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Viral myocarditis: identification of five differentially expressed genes in coxsackievirus B3-infected mouse heart.

Differences in host susceptibility to viral myocarditis caused by a given strain of coxsackievirus B3 (CVB3) are known to be largely related to host genetic factors. Little is known, however, about the key genes that encode determinants (mediators) of myocarditis development or the nature of injury. To identify these genes and further understand the molecular mechanisms of the disease process, we have used a murine model and the differential display technique to fingerprint mRNAs from CVB3-infected mouse hearts. Total RNA was extracted from hearts of 4- and 10-week-old A/J(H-2(a)) mice at day 4 after CVB3 infection, and mRNAs were detected by reverse transcriptase-polymerase chain reaction and subsequently analyzed on polyacrylamide DNA sequencing gels. The differentially displayed bands were confirmed by Northern hybridization using the bands as cDNA probes. Twenty-eight upregulated or downregulated bands were selected from the sequencing gels; among these, 2 upregulated and 3 downregulated cDNA fragments were confirmed by Northern hybridization. DNA sequence analysis and GenBank searching have determined that 4 of the 5 candidate genes are homologous to genes encoding Mus musculus inducible GTPase, mouse mitochondrial hydrophobic peptide (a subunit of NADH dehydrogenase), mouse beta-globin, and Homo sapiens cAMP-regulated response element binding protein (CREB) binding protein (CBP), respectively. The remaining candidate gene matches an unpublished cDNA clone, M musculus Nip21 mRNA (GenBank accession number, AF035207), which is homologous to human Nip2, a Bcl-2 binding protein. Our data suggest preliminarily that both structural and nonstructural genes are involved in myocarditis development. For the structural gene, beta-globin, we further confirmed its downregulation at the protein level by measuring the mean cell volume of red blood cells and found it was marginally reduced in the CVB3-infected group (P<0.06), with no change in hemoglobin concentration. Cardiac myoglobin concentration was also measured and found to be decreased (P<0.005), with a parallel decrease in total soluble protein in the CVB3-infected mouse myocardium (P<0.01). We also noted that the ratio of myoglobin to total protein was not significantly changed; this may be due to the downregulation of additional genes in the host heart, a number being observed on the differential display gels. The significant downregulation of beta-globin major gene expression in the heart may be relevant to impaired cardiac function in both the early and late postinfection period. The other identified nonstructural genes are known to be involved in regulation of gene expression, signal transduction pathways, and apoptotic cell death. The altered expression of structural and nonstructural genes may play important roles in the mediation of myocarditis development and perhaps other pathological processes in the heart.

Animals↗

Mutations in the desert hedgehog (DHH) gene in patients with 46,XY complete pure gonadal dysgenesis.

Mutations of SRY are the cause of complete pure gonadal dysgenesis (PGD) in 10-15% of patients. In the remaining individuals, it has been suggested that mutations in other genes involved in the testis-determining pathway could be causative. We describe the first report in which three cases of 46,XY complete PGD are attributed to mutations of the Desert hedgehog (DHH) gene. DHH was sequenced using genomic DNA from paraffin-embedded gonadal tissue from six patients with complete 46,XY PGD. Mutations were found in three patients: a homozygous mutation in exon 2, responsible for a L162P, and a homozygous 1086delG in exon 3. Mutated individuals displayed 46,XY complete PGD, differentiating from the only previously described patient with a homozygous DHH mutation, who exhibited a partial form of PGD with polyneuropathy, suggesting that localization of mutations influence phenotypic expression. This constitutes the first report where mutations of DHH are associated with the presence of 46,XY complete PGD, demonstrating that the genetic origin of this entity is heterogeneous and that disorders in other genes, different from SRY, involved in the testis-determining pathway are implicated in abnormal testicular differentiation in humans. These data extend previous reports demonstrating DHH is a key gene in gonadal differentiation.

Adolescent↗

Emerging biomarker technologies.

New technology offers great potential for advances in cancer biomarker research. Here, we describe a number of new technologies and discuss their potential for use in molecular cancer epidemiology. The successful sequencing of the human genome has revealed several new insights, including the fact that the human genome consists of only 40,000 genes and is highly variable, with approximately 60,000 functional polymorphisms. High-throughput genomic technologies continue to facilitate the identification and analysis of mutations and polymorphisms in key genes and expand the spectrum of available genomic biomarkers. The next major challenge is the identification of novel proteins and understanding the structure, function and interaction of proteins and other molecules--information that cannot be obtained from genomics alone. Emerging technologies including arrays, proteomics and nanotechnology provide new platforms for high-throughput, highly sensitive, functional assays. These technologies will complement existing and emerging genomic technologies and result in the identification of new biomarkers of cancer risk. They will, however, require extensive validation in epidemiological studies.

Biomarkers↗

[A preliminary study on gene expression profile induced by water stress in wheat (Triticum aestivum L.) seedling].

In the present research, suppression subtractive hybridization (SSH) and high density membrane techniques were employed to analysis genes induced by water stress in wheat seedling at 2-leaf stage. The purpose was to comprehensively understand the genetic bases of drought resistance and to find the key genes related to drought resistance in wheat. A total of 181 positive clones were obtained by screening the SSH library including 1 530 individual recombinant clones. The result of the sequence homologous comparison and function querying showed that 83.2% differentially expressed genes were high homologous with those induced by abiotic or biotic stresses in plant and their functions were to protect the cell directly or indirectly from stress strain. Seventeen differentially expressed ESTs found first were registered in GenBank. After further identifying by reverse Northern, RT-PCR and Northern, the gene expression profile induced by water stress in wheat seedling was preliminarily revealed.

Blotting, Northern↗

Decreased expression and activity of the immediate-early growth response (Egr-1) gene product during cellular senescence.

Human diploid fibroblasts (HDFs) undergo a limited number of population doublings in culture before reaching the end of their proliferative life span, an event termed in vitro cellular senescence. Considerable evidence suggests that altered expression of key genes involved in the mitogenic response may be responsible for the inability of senescent cells to proliferate. Here we examined the expression and activity of the early growth response-1 (egr-1) gene, an "immediate-early" gene that is believed to link extracellular mitogenic signals to cell-cycle progression. We found that egr-1 was strongly downregulated in senescent HDFs at the level of mRNA, protein, and DNA binding activity. Decreased DNA binding activity of Egr-1 in vitro corresponded to decreased transcriptional activation in vivo. To further understand the mechanism of egr-1 downregulation, we examined the potential role of the serum response elements (SREs) present in the egr-1 promoter. Electrophoretic mobility shift studies using young and old cell nuclear extracts showed a marked decrease in serum response factor (SRF) binding activity to the SRE in old compared to young cells. Loss of SRF binding activity has been correlated with the loss of expression of another growth-related immediate-early gene (c-fos). These results suggest a common mechanism for the downregulation of c-fos, egr-1, and other SRE-dependent, mitogen-responsive genes during cellular senescence.

Cells, Cultured↗

Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays.

A comparative analysis of gene expression profiles during cold acclimation and deacclimation is necessary to elucidate the molecular mechanisms of cold stress responses in higher plants. We analyzed gene expression profiles in the process of cold acclimation and deacclimation (recovery from cold stress) using two microarray systems, the 7K RAFL cDNA microarray and the Agilent 22K oligonucleotide array. By both microarray analyses, we identified 292 genes up-regulated and 320 genes down-regulated during deacclimation, and 445 cold up-regulated genes and 341 cold down-regulated genes during cold acclimation. Many genes up-regulated during deacclimation were found to be down-regulated during cold acclimation, and vice versa. The genes up-regulated during deacclimation were classified into (1) regulatory proteins involved in further regulation of signal transduction and gene expression and (2) functional proteins involved in the recovery process from cold-stress-induced damages and plant growth. We also applied expression profiling studies to identify the key genes involved in the biosynthesis of carbohydrates and amino acids that are known to play important roles in cold acclimation. We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process.

Acclimatization↗

Quantification of virulence-associated gene transcripts in epidemic methicillin resistant Staphylococcus aureus by real-time PCR.

The control of Staphylococcus aureus virulence gene expression is complex and few data are available for the epidemic methicillin resistant S. aureus clones circulating in the UK. Quantitative real-time PCRs were developed for key gene transcripts involved in S. aureus infection (RNAIII, hla and spa) and for the 16S rRNA. These assays were applied to log and stationary phase cultures of the important EMRSA strains. To correct for inconsistencies in extract yield, results were calculated as ratios using the 16S rRNA values as denominator. The quantitative assays were sensitive and reproducible. The number of copies of each transcript present differed greatly between the EMRSA strains tested. Strains within an EMRSA clone or type gave similar results. High levels of RNAIII transcripts were not consistently linked to elevated levels of hla transcripts or to low levels of the spa transcript. In addition, strains showed significant variations in their patterns of induction (or repression) of all three transcripts. A complex interplay exists between the regulatory factors that control the expression of proteins required for colonisation and survival in the host. The transcript level data suggest that this pattern shows great diversity among the currently important EMRSA strains.

Bacterial Proteins↗

deCODE genetics, Inc.

deCODE genetics, Inc. has compiled the world's most comprehensive collection of population data on genealogy, genotypes and phenotypes. This combination of resources provides an effective system for identifying key genes linked to common diseases and to the regulation of drug response. deCODE has successfully mapped genes in over 25 common complex diseases and isolated genes in eight of these. The methodology used to map these genes is based upon the company's genealogical database of the Icelandic population, which enables deCODE scientists to efficiently conduct population- and genome-wide linkage studies to identify key genetic factors involved in phenotypes ranging from diseases to drug response. In its growing pharmacogenomics program, deCODE has combined this linkage approach with high-throughput expression profiling to develop accurate tests that can predict individual responsiveness to virtually any drug of interest. deCODE is applying its unrivaled discovery capabilities to bring to market new drugs, DNA-based diagnostic products and pharmacogenomic tests. The company believes that such tests will play a crucial role in delivering personalized medicine - contributing to the development of more effective means of diagnosing and treating disease by matching each patient with the most suitable drug.

Chromosome Mapping↗

Gene modification strategies to induce tumor immunity.

The immune system provides an attractive option for use in cancer therapy. Our increasing understanding of the molecular events important in the generation of an effective immune response presents us with the opportunity to manipulate key genes to boost the immune response against cancer. Genetic modification is being employed to enhance a range of immune processes including antigen presentation, activation of specific T cells, and localization of immune effectors to tumors. In this review, we describe how many diverse cell types, including dendritic cells, T cells, and tumor cells, are being modified with a variety of genes, including those encoding antigens, cytokines, and chemokines, in order to enhance tumor immunity.

Antigens↗

Effects of all-trans retinoic acid and interferon-gamma on expression of RAR beta gene in Tca8113 cells.

OBJECTIVE: All-trans-retinoic acid (ATRA) and interferons (IFNs) have been proven to synergistically amplify growth inhibition and apoptosis in the tongue squamous carcinoma cell line (Tca8113). Nuclear retinoic acid receptor-beta (RAR beta) was the key gene that mediated retinoid activity for squamous carcinoma cells. In order to understand the mechanism of ATRA combined with IFN gamma inhibiting growth of Tca8113 cells, this investigation focused on RAR beta mRNA expression. MATERIALS AND METHODS: In this experiment, RT-PCR method was used to analyze the RAR beta expression level, and viable cell count assay was carried out for growth inhibition studies. RESULTS: All-trans-retinoic acid (1 microM) and IFN gamma (1000 u/mL) inhibited cell growth by 39.2% and 44.4%, respectively. Synergistic inhibition of cell proliferation by 86.7% was found under combined treatment. The combination of suboptimal concentrations of ATRA (0.1 microM) with IFN gamma (1000 u/mL) showed a much stronger additive inhibitory effect on cell proliferation. ATRA (1 microM) and IFN gamma (1000 u/mL) increased RAR beta expression to 4 times and 3 times, respectively. The expression of RAR beta increased 12 times after treatment with combined ATRA and IFN gamma treatment. CONCLUSIONS: These observations indicated that the use of combined ATRA and IFN may lead to enhanced antitumor effects. These results also suggested that ATRA and IFN mediated upregulating expression of RAR beta may play an important role in synergistic inhibition of proliferation in Tca8113 cells.

Carcinoma, Squamous Cell↗

Gene expression analysis of the rat testis after treatment with di(2-ethylhexyl) phthalate using cDNA microarray and real-time RT-PCR.

To investigate the effects of di(2-ethylhexyl) phthalate (DEHP) on gene expression in rat testis, 6-week-old male Sprague-Dawley rats were given a single oral dose of 20 or 2000 mg/kg and euthanized 3, 6, 24, or 72 h thereafter. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL)-positive cells were significantly increased in the testis at 24 and 72 h after the exposure to 2000 mg/kg of DEHP. On cDNA microarray analysis, in addition to apoptosis-related genes, genes associated with atrophy, APEX nuclease, MutS homologue (E. coli), testosterone-repressed-prostatic-message-2 (TRPM-2), connective tissue growth factor, collagen alpha 2 type V, and cell adhesion kinase were differentially expressed. To investigate the relationship between histopathological alteration and gene expression, we selected genes associated with apoptosis and analyzed their expression by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR). With 20 mg/kg of DEHP treatment, bcl-2, key gene related to apoptosis, was increased. Up-regulation of bcl-2, inhibitor of Apaf-1/caspase-9/caspase-2 cascade of apoptosis, may be related to the fact that no morphological apoptotic change was induced after dosing of 20 mg/kg DEHP. With 2000 mg/kg of DEHP treatment, the apoptotic activator cascade, Fas/FasL, FADD/caspase-8/caspase-3 cascade, and Apaf-1/caspase-9/caspase-2 cascade were increased and bcl-2 was decreased. Thus, these gene regulations might lead the cells into apoptosis in the case of high exposure to DEHP. In contrast, FADD/caspase-10/caspase-6 cascade and caspase-11/caspase-3 cascade were not increased. These results indicate that the cascades of FADD/caspase-10/caspase-6 and caspase-11/caspase-3 are not related to apoptosis with DEHP treatment.

Animals↗

Analysis of gene expression in subpopulations of murine hematopoietic stem and progenitor cells.

OBJECTIVE: The aim of the present work was to study how functional differences between subsets of the murine hematopoietic stem/progenitor cell compartment are manifested on the level of different patterns of gene expression in these subsets. MATERIALS AND METHODS: Amplified 3' terminal total cDNA fragment populations from four stem and progenitor cell fractions sorted using differential staining with Rhodamine 123 were prepared, and gene expression patterns were analyzed by Southern hybridization with a panel of gene markers. RESULTS: For the vast majority of lineage-specific markers, no expression was detected in the long-term repopulating stem cell fraction. Expression of a number of key genes positively regulating entry and progression through the cell cycle was down-regulated in long-term repopulating cells, in accordance with the quiescent state of the latter. In contrast, certain but not all cell division kinase inhibitors were significantly up-regulated in long- and short-term repopulating stem cell fractions. Expression of several genes important for entry into the apoptotic pathway was moderately reduced in long-term repopulating cells. Messenger RNA levels of the transcription factors GATA-1, GATA-2, c-Myb and SCL were down-regulated in long-term repopulating cells, as compared to more mature stem/progenitor cells. Finally, expression of the MDR1a gene encoding the Pgp efflux pump was highest in long-term repopulating cells, and progressively decreased with maturation. CONCLUSION: The patterns of gene expression in the stem/progenitor cell fractions are in good correlation with the known properties of adult hematopoietic stem/progenitor cells and may provide insight into molecular mechanisms underlying stem cell physiology.

Animals↗

Dissecting the molecular mechanisms of human cancer: translating laboratory advances into clinical practice.

There are multiple molecular mechanisms involved in human cancers with many genes involved, complex interactions and a variety of ways to examine them. Some events are already emerging as clinically important; others will turn out to be bystanders. By focussing on key genes, such as p53, the clinical implications of genetic changes and the pathways they link into are becoming apparent. Using the complex methodologies now available allied to disciplines such as mathematics we are improving our understanding of malignancy. This is beginning to impact on the management of patients with cancer; meanwhile, a good surgical operation performed timeously is still the best chance a patient has of a cure for most types of solid cancers.

Biopsy, Needle↗

Mutant SOD1 alters the motor neuronal transcriptome: implications for familial ALS.

Familial amyotrophic lateral sclerosis (FALS) is caused, in 20% of cases, by mutations in the Cu/Zn superoxide dismutase gene (SOD1). Although motor neuron injury occurs through a toxic gain of function, the precise mechanism(s) remains unclear. Using an established NSC34 cellular model for SOD1-associated FALS, we investigated the effects of mutant SOD1 specifically in cells modelling the vulnerable cell population, the motor neurons, without contamination from non-neuronal cells present in CNS. Using gene expression profiling, 268 transcripts were differentially expressed in the presence of mutant human G93A SOD1. Of these, 197 were decreased, demonstrating that the presence of mutant SOD1 leads to a marked degree of transcriptional repression. Amongst these were a group of antioxidant response element (ARE) genes encoding phase II detoxifying enzymes and antioxidant response proteins (so-called 'programmed cell life' genes), the expression of which is regulated by the transcription factor NRF2. We provide evidence that dysregulation of Nrf2 and the ARE, coupled with reduced pentose phosphate pathway activity and decreased generation of NADPH, represent significant and hitherto unrecognized components of the toxic gain of function of mutant SOD1. Other genes of interest significantly altered in the presence of mutant SOD1 include several previously implicated in neurodegeneration, as well as genes involved in protein degradation, the immune response, cell death/survival and the heat shock response. Preliminary studies on isolated motor neurons from SOD1-associated motor neuron disease cases suggest key genes are also differently expressed in the human disease.

Amyotrophic Lateral Sclerosis↗

Functional, structural, and metabolic abnormalities of the hippocampal formation in Williams syndrome.

Williams syndrome (WS), caused by microdeletion of some 21 genes on chromosome 7q11.23, is characterized by dysmorphic features, mental retardation or learning difficulties, elastin arteriopathy, and striking neurocognitive and social-behavioral abnormalities. Recent studies of murine knockouts of key genes in the microdeleted region, LIM kinase 1 (LIMK1) and cytoplasmatic linker protein 2 (CYLN2), demonstrated significant functional and metabolic abnormalities, but grossly normal structure, in the hippocampal formation (HF). Furthermore, deficits in spatial navigation and long-term memory, major cognitive domains dependent on hippocampal function, have been described in WS. We used multimodal neuroimaging to characterize hippocampal structure, function, and metabolic integrity in 12 participants with WS and 12 age-, sex-, and IQ-matched healthy controls. PET and functional MRI studies showed profound reduction in resting blood flow and absent differential response to visual stimuli in the anterior HF in WS. Spectroscopic measures of N-acetyl aspartate, considered a marker of synaptic activity, were reduced. Hippocampal size was preserved, but subtle alterations in shape were present. These data demonstrate abnormalities in HF in WS in agreement with murine models, implicate LIMK1 and CYLN2 in human hippocampal function, and suggest that hippocampal dysfunction may contribute to neurocognitive abnormalities in WS.

Adult↗

Drugs that target gene expression: an overview.

Over the last few years, it has become apparent that regulation of many normal physiological pathways, as well as the response to a wide variety of disease states, involves specific changes in gene transcription. The concept of drugs that regulate gene transcription is now firmly established. There are multiple, highly effective drugs in widespread use whose primary mechanism of action is to affect gene transcription. A major goal at Oncogene Science is to develop drugs that can modulate the normal physiological responses associated with disease by specifically increasing or decreasing the transcription of key genes. In this article, we review several examples of drugs that have been shown to act by regulating gene transcription and describe the approach Oncogene Science has pioneered.

Drug Evaluation, Preclinical↗

Dopaminergic gene expression during amphetamine withdrawal.

Animals and humans display a constellation of behavioral and neurochemical signs after termination of psychostimulant administration. Amphetamine withdrawal could involve the dopaminergic systems that are thought to underlie psychostimulant rewarding effects, and may thus conceivably alter expression of key genes for dopaminergic transmission, including those encoding tyrosine hydroxylase (TH), the membrane dopamine transporter (DAT) and the synaptic vesicle amine transporter (SVAT). Withdrawal from 7.5 mg kg-1 i.p. amphetamine (b.i.d. for a two week duration) yields no significant changes in rat DAT mRNA. TH mRNA levels are modestly enhanced over the same week of withdrawal, during which dopamine levels and behavioral novelty responses are both depressed. SVAT expression is significantly blunted following chronic amphetamine treatment. Altered TH and/or SVAT gene expression might contribute to restoring normal function to neurons "withdrawing" from amphetamine treatments.

Animals↗

Analysis of flowering pathway integrators in Arabidopsis.

Flowering is regulated by an integrated network of several genetic pathways in Arabidopsis. The key genes integrating multiple flowering pathways are FT, SOC1 and LFY. To elucidate the interactions among these integrators, genetic analyses were performed. FT and SOC1 share the common upstream regulators CO, a key component in the long day pathway, and FLC, a flowering repressor integrating autonomous and vernalization pathways. However, the soc1 mutation further delayed the flowering time of long day pathway mutants including ft, demonstrating that SOC1 acts partially independently of FT. Although soc1 did not show an obvious defect in flower meristem determination on its own, it dramatically increased the number of coflorescences in a lfy mutant, which is indicative of a defect in floral initiation. Therefore, double mutant analysis shows that the three integrators have both overlapping and independent functions in the determination of flowering time and floral initiation. The expression analysis showed that FT regulates SOC1 expression, and SOC1 regulates LFY expression, but not vice versa, which is consistent with the fact that FT and LFY have the least overlapping functions among the three integrators. The triple mutation ft soc1 lfy did not block flowering completely under long days, indicating the presence of other integrators. Finally, vernalization accelerated flowering of flc ft soc1 and ft soc1 lfy triple mutants, which shows that the vernalization pathway also has targets other than FLC, FT, SOC1 and LFY. Our genetic analysis reveals the intricate nature of genetic networks for flowering.

Arabidopsis↗