Two Thalamic Regions Screened Using Laser Capture Microdissection with Whole Human Genome Microarray in Schizophrenia Postmortem Samples.

Editor's evaluation: Comparative transcriptomic analysis reveals translationally relevant processes in mouse models of malaria

P-1256 - Thalamic anterior nucleus microarray screening in schizophrenia

Because the respiratory chain is the major site of oxidation of the reduced equivalents and of energy production in aerobic cells, its inhibition has severe impact on the cells. Communication pathways from the respiratory chain are required to allow the cell to sense the defect and respond to it. In this work, we studied changes in gene expression induced by the treatment of yeast cells with myxothiazol, an inhibitor of the bc(1) complex, an enzyme of the respiratory chain. The pattern and time-course expression of the genes resemble those of the environmental stress response, a common gene expression program induced by sudden changes in the environment. In addition, the changes were, for most of the genes, mediated through the transcription factors Msn2/4, which play a central role in the cellular response to these stresses. By using a mutant with a myxothiazol-resistant bc(1) complex, we showed that the changes of expression of the majority of the genes was caused by the inhibition of the bc(1) complex but that other stresses might be involved. The expression pattern of CTT1, coding for a cytoplasmic catalase, was further studied. The expression of this gene was largely dependent on Msn2/4 and the inhibition of the cytochrome bc(1). Addition of oxidants of NADH was found to decrease the expression of CTT1 induced by myxothiazol treatment, suggesting that the accumulation of NADH caused by the inhibition of the respiratory chain may be involved in the signaling pathway from the mitochondria to the transcription factor.

A Cellular Memory of Developmental History Generates Phenotypic Diversity in C. elegans

New and old regulators of uterine leiomyoma growth from screening with DNA arrays

Chapter 9 - Changes in cortical gene expression in major depressive disorders: More evidence implicating inflammatory-related pathways in disease etiology

Effects of turmeric (Curcuma longa) on the expression of hepatic genes associated with biotransformation, antioxidant, and immune systems in broiler chicks fed aflatoxin

Activation of the mesolimbic dopamine reward pathway by acute ethanol produces reinforcement and changes in gene expression that appear to be crucial to the molecular basis for adaptive behaviors and addiction. The inbred mouse strains DBA/2J and C57BL/6J exhibit contrasting acute behavioral responses to ethanol. We used oligonucleotide microarrays and bioinformatics methods to characterize patterns of gene expression in three brain regions of the mesolimbic reward pathway of these strains. Expression profiling included examination of both differences in gene expression 4 h after saline injection or acute ethanol (2 g/kg). Using a rigorous stepwise method for microarray analysis, we identified 788 genes differentially expressed in control DBA/2J versus C57BL/6J mice and 307 ethanol-regulated genes in the nucleus accumbens, prefrontal cortex, and ventral tegmental area. There were strikingly divergent patterns of ethanol-responsive gene expression in the two strains. Ethanol-responsive genes also showed clustering at discrete chromosomal regions, suggesting local chromatin effects in regulation. Ethanol-regulated genes were generally related to neuroplasticity, but regulation of discrete functional groups and pathways was brain region specific: glucocorticoid signaling, neurogenesis, and myelination in the prefrontal cortex; neuropeptide signaling and developmental genes, including factor Bdnf, in the nucleus accumbens; and retinoic acid signaling in the ventral tegmental area. Bioinformatics analysis identified several potential candidate genes for quantitative trait loci linked to ethanol behaviors, further supporting a role for expression profiling in identifying genes for complex traits. Brain region-specific changes in signaling and neuronal plasticity may be critical components in development of lasting ethanol behavioral phenotypes such as dependence, sensitization, and craving.

See related article, pages 200–208 The endothelium is an expansive spatially distributed organ.1 Endothelial cells participate in a large number of physiological processes including the control of vasomotor tone, the trafficking of cells and nutrients, the regulation of permeability, and the maintenance of blood fluidity. In addition, the endothelium mediates new blood vessel formation, contributes to the balance of pro- and antiinflammatory mediators, and may play a role in antigen presentation. In accomplishing these tasks, the endothelium exhibits a remarkable “division of labor”. For example, arteriolar endothelium is primarily responsible for mediating vasomotor tone; endothelium in postcapillary venules regulates leukocyte trafficking; capillary endothelial cells display organ-specific barrier properties (eg, blood brain barrier versus fenestrated, discontinuous endothelium in hepatic sinusoids); and endothelial cells from different vascular beds balance local hemostasis via the expression of site-specific patterns of anticoagulants and procoagulants.2 In recent years, in vivo phage display and direct proteome mapping of the intact vasculature have revealed a rich diversity in endothelial cell surface markers.3,4 Any consideration of the mechanisms underlying endothelial heterogeneity is best framed around the time-honored debate of nature versus nurture (which will be addressed here in reverse order) (Figure). Mechanisms of endothelial cell heterogeneity. Relative importance of epigenetics and microenvironment in mediating site-specific phenotypes is indicated by +. The table is designed to provide a conceptual framework; the scores are largely speculative and will require ongoing experimental validation. ### Nurture Site-specific endothelial cell phenotypes may be initiated and maintained by signals residing in the extracellular environment. The endothelium is analogous to a barcode reader, constantly taking inventory of its surrounding extracellular environment on the luminal side (circulating blood and its constituents), the abluminal side, and at the endothelial junctions. Environmental cues may be classified into biomechanical or biochemical. Biochemical forces include shear stress and strain. …

Cerebral vasospasm (CV) and related ischemic injury is a major contributor to death and disability after aneurysmal subarachnoid hemorrhage (aSAH). Our overall goal is to understand molecular mechanisms of action of endogenous mechano-growth factor (MGF), a splice variant of insulin-like growth factor 1 (IGF-1), in the brain. MGF was found to be neuroprotective after stroke in a gerbil model of ischemic injury and may serve as a potential therapeutic target to prevent CV-induced brain damage. In our studies, we characterized hypoxia induced changes in MGF expression in different brain regions, commonly affected by CV, at different time points (from 2 hours to 7 days) post 4h hypoxia treatments (6, 8,10 or 12% oxygen). The brain regions analyzed were motor cortex, hippocampus, striatum and hypothalamus. In addition, we characterized changes in MGF expression in microparticle (MP) fractions isolated from cerebrospinal fluid (CSF) extracted from CV patients. Microparticle fractions were isolated from CSF samples using serial ultracentrifugation. We used real time RT-PCR, western blots, and enzyme immunosorbent assay to quantify changes in gene expression and protein levels. In the animal model, our results showed that there were time, dose and brain region specific changes in MGF expression that correlated with changes in the expression of heme oxygenase 1 (HO-1) and biliverdin reductase A, which are molecules involved in neuroprotection, and caspases, apoptotic markers. These results suggest that changes in endogenous MGF due to hypoxia may activate neuroprotective pathways in the brain. In CSF MPs isolated from CV patients, we observed an increase in MGF expression that correlated with the CV onset window and with an increase in HO-1, suggesting that similar pathways are activated post-CV in humans and post-hypoxia in animals. These data indicate that endogenous MGF may play a role in CV onset and may be a neuroprotective target in CV papteins. However, further studies are required to elucidate the molecular mechanisms of MGF and its exact role in CV development and patient outcome.

Sex- and Brain Region-specific Changes in Gene Expression in Male and Female Rats as Consequences of Methamphetamine Self-administration and Abstinence

Differential activation of anterior and midline thalamic nuclei following retrieval of aversively motivated learning tasks

Phenotypic plasticity in Astatotilapia burtoni allows individual males to alternate between dominant and subordinate status, two physiologically and behaviorally distinct phenotypes. Because these phenotypes are completely reversible, they provide an excellent model for studying the molecular mechanisms of phenotypic plasticity. The ability to express alternate phenotypes in A. burtoni depends on the ability to regulate gene expression on both short- and long-term time scales. Previous studies have demonstrated that dominant males, who have increased reproductive capacity, have higher expression of several genes involved in reproduction (e.g., genes for steroid receptors). These differences in gene expression and reproductive physiology are controlled by interactions among males. Recently, it was found that the same interactions that lead to stable long-term changes in gene expression also induce short-term and transient changes in expression of egr-1, an immediate-early gene transcription factor. This immediate-early gene response is part of a general mechanism for mediating changes in gene expression that underlie phenotypic plasticity. Longer stable changes in gene expression must involve other mechanisms, such as dynamic modifications of the epigenome. Recent data suggests a direct link between the immediate-early gene response and epigenetic modifications. These mechanisms which link behavioral interactions to changes in gene expression allow phenotypic variation to occur without corresponding changes in the genome and, as a consequence, they have implications for evolution. In the case of A. burtoni, phenotypic plasticity is likely to slow evolution because it produces highly adapted phenotypes under the primary niches encountered in the life-history of the species and the plasticity itself is likely to be an adaptive trait.

Gene profiling methods have been widely useful for delineating changes in gene expression as an approach for gaining insight into the mechanism of rejection or disease pathology. Herein, we use gene profiling to compare changes in gene expression associated with different orthotopic cardiac xenotransplantation (OCXTx) outcomes and to identify potential effects of OCXTx on cardiac physiology. We used the Affymetrix GeneChip Porcine Genomic Array to characterize three types of orthotopic cardiac xenograft outcomes: 1) rejected hearts that underwent delayed xenograft rejection (DXR); 2) survivor hearts in which the xenograft was not rejected and recipient death was due to model complications; and 3) hearts which failed to provide sufficient circulatory support within the first 48 h of transplant, termed "perioperative cardiac xenograft dysfunction" (PCXD). Gene expression in each group was compared to control, not transplanted pig hearts, and changes in gene expression > 3 standard deviations (±3SD) from the control samples were analyzed. A bioinformatics analysis was used to identify enrichments in genes involved in Kyoto Encyclopedia of Genes and Genomes pathways and gene ontogeny molecular functions. Changes in gene expression were confirmed by quantitative RT-PCR. The ±3SD data set contained 260 probes, which minimally exhibited a 3.5-fold change in gene expression compared to control pig hearts. Hierarchical cluster analysis segregated rejected, survivor and PCXD samples, indicating a unique change in gene expression for each group. All transplant outcomes shared a set of 21 probes with similarly altered expression, which were indicative of ongoing myocardial inflammation and injury. Some outcome-specific changes in gene expression were identified. Bioinformatics analysis detected an enrichment of genes involved in protein, carbohydrate and branched amino acid metabolism, extracellular matrix-receptor interactions, focal adhesion, and cell communication. This is the first genome wide assessment of changes in cardiac gene expression after OCXTx. Hierarchical cluster analysis indicates a unique gene profile for each transplant outcome but additional samples will be required to define the unique classifier probe sets. Quantitative RT-PCR confirmed that all transplants exhibited strong evidence of ongoing inflammation and myocardial injury consistent with the effects of cytokines and vascular antibody-mediated inflammation. This was also consistent with bioinformatic analysis suggesting ongoing tissue repair in survivor and PCXD samples. Bioinformatics analysis suggests for the first time that xenotransplantation may affect cardiac metabolism in survivor and rejected samples. This study highlights the potential utility of molecular analysis to monitor xenograft function, to identify new molecular markers and to understand processes, which may contribute to DXR.

Introduction: Integrins can stimulate cellular growth and proliferation, as well as apoptosis, and are important factors in AKT cell signaling. To assess their binding, a recombinant protein of the G3 domain of laminin-5 (rG3) that specifically binds the alpha subunit expressed on metastatic MDA-MB-231 cells in vitro was produced. Studying changes in expression of genes involved in cell signaling and the apoptosis cascade, specifically CDKN1B, GRB10, and Caspase 9, can help improve understanding of signaling pathways of metastatic cells and the AKT pathway. Methods: rG3 was produced using ArcticExpress Competent Cells (Stratagene). Plasmid DNA was transformed into competent cells and transferred to ampicillin plates for colony production of successful transformation. A single colony was used to inoculate LB broth containing gentamycin and ampicillin for an overnight incubation at 37°C. LB without antibiotics was inoculated with the overnight culture and incubated at 30°C for 3 hours. The temperature was lowered to 11.5°C before the expression was induced using IPTG at a final concentration of 1mM. SDS-PAGE/immunoblotting confirmed successful soluble rG3 protein expression. MDA-MB-231 human breast cancer cells from ATCC were grown in tissue culture flasks and maintained until confluent. Cells were plated at 3 × 106 cells/well in a 6-well tissue culture plate in a 2 ml volume of DMEM without pen/strep in duplicate. rG3 was added to wells at a final concentration of 175 µg/ml for treated cells and corresponding control buffer for untreated cells. After incubation overnight, cells were collected at time points within 0-60 hours and RNA was isolated using Qiagen RNeasy. An eppendorf Realplex 96-well plate reader was used for PCR analysis using a β-actin standard curve. Differences in gene expression were shown in fold change using Pfaffl's Method. Results: Our preliminary data show there are changes in gene expression after treatment with rG3.We are further investigating these changes in expression. Preliminary results suggest that changes in gene expression after treatment may be informative in understanding the AKT signaling pathway. Conclusion: The study of these changes in gene expression after altering the AKT pathway from treatment with rG3 could prove to be a helpful tool in understanding the signaling mechanisms of metastatic cells and the details of the signaling pathways involved in apoptosis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1954. doi:10.1158/1538-7445.AM2011-1954