Microarray analysis

Clarke PA, te Poele R, Wooster R, Workman P (2001) Gene expression microarray analysis in cancer biology, pharmacology, and drug development progress and potential. Biochem Pharmacol 62 1311-1336... 

Examples of biomarker assays operating at different levels are given in Table 4.2. The recent development of omics technology should provide strong support to this approach (Box 4.3). Microarray analysis, for instance, can give a time-related sequence of gene responses that relate to the cellular changes of toxicity. 

Raponi M, Belly RT, Karp JE, Lancet JE, Atkins D, Wang Y. Microarray analysis reveals genetic pathways modulated by tipifarnib in acute myeloid leukemia. BMC Cancer 2004 4 56. 

Nemeth KR, Charlap JH, O Hara MF, Craig RC, Knudsen TB. 2002. Microarray analysis of developmental toxicity ontogenetic profiles of susceptibility in the mouse embryonic eye. Toxicologist 66 28. 

Chen, M.-L. Chen, C.-H. (2005b). Microarray analysis of differentially expressed genes in rat frontal cortex under chronic risperidone treatment. Neuropsychopharmacology, 30(2), 268-77. 

Hihara, Y., A. Kamei, M. Kanehisa, A. Kaplan, and M. Ikeuchi (2001). DNA microarray analysis of cyanobac-terial gene expression during acclimation to high light. Plant Cell 13(4) 793-806. 

Apart from SR-BI, SR-BII, CD36, and ABCA1, a microarray analysis of gene expression in human RPE reveals some additional lipid transporters that might potentially be involved in intracellular transport of carotenoids and/or their efflux from the RPE cells into the neural retina or out of the retina into the choroidal blood (van Soest et al., 2007). These include other ABC... 

Villaret DB et al. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope 2000 11 374-381. 

Chang YE et al. Microarray analysis identifies interferon-inducible genes and Stat-1 as major transcriptional targets of human papillomavims type 31. J Virol 2000 74 4174-4182. 

Ichikawa JK et al. Interaction of Pseudomonas aeruginosa with epithelial cells identification of differentially regulated genes by expression microarray analysis of humans. Proc Natl Acad Sci USA 2000 97 9659-9664. 

Waring JF et al. Microarray analysis of hepatotoxins in vitro reveals a correlation between expression profiles and mechanisms of toxicity. Toxicol Lett 2001 120 359-368. 

Andrews J et al. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanoga-ster testis. Genome Res 2000 10 2030-2043. 

Arava, Y. (2003). Isolation of polysomal RNA for microarray analysis. Methods Mol. Biol. 224, 79-87. 

Figure 10.1 Experimental schemes for microarray analysis. All experimental schemes start with a separation step of the cell lysate by velocity sedimentation in a sucrose gradient (top scheme). Collection of the desired fractions is assisted by a continuous ultraviolet (UV) reading of the gradient (an example of such UV reading is shown in each section). This allows determination of the sedimentation position of the 40S, 60S, 80S, and polyribosomal complexes (2,3, and more).Three general ways for fraction collection and analysis are presented (sections A, B, and C) (A) Collection of two fractions (free and polysomes) and direct comparison between them, with the free mRNA fraction labeled with green dye and the polysome fraction labeled with red dye. (B) Collection of two fractions and indirect comparison between them by utilizing an unfractionated reference RNA. (C) Collection of multiple fractions (four in this case), where each fraction is compared to an unfractionated reference sample. The blue arrows indicate the addition of spike-in RNA to each fraction and to the reference RNA.

There are numerous protocols for polysomal gradients preparations that differ mainly at the step for harvesting the cells, and the gradient composition and separation times. The protocol presented later was optimized for isolation of polysomal mRNA from the yeast Saccharomyces cerevisiae, yet many steps will be similar to other eukaryotes and the procedure can easily be modified for other organisms. We will use this protocol as a template on which we will indicate and highlight points that are critical for the microarray analysis. Generally, the RNA isolated by this protocol can be used for analysis by DNA microarray, Northern blot, or RT-PCR. 

Linton KM, Hey Y, Saunders E, et al. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br. J. Cancer 2008 98 1398-1402. 

Microarray analysis of Potential Transcription Factor Targets... 

Le Berre, V. Trevisiol, E. Dagkessamanskaia, A. Sokol, S. Caminade, A. M. Majoral, J. P. Meunier, B. Francois, J., Dendrimeric coating of glass slides for sensitive DNA microarrays analysis, Nucleic Acids Res. 2003, 31, e88... 

Miyazato, A., et al., "Identification of Myelodysplastic Syndrome-Specific Genes by DNA Microarray Analysis with Purified Hematopoietic Stem Cell Fraction," Blood, 98, 422-427 (2001). 

A number of studies have also involved the use of microarrays as tools for the evaluation of mechanisms of immunotoxicology. For example, toxic effects of ricin,23 hexachlorobenzene,24 and nickel,25 revealed an unexpected role for inflammatory processes. These findings illustrate the value of microarray analysis in identifying inflammation as a mechanism involved in the toxicopathology following exposure to a particular compound and highlight the underestimated importance of inflammatory processes in immunotoxicity. 

The current practice of using a T-cell-dependent antibody response or natural killer cell function is based on analyses suggesting that these parameters would suffice to identify the vast majority of immunotoxicants.12 However, it is clear that there are exceptions12 and that some immunotoxicants are not effectively identified by these functional tests or by histopathology.3 Thus, it remains possible, particularly if the cost of microarray analysis decreases, that microarrays will eventually prove to be the most practical method available to identify immunotoxicants. 

Rogers, P. D. et al., Differential expression of genes encoding immunomodulatory proteins in response to amphotericin B in human mononuclear cells identified by cDNA microarray analysis, J. Antimicrob. Chemother., 50, 811, 2002. 

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