Designer Microarrays: From Soup To Nuts

Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Kentucky 40292, USA.
The Journals of Gerontology Series A Biological Sciences and Medical Sciences (Impact Factor: 5.42). 12/2002; 57(11):B400-5. DOI: 10.1093/gerona/57.11.B400
Source: PubMed


The recognition that multigene mechanisms control the pathways determining the aging process renders gene screening a necessary skill for biogerontologists. In the past few years, this task has become much more accessible, with the advent of DNA chip technology. Most commercially available microarrays are designed with prefixed templates of genes of general interest, allowing investigators little freedom of choice in attempting to focus gene screening on a particular thematic pathway of interest. This report describes our "designer microarray" approach as a next generation of DNA chips, allowing individual investigators to engage in gene screening with a user friendly, do-it-yourself approach, from designing the probe templates to data mining. The end result is the ability to use microarrays as a platform for versatile gene discovery.

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    • "Samples of small RNA were labeled at the 3 0 end with digoxigenin (DIG) using the DIG Oligonucleotide Tailing Kit, 2nd Generation (Roche Diagnostics , Indianapolis, IN). 1.0 lg of small RNA was labeled in a total volume of 20 lL, as previously described by Wang et al. (2002). Rat miRNA microarrays (MMChips) bore 367 antisense DNA sequences of rat miRNAs obtained from miRBase (http://microrna. "
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    ABSTRACT: Background Over-expression of the heme-degrading enzyme, heme oxygenase-1 (HO-1) promotes iron deposition, mitochondrial damage, and autophagy in astrocytes and enhances the vulnerability of nearby neuronal constituents to oxidative injury. These neuropathological features and aberrant brain microRNA (miRNA) expression patterns have been implicated in the etiopathogeneses of various neurodevelopmental and aging-related neurodegenerative disorders.Objective To correlate glial HO-1 overexpression with altered miRNA patterns, which have been linked to the aforementioned “core” neuropathological features.MethodsmiRNA microchip assays were performed on HMOX1- and sham-transfected primary rat astroglia and affected miRNAs were further validated by qPCR. The roles of the heme degradation products, carbon monoxide (CO), iron (Fe) and bilirubin on miRNA expression were assessed and salient mRNA targets of the impacted miRNAs were ascertained.ResultsIn HMOX1-transfected astrocytes, rno-miR-140*, rno-miR-17, and rno-miR-16 were significantly up-regulated, and rno-miR-297, rno-miR-206, rno-miR-187, rno-miR-181a, rno-miR-138 and rno-miR-29c were down-regulated, compared to sham-transfected controls. CO and Fe were implicated in the HMOX1 effects, whereas bilirubin was inert or counteracted the HMOX1-related changes. mRNA levels of Ngfr, Vglut1, Mapk3, Tnf-α, and Sirt1, known targets of the down-regulated miRNAs and abnormal in various human brain disorders, were significantly increased in the HMOX-1-transfected astrocytes.Conclusions In chronic CNS disorders, altered expression of salient miRNAs and their mRNA targets may contribute to the neural damage accruing from the over-expression of glial HO-1. © 2015 Wiley Periodicals, Inc.GLIA 2015
    Glia 03/2015; 63(7). DOI:10.1002/glia.22823 · 6.03 Impact Factor
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    • "Samples of small RNA were labeled on their 3' end with digoxigenin (DIG) using the DIG Oligonucleotide Tailing Kit, 2nd Generation (Roche Diagnostics, Indianapolis, IN). 1.0 µg of small RNA was labeled in a total volume of 20 µL, as described by Wang et al. (Wang et al. 2002). Mouse miRNA microarrays (MMChips) bore 367 anti-sense DNA sequences of mouse miRNAs obtained from miRBase ( "
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    ABSTRACT: The Ames dwarf mouse is well known for its remarkable propensity to delay the onset of aging. Although significant advances have been made demonstrating that this aging phenotype results primarily from an endocrine imbalance, the post-transcriptional regulation of gene expression and its impact on longevity remains to be explored. Towards this end, we present the first comprehensive study by microRNA (miRNA) microarray screening to identify dwarf-specific lead miRNAs, and investigate their roles as pivotal molecular regulators directing the long-lived phenotype. Mapping the signature miRNAs to the inversely expressed putative target genes, followed by in situ immunohistochemical staining and in vitro correlation assays, reveals that dwarf mice post-transcriptionally regulate key proteins of intermediate metabolism, most importantly the biosynthetic pathway involving ornithine decarboxylase and spermidine synthase. Functional assays using 3'-untranslated region reporter constructs in co-transfection experiments confirm that miRNA-27a indeed suppresses the expression of both of these proteins, marking them as probable targets of this miRNA in vivo. Moreover, the putative repressed action of this miRNA on ornithine decarboxylase is identified in dwarf mouse liver as early as 2 months of age. Taken together, our results show that among the altered aspects of intermediate metabolism detected in the dwarf mouse liver--glutathione metabolism, the urea cycle and polyamine biosynthesis--miRNA-27a is a key post-transcriptional control. Furthermore, compared to its normal siblings, the dwarf mouse exhibits a head start in regulating these pathways to control their normality, which may ultimately contribute to its extended health-span and longevity.
    Aging cell 10/2009; 9(1):1-18. DOI:10.1111/j.1474-9726.2009.00529.x · 6.34 Impact Factor
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    • "The human microRNA microarray (MMchip) consisted at the time of 462 human anti-sense DNA sequences of mature miRNAs obtained from miRBase (, version 8.2), spotted and UV crosslinked on nitrocellulose membrane, as described (Wang et al., 2002). "
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    ABSTRACT: MicroRNAs (miRNAs) are small non-coding RNAs that regulate diverse genetic expression networks through their control of mRNA stability or translation. Their role in aging mechanisms has been proposed in various model systems. In this report, the expression profiling of 462 human miRNAs in the reversible growth arrest state of quiescence, and irreversible states of replicative senescence and hydrogen peroxide-induced premature senescence, are compared to young replicating lung fibroblasts. Greater numbers of up-regulated than down-regulated miRNAs are observed when cells stop proliferating, particularly in premature senescence, somewhat less in replicative senescence, and less still in quiescence. Several altered miRNA expressions are shared by the three growth arrest states, including the up-regulation of miR-34a, -624, -638 and miR-377, and the down-regulation of miR-365 and miR-512-5p. miRNAs up-regulated in both permanent growth arrest states but not in quiescence include let-7g, miR-26a, -136, -144, -195 and miR-200b. In each of the growth arrest states, miR-34a and let-7f have the most robust up-regulation in H(2)O(2)-induced premature senescence, followed by miR-638 and miR-663 in replicative senescence, and finally, miR-331-3p and miR-595 in quiescence. Our comprehensive evaluation of miRNA target correlations with known biomarkers for replicative senescence suggests that miRNAs may repress pathways controlling not only cell cycle traverse and proliferation, but also insulin-like signaling, DNA repair and apoptosis, all of which are cellular functions deficient in senescent human fibroblasts.
    Journal of Cellular Physiology 10/2009; 221(1):109-19. DOI:10.1002/jcp.21834 · 3.84 Impact Factor
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