
- Institute for Cellular & Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
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6
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Torres A, Storey L, Anders M, Miller R, Bulbulian B, Jin J, Raghavan S, Lee J, Slade H, Birmachu W. Microarray analysis of aberrant gene expression in actinic keratosis: effect of the Toll-like receptor-7 agonist imiquimod. Br J Dermatol 2007; 157:1132-47. [DOI: 10.1111/j.1365-2133.2007.08218.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Lauss M, Vierlinger K, Weinhaeusel A, Szameit S, Kaserer K, Noehammer C. Comparison of RNA amplification techniques meeting the demands for the expression profiling of clinical cancer samples. Virchows Arch 2007; 451:1019-29. [DOI: 10.1007/s00428-007-0522-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 09/27/2007] [Accepted: 09/28/2007] [Indexed: 11/30/2022]
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8
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Conrad C, Zhu J, Conrad C, Schoenfeld D, Fang Z, Ingelsson M, Stamm S, Church G, Hyman BT. Single molecule profiling of tau gene expression in Alzheimer's disease. J Neurochem 2007; 103:1228-36. [PMID: 17727636 DOI: 10.1111/j.1471-4159.2007.04857.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tau is a microtubule-associated protein that is important for establishing and maintaining neuronal morphology. In addition to its role in normal cells, tau protein is involved in many neurodegenerative diseases, e.g. Alzheimer's disease (AD) and frontotemporal dementia, as the main component of intraneuronal aggregates. Alternative splicing of tau gene in the brain can give rise to at least six protein variants. A causative role of skewed tau exon 10 inclusion has been defined in frontotemporal dementia; however, no link was established between the aberrant splicing of tau and AD. Here, we applied a single-molecule-based technology, polymerase colony or polony, to simultaneously monitor tau splicing variant and haplotype profile in sporadic AD and normal brains. We found that the coordinated expression of tau exons 2 and 10 is altered in AD. Additional investigations of cis and trans mechanisms of this observation revealed a decreased protein expression of a known tau splicing factor, htra2-beta-1 in AD, thereby implicating a trans mechanism. Our results demonstrate that dysregulation of combinatorial splicing might serve as a signature for aging-related diseases, and the polony assay could be widely adapted for the study of other tauopathies. Furthermore, splicing-based therapeutics is an emerging area of drug development, and a well-defined and quantitative assay for monitoring single-gene transcriptome will be relevant for such development.
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Affiliation(s)
- Chris Conrad
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease (MIND), Charlestown, Massachusetts, USA.
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9
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Yauk CL, Berndt ML. Review of the literature examining the correlation among DNA microarray technologies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:380-94. [PMID: 17370338 PMCID: PMC2682332 DOI: 10.1002/em.20290] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNA microarray technologies are used in a variety of biological disciplines. The diversity of platforms and analytical methods employed has raised concerns over the reliability, reproducibility and correlation of data produced across the different approaches. Initial investigations (years 2000-2003) found discrepancies in the gene expression measures produced by different microarray technologies. Increasing knowledge and control of the factors that result in poor correlation among the technologies has led to much higher levels of correlation among more recent publications (years 2004 to present). Here, we review the studies examining the correlation among microarray technologies. We find that with improvements in the technology (optimization and standardization of methods, including data analysis) and annotation, analysis across platforms yields highly correlated and reproducible results. We suggest several key factors that should be controlled in comparing across technologies, and are good microarray practice in general.
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Affiliation(s)
- Carole L Yauk
- Environmental and Occupational Toxicology Division, Safe Environments Programme, Health Canada, Ottawa, Ontario, Canada K1A 0K9.
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10
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Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppée JY, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC. Long oligonucleotide microarrays for African green monkey gene expression profile analysis. FASEB J 2007; 21:3262-71. [PMID: 17507667 DOI: 10.1096/fj.07-8271com] [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: 11/11/2022]
Abstract
Nonhuman primates, including African green monkey (AGM), are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25-mer). Using the long oligonucleotide arrays, we detected 4-fold more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4+ T cells vs. nonactivated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be regulated in human CD4+ T cell activation. Finally, tissue specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles.
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Affiliation(s)
- Béatrice Jacquelin
- Unité de Régulations des Infections Rétrovirales, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris cedex 15, France
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11
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Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
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Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
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12
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Wagner F, Radelof U. Performance of different small sample RNA amplification techniques for hybridization on Affymetrix GeneChips. J Biotechnol 2007; 129:628-34. [PMID: 17408796 DOI: 10.1016/j.jbiotec.2007.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 02/14/2007] [Accepted: 02/19/2007] [Indexed: 11/17/2022]
Abstract
A key issue in RNA amplification techniques is the preservation of original transcript abundance, however popular high-grade RNA amplification methods lack sufficient validation regarding the potential bias of gene expression profiles. This study evaluated a double-round T7-based and a PCR-based amplification protocol, using the Affymetrix GeneChip platform. Both small sample methods performed excellently in terms of yield and reproducibility (r>0.99), and also the within-method concordance with respect to differential gene expression was as high as with standard single-round T7-based amplification. However, when comparing the overlap of all differentially expressed genes between standard and small sample methods, this was only moderate for the double-round T7 (48.7-55.0%) as well as for the PCR-based amplification protocol (51.9-58.0%). In contrast, the concordance for the top 100 genes with highest fold changes was significantly higher, indicating that both small sample methods generate reliable results when focusing on strongly regulated genes.
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Affiliation(s)
- Florian Wagner
- RZPD German Resource Center for Genome Research, Heubnerweg 6, Berlin, Germany.
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13
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Ju Z, Wells MC, Heater SJ, Walter RB. Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:134-44. [PMID: 16916623 DOI: 10.1016/j.cbpc.2006.06.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 06/18/2006] [Accepted: 06/19/2006] [Indexed: 12/22/2022]
Abstract
Due in part to human population growth watersheds and coastal estuaries have been receiving increasing run-off of nutrients and genotoxins. As a consequence, the occurrences of nutrient-driven hypoxia in coastal waters appear to be increasing. Thus, understanding the molecular genetic response to hypoxia by model aquatic organisms is of interest both from environmental and physiological viewpoints. The major objectives of this study are to determine genome-wide gene expression profiles and to better understand how hypoxia influences global gene expression in medaka (Oryzias latipes), a well utilized aquatic model species. Herein we detail our development of a microarray containing 8046 medaka unigenes and describe our experimental results for measuring gene expression changes in the brain, gill, and liver of hypoxia exposed fish. Using conservative selection criteria, we determined that 501 genes in the brain, 442 in the gill, and 715 in the liver were differentially expressed in medaka exposed to hypoxia. These differentially expressed genes fell into a number of biological gene ontology groups related to general metabolism, catabolism, RNA and protein metabolism, etc. Two biological pathways, ubiquitin-proteasome and phosphatidylinositol signaling, were significantly dysregulated in medaka upon hypoxia exposure. Comparative genomics between medaka and human identified several human orthologies associated with known diseases.
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Affiliation(s)
- Zhenlin Ju
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666-4616, USA.
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14
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Ju Z, Wells MC, Walter RB. DNA microarray technology in toxicogenomics of aquatic models: methods and applications. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:5-14. [PMID: 16828578 DOI: 10.1016/j.cbpc.2006.04.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 04/10/2006] [Accepted: 04/21/2006] [Indexed: 10/24/2022]
Abstract
Toxicogenomics represents the merging of toxicology with genomics and bioinformatics to investigate biological functions of genome in response to environmental contaminants. Aquatic species have traditionally been used as models in toxicology to characterize the actions of environmental stresses. Recent completion of the DNA sequencing for several fish species has spurred the development of DNA microarrays allowing investigators access to toxicogenomic approaches. However, since microarray technology is thus far limited to only a few aquatic species and derivation of biological meaning from microarray data is highly dependent on statistical arguments, the full potential of microarray in aquatic species research has yet to be realized. Herein we review some of the issues related to construction, probe design, statistical and bioinformatical data analyses, and current applications of DNA microarrays. As a model a recently developed medaka (Oryzias latipes) oligonucleotide microarray was described to highlight some of the issues related to array technology and its application in aquatic species exposed to hypoxia. Although there are known non-biological variations present in microarray data, it remains unquestionable that array technology will have a great impact on aquatic toxicology. Microarray applications in aquatic toxicogenomics will range from the discovery of diagnostic biomarkers, to establishment of stress-specific signatures and molecular pathways hallmarking the adaptation to new environmental conditions.
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Affiliation(s)
- Zhenlin Ju
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA
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15
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Torres A, Storey L, Anders M, Miller RL, Bulbulian BJ, Jin J, Raghavan S, Lee J, Slade HB, Birmachu W. Immune-mediated changes in actinic keratosis following topical treatment with imiquimod 5% cream. J Transl Med 2007; 5:7. [PMID: 17257431 PMCID: PMC1796543 DOI: 10.1186/1479-5876-5-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2006] [Accepted: 01/26/2007] [Indexed: 12/15/2022] Open
Abstract
Background The objective of this study was to identify the molecular processes responsible for the anti-lesional activity of imiquimod in subjects with actinic keratosis using global gene expression profiling. Methods A double-blind, placebo-controlled, randomized study was conducted to evaluate gene expression changes in actinic keratosis treated with imiquimod 5% cream. Male subjects (N = 17) with ≥ 5 actinic keratosis on the scalp applied placebo cream or imiquimod 3 times a week on nonconsecutive days for 4 weeks. To elucidate the molecular processes involved in actinic keratosis lesion regression by imiquimod, gene expression analysis using oligonucleotide arrays and real time reverse transcriptase polymerase chain reaction were performed on shave biopsies of lesions taken before and after treatment. Results Imiquimod modulated the expression of a large number of genes important in both the innate and adaptive immune response, including increased expression of interferon-inducible genes with known antiviral, anti-proliferative and immune modulatory activity, as well as various Toll-like receptors. In addition, imiquimod increased the expression of genes associated with activation of macrophages, dendritic cells, cytotoxic T cells, and natural killer cells, as well as activation of apoptotic pathways. Conclusion Data suggest that topical application of imiquimod stimulates cells in the skin to secrete cytokines and chemokines that lead to inflammatory cell influx into the lesions and subsequent apoptotic and immune cell-mediated destruction of lesions.
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MESH Headings
- Adaptive Immunity/drug effects
- Adaptive Immunity/genetics
- Adjuvants, Immunologic/pharmacology
- Administration, Topical
- Aged
- Aged, 80 and over
- Aminoquinolines/administration & dosage
- Aminoquinolines/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Cell Proliferation/drug effects
- Chemokines/genetics
- Chemokines/metabolism
- Demography
- Dendritic Cells/drug effects
- Dendritic Cells/metabolism
- Dosage Forms
- Gene Expression Profiling
- Gene Expression Regulation/drug effects
- Humans
- Imiquimod
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Interferon Type I/pharmacology
- Keratosis, Actinic/drug therapy
- Keratosis, Actinic/genetics
- Keratosis, Actinic/immunology
- Keratosis, Actinic/pathology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Macrophages/drug effects
- Macrophages/metabolism
- Male
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Receptors, Pattern Recognition/metabolism
- Reproducibility of Results
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Abel Torres
- Dermatology Office, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Leslie Storey
- Dermatology Office, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Makala Anders
- Dermatology Office, Loma Linda University Medical Center, Loma Linda, California, USA
| | | | | | - Jizhong Jin
- Pharmacology, 3M Pharmaceuticals, St Paul, Minnesota, USA
| | | | - James Lee
- Medical & Scientific Affairs, 3M Pharmaceuticals, St Paul, Minnesota, USA
| | - Herbert B Slade
- Medical & Scientific Affairs, 3M Pharmaceuticals, St Paul, Minnesota, USA
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Ehrenkaufer GM, Haque R, Hackney JA, Eichinger DJ, Singh U. Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol 2007; 9:1426-44. [PMID: 17250591 DOI: 10.1111/j.1462-5822.2006.00882.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. The protozoan parasite Entamoeba histolytica converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Identification of genes involved in the developmental pathway has been severely hindered by the inability to generate E. histolytica cysts in vitro. Using parasite strains derived from recent human infections and whole-genome transcriptional profiling, we determined that 1439 genes (approximately 15% of annotated genes) were potentially developmentally regulated. Genes enriched in cysts (672 in total) included cysteine proteinases and transmembrane protein kinases, which may be involved in signal transduction. Genes enriched in trophozoites (767 in total) included genes typically thought of as important in tissue invasion by trophozoites, including the Gal/GalNAc lectin light subunit and cysteine protease 1. Putative regulators of differentiation including possible G-protein coupled receptors, signal transduction proteins and transcription factors were identified. A number of E. histolytica stage-specific genes were also developmentally regulated in the reptilian parasite E. invadens, indicating that they likely have conserved functions in Entamoeba development. These advances lay the groundwork for dissection of the molecular signals that initiate stage conversion and development of novel diagnostic and therapeutic measures targeting E. histolytica cysts.
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Affiliation(s)
- Gretchen M Ehrenkaufer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Assessment of reducing RNA input for Agilent oligo microarrays. Anal Biochem 2007; 363:315-7. [PMID: 17320029 DOI: 10.1016/j.ab.2007.01.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 01/15/2007] [Indexed: 11/28/2022]
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Bak M, Conley L, Hedegaard J, Larsen LA, Sørensen P, Bendixen C, Tommerup N. Evaluation of two methods for generating cRNA for microarray experiments from nanogram amounts of total RNA. Anal Biochem 2006; 358:111-9. [PMID: 16996470 DOI: 10.1016/j.ab.2006.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 08/22/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
Several methods have been developed for amplification of RNA, making it possible to use cDNA microarrays for analysis of samples limited in amount of total RNA. The most widely used amplification protocol, the Eberwine method, amplifies RNA in a linear manner through in vitro transcription (IVT). However, when starting material is limited to nanogram amounts of total RNA, several rounds of amplification are necessary, making this method both expensive and labor-intensive. Amplification by PCR is robust and is able to amplify extremely limiting material. However, it is possible that the nonlinear nature of PCR could result in reduced reproducibility of the amplification compared with IVT. We have evaluated two methods that use a combination of PCR and IVT for amplification of nanogram amounts of total RNA. We have compared microarray results obtained by these methods with results obtained by two established methods: indirect labeling of 20 microg total RNA and Eberwine amplification of 1 microg total RNA. Starting from as little as 5 ng of total RNA, both methods yielded results in concordance with the Eberwine method.
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Affiliation(s)
- Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Medical Biochemistry and Genetics, Panum Institute, University of Copenhagen, DK-2200N Copenhagen, Denmark.
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Yue C, Mutsuga N, Verbalis J, Gainer H. Microarray analysis of gene expression in the supraoptic nucleus of normoosmotic and hypoosmotic rats. Cell Mol Neurobiol 2006; 26:959-78. [PMID: 16699879 PMCID: PMC11520591 DOI: 10.1007/s10571-006-9017-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 01/24/2006] [Indexed: 10/24/2022]
Abstract
1. Hypoosmolality produces a dramatic inhibition of vasopressin (VP) and oxytocin (OT) gene expression in the supraoptic nucleus (SON). This study examines the effect of sustained hypoosmolality on global gene expression in the OT and VP magnocellular neurons (MCNs) of the hypothalamo-neurohypophysial system (HNS), in order to detect novel genes in this system that might be involved in osmoregulation in the MCNs. 2. For this purpose, we used Affymetrix oligonucleotide arrays to analyze the expression of specific genes in laser microdissected rat SONs, and their changes in expression during chronic hypoosmolality. We identified over 40 genes that had three-fold or more greater expression in the SON versus total hypothalamus, and that also changed more than two fold in expression as a result of the chronic hypoosmolar treatment. These genes contained both novel as well as genes previously known to be present in the SON. All of the raw data for the genes that are expressed in the SON and altered by hypoosmolality can be found on the following NINDS website URL address: http://data.ninds.nih.gov/Gainer/Publications.
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Affiliation(s)
- Chunmei Yue
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
| | - Noriko Mutsuga
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
| | - Joseph Verbalis
- Department of Medicine, Division of Endocrinology and Metabolism, Georgetown University, Washington, DC 20007 USA
| | - Harold Gainer
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
- Molecular Neuroscience Section, Laboratory of Neurochemistry, National Institute of Neurological Disorder and Stroke, National Institutes of Health, Bldg. 49, Rm 5A78, Bethesda, MD 20892 USA
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Jones GM, Song B, Cram DS, Trounson AO. Optimization of a microarray based approach for deriving representative gene expression profiles from human oocytes. Mol Reprod Dev 2006; 74:8-17. [PMID: 16941669 DOI: 10.1002/mrd.20621] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The purpose of the present study was to optimize a protocol for deriving reproducible and representative gene expression profiles from very rare research samples of human oocytes using microarrays. Immature oocytes produced as a result of administration of gonadotrophins for the treatment of infertility were donated to research. Linear amplification (L-amp) and exponential amplification (E-amp) were both capable of generating sufficient product for hybridization to the microarrays even from the low amount of template mRNA present in a single human oocyte. Slightly higher numbers of transcripts were detected by microarray following linear rather than E-amp but both techniques generated a product with reliably reproducible sensitivity and fidelity providing oocytes were pooled in minimum numbers of three. The majority of the variance associated with amplification and hybridization to arrays comes from the molecular processing. Slightly greater additional variance is associated with biological differences in immature oocytes from the same or different donors. The findings suggest that representative gene expression profiles can be generated from human oocytes for comparative purposes following L-amp and hybridization to microarray. However, oocytes must be pooled for the starting template for each array and sufficient independent microarray experiments performed to minimize the variance associated with molecular processing.
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Affiliation(s)
- Gayle M Jones
- Monash Immunology and Stem Cell Laboratories, Monash University, Clayton, Australia.
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