Biomedical subjects

Gary M Hellmann

Publications and source records attributed to Gary M Hellmann.

7 recordsLinked to original sources

PubMed2005

Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates.

The high degree of sequence similarity between human and nonhuman primate (NHP) genomic DNA suggests that human genome sequence-based DNA microarrays may be used effectively to study gene expression in NHP disease models. In the present study, two distinct commercially available human genome microarray platforms, the Affymetrix HG U133A GeneChip System utilizing Human Genome U133A GeneChips and the Applied Biosystems Expression Array System utilizing the Human Genome Survey Microarray, were used to identify and characterize gene expression changes in the anterior cerebellum of a macaque monkey model of human alcoholism. The Affymetrix microarray consists of eleven short oligonucleotide probe sets for each gene while the Applied Biosystems Microarray uses a single long oligonucleotide per gene. Cross-mapping of probes revealed a total of 11,542 genes that are represented on both microarray platforms. Absolute measures of gene expression ("present calls") from the cerebellum RNA samples were 65-70% (Applied Biosystems Expression Array System) and 27-30% (AffymetrixGeneChip System) among these common gene targets. Analysis of variance (ANOVA; p<0.05; >1.2 fold change; detected on at least 50% of the arrays) indicated 932 and 515 differentially expressed genes for the Applied Biosystems and Affymetrix microarrays, respectively. Significance analysis of microarrays (SAM) identified 255 significant genes at 5% false discovery rate (FDR) for the Applied Biosystems data set and five significant genes at 60% FDR (minimum FDR) for the Affymetrix data set. TaqMan assay-based real-time PCR validation of a number of differentially-expressed genes yielded results that agreed well with the array data in the majority of comparisons. This study demonstrates that human sequence-based DNA arrays can be used effectively to detect differential gene expression in an NHP disease model and provides evidence that the use of this long oligonucleotide-based microarray platform may be more suitable for cross-species gene expression studies than a short oligonucleotide-based system.

Alcohol Drinking↗

PubMed2005

Kinetic analysis of cytokine response to cigarette smoke condensate by human endothelial and monocytic cells.

Atherosclerosis is generally considered an inflammatory disease characterized by the accumulation of lipid in large and medium elastic arteries. Individuals who smoke are at increased risk for developing atherosclerosis and the clinical events associated with this disease. Underlying the mechanisms involved in atherosclerotic lesion development exists a complex pattern of signaling, involving molecules (cytokines and chemokines) that mediate the progression of arterial lesions. The unique nature of exposure to tobacco-related toxicants during the process of smoking prompted our investigation of the time-dependent responses of two critical cell types to cigarette smoke condensate exposure. In this study, we examined the kinetic responses, using suspension array technology and RT-PCR of 17 cytokines (IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12, IL-13, IL-17 GM-CSF, G-CSF, INF-gamma, TNF-alpha, MCP-1 and MIP-1beta) in human aortic endothelial cells (HAECs) and THP-1 monocyte macrophages following exposure to cigarette smoke condensate (CSC) for 24h. In HAECs, IL-8 and IL-4 were rapidly stimulated by CSC exposure while, surprisingly, MCP-1 expression was downregulated. In THP-1 macrophages, IL-6, MIP-1beta, MCP-1 and IL-1beta protein expression were suppressed upon CSC exposure. All other measurable cytokines in THP-1 cells exposed to CSC had levels of protein and mRNA similar to controls. Depending on cell type, CSC uniquely influences the expression of cytokines. The complex interplay of these signaling molecules within the framework of atherosclerosis points to the ability of cigarette smoke components to alter such signaling following acute exposure, and by this mechanism may alter the course of both atherogenesis initiation and progression.

Aorta↗

PubMed2004

Increased DNA methylation in the HoxA5 promoter region correlates with decreased expression of the gene during tumor promotion.

Promoter-region DNA methylation inhibits transcription. A two-stage SENCAR (sensitive to mouse carcinogenesis) mouse skin carcinogenicity model was used to examine gene-specific changes in methylation during skin tumor promotion. Analysis was performed on 7,12-dimethylbenz[a]anthracene (DMBA)-initiated skin promoted with 9, 18, 27, or 36 mg cigarette smoke condensate (CSC) for 9 wk, or 27 mg CSC for 9 wk and sacrificed 6 wk afterwards (recovery group). Additionally, tumors arising following promotion with 27 mg CSC for 29 wk were assessed. Gene array analysis identified differentially expressed genes. Expression of HoxA5, a tumor suppressor gene, was decreased following 9 wk of treatment with 27 mg CSC, and returned to control levels during recovery. HoxA5 promoter methylation was measured with the enzymatic regional methylation assay (ERMA). DNA was bisulfite-modified, PCR-amplified with primers containing dam sites, incubated with [14C-methyl] S-adenosyl-L-methionine (SAM) and dam methyltransferase for DNA quantification, then incubated with [3H-methyl] SAM and SssI methylase to quantify methylation status. Higher 3H/14C ratios indicate increased methylation. The 3H/14C ratios of animals promoted with 27 or 36 mg CSC (48.2 +/- 6.9 and 24.2 +/- 6.1, respectively) were higher than the control or recovery group ratios (12.3 +/- 0.1 and 12.6 +/- 0.3, respectively); sequence analysis supported these findings. Increased methylation of p16 or O6 methylguanine methyltranferase (MGMT) was detected in 4/8 (50%) of the tumor samples from mice promoted with 27 mg CSC. These data suggest that increased DNA methylation contributes to the downregulation of HoxA5, and combined with hypermethylation of p16 or MGMT, this might facilitate the clonal expansion of increasingly aberrant cells during promotion.

Animals↗

PubMed2004

Confirming microarray data--is it really necessary?

The generation of corroborative data has become a commonly used approach for ensuring the veracity of microarray data. Indeed, the need to conduct corroborative studies has now become official editorial policy for at least 2 journals, and several more are considering introducing such a policy. The issue of corroborating microarray data is a challenging one-there are good arguments for and against conducting such experiments. However, we believe that the introduction of a fixed requirement to corroborate microarray data, especially if adopted by more journals, is overly burdensome and may, in at least several applications of microarray technology, be inappropriate. We also believe that, in cases in which corroborative studies are deemed essential, a lack of clear guidance leaves researchers unclear as to what constitutes an acceptable corroborative study. Guidelines have already been outlined regarding the details of conducting microarray experiments. We propose that all stakeholders, including journal editorial boards, reviewers, and researchers, should undertake concerted and inclusive efforts to address properly and clarify the specific issue of corroborative data. In this article we highlight some of the thorny and vague areas for discussion surrounding this issue. We also report the results of a poll in which 76 life science journals were asked about their current or intended policies on the inclusion of corroborative studies in papers containing microarray data.

Animals↗

PubMed2004

MMP-1 polymorphic expression in aortic endothelial cells: possible role in lesion development in smokers and nonsmokers.

Matrix metalloproteinase-1 (MMP-1) is involved in the degradation of extra-cellular matrix components and is thought to play a key role in atherogenesis. The objective of the present study was to determine: (1) whether MMP-1 differential gene expression observed in primary cultures of human aortic endothelial cells (HAEC) exposed to cigarette smoke condensate (CSC) was associated with a single nucleotide polymorphism (SNP) in its promoter region and (2) if the SNP altered atherosclerotic lesion development in smokers and nonsmokers. Genotype analysis of six HAEC lines revealed that those homozygous for the 1G-variant exhibited low levels of gene expression. Cells homozygous for the 2G-variant or heterozygous (1G/2G) had elevated levels of both mRNA and protein. These relative levels were also seen after CSC expo-sure. MMP-1 genotypes of 104 Caucasian males acquired from the Pathobiological Determinants of Atherosclerosis in Youth study were compared with the extent of atherosclerotic lesion development in the aorta. The results indicate that, although the MMP-1 SNP influences MMP-1 gene expression in cultured HAEC exposed to CSC, differences in lesion development were not observed based on this polymorphism in young Caucasian males.

Arteries↗

PubMed2003

Matrix-degrading and pro-inflammatory changes in human vascular endothelial cells exposed to cigarette smoke condensate.

Cigarette smoking has been associated with an increase in the severity and prevalence of atherosclerosis in the abdominal aorta. To begin our investigation of this finding, we used an integrated approach combining gene expression profiling, protein analysis, cytokine measurements, and cytotoxicity determinations to examine molecular responses of cultured human aortic and coronary endothelial cells exposed to cigarette smoke condensate (CSC) and nicotine. Exposure of endothelial cells to CSC (30 and 60 microg/mL TPM) for 24 h resulted in minimal cytotoxicity, and the upregulation of genes involved in matrix degradation (MMP-1, MMP-8, and MMP-9), xenobiotic metabolism (HO-1 and CYP1A2), and downregulation of genes involved in cell cycle regulation (including TOP2A, CCNB1, CCNA, CDKN3). Exposure of cells to a high physiological concentration of nicotine resulted in few differentially expressed genes. Immunoblot analysis of proteins selected from genes shown to be differentially regulated by microarray analysis revealed similar responses. Finally, a number of inflammatory cytokines measured in culture media were elevated in response to CSC. Together, these results describe a complex proinflammatory response, possibly mediating the recruitment of leukocytes through cytokine signaling. Additionally, fibrous cap destabilization may be facilitated by matrix metalloproteinase upregulation.

Adult↗

PubMed2002

Induction of GADD45 and GADD153 in neuroblastoma cells by dopamine-induced toxicity.

Dopamine (DA) metabolism and oxidation produce both reactive oxygen species (ROS) and reactive quinones. These chemical species are implicated in dopamine neurotoxicity and neurodegeneration. In the present studies, human neuroblastoma (SK-N-SH) cells were exposed to toxic concentrations of dopamine (333 microM) in order to investigate molecular pathways involved in dopamine toxicity. cDNA hybridization array (microarray) technology demonstrated that GADD45 and GADD153 (growth arrest and DNA-damage inducible) gene expression was increased in dopamine-treated cells (333 microM for 18 h). Subsequent Northern and Western blot analysis confirmed these changes in GADD45 and GADD153 gene expression. The antioxidant, ascorbic acid, significantly reduced the increase in GADD45 gene expression but did not significantly reduce GADD153 gene expression. Currently, the precise function of the GADD gene products is not known. It is known, however, that these genes are upregulated in response to stress to allow cells time to repair macromolecular damage. In the present case, GADD gene expression (manifested as increased mRNA and protein levels) preceded dopamine-induced cytotoxicity. It appears that dopamine, through the formation of reactive oxygen species and quinones, may damage cellular macromolecules to the point of inducing GADD gene expression. Other genes that displayed changes, but that have not been subjected to post-hoc confirmation, include clusterin (increased), ubiquitin (increased), CD27 ligand (increased), CD27BP (increased), and rac-PK-beta (decreased).

Ascorbic Acid↗