870 research outputs found
Introduction to Large-scale Gene Expression Data Analysis.
No full textThe high-density DNA microarray is the most powerful, versatile and widely used tools for gene expression analysis. It is based on the principle of specificity and complimentary hybridization of nucleotide sequences. Thousands of individual nucleic acid species called probes is hybridized with the complex mixture of labeled nucleic acids called target that have a designated spots on a solid surface. The fluorescent-labeled probe fragments bind to their appropriate partners and the intensity of emission can be assessed by an ion laser. The two main microarray technologies that are widely used are oligonucleotide and cDNA arrays
Role of cannabinoidergic mechanisms in ethanol self-administration and ethanol seeking in rat adult offspring following perinatal exposure to Delta9-tetrahydrocannabinol
No full textThe present study evaluated the consequences of perinatal Delta(9)-tetrahydrocannabinol (Delta(9)-THC) treatment (5 mg/kg/day by gavage), either alone or combined with ethanol (3% v/v as the only fluid available), on ethanol self-administration and alcohol-seeking behavior in rat adult offspring. Furthermore, the effect of the selective cannabinoid CB(1) receptor antagonist, SR-141716A, on ethanol self-administration and on reinstatement of ethanol-seeking behavior induced either by stress or conditioned drug-paired cues was evaluated in adult offspring of rats exposed to the same perinatal treatment. Lastly, microarray experiments were conducted to evaluate if perinatal treatment with Delta(9)-tetrahydrocannabinol, ethanol or their combination causes long-term changes in brain gene expression profile in rats. The results of microarray data analysis showed that 139, 112 and 170 genes were differentially expressed in the EtOH, Delta(9)-THC, or EtOH+Delta(9)-THC group, respectively. No differences in alcohol self-administration and alcohol seeking were observed between rat groups. Intraperitoneal (IP) administration of SR-141716A (0.3-3.0 mg/kg) significantly reduced lever pressing for ethanol and blocked conditioned reinstatement of alcohol seeking. At the same doses SR-141716A failed to block foot-shock stress-induced reinstatement of alcohol seeking. The results reveal that perinatal exposure to Delta(9)-THC ethanol or their combination results in evident changes in gene expression patterns. However, these treatments do not significantly affect vulnerability to ethanol abuse in adult offspring. On the other hand, the results obtained with SR-141716A emphasize that endocannabinoid mechanisms play a major role in ethanol self-administration, as well as in the reinstatement of ethanol-seeking behavior induced by conditioned cues, supporting the idea that cannabinoid CB(1) receptor antagonists may represent interesting agents for the pharmacotherapy of alcoholism
Microarrays in neuroscience
No full textGene expression analysis has progressed rapidly over the past decade from the historical analyses of individual genes to the sophisticated genome surveys routinely performed today. DNA biochips have facilitated this progression and helped accelerate target validation and drug discovery efforts by the pharmaceutical industry. The increasing use and acceptance of biochips to study genetic and cellular processes is clearly demonstrated by the large number of publications in recent years and the emergence of several robust commercial microarray platforms (1-3). Affymetrix (Santa Clara, Ca) pioneered this field and has been the market leader for many years, applying photolithographic technologies derived from the semiconductor industry to the fabrication of high-density 25-mer oligonucleotide microarrays. Alternative commercial platforms equally as robust have emerged including array platforms from Agilent, Amersham, Illumina and Applied Biosystems (see Chapter 1 of this book for further discussion of the technology platforms)
Abstract LB-224: A novel model of pediatric spinal ependymoma using conditionally reprogrammed cells from a primary tumor demonstrates aberrant expression of <i>HMGA, HOX, MYC</i> and other Wnt target genes
No full textAbstract
Pediatric spinal ependymomas are rare tumors of the central nervous system with limited treatment options. Successful outcomes depend primarily upon the extent of surgical resection, although significant impairment is common, particularly in children with developing nervous systems. Because these tumors are uncommon, there are no established tumor models nor are there many studies to define underlying molecular lesions. Here, we describe an innovative spinal ependymoma (SE) tumor model based on the recent discovery that primary carcinoma cells can be cultured indefinitely ex vivo on fibroblast feeder cells in the presence of a rho kinase inhibitor; these cells are denoted conditionally reprogrammed cells (CRCs). In prior studies, CRCs form spheres in vitro, replicate tumor pathology as xenografts in vivo, and predict drug responses to the primary tumor. We therefore adopted this strategy to generate a cell line from a 12 year-old girl with a spinal myxopapillary ependymoma. The cell line and primary tumor are of human origin and identical with respect to short tandem repeat (STR) analysis. Using targeted gene expression analysis, we discovered that genes encoding the of High Mobility Group Protein AT-hook 1 (HMGA1), High Mobility Group Protein AT-hook 2 (HMGA2), cMYC, HOXB13, and HOXA10 proteins are all up-regulated compared to their expression in spinal cord tissue from a normal individual. In primary pediatric tumors, HMGA1 gene expression was also higher in spinal ependymomas as compared to supratentorial or posterior fossa ependymomas. There was also a significant positive correlation between HMGA1 and HOX genes, including HOXA10, HOXD13, HOXD1, and HOXB7 in primary tumors. In addition, HMGA1 and cMYC, together with other Wnt target genes, were positively correlated in primary spinal ependymoma. Pathway analysis showed that HMGA1 expression correlated with the following pathways: 1) metabolic pathways, 2) osteoclast differentiation, 3) MAPK signaling, and, 4) Neurotropin signaling. Studies are underway to generate additional cell lines from primary tumor samples and to elucidate the mechanisms that account for up-regulation in HMGA1, HOX and Wnt genes. We will harness this information to identify novel therapeutic targets and agents for children and young adults with spinal ependymoma.
Citation Format: Li Z. Luo, Ewa Krawczyk, Anbarasu Lourdusamy, Lisa C. Storer, Lingling Xian, Kenneth J. Cohen, Richard Schlegel, Richard Grundy, Linda Resar. A novel model of pediatric spinal ependymoma using conditionally reprogrammed cells from a primary tumor demonstrates aberrant expression of HMGA, HOX, MYC and other Wnt target genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-224. doi:10.1158/1538-7445.AM2017-LB-224</jats:p
Expression alterations define unique molecular characteristics of spinal ependymomas
No full textEpendymomas are glial tumors that originate in either intracranial or spinal regions. Although tumors from different regions are histologically similar, they are biologically distinct. We therefore sought to identify molecular characteristics of spinal ependymomas (SEPN) in order to better understand the disease biology of these tumors. Using gene expression profiles of 256 tumor samples, we identified increased expression of 1,866 genes in SEPN when compared to intracranial ependymomas. These genes are mainly related to anterior/posterior pattern specification, response to oxidative stress, glial cell differentiation, DNA repair, and PPAR signalling, and also significantly enriched with cellular senescence genes (P = 5.5 × 10-03). In addition, a high number of significantly down-regulated genes in SEPN are localized to chromosome 22 (81 genes from chr22: 43,325,255 – 135,720,974; FDR = 1.77 × 10-23 and 22 genes from chr22: 324,739 – 32,822,302; FDR = 2.07 × 10-09) including BRD1, EP300, HDAC10, HIRA, HIC2, MKL1, and NF2. Evaluation of NF2 co-expressed genes further confirms the enrichment of chromosome 22 regions. Finally, systematic integration of chromosome 22 genes with interactome and NF2 co-expression data identifies key candidate genes. Our results reveal unique molecular characteristics of SEPN such as altered expression of cellular senescence and chromosome 22 genes
microRNA network analysis identifies miR-29 cluster as key regulator of LAMA2 in ependymoma
No full textThe endogenous and reactive depression subtypes revisited: integrative animal and human studies implicate multiple distinct molecular mechanisms underlying major depressive disorder
No full textTraditional diagnoses of major depressive disorder (MDD) suggested that the presence or absence of stress prior to onset results in either 'reactive' or 'endogenous' subtypes of the disorder, respectively. Several lines of research suggest that the biological underpinnings of 'reactive' or 'endogenous' subtypes may also differ, resulting in differential response to treatment. We investigated this hypothesis by comparing the gene-expression profiles of three animal models of 'reactive' and 'endogenous' depression. We then translated these findings to clinical samples using a human post-mortem mRNA study
Sequential 3D OrbiSIMS and LESA-MS/MS-based metabolomics for prediction of brain tumor relapse from sample-limited primary tissue archives
No full textRaw and processed data used for the publication entitled "Predicting tumor relapse from serial in situ surface mass spectrometry metabolite profiles of pediatric brain tumor tissue microarrays
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