Virus infection induces an antiviral response that is predominantly associated with the synthesis and secretion of soluble interferon. Here, we report that herpes simplex virus type 1 virions induce an interferonindependent antiviral state in human embryonic lung cells that prevents plaquing of a variety of viruses. Microarray analysis of 19,000 human expressed sequence tags revealed induction of a limited set of host genes, the majority of which are also induced by interferon. Genes implicated in controlling the intracellular spread of virus and eliminating virally infected cells were among those induced. Induction of the cellular response occurred in the absence of de novo cellular protein synthesis and required viral penetration. In addition, this response was only seen when viral gene expression was inhibited, suggesting that a newly synthesized viral protein(s) may function as an inhibitor of this response.
RNA polymerase II lacking the Rpb9 subunit uses alternate transcription initiation sites in vitro and in vivo and is unable to respond to the transcription elongation factor TFIIS in vitro. Here, we show that RPB9 has a synthetic phenotype with the TFIIS gene. Disruption of RPB9 in yeast also resulted in sensitivity to 6-azauracil, which is a phenotype linked to defects in transcription elongation. Expression of the TFIIS gene on a high-copy plasmid partially suppressed the 6-azauracil sensitivity of ⌬rpb9 cells. We set out to determine the relevant cellular role of yeast Rpb9 by assessing the ability of 20 different site-directed and deletion mutants of RPB9 to complement the initiation and elongation defects of ⌬rpb9 cells in vivo. Rpb9 is composed of two zinc ribbons. The N-terminal zinc ribbon restored the wild-type pattern of initiation start sites, but was unable to complement the growth defects associated with defects in elongation. Most of the site-directed mutants complemented the elongation-specific growth phenotypes and reconstituted the normal pattern of transcription initiation sites. The anti-correlation between the growth defects of cells disrupted for RPB9 and the selection of transcription start sites suggests that this is not the primary cellular role for Rpb9. Genome-wide transcription profiling of ⌬rpb9 cells revealed only a few changes, predominantly in genes related to metabolism.RNA polymerase II comprises 12 subunits in yeast (1). Four of the subunits, Rpb1, Rpb2, Rpb3, and Rpb11, form a catalytic core that is homologous in structure and function to the prokaryotic core RNA polymerase (2, 3). The other eight eukaryotic subunits are less well characterized. Five of these subunits, Rpb5, Rpb6, Rpb8, Rpb10, and Rpb12, are found in all three eukaryotic RNA polymerases (4 -6). The other three, Rpb4, Rpb7, and Rpb9, are unique to RNA polymerase II, although both Rpb7 and Rpb9 have sequence homologues in RNA polymerases I and III (7). The gene for Rpb9 is not essential for yeast cell viability, but is essential in Drosophila (8).Rpb9 has roles both in transcription initiation and in transcription elongation. In the initiation reaction, Rpb9 modulates the selection of the transcription start site. In cells lacking Rpb9 and in reconstituted transcription reactions lacking Rpb9, the population of start sites is shifted upstream at a variety of promoters (9 -11). In the elongation reaction, Rpb9 is required, along with TFIIS, to effect transcription through blocks to elongation encoded by the DNA template (12). A role in the modulation of initiation and elongation is consistent with the localization of Rpb9 in the three-dimensional structure of yeast RNA polymerase II. Rpb9 is located at the tip of the so-called "jaws" of the enzyme, which is thought to function by clamping the DNA downstream of the active site (3, 13, 14). The Rpb9 homologue in RNA polymerase III, C11, also has been implicated in regulating RNA chain elongation (15).Rpb9 comprises two zinc ribbon domains joined by a 30-amino acid l...
Array comparative genomic hybridization (aCGH) and microarray expression profiling were used to subclassify DNA and RNA alterations associated with differential response to chemotherapy in ovarian cancer. Two to 4 Mb interval arrays were used to map genomic imbalances in 26 sporadic serous ovarian tumors. Cytobands 1p36, 1q42-44, 6p22.1-p21.2, 7q32.1-q34 9q33.3-q34.3, 11p15.2, 13q12.2-q13.1, 13q21.31, 17q11.2, 17q24.2-q25.3, 18q12.2, and 21q21.2-q21.3 were found to be statistically associated with chemotherapy response, and novel regions of loss at 15q11.2-q15.1 and 17q21.32-q21.33 were identified. Gene expression profiles were obtained from a subset of these tumors and identified a group of genes whose differential expression was significantly associated with drug resistance. Within this group, five genes (GAPD, HMGB2, HSC70, GRP58, and HMGB1), previously shown to form a nuclear complex associated with resistance to DNA conformation-altering chemotherapeutic drugs in in vitro systems, may represent a novel class of genes associated with in vivo drug response in ovarian cancer patients. Although RNA expression change indicated only weak DNA copy number dependence, these data illustrate the value of molecular profiling at both the RNA and DNA levels to identify small genomic regions and gene subsets that could be associated with differential chemotherapy response in ovarian cancer.
Molecular diagnostics is a rapidly advancing field in which insights into disease mechanisms are being elucidated by use of new gene-based biomarkers. Until recently, diagnostic and prognostic assessment of diseased tissues and tumors relied heavily on indirect indicators that permitted only general classifications into broad histologic or morphologic subtypes and did not take into account the alterations in individual gene expression. Global expression analysis using microarrays now allows for simultaneous interrogation of the expression of thousands of genes in a high-throughput fashion and offers unprecedented opportunities to obtain molecular signatures of the state of activity of diseased cells and patient samples. Microarray analysis may provide invaluable information on disease pathology, progression, resistance to treatment, and response to cellular microenvironments and ultimately may lead to improved early diagnosis and innovative therapeutic approaches for cancer.
Genome-wide monitoring of gene expression using DNA microarrays represents one of the latest breakthroughs in experimental molecular biology and provides unprecedented opportunity to explore the biological processes underlying human diseases by providing a comprehensive survey of a cell's transcriptional landscape. In the cancer field, this revolutionary technology allows the simultaneous assessment of the transcription of tens of thousands of genes, and of their relative expression between normal cells and malignant cells. As microarray analysis emerges from its infancy, there is widespread hope that microarrays will significantly impact on our ability to explore the genetic changes associated with cancer etiology and development, and ultimately lead to the discovery of new biomarkers for disease diagnosis and prognosis prediction, and of new therapeutic tools. This review provides an overview of microarray technology, specifically in the context of cancer research and describes some of its recent applications to the study of cancer. In addition, the challenges of translating microarray findings into molecular cancer diagnosis and prognosis tools, with the potential of altering clinical practice through individualized cancer care and ultimately of contributing to the battle against cancer, are discussed.
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