Absolute Fold Change Research Articles

Genome-wide gene expression profiling and mutation analysis of Saudi patients with Canavan disease

PurposeCanavan disease, caused by a deficiency of aspartoacylase, is one of the most common cerebral degenerative diseases of infancy. The aims of this study were to identify the mutations associated with Canavan disease in Saudi Arabia and to identify differentially expressed genes likely to contribute to the development of this disease. MethodsPolymerase chain reaction, long polymerase chain reaction, multiplex ligation-dependent probe amplification, sequencing, array comparative genomic hybridization (aCGH), and global gene expression profiling were used to determine putative mutations and likely gene signatures in cultured fibroblasts of patients from Saudi Arabia. ResultsOne novel and one known large deletion and two previously known mutations (IVS4 + 1G>T and G27R) were identified. Compared with controls, 1440 genes were significantly modulated in Canavan patients (absolute fold change [FC] ≥4). Genome-wide gene expression profiling results indicated that some genes, involved in apoptosis, muscle contraction and development, mitochondrial oxidation, inflammation and glutamate, and aspartate metabolism, were significantly dysregulated. ConclusionsOur findings indicate that the presence of muscle weakness and hypotonia in patients may be associated with the dysregulated gene activities of cell motility, muscle contraction and development, actin binding, and cytoskeletal-related activities. Overall, these observations are in accordance with previous studies performed in a knockout mouse model.

Endometrial-Peritoneal Interactions during Endometriotic Lesion Establishment

The pathophysiology of endometriosis remains unclear but involves a complex interaction between ectopic endometrium and host peritoneal tissues. We hypothesized that disruption of this interaction would suppress endometriotic lesion formation. We hoped to delineate the molecular and cellular dialogue between ectopic human endometrium and peritoneal tissues in nude mice as a first step toward testing this hypothesis. Human endometrium was xenografted into nude mice, and the resulting lesions were analyzed using microarrays. A novel technique was developed that unambiguously determined whether RNA transcripts identified via microarray analyses originated from human cells (endometrium) or mouse cells (mesothelium). Four key pathways (ubiquitin/proteasome, inflammation, tissue remodeling/repair, and ras-mediated oncogenesis) were revealed, demonstrating communication between host mesothelial cells and ectopic endometrium. Morphometric analysis of nude mouse lesions confirmed that necrosis, inflammation, healing and repair, and cell proliferation occurred during xenograft development. These processes were entirely consistent with the molecular networks revealed by the microarray data. The transcripts detected in the xenografts overlapped with differentially expressed transcripts in a comparison between paired eutopic and ectopic endometria from human endometriotic patients. For the first time, components of the interaction between ectopic endometrium and peritoneal stromal tissues are revealed. Targeted disruption of this dialogue is likely to inhibit endometriotic tissue formation and may prove to be an effective therapeutic strategy for endometriosis.

A distinct epigenetic signature at targets of a leukemia protein

BackgroundHuman myelogenous leukemia characterized by either the non random t(8; 21)(q22; q22) or t(16; 21)(q24; q22) chromosome translocations differ for both their biological and clinical features. Some of these features could be consequent to differential epigenetic transcriptional deregulation at AML1 targets imposed by AML1-MTG8 and AML1-MTG16, the fusion proteins deriving from the two translocations. Preliminary findings showing that these fusion proteins lead to transcriptional downregulation of AML1 targets, marked by repressive chromatin changes, would support this hypothesis. Here we show that combining conventional global gene expression arrays with the power of bioinformatic genomic survey of AML1-consensus sequences is an effective strategy to identify AML1 targets whose transcription is epigenetically downregulated by the leukemia-associated AML1-MTG16 protein.ResultsWe interrogated mouse gene expression microarrays with probes generated either from 32D cells infected with a retroviral vector carrying AML1-MTG16 and unable of granulocyte differentiation and proliferation in response to the granulocyte colony stimulating factor (G-CSF), or from 32D cells infected with the cognate empty vector. From the analysis of differential gene expression alone (using as criteria a p value < 0.01 and an absolute fold change > 3), we were unable to conclude which of the 37 genes downregulated by AML1-MTG16 were, or not, direct AML1 targets. However, when we applied a bioinformatic approach to search for AML1-consensus sequences in the 10 Kb around the gene transcription start sites, we closed on 17 potential direct AML1 targets. By focusing on the most significantly downregulated genes, we found that both the AML1-consensus and the transcription start site chromatin regions were significantly marked by aberrant repressive histone tail changes. Further, the promoter of one of these genes, containing a CpG island, was aberrantly methylated.ConclusionThis study shows that a leukemia-associated fusion protein can impose a distinct epigenetic repressive signature at specific sites in the genome. These findings strengthen the conclusion that leukemia-specific oncoproteins can induce non-random epigenetic changes.

Gene expression in giant cell myocarditis: Altered expression of immune response genes

Background Giant cell myocarditis is a rapidly progressive and often fatal condition without a clear etiology or treatment. A better understanding of giant cell myocarditis pathogenesis is critical to developing treatments to prevent progression and reverse damage. We compared the gene expression of giant cell myocarditis with that of nonfailing hearts. Methods Left ventricular samples from two giant cell myocarditis patients harvested during ventricular assist device placement and six unused donor hearts were examined using Affymetrix U133A microarrays. Differential gene expression was defined with a Bonferroni-adjusted p value ≤ 0.05 from a Student's t-test and an absolute fold change ≥ 2.0. Select gene expression was confirmed with quantitative PCR. Results Of 115 differentially expressed genes, most were upregulated in giant cell myocarditis and involved in immune response, transcriptional regulation, and metabolism. T-cell activation genes included chemokine receptor 4; chemokine ligands 5, 9, 13, and 18; interleukin-10 receptor alpha; and beta-2 integrin. Conclusions Gene expression analysis of giant cell myocarditis offers novel insights into its pathogenesis, namely the role of T-cell activators of the Th1 subset and immune response genes previously implicated in heart failure. This forms the basis for future work aimed at defining novel therapeutic targets for giant cell myocarditis.

Intrinsic pollen NADPH oxidases induce genes by activating innate immune responses in human bronchial epithelial cells

Rationale We recently identified intrinsic NADPH-oxidase activity (NOA) in ragweed pollen extract (RWE) that induces oxidative stress in cultured bronchial epithelial cells and in vivo in the airway epithelial cells of mice. This NOA plays a key role in allergic inflammation (Boldogh et al). We hypothesized that NOA may directly modulate gene expression in airway epithelial cells via innate immune pathways. Methods A549 cells, a human bronchial epithelial cell line, were exposed to RWE for 1, 3, and 6 hours, and compared to an unexposed control. Cellular mRNA was analyzed for 15,000 genes by Affymetrix® HG-U133A GeneChip® microarray. Probe sets with an absolute fold change ≥2X from control were compared using a Venn analysis. Candidate genes were compared to three model time-course profiles and ranked by their correlation coefficient against the model trajectory: 1) progressively up/down with time, 2) up/down at 1 hour post-exposure, and 3) up/down at 3 hours post-exposure. Results Venn analysis showed that RWE with NOA had up-regulated 155 genes by 1 hour, 213 genes by 3 hours, and 193 genes by 6 hours more than 2 fold relative to the control. Likewise, RWE with NOA had down-regulated 100 genes by 1 hour, 118 genes by 3 hours, and 80 genes by 6 hours. Profile searches identified 68 genes that positively or negatively correlated at the 95% limit with profile 1, 63 with profile 2 and 82 with profile 3. Conclusions NOA modulates many genes in bronchial epithelial cells by activation of innate immune networks in epithelial cells.