Biomedical subjects

Zihua Hu

Publications and source records attributed to Zihua Hu.

6 recordsLinked to original sources

PubMed2006

Identification of common transcriptional regulatory elements in interleukin-17 target genes.

Interleukin (IL)-17 is the founding member of a novel family of inflammatory cytokines. Although produced by T cells, IL-17 activates genes and signals typical of innate immune mediators such as tumor necrosis factor (TNF)-alpha and IL-1beta. Most IL-17 target genes characterized to date are cytokines or neutrophil-attractive chemokines. Our recent microarray studies identified an acute phase response gene, 24p3/lipocalin 2, as a novel IL-17-induced gene. Here we describe a detailed analysis of the 24p3 promoter. We find that, unlike cytokine or chemokine gene target genes, 24p3 is regulated primarily at the level of transcription rather than mRNA stability and that synergy between IL-17 and TNFalpha occurs at the level of the 24p3 promoter. Two key transcription factor binding sites (TFBS) were identified, corresponding to NF-kappaB and CCAAT/enhancer-binding protein (C/EBP). Deletion of either site eliminated 24p3 promoter activity in response to IL-17. These findings were strikingly similar to the IL-6 promoter, where IL-17-mediated regulation of both NF-kappaB and C/EBP is essential. To determine whether joint use of NF-kappaB and C/EBP is common to all IL-17 target genes, we performed a computational analysis on 18 well documented IL-17 target promoters to assess statistical enrichment of specific TFBSs. Indeed, NF-kappaB and C/EBP sites were over-represented in these genes, as were AP1 and OCT1 sites. Moreover, these promoters fell into three definable subcategories based on TFBS location and usage. Analysis of IL-17 target gene regulation is key for understanding this important host-defense molecule and also contributes to an understanding of upstream signaling mechanisms used by IL-17, either alone or in concert with TNFalpha.

Acute-Phase Proteins↗

PubMed2006

Diabetes-altered gene expression in rat skeletal muscle corrected by oral administration of vanadyl sulfate.

Treatment with vanadium, a representative of a class of antidiabetic compounds, alleviates diabetic hyperglycemia and hyperlipidemia. Oral administration of vanadium compounds in animal models and humans does not cause clinical symptoms of hypoglycemia, a common problem for diabetic patients with insulin treatment. Gene expression, using Affymetrix arrays, was examined in muscle from streptozotocin-induced diabetic and normal rats in the presence or absence of oral vanadyl sulfate treatment. This treatment affected normal rats differently from diabetic rats, as demonstrated by two-way ANOVA of the full array data. Diabetes altered the expression of 133 genes, and the expression of 30% of these genes dysregulated in diabetes was normalized by vanadyl sulfate treatment. For those genes, the ratio of expression in normal animals to the expression in diabetic animals showed a strong negative correlation with the ratio of expression in diabetic animals to the expression in diabetic animals treated with vanadyl sulfate (P = -0.85). The genes identified belong to six major metabolic functional groups: lipid metabolism, oxidative stress, muscle structure, protein breakdown and biosynthesis, the complement system, and signal transduction. The identification of oxidative stress genes, coupled with the known oxidative chemistry of vanadium, implicates reactive oxygen species in the action of this class of compounds. These results imply that early transition metals or compounds formed from their chemical interactions with other metabolites may act as general transcription modulators, a role not usually associated with this class of compounds.

Administration, Oral↗

PubMed2006

Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.

BACKGROUND: The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess the relative performance of probe set algorithms. Given the fact that the spiked-in cRNAs do not represent endogenously expressed genes in experiments, it becomes increasingly important to have methods to study whether a particular probe set algorithm is more appropriate for a specific dataset, without using such external reference data. RESULTS: We propose the use of the probe set redundancy feature for evaluating the performance of probe set algorithms, and have presented three approaches for analyzing data variance and result bias using two sample t-test statistics from redundant probe sets. These approaches are as follows: 1) analyzing redundant probe set variance based on t-statistic rank order, 2) computing correlation of t-statistics between redundant probe sets, and 3) analyzing the co-occurrence of replicate redundant probe sets representing differentially expressed genes. We applied these approaches to expression summary data generated from three datasets utilizing individual probe set algorithms of MAS5.0, dChip, or RMA. We also utilized combinations of options from the three probe set algorithms. We found that results from the three approaches were similar within each individual expression summary dataset, and were also in good agreement with previously reported findings by others. We also demonstrate the validity of our findings by independent experimental methods. CONCLUSION: All three proposed approaches allowed us to assess the performance of probe set algorithms using the probe set redundancy feature. The analyses of redundant probe set variance based on t-statistic rank order and correlation of t-statistics between redundant probe sets provide useful tools for data variance analysis, and the co-occurrence of replicate redundant probe sets representing differentially expressed genes allows estimation of result bias. The results also suggest that individual probe set algorithms have dataset-specific performance.

Algorithms↗

PubMed2006

Methamphetamine modulates gene expression patterns in monocyte derived mature dendritic cells: implications for HIV-1 pathogenesis.

BACKGROUND: The US is currently experiencing a grave epidemic of methamphetamine use as a recreational drug, and the risk for HIV-1 infection attributable to methamphetamine use continues to increase. Recent studies show a high prevalence of HIV infection among methamphetamine users. Dendritic cells (DCs) are potent antigen presenting cells that are the initial line of defense against HIV-1 infection. In addition, DCs also serve as reservoirs for HIV-1 and function at the interface between the adaptive and the innate immune systems, which recognize and internalize pathogens and subsequently activate T cells. Exposure to methamphetamine results in modulation of immune functional parameters that are necessary for host defense. Chronic methamphetamine use can cause psychiatric co-morbidity, neurological complications, and can alter normal biological processes and immune functions. Limited information is available on the mechanisms by which methamphetamine may influence immune function. This study explores the effect of methamphetamine on a specific array of genes that may modulate immune function. We hypothesize that methamphetamine treatment results in the immunomodulation of DC functions, leading to dysregulation of the immune system of the infected host. This suggests that methamphetamine has a role as a cofactor in the pathogenesis of HIV-1. METHODS: We used the high-throughput technology of gene microarray analysis to understand the molecular mechanisms underlying the genomic changes that alter normal biological processes when DCs are treated with methamphetamine. Additionally, we validated the results obtained from microarray experiments using a combination of quantitative real-time PCR and Western blot analysis. RESULTS: These data are the first evidence that methamphetamine modulates DC expression of several genes. Methamphetamine treatment alters categories of genes that are associated with chemokine regulation, cytokinesis, signal transduction mechanisms, apoptosis, and cell cycle regulation. This report focuses on a selected group of genes that are significantly modulated by methamphetamine treatment and that have been associated with HIV-1 pathogenesis. DISCUSSION/CONCLUSION: The purpose of this study was to identify genes that are unique and/or specific to the complex immunomodulatory mechanisms that are altered as a result of methamphetamine abuse in HIV-1-infected patients. These studies will help to identify the molecular mechanisms that underlie methamphetamine toxicity, and several functionally important classes of genes have emerged as targets in methamphetamine-mediated immunopathogenesis of HIV-1. Identification of novel DC-specific and methamphetamine-responsive genes that modulate several biological, molecular, and signal transduction functions may serve as methamphetamine- and/or HIV-1-specific drug targets.

Adult↗

PubMed2005

REDfly: a Regulatory Element Database for Drosophila.

Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.

Animals↗

PubMed2003

Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm.

We have taken a genomic approach to examine global gene expression in the maize endosperm in relation to dosage and parental effects. Endosperm of eight hybrids generated by reciprocal crosses and their seven inbred parents were sampled at three developmental stages: 10, 14, and 21 days after pollination (DAP). These samples were subjected to GeneCalling, an open-ended mRNA-profiling technology, which simultaneously analyzes thousands of genes. Results indicated that the overall level of gene expression in the maize endosperm was dosage-dependent, that is, the gene expression was proportional to the parental genome contribution of 2n maternal : 1n paternal. However, approximately 8% of the genes deviated from such allelic additive expression and exhibited differential expression in hybrids of reciprocal crosses, resembling either maternally or paternally expressed genes. There were more genes with maternal-like expression (MLE) than those with paternal-like expression (PLE). Allele-specific expression analysis of four selected genes using the WAVE denaturing HPLC (dHPLC) system revealed several mechanisms responsible for the deviation from the allelic additive expression in the hybrid endosperm: heterochronic allelic variation, allelic variation in the level of expression, and genomic imprinting. We discovered a novel imprinted gene no-apical-meristem (NAM) related protein1 (nrp1) that was expressed only in the endosperm and regulated by gene-specific imprinting. The nrp1 gene, a putative transcriptional factor, may play an important role in endosperm development.

Alleles↗