High density synthetic oligonucleotide arrays

Lipshutz, Robert J.; Fodor, Stephen P. A.; Gingeras, T; Lockhart, David J.

doi:10.1038/4447

Cited by 2,000 publications

(1,119 citation statements)

References 28 publications

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“…The microarray method allows high-throughput analysis of gene expression patterns (Khan et al, 1999;Lipshutz et al, 1999), and it is particularly useful for studying cocaineinduced gene expression changes (Bibb et al, 2001;Freeman et al, 2001a, b;Toda et al, 2002;McClung and Nestler, 2003;Yuferov et al, 2003;Tang et al, 2003;Yao et al, 2004;Albertson et al, 2004). Despite these studies, the gene expression profile induced by chronic cocaine through the DA D1 receptors remains unclear.…”

Section: Introductionmentioning

confidence: 99%

Repeated Cocaine Administration Induces Gene Expression Changes through the Dopamine D1 Receptors

Zhang

Tang

et al. 2005

Neuropsychopharmacol

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Drug addiction involves compulsive drug-seeking and drug-taking despite known adverse consequences. The enduring nature of drug addiction suggests that repeated exposure to abused drugs leads to stable alterations that likely involve changes in gene expression in the brain. The dopamine D1 receptor has been shown to mediate the long-term behavioral effects of cocaine. To examine how the persistent behavioral effects of cocaine correlate with underlying changes in gene expression, we have used D1 receptor mutant and wild-type mice to identify chronic cocaine-induced gene expression changes mediated via the D1 receptors. We focused on the caudoputamen and nucleus accumbens, two key brain regions that mediate the long-term effects of cocaine. Our analyses demonstrate that repeated cocaine administration induces changes in the expression of 109 genes, including those encoding the stromal cell-derived factor 1, insulin-like growth factor binding protein 6, sigma 1 receptor, regulators of G-protein signaling protein 4, Wnt1 responsive Cdc42 homolog, Ca 2 þ /calmodulin-dependent protein kinase II a subunit, and cyclin D2, via the D1 receptors. Moreover, the seven genes contain AP-1 binding sites in their promoter regions. These results suggest that genes encoding certain extracellular factors, membrane receptors and modulators, and intracellular signaling molecules, among others, are regulated by cocaine via the D1 receptor, and these AP-1 transcription complex-regulated genes might contribute to persistent cocaine-induced behavioral changes.

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Section: Introductionmentioning

confidence: 99%

Repeated Cocaine Administration Induces Gene Expression Changes through the Dopamine D1 Receptors

Zhang

Tang

et al. 2005

Neuropsychopharmacol

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“…In this work we have used high-density oligonucleotide arrays (Lipshutz et al, 1999;Rogge et al, 2000) to analyse the expression pattern of about 7000 genes in RNA samples from melanoma cell lines sensitive or resistant to IFN-α induced inhibition of proliferation and HLA class I induction. Furthermore, by applying the same technology, we have evaluated the gene expression profiles induced by IFN-α in cells sensitive or resistant to these discrete effects.…”

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confidence: 99%

High density oligonucleotide array analysis of interferon-α2a sensitivity and transcriptional response in melanoma cells

et al. 2001

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Summary Interferon alpha (IFN-α) represents an adjuvant therapy of proven effectiveness in increasing disease-free interval and survival in subgroups of melanoma patients. Since high doses of cytokine are required, the treatment is often accompanied by toxic side effects. Furthermore, naturally occurring insensitivity to IFN-α may hamper its therapeutic efficacy. Clinical, molecular or immunological markers enabling the selection of potential responders have not been identified so far. To explore the molecular basis of IFN-α responsiveness, we analysed the expression pattern of about 7000 genes in IFN-α sensitive and resistant cell lines and we compared the transcription profiles of cells cultured in the presence or absence of the cytokine using high-density oligonucleotide arrays. Melanoma cell lines were screened for their sensitivity to proliferation inhibition and HLA class I induction upon IFN-α treatment by standard 3H-thymidine incorporation and flowcytometry. The study of 4 sensitive and 2 resistant cell lines allowed the identification of 4 genes (RCC1, IFI16, hox2 and h19) preferentially transcribed in sensitive cells and 2 (SHB and PKC-ζ) preferentially expressed in resistant cells. IFN-α stimulation resulted in the expression of a panel of 19 known inducible genes in sensitive but not in resistant cells. Moreover a group of 30 novel IFN-α inducible genes was identified. These data may provide a useful basis to develop diagnostic tools to select potential IFN-α responders eligible for treatment, while avoiding unnecessary toxicity to non-responders. Furthermore, by extending the knowledge of the polymorphic effects of IFN-α on gene expression, they offer novel clues to the study of its pleiotropic toxicity.

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“…One company (Affymetrix) produces high-density oligonucleotide R As by using masked photolithography with ~2.4 million 25-mer oligos and 8 µm feature size (33). This enables the sequencing of ~300 Kb/chip.…”

Section: Sequencing By Hybridizationmentioning

confidence: 99%

Applying Rapid Genome Sequencing Technologies To Characterize Pathogen Genomes

Steinberg¹,

Okou²,

Zwick³

2008

Anal. Chem.

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R ecent predictions of the worldwide burden of diseases under a variety of scenarios suggest that infectious diseases will continue to negatively impact the health of human populations well into the future (1). Although economic, social, and technological developments will surely influence these projections, the impact of the constantly changing interaction between hosts and infectious agents is rarely considered. Throughout evolutionary history, human populations were selected to develop immune responses to microbial challenges. The resulting human adaptations then caused pathogen populations to develop resistance via mechanisms such as antigenic variation to evade the immune system. The human host, in turn, counteradapted to the pathogens, not only with genetic changes but also with technologies, such as vaccines and therapeutics, that better recognize and combat the more virulent pathogens. This pattern of host-pathogen coevolution, where changes in allele frequencies in one population exert selection pressures affecting allele frequencies in the other population, creates a complex evolutionary arms race whose course may be difficult to predict (2).Analyzing pathogen and host genomes can elucidate the mechanisms underlying novel adaptations that arise as a consequence of this ongoing evolutionary arms race. Pathogen genomes, because of their relatively small size, were the first to be completely sequenced and have provided researchers fundamental insights into the biology of the organisms, evolutionary relationships, and the determinants of virulence (3).

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High density synthetic oligonucleotide arrays

Cited by 2,000 publications

References 28 publications

Repeated Cocaine Administration Induces Gene Expression Changes through the Dopamine D1 Receptors

Repeated Cocaine Administration Induces Gene Expression Changes through the Dopamine D1 Receptors

High density oligonucleotide array analysis of interferon-α2a sensitivity and transcriptional response in melanoma cells

Applying Rapid Genome Sequencing Technologies To Characterize Pathogen Genomes

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