Biomedical subjects

Milton W Taylor

Publications and source records attributed to Milton W Taylor.

6 recordsLinked to original sources

PubMed2006

Model-based identification of cis-acting elements from microarray data.

Identification of transcriptional regulatory motifs continues to be a challenging problem in computational biology. We report a model-based procedure, MotifModeler, that uses global gene expression data to (1) identify cis-acting elements (CAE) that regulate gene expression under a given condition and (2) estimate the effects of the CAE on gene expression. MotifModeler repeatedly tests random subsets of all possible motifs of a given size and selects those that best fit a combinatorial model of the expression levels. We tested MotifModeler using data from a microarray experiment on the effects of interferon-alpha in peripheral blood monocytes. Focusing on 6-bp motifs, we predicted 16 stimulatory and 4 inhibitory motifs. Motifs were extended and compared to known binding sites in the TRANSFAC database using position-specific scoring matrices. Many predicted CAE match sites known to be involved in interferon action. MotifModeler demonstrated the potential to computationally identify CAE important in gene regulation.

Amino Acid Motifs↗

PubMed2006

REFINEMENT: a search framework for the identification of interferon-responsive elements in DNA sequences--a case study with ISRE and GAS.

Interferons (IFN) are a family of pleiotropic secreted proteins that play a key role in mediating antiviral and apoptotic responses, and in immune modulation. Interferons induce a large number of genes through activating the janus tyrosine kinase (JAK)-signal transducers and activators of transcription proteins (STAT) pathway, and the binding of transcription factors to upstream regions of the inducible genes (interferon-stimulated gene, ISG) at specific DNA regulatory elements known as interferon-stimulated response element (ISRE) and gamma-activated sequence (GAS). We have previously performed DNA micro-arrays on peripheral blood mononuclear cells (PBMC) treated with interferon-alpha in culture and showed that approximately 700 genes are significantly modulated (P < or = 0.001). In order to search for ISRE and GAS we have developed a framework called regulatory element finding with iteration and effective model refinement (REFINEMENT) using an existing program (HMMER) and a standard discriminating scoring technique. Although REFINEMENT uses existing programs, our framework itself is novel as it effectively discriminates occurrences using an iterative model refinement technique. REFINEMENT has detected either ISRE or GAS sequence in all of the genes shown to be induced at a P-value < or = 0.001. There were far more functional occurrences in ISRE than in GAS, suggesting that ISRE plays a greater role in response to interferon-alpha than GAS sequences. This method can be used to identify such sequences in any set of genes. REFINEMENT is non-commercial and is accessible at .

Base Sequence↗

PubMed2006

Differential gene induction by type I and type II interferons and their combination.

Type I and type II interferons (IFNs) bind to different cell surface receptors but activate overlapping signal transduction pathways. We examined the effects of a type I IFN (IFN-alphacon1) and a type II IFN (IFN-gamma1b) on gene expression in A549 cells and demonstrate that there is a common set of genes modulated by both IFNs as well as a set of genes specifically regulated by each, reflecting the activation of different signaling pathways. In particular, IFN-gamma induced many more genes of the signaling pathways, apoptosis, and cytokine interactions than did IFN-alpha. Even with genes induced by both IFNs there were distinctive quantitative differences in expression. IFN-gamma1b plays a major role in the induction and regulation of the complement pathway. Previous work has shown a synergistic antiviral and antiproliferative effect of type I and type II IFNs in cell culture and in the treatment of tumors in mice. We demonstrate that a majority of genes showed an additive effect of IFN-alphacon1 and IFN-gamma1b, but a subset of genes is synergistically induced; these include ISG20, MX2, OAS2, and other genes known to be involved in the antiviral response, TRAIL (TNFSF10) and caspases involved in apoptosis and chemokine genes RANTES, CXCL10, and CXCL11. Greater than additive transcription of some of these genes in the presence of both IFNs was confirmed by real-time kinetic RT-PCR. Elevated induction of many of these genes may be sufficient to explain the synergistic antiviral and antitumor effects of this combination of IFNs in vivo.

Antineoplastic Agents↗

PubMed2004

Global effect of PEG-IFN-alpha and ribavirin on gene expression in PBMC in vitro.

Using oligonucleotide microarrays, we have examined the expression of 22,000 genes in peripheral blood cells treated with pegylated interferon-alpha2b (PEG-IFN-alpha) and ribavirin. Treatment with ribavirin had very little effect on gene expression, whereas treatment with PEG-IFN-alpha had a dramatic effect, modulating the expression of approximately 1000 genes (at p < 0.001). In addition to genes previously reported to be induced by type I or type II IFNs, many novel genes were found to be upregulated, including transcription factors, such as ATF3, ATF4, properdin, a key regulator of the complement pathway, a homeobox gene (HESX1), and an RNA editing enzyme (apobec3). Chemokines CXCL10 and CXCL11 were upregulated, whereas CXCL5 was downregulated. Cytokines interleukin-15 (IL-15) and IL-18 were also significantly induced, whereas IL-1alpha and IL-1beta were downregulated. Most other interleukins were not affected. The results of the microarrays were confirmed by kinetic real-time PCR. These data indicate that IFN treatment causes upregulation of genes associated with the stress response, apoptosis, and signaling, and an equal number of genes are downregulated, including those associated with protein synthesis, specific cytokines and chemokines and other biosynthetic functions.

Cells, Cultured↗

PubMed2003

Identification of a novel promoter in the E2 open reading frame of the human papillomavirus type 18 genome.

Northern blot and RT-PCR analyses indicated that the human papillomavirus E4 open reading frame is expressed in HeLa cells. Because integration at the E1 or E2 open reading frame would place the viral upstream regulatory region downstream of the viral late genes, the expression of E4 in HeLa cells is most likely regulated by host cellular promoter(s) or unidentified viral promoter(s) in the E2 region. Primer extension analysis and transient transfection experiments with luciferase reporter constructs under the transcriptional control of various subgenomic fragments of HPV-18 were carried out to identify and characterize functional promoters within the E2 region. The in vivo activity of a novel promoter located within the 5'-end region of the E2 open reading frame of human papillomavirus type 18 is demonstrated.

5' Untranslated Regions↗

PubMed2002

Induction of IL-1Ra in resistant and responsive hepatitis C patients following treatment with IFN-con1.

Hepatitis C virus (HCV) infection is resistant to interferon-alpha (IFN-alpha) in some patients. The mechanism of this resistance is unknown. Interleukin-1 receptor antagonist (IL-1Ra) is induced by IFN-alpha and is a good indicator of IFN activity. In the current study, we compared IL-1Ra levels in rapid virologic responders and flat responders who showed resistance to IFN. Three groups of patients were examined, including those who received a single dose of consensus IFN (IFN-con1), patients who received daily IFN-con1 for 1 week, and patients who received IFN-con1 daily for 24 weeks. Serum IL-1Ra, IL-6, and HCV RNA were measured serially in all groups. Serum IL-1Ra levels increased rapidly in all patients with hepatitis C after IFN-alpha administration, irrespective of their virologic response. IL-1Ra levels remained elevated at 1 week but were similar to baseline by week 2 of treatment in patients receiving continuous therapy. IL-6 levels also increased acutely but rose more slowly than IL-1Ra levels. The increase in IL-1Ra and IL-6 observed in both flat and rapid virologic responders indicates that IFN receptors are functioning in patients with IFN-resistant hepatitis C and that the lack of response is related to other virologic or immunologic factors.

Adult↗