Single-amino-acid mutations in Sindbis virus proteins can convert clinically silent encephalitis into uniformly lethal disease. However, little is known about the host gene response during avirulent and virulent central nervous system (CNS) infections. To identify candidate host genes that modulate alphavirus neurovirulence, we utilized GeneChip Expression analysis to compare CNS gene expression in mice infected with two strains of Sindbis virus that differ by one amino acid in the E2 envelope glycoprotein. Infection with Sindbis virus, dsTE12H (E2-55 HIS), resulted in 100% mortality in 10-day-old mice, whereas no disease was observed in mice infected with dsTE12Q (E2-55 GLN). dsTE12H, compared with dsTE12Q, replicated to higher titers in mouse brain and induced more CNS apoptosis. Infection with the neurovirulent dsTE12H strain was associated with both a greater number of host genes with increased expression and greater changes in levels of host gene expression than was infection with the nonvirulent dsTE12Q strain. In particular, dsTE12H infection resulted in greater increases in the levels of mRNAs encoding chemokines, proteins involved in antigen presentation and protein degradation, complement proteins, interferon-regulated proteins, and mitochondrial proteins. At least some of these increases may be beneficial for the host, as evidenced by the demonstration that enforced expression of the antiapoptotic mitochondrial protein peripheral benzodiazepine receptor (PBR) protects neonatal mice against lethal Sindbis virus infection. Thus, our findings identify specific host genes that may play a role in the host protective or pathologic response to neurovirulent Sindbis virus infection.

To identify new and differentially expressed genes in rat fetal liver epithelial stem/progenitor cells during their proliferation, lineage commitment, and differentiation, we used a high throughput method-mouse complementary DNA (cDNA) microarrays-for analysis of gene expression. The gene expression pattern of rat hepatic cells was studied during their differentiation in vivo: from embryonic day (ED) 13 until adulthood. The differentially regulated genes were grouped into two clusters: a cluster of up-regulated genes comprised of 281 clones and a cluster of down-regulated genes comprised of 230 members. The expression of the latter increased abruptly between ED 16 and ED 17. Many of the overexpressed genes from the first cluster fall into distinct, differentially expressed functional groups: genes related to development, morphogenesis, and differentiation; calcium-and phospholipid-binding proteins and signal transducers; and cell adhesion, migration, and matrix proteins. Several other functional groups of genes that are initially down-regulated, then increase during development, also emerged: genes related to inflammation, blood coagulation, detoxification, serum proteins, amino acids, lipids, and carbohydrate metabolism. Twenty-eight genes overexpressed in fetal liver that were not detected in adult liver are suggested as potential markers for identification of liver progenitor cells. In conclusion, our data show that the gene expression program of fetal hepatoblasts differs profoundly from that of adult hepatocytes and that it is regulated in a specific manner with a major switch at ED O ver the years, substantial evidence has accumulated suggesting the existence of potential liver stem cells (LSCs) in the adult liver. This evidence is indirect, because in all reports the putative LSCs were activated to proliferate and differentiate into liver progenitor cells only when the regenerative capacity of terminally differentiated hepatocytes was compromised. 1-3 Because these cells are not under constant renewal-in contrast to epithelial cells of the intestine or the skin-they escape detection in the quiescent liver. For this reason, a unique specific marker for LSCs in adult liver has not yet been identified, and the LSCs have not yet been isolated.To study liver stem/progenitor cells (LS/PCs), we took a different approach. We began to analyze the gene expression profile of hepatic cells in fetal liver. Around embryonic day (ED) 8.5 in the mouse and 1 day later in the rat, primitive epithelial cells of the ventral foregut come in contact with cardiac mesoderm and fibroblast growth factor signaling, leading to formation of the hepatic diverticulum. 4-6 Subsequently, cells of the primary liver diverticulum invade the septum transversum and, under the inductive signals of bone morphogenic proteins, proliferate extensively and differentiate further. 6 These cells are considered committed hepatic epithelial cells and have been termed hepatoblasts. [4][5][6] Some of these cells are at a very early stage of their differen...

The prefrontal cortex has been implicated in schizophrenia (SZ) and affective disorders by gene expression studies. Owing to reciprocal connectivity, the thalamic nuclei and their cortical fields act as functional units. Altered thalamic gene expression would be expected to occur in association with cortical dysfunction. We screened the expression of the entire human genome of neurons harvested by laser-capture microdissection (LCM) from the thalamic primary relay to dorsolateral prefrontal cortex in three psychiatric disease states as compared with controls. Microarray analysis of gene expression showed the largest number of dysregulated genes was in SZ, followed by major depression (MD) and bipolar mood bipolar (BP) (1152, 385 and 288, respectively). Significantly, IGF1-mTOR-, AKT-, RAS-, VEGF-, Wnt-and immune-related signaling, eIF2-and proteasome-related genes were unique to SZ. Vitamin D receptor and calcium signaling pathway were unique to BP. AKAP95 pathway and pantothenate and CoA biosynthesis were unique to MD. There are significant differences among the three psychiatric disorders in MDNp cells. These findings offer new insights into the transcriptional dysregulation in the thalamus of SZ/BP/MD subjects.

The development of microarray technology has revolutionized RNA and deoxyribonucleic acid (DNA) research. In contrast with traditional biological assays, microarrays allow the simultaneous measurement of tens of thousands of messenger RNA (mRNA) transcripts for gene expression or of genomic DNA fragments for copy number variation analysis. Over the past decade, genome-wide RNA or DNA microarray analysis has become an essential component of biology and biomedical research. The successful use of microarrays requires attention to unique issues of experimental design and execution. This chapter provides an overview of the methodology and applications of RNA and DNA microarrays in various areas of biological research.

Schizophrenia is a highly complex inheritable disease characterized by numerous genetic susceptibility elements, each contributing a modest increase in risk for the disease. Although numerous linkage or association studies have identified a large set of schizophrenia-associated loci, many are controversial. In addition, only a small portion of these loci overlaps with the large cumulative pool of genes that have shown changes of expression in schizophrenia. Here, we applied a genomic gene-function approach to identify susceptibility loci that show direct effect on gene expression, leading to functional abnormalities in schizophrenia. We carried out an integrated analysis by cross-examination of the literature-based susceptibility loci with the schizophrenia-associated expression gene list obtained from our previous microarray study (Journal of Human Genetics (2009) 54: 665-75) using bioinformatic tools, followed by confirmation of gene expression changes using qPCR. We found nine genes (CHGB, SLC18A2, SLC25A27, ESD, C4A/C4B, TCP1, CHL1 and CTNNA2) demonstrate gene-function correlation involving: synapse and neurotransmission; energy metabolism and defense mechanisms; and molecular chaperone and cytoskeleton. Our findings further support the roles of these genes in genetic influence and functional consequences on the development of schizophrenia. It is interesting to note that four of the nine genes are located on chromosome 6, suggesting a special chromosomal vulnerability in schizophrenia.

Glucose disposal induces a signal that modulates the transcriptional regulation of genes involved in the glycolysis and lipogenesis pathways. To investigate the role of glucose metabolism on hepatic gene expression independently from insulin action, we overexpressed glucokinase, the limiting enzyme in the glycolysis pathway, in the liver of streptozotocin-induced type 1 diabetic rats. By microarray analysis, we observed that critical genes such as livertype pyruvate kinase, malic enzyme, fatty acid synthase, and stearoyl-CoA desaturase 1 were enhanced multiple-fold, whereas genes involved in mitochondrial fatty acid oxidation and the Krebs cycle were downregulated. Despite the increase in expression of fatty acid synthesis genes and the presence of steatosis, no major alterations to the levels of genes involved in VLDL assembly and secretion, such as diacylglycerol acyltransferases 1 and 2 and microsomal triglyceride transfer protein, were observed. Overall, our data suggest that the gene expression pattern induced by glucose metabolism favors fatty acid storage in the liver rather than secretion into the circulation.-Morral, N., H. J. Edenberg, S. R. Witting, J. Altomonte, T. Chu, and M. Brown. Effects of glucose metabolism on the regulation of genes of fatty acid synthesis and triglyceride secretion in the liver. J. Lipid Res.

SummaryGonadotropin-releasing hormone (GnRH) regulates biosythesis in the pituitary gonadotrope via a complex signaling and gene network. Small non-coding microRNAs (miRNA) can play important roles in gene expression. We investigated the microtranscriptome in the mouse LβT2 gonadotrope cell line using microarray, single molecule coincidence detection assays, hairpin real time PCR and LNA (locked nucleic acid) primer-extension PCR. Expression of nearly 200 miRNAs were detected by array and a panel of 101 hairpin real-time PCR assays. Within this broad family of expressed miRNAs, GnRH induced upregulation of two miRNA products of the same primary transcript, miR-132 and miR-212, a result confirmed by single molecule, hairpin and LNA assays. Induction peaked 6 hours after GnRH exposure and showed no significant frequency sensitivity. Bioinformatics analysis was used to predict potential targets of each of these GnRH-regulated miRNAs. These findings suggest the importance of the microtranscriptome in gene control in the gonadotrope and implicate miR-132 and miR-212 in the regulation of GnRH-stimulated biosynthetic response.

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