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Objective:To establish a mouse model of intra-jugular arteriovenous fistula (AVF) to screen differentially expressed genes in the process of intimal stenosis of AVF for investigating the abnormal expression signaling pathways and the mechanisms.Methods:Forty-six male C57BL/6 mice were randomly divided into AVF group ( n=23) and sham-operated group ( n=23). The AVF group underwent internal jugular arteriovenous fistuloplasty, and the sham-operated group separated the right external jugular vein and common carotid artery and then sutured the incision. The whole-genome sequences of mice with AVF stenosis were determined by transcriptomic reversible chain terminator and synthetic sequencing. The microarray data set was established, and the Benjamini & Hochberg method of gene microarray data analysis was applied to screen the differentially expressed genes. The differentially expressed genes were screened by R-language enrichment analysis. Then, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were performed. The subcellular localization of the differentially expressed genes was performed by BUSCA software. The protein network interaction of differentially expressed genes was analyzed by using STRING database and Cytoscape software. Results:In the AVF group, 21 mice were successfully modeled and 2 mice failed. Therefore, there were 21 mice in the AVF group and only 21 mice in the sham-operated group. This mouse internal jugular AVF model was innovated using the continuous-interrupted suture method, which improved the success rate of modeling this model. The differential gene sequencing analysis showed that there were 2 514 differentially expressed genes in the AVF process, including 1 323 up-regulated genes and 1 191 down-regulated genes. GO functional enrichment analysis showed that the differential genes were mainly enriched in metabolic process, activation, redox, mitochondria and so on. KEGG pathway enrichment analysis showed that the differential genes were enriched in metabolism, energy substance synthesis, diabetes, oxidative stress and so on. Statistical analysis of subcellular localization showed that the differences were mainly in mitochondrial proteins (24.24%), cytoplasmic proteins (17.51%), nuclear proteins (13.13%), cell membrane proteins (11.45%), and extracellular proteins (10.77%).Conclusions:Mitochondrial oxidative stress injury may be involved in the pathological damage process of endothelial proliferation stenosis in the AVF.
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【Objective】 To study the level of occult hepatitis B virus methylation and replication related genes, and to explore the effect of the former on the latter. 【Methods】 The cases in control group (healthy control, n=3), occult hepatitis B group (occult HBV group, n=3) and hepatitis B group (HBV group, n=3) were detected by Illumina methylation 850k chip. The difference analysis, GO analysis and KEGG analysis were carried out. The methylation and virus replication related genes DNMT1, DNMT2, Dnmt3a and ZHX2 were screened for RT-PCR. 【Results】 The methylation level of occult HBV group and HBV group was significantly higher than that of the control group. Difference analysis showed that there were 1 050 differential methylation sites in occult HBV group with the methylation level greater than non-methylation level, and 1 340 differential methylation sites as the opposite compared with the control group. In HBV group, there were 1 008 differential methylation sites with methylation level greater than non-methylation level, and 1 242 differential methylation sites as the opposite. Go analysis showed that compared with the control group, the differential gene expression in occult HBV group and HBV group was significantly related to many anabolic processes in biological process (BP), cell composition (CC) and molecular function (MF). The enrichment analysis of KEGG pathway between the control group and the occult HBV group showed that the differential genes were mainly involved in adhesion junction, basal cell carcinoma, endometrial carcinoma, EB virus infection, hepatocellular carcinoma and other signal pathways. The enrichment analysis of KEGG pathway in occult HBV group and HBV group showed that the differential genes were mainly involved in AMPK signal pathway, cell cycle, endometrial cancer, hepatitis C, hepatocellular carcinoma and other signal pathways. DNMT1 and DNMT3a in occult HBV group and HBV group were significantly higher while ZHX2 was significantly lower than those in control group. 【Conclusion】 The methylation level of occult HBV group and HBV group increased significantly while ZHX2 decreased significantly. Hypermethylation inhibited the expression of ZHX2 and changed the replication of hepatitis B virus. Hepatitis B virus DNA methylation provides a theoretical basis for the replication mechanism of hepatitis B virus and a new method for the treatment of hepatitis B virus.
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Introdução: a Síndrome do X Frágil (FXS) é a forma mais prevalente de deficiência intelectual herdável, e é a principal causa monogênica para o desenvolvimento de Transtorno de Espectro do Autismo (TEA). Objetivo: o objetivo do presente estudo é identificar RNAm associados à possíveis vias neurocomportamentais na SFX como no TEA, através de ferramentas de bioinformática. Metodologia: para identificação de possíveis vias alteradas entre a SFX e pacientes com TEA, utilizamos os bancos de dados GSE65106 e GSE21348 para anotação, visualização e descoberta integrada (DAVID 6.8). O valor de p <0,05 e fold change maior que 2 vezes (FC > 2) definidos como os limiares para a identificação de genes diferencialmente expressos (DE-RNAm). Resultados: foi possível identificar cerca de 32 DE-RNAm com funções em vias de spliceossomo, apoptose, transcrição, e em vias neurológicas comportamentais expressos exclusivamente na SFX. Os genes CAPNS1, HNRNPK, HNRPM, foram identificados como hipoexpressos em indivíduos com síndrome do X Frágil. Estes genes tem importante função moduladora nas respostas do potencial de longo prazo (LTP), plasticidade neural, e em transportadores de serotonina (SERT) alterando respostas que englobam humor, cognição e comportamentos, além de interferirem no receptor de dopamina (D2R) alterando as funções motoras e circuitos de recompensa. Conclusão: os genes CAPNS1, HNRNPK, HNRNPM foram identificados como marcadores genéticos eurocomportamentais importantes para a síndrome do X-frágil com expressão diminuída na doença, indicando uma possível modulação desses genes em aspectos fenotípicos marcantes da doença.
Introduction: fragile X Syndrome (FXS) is the most prevalent form of inheritable intellectual disability, and is the leading monogenic cause for the development of Autism Spectrum Disorder (ASD). Objective: the aim of this study is to identify mRNA associated with possible neurobehavioral pathways in SFX as in ASD, using bioinformatics tools. Methodology: to identify possible altered pathways between SFX and ASD patients, we used the GSE65106 and GSE21348 databases for annotation, visualization and integrated discovery (DAVID 6.8). The p value <0.05 and fold change greater than 2 times (HR> 2) are defined as the thresholds for the identification of differentially expressed genes (DE-mRNA). Results: it was possible to identify about 32 DE-mRNA with functions in spliceosome, apoptosis, transcription, and behavioral neurological pathways expressed exclusively in SFX. CAPNS1, HNRNPK, HNRPM genes were identified as hypoexpressed in individuals with fragile X syndrome. These genes play an important modulating role in long-term potential (LTP), neural plasticity, and serotonin transporters (SERT) responses by altering mood, cognition, and behavioral responses, and by interfering with dopamine receptor (D2R) by motor functions and reward circuits. Conclusion: the CAPNS1, HNRNPK, HNRNPM genes have been identified as important neurobehavioral genetic markers for impaired X-syndrome, indicating a possible modulation of these genes into marked phenotypic aspects of the disease.
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Humans , Gene Expression , Autism Spectrum Disorder , Fragile X Syndrome , Genes , DatabaseABSTRACT
Objective To compare and analyze the differences in the transcriptomics between mycelium and early yeast phases of Sporothrix schenckii (S.schenckii),and to realize the changes in transcriptome expression profiles during mycelium-to-yeast transformation.Methods A standard strain of S.schenckii (ATCC 10268) was subjected to 96-hour culture with Sabouraud medium at 25 ℃ or 36-hour culture with brain-heart infusion medium at 37 ℃ to obtain the mycelium and yeast form of S.schenckii,and then,their transcriptomes were sequenced.Functional annotation was performed for screened unigenes by comparison using several databases (such as NR,Swiss-Prot,KEGG,COG,KOG,GO and Pfam),coding sequence prediction,and gene expression analysis in each sample.Finally,the differentially expressed genes were subjected to pattern clustering,functional annotation and enrichment analysis.Results A total of 14.76 Gb valid data (clean data) were obtained,and functional annotation results were acquired in 28 094 of 43 863 assembled unigene clusters.Compared with S.schenckii in mycelium phase,there were 10 969 up-regulated genes and 199 down-regulated genes in S.schenckii in yeast phase.These differentially expressed genes were involved in protein phosphorylation,intracellular protein transport,cellular protein modification,small guanosine triphosphate-mediated signal transduction,vesicle-mediated transport,translation,intracellular signal transduction,microtubule formation,adenosine triphosphate synthesis,coupled proton transport and so on.Sixteen genes in the mitogen-activated protein kinase (MAPK) pathway and two-component signaling pathway,which were two important signal transduction pathways involved in fungal morphogenesis,and 16 genes involved in chitin synthesis and metabolism were all confirmed to be up-regulated in S.schenckii in yeast phase.Conclusions Compared with S.schenckii in mycelium phase,great changes in gene expression profiles were observed in S.schenckii in yeast phase.These differentially expressed genes are involved in many functions,suggesting that the dimorphic transition of S.schenckii is regulated by a multi-gene network system.
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Objective To establish tree shrew model of type 2 diabetes mellitus (T2DM) combined with cerebral ischemia (IS),and to explore the regulatory mechanism of ischemic postconditioning (PC) on gene differential expression in cerebral cortex under metabolic abnormalities and cerebral ischemia condition.Methods Seventy tree shrews were divided into control,T2DM,IS,T2DM+IS and T2DM +IS +PC groups (n =14 each group).The experimental diabetes model was established by the combined use of high fat diet breeding with streptozocin injection in tree shrew.The local cerebral thrombosis was induced by photochemical reaction in tree shrews,and ischemic PC was established at 4h after cerebral ischemia followed by clipped ipsilateral common carotid artery three times (5 min/time).The metabolic status of tree shrews was measured by serum biochemical markers.TTC staining,HE staining,and electron microscopy were used to observe the changes of the body's metabolic status at 24h after IS.RNA-seq was used to analyze differentially expressed genes.Results The ultrastructure of brain cells was abnormal and the cerebral infarction area was the largest in T2DM+IS tree shrews (P＜0.01).Compared with control group,body weight of tree shrews in T2DM + IS group was significantly reduced (P＜ 0.01) while blood glucose,total cholesterol,low density lipoprotein-cholesterol,triglyceride,and C-reactive protein (CRP) levels were markedly increased(all P＜0.01).The RNA-seq analysis showed that there were 1 629 differentially expressed genes (1 109 up-regulated genes and 520 down-regulated genes) in T2DM + IS group vs control group.However,ischemic PC deceased the cortical infarction area (P＜0.01)and reduced blood glucose,lipid and CRP levels (P＜0.05),with 520 differential expression genes (203 up-regulated genes and 317 down-regulated genes).Conclusion Ischemic PC improves the metabolic disturbance-aggravated ischemic brain injury in T2DM tree shrews,which may be related to its regulation on gene expression in cerebral cortex.
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Para acortar la brecha entre lo molecular y la clínica, el personal de atención médica debe tener un conocimiento básico de los mecanismos moleculares que gobiernan la identidad celular, mediante la activación selectiva de genes. La expresión diferencial de genes permite a las células sintetizar las proteínas requeridas para cumplir con sus funciones biológicas, y ello posibilita a las células responder a estímulos internos y externos. Para esto se debe tener primero acceso a los genes que codifican las proteínas, determinando el fenotipo celular. Modificaciones en la estructura de la cromatina permiten a la maquinaria transcripcional tener acceso a secuencias de ADN. El ADN es transcripto en ARNm, que sufre diversas modificaciones antes de salir del núcleo para ser traducido en una proteína en el citoplasma. Cualquier desregulación en alguno de los procesos asociados se presenta como una patología. A inicios del siglo XXI se reportó la secuenciación del genoma humano, y sorprendentemente uno de los principales hallazgos fue que solo un 2% de la secuencia codifica para proteínas, lo cual dejó un interrogante sobre cómo funcionan y se regulan los procesos genéticos que llevan a la identidad celular. Desde entonces las investigaciones han permitido utilizar los principios que rigen estos procesos para ampliar el conocimiento de los mecanismos asociados a enfermedades. Gracias a estos avances, se ha buscado determinar aplicaciones clínicas dirigidas a los procesos involucrados en la expresión génica diferencial, lograr una mejor comprensión sobre los procesos patológicos de la enfermedad y desarrollar herramientas diagnósticas.
To narrow the gap between the bench and the clinic, healthcare personnel should have a basic understanding of molecular mechanisms ruling cell identity, since it establishes the key differences between health and disease states. Differential gene expression allows for protein synthesis required for the cell's biological function. In this process genes are selected from the entire genome to meet the cell's biological functioning and respond to internal and external stimuli. To this end, first the chromatin must be remodeled for the transcriptional machinery to gain access to DNA sequences coding for particular genes. DNA can then be transcribed into mRNA, followed by different processes leading to mature mRNA leaving the nucleus for protein synthesis in the cytoplasm. Any dysregulation in these processes results in disease. In the beginning of this millennium the human genome project sequenced the whole genome. Surprisingly, one of the main findings was only 2% of the genome represented protein coding sequences, which raised the question about the remainder of the genome and cell identity. Based on principles derived from the human genome project many investigations have shed light on mechanisms associated with disease. Thanks to advancements in differential gene expression, researchers are seeking for a better understanding in pathological processes associated with disease and the development of diagnostic tools.
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Humans , Epigenomics , Acetylation , MethylationABSTRACT
Abstract Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13 × 3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13 × 3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.
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Pleurotus/genetics , Gene Expression Profiling , Alleles , Genes, FungalABSTRACT
AIM:To study the protective effect of heat shock factor1(HSF1) on the mice with lipopolysaccha-ride (LPS)-induced acute lung injury(ALI),and to screen the relevant differentially-expressed genes. METHODS:ALI mouse model was established by LPS intracheal instillation. The macroscopic and pathological changes of the lung tissue were observed,and the concentrations of total protein,TNF-α, IL-β, IL-6 and VEGF in the bronchoalveolar lavage fluid (BALF) were analyzed. Differentially-expressed genes in the lung tissues of HSF1 +/ +mice and HSF1 -/- mice with ALI induced by LPS were screened by gene chips. The key gene was verified by real-time qPCR. RESULTS:The macroscopic and pathological changes of the lung injury in HSF1 -/- +LPS mice were more serious than those in HSF1 +/ ++LPS mice.The concentrations of total protein,VEGF,TNF-α,IL-1β and IL-6 in the BALF of HSF1 -/- +LPS mice were significantly higher than those of HSF1 +/ ++LPS mice(P<0.05). Compared with the HSF1 +/ +mice,a total of 918 differentially-ex-pressed genes were indentified in the HSF1 -/- mice, among which the expression levels of 65 genes had obvious diffe-rence,with 28 genes up-regulated,including Atg7,ccr1,cxcr2,Tbl1xr1,Mmp9,Pparg,Plcb2,Arrb2,Cntn1,Col4a6, etc, and 37 genes down-regulated,including Fgfr1,Fgfr2,Map4k4,Ddx58,Tfg,Stat3,Smad4,Lamc1,Sdc3,etc. The results of real-time qPCR showed that the mRNA level of CXCR2 in HSF1 -/- + LPS mice was significantly higher than that in HSF1 +/ ++ LPS mice,which was consistent with the results of gene chips. CONCLUSION:HSF1 has protective effect on the mice with LPS-induced ALI. CXCR2 may be involved in the protective effect of HSF1 on this process.
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Objective To analyze gene expression profiles of biopsy specimens from breast cancer patients who were treated with neoadjuvant chemotherapy(NAC) after biopsies, and to identify the genes which are closely associated with the efficacy of neoadjuvant chemotherapy with T/FAC [docetaxel(Taxotere), 5-fluorouracil, doxorubicin and cyclophosphamide] or T/FEC (Taxotere, 5-fluorouracil, epirubicin and cyclophosphamide) regimen.Methods We retrieved and collected gene expression profiles from publicly available databases.Four datasets, a total of 844 samples, were finally retained because all the patients had received a uniform neoadjuvant chemotherapy regimen.Response to neoadjuvant chemotherapy was categorized as a pathological complete response (pCR) or residual invasive cancer (RD).The differentially expressed genes (adjusted P-value<0.05) and therapeutic efficacy were analyzed and explored.Results After differential analysis, genes whose expressions were higher or lower in pCR group than in RD group were identified in each of the four datasets, respectively.There were 34 and 42 genes which were simultaneously more highly expressed or more lowly expressed in pCR group than in RD group in the four datasets.The unsupervised clustering, based on the 76 intersection genes, showed that the pCR specimens tended to form one cluster and the RD tended to form the other.Conclusion The seventy-six differentially expressed genes are associated with the efficacy of neoadjuvant chemotherapy and are likely to be novel predictive biomarkers for the efficacy of neoadjuvant chemotherapy.
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To screen the differentially-expressed microRNAs (miRNAs) in mouse models with renal ischemia-reperfusion injury (IRI),aiming to offer foundation for unraveling the molecular mechanism of the incidence and progression of IRI.Methods The mouse models with acute IRI were established by renal artery clamping.Fifteen mice were divided into the IRI group and sham surgery group (E group).The animals in the IRI group were subdivided into the A group (45 min ischemia followed by 24 h reperfusion),B group (25 min ischemia followed by 24 h reperfusion),C group (45 min ischemia followed by 4 h reperfusion) and D group (25 min ischemia followed by 4 h reperfusion) (n=3 for each group).The severity ofIRI was evaluated by histological changes and renal function.The differentially-expressed miRNAs in the IRI mouse models at different ischemia time (25 and 45 min) and reperfusion time (4 and 24 h) were screened by using cluster analysis of miRNAs microarray data.The differential expression of miR-695 and miR-145 was validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR).Results Both histological changes and renal function confirmed that the IRI mouse models were successfully established.Compared with the sham surgery group,71 differentially-expressed miRNAs were detected in the IRI group including 30 down-regulated miRNAs and 40 up-regulated miRNAs.The results of qRT-PCR demonstrated that if the standardized expression level of miRNAs in the E group was 1,the relative expression levels of miR-695 and miR-145 were 11.82 and 0.31 in the IRI group (both P＜0.05),which were consistent with the chip results.Conclusions After renal IRI,different changes occur in the gene expression profile of miRNAs.These differentially-expressed miRNAs act as molecular biomarkers for renal IRI with potential clinical and scientific research values.
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Objective To screen the tumor metastasis related differentially expressed genes in hepatocelluar carcinoma (HCC)cells 7402 after stable transfection with FATE/BJ‐HCC‐2 gene .Methods Total RNA was extracted from FATE/BJ–HCC‐2‐transfected HCC(5B4)cells and empty vector control (Mock)cells respectively .Differentially expressed genes were obtained using cDNA microarray .Results Compared with Mock cells ,a total of 1 694 differentially expressed genes were screened out in 5B4 cells ,the 11 gene expressions had obvious differences ,among which the expression amounts in 7 genes were significantly in‐creased ,including MMP‐1 ,PTGS2 ,FN ,CA9 ,IL‐8 ,ILK and Areg .The fold changes were 81 .80 ,49 .86 ,11 .30 ,16 .26 ,3 .48 ,2 .79 and 2 .20 ,respectively .The expression amounts in 4 genes were significantly decreased ,including E‐cadherin ,E‐cadherin , RHOBTB3 ,ALPP and HLA‐DRB4 .The fold changes were -5 .42 ,-2 .23 ,-5 .93 and -8 .03 ,respectively .Conclusion Adopting gene microarray technology can carefully screen the differentially expressed genes of FATE/BJ‐HCC‐2 involved HCC metastasis ,its final goal is to lay a solid theoretical foundation for studying the HCC metastasis mechanism .
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OBJECTIVES@#To study the differential genes expression in the early stage of acute renal ischemia-reperfusion injury and explore potential molecular mechanisms.@*METHODS@#The ischemia-reperfusion model was made via clamping renal artery of rat. The microarray detection and bioinformatics analyzing of the genes expression were performed. Differentially expressed genes were screened and related cellular activities and signaling pathways were analyzed in early stage of acute kidney injury. Meanwhile, molecules closely relative to acute kidney injury were explored by establishing a biological network of the differentially expressed genes, and the results were verified by real-time PCR.@*RESULTS@#A total of 151 genes showed differential expression in this study, including 132 up-regulated and 19 down-regulated genes. Cell proliferation, cytokines mediated signaling transduction and immune responses were greatly enriched by GO and KEGG analysis. The results of real-time PCR showed that compared with control groups, three selected genes （ANXA1, PHLDA1 and KLF6） which related to the acute kidney injury had an obvious differential expression in the early stage of disease. The multiple of increase was essentially the same as the multiple detected by microarray.@*CONCLUSIONS@#This study shows differential gene expression profile, related biological processes and signaling pathways involved in the early stage of acute kidney injury. ANXA1, PHLDA1 and KLF6 may play a role in the pathogenesis of acute kidney injury.
Subject(s)
Animals , Rats , Acute Kidney Injury/genetics , Annexin A1/genetics , Apoptosis Regulatory Proteins/genetics , Gene Expression , Kidney/pathology , Kruppel-Like Factor 6/genetics , Real-Time Polymerase Chain Reaction , Reperfusion Injury/genetics , Signal TransductionABSTRACT
Objective To investigate the effect of testosterone on mitotic orientation in rat prostate epithelial cells and the relative differential gene expression.Methods Twenty SPF male SD rats were divided into 2 groups at random and then subjected to castration.One group of rats was administrated with testosterone 3.7 mg daily for 30 days and the control group was only injected with olive oil.Microscopic analysis was performed using immunohistochemistry.Differential gene expression analysis was conducted by gene microarray and RT-PCR techniques.Results In the testosterone-adminis-trated group, there was a significant mitosis orientation parallel to the basement membrane.But in the control group, mito-sis orientation was oriented perpendicular to the basement membrane.Using the gene microarray and RT-PCR techniques, the cell proliferation genes such as Ran, Tgm4 and Wnt2 in Wnt signal pathway were up-regulated in the testosterone group.Conversely, suppressor cell proliferation genes such as Dkk3 and Fas were down-regulated.Conclusions Mitotic orientation of prostate epithelia cells is changed after testosterone administration.Wnt signal pathway and AR singling path-way also have an influence on the mitosis orientation and cell proliferation.
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In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.
Subject(s)
Animals , Male , Female , Bees/genetics , Diploidy , Cytogenetic Analysis , Gene Expression , Real-Time Polymerase Chain ReactionABSTRACT
Quantification of the differential expression of metabolic enzyme and heat-shock protein genes (Hsp) during early embryogenesis in diapause and non-diapause eggs of the silkworm B. mori was carried out by semi-quantitative RT-PCR. Data analysis revealed that, the phosphofructokinase (PFK) expression started at a higher level in the early stage (6 h after oviposition) in non-diapause eggs, while in diapause induced eggs, it started at a lower level. However, the PFK gene expression in diapause eggs was comparatively higher than in non-diapause eggs. PFK facilitates use of carbohydrate reserves. The lower level of PFK gene expression in the early stage of diapause induced eggs but comparatively higher level of expression than in non-diapause eggs is due to enzyme inactivation via protein phosphorylation during early embryogenesis followed by de-phosphorylation in later stage. The sorbitol dehydrogenase-2 (SDH-2) gene was down regulated in diapause induced eggs up to 24 h and its expression levels in diapause induced eggs coincided with that of PFK gene at 48h in non-diapause eggs. During carbohydrate metabolism, there is an initial temporary accumulation of sorbitol which acts as protectant. The down regulation of SDH-2 gene during the first 24 hours in diapause induced eggs was due to the requirement of sorbitol as protectant. However, since the diapause process culminates by 48 h, the SDH-2 gene expression increased and coincided with that of PFK gene expression. The trehalase (Tre) gene expression was at a lower level in diapause induced eggs compared to non-diapausing eggs. The induction of Tre activity is to regulate uptake and use of sugar by the tissues. The non-diapause eggs revealed maximum expression of GPase gene with major fluctuations as well as an overall higher expression compared to diapause induced eggs. The diapause process requires less energy source which reflects lower activity of the gene. Heat shock protein (Hsp)genes (Hsp20.4, 40, 70, and 90) revealed differential levels of expression in both the eggs at all stages of embryonic development. The present study thus provides an overview of the differential expression levels of metabolic enzyme and Hsp genes in non-diapause and diapause induced eggs of multivoltine silkworm B. mori within 48 h after oviposition, confirming the major role of in early embryogenesis.
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Diffuse infiltrating gliomas are the most common tumors of the central nervous system. Gliomas are classified by the WHO according to their histopathological and clinical characteristics into four classes: grade I (pilocytic astrocytoma), grade II (diffuse astrocytoma), grade III (anaplastic astrocytoma), and grade IV (glioblastoma multiforme). Several genes have already been correlated with astrocytomas, but many others are yet to be uncovered. By analyzing the public SAGE data from 21 patients, comprising low malignant grade astrocytomas and glioblastomas, we found COL6A1 to be differentially expressed, confirming this finding by real time RT-PCR in 66 surgical samples. To the best of our knowledge, COL6A1 has never been described in gliomas. The expression of this gene has significantly different means when normal glia is compared with low-grade astrocytomas (grades I and II) and high-grade astrocytomas (grades III and IV), with a tendency to be greater in higher grade samples, thus rendering it a powerful tumor marker.
Subject(s)
Humans , Astrocytoma/genetics , Collagen Type VI/genetics , Gene Expression Profiling , Astrocytoma/pathology , Gene Expression Regulation, Neoplastic , Reverse Transcriptase Polymerase Chain Reaction , RNA, NeoplasmABSTRACT
BACKGROUND: The normal functions of the cell cycle inhibitor p16INK4a are frequently inactivated in many human cancers. Over 80% of hepatocellular carcinoma (HCC) cases lack a functional p16/Rb pathway. p16/Rb pathway, as well as p53 pathway, is considered as one of key components of tumor suppression. METHODS: To study the roles of p16INK4a in HCC, a stable cell line expressing exogenous p16 was generated from SNU-449 hepatocellular carcinoma cells lacking endogenous p16, and suppression subtractive hybridization (SSH) was performed in parallel with the control cells. RESULTS: 1) SSH identifies fibronectin (FN1), crystallin alphaB (CRYAB), Rac1, WASP, RhoGEF, and CCT3 as differentially-expressed genes. 2) Among the selected genes, the up- regulation of FN1 and CRYAB was confirmed by Northern blot, RT-PCR and by proteomic methods. CONCLUSION: These genes are likely to be associated with the induction of stress fiber and stabilization of cytoskeleton. Further studies are required to clarify the possible role of p16 in the signal transduction pathway.
Subject(s)
Humans , Blotting, Northern , Carcinoma, Hepatocellular , Cell Cycle , Cell Line , Crystallins , Cytoskeleton , Fibronectins , Gene Expression , Rho Guanine Nucleotide Exchange Factors , Signal Transduction , Stress Fibers , WaspsABSTRACT
BACKGROUND/AIMS: It has been acknowleged that diverse factors such as Hepatitis B or C virus, alcohol, food carcinogens, and environmental or genetic factors are involved in hepatocellular carcinogenesis. In the molecular biologic aspect, suppression of tumor suppressor gene or amplification of oncogene, abnormal regulation of cell cycle-related proteins, abnormal apoptosis mechanism, and diverse growth factors are reported to be factors that contribute to hepatocellular carcinogenesis. In this study, the genetic difference between hepatocellular carcinoma tissue and surrounding non-hepatocellular carcinoma tissue has been investigated to identify genes that are deleted, diminished, amplified, or newly developed in hepatocellular carcinoma using differential gene expression. METHOD: We studied each of 12 biopsy samples of hepatocellular carcinoma and surrounding non-hepatocellular carcinoma tissues obtained during surgical resections. Random arbitrarily primed-polymerase chain reaction (RAP-PCR) was applied for differential gene expression. The genes that are deleted, diminished, or amplified, newly developed in hepatocellular carcinoma are cloned, sequenced, and then identified by BLAST search, some genes are characterized by eletrophoresis motility shift assay (EMSA) and in situ hybridization. RESULTS: We identified the various, diverse genes classified as tumor suppressor genes, oncogenes, growth factor genes, and some kinds of transcription factors. Some of these genes were identified to be repressed, deleted or diminished, others were amplified, or newly developed in hepatocellular carcinoma tissues. CONCLUSIONS: RAP-PCR is a good method in the identification of the gene associated with hepatocellular carcinoma. The result in this study shows that so many genes are different between hepatocellular carcinoma and surrounding non- hepatocellular carcinoma tissues, and that the genes related with hepatocellular carcinogenesis may be predicted. Further studies are necessary for analyzing the relationship bet
Subject(s)
Apoptosis , Biopsy , Carcinogenesis , Carcinogens , Carcinoma, Hepatocellular , Clone Cells , Gene Expression , Genes, Tumor Suppressor , Hepatitis B , In Situ Hybridization , Intercellular Signaling Peptides and Proteins , Oncogenes , Transcription FactorsABSTRACT
PURPOSE: To know whether amniotic membrane (AM) extract could protect cell from toxic stimuli by changing gene expression such as inflammatory and apoptosis-related genes, cultured corneal fibroblasts were used. METHODS: After AM was pulverized in the liquid nitrogen and homogenized under the 4(C, it was centrifuged and its supernatant was obtained. Human corneal fibroblasts (HCFs) were divided into 2 groups - one group treated with AM extracts and TNF-alpha, and the other with TNF-alpha only. Cell morphology and viability were assessed and differential gene expression through cDNA array was performed. RESULTS: Viability of HCF cultured in AM extracts and TNF-alpha was better than that of cells in TNF-alpha only. Cells in TNF-alpha only were morphologically changed and dead. cDNA array showed the decrease in IL-1 , IL-1 receptor type 1 and caspases-1,-3,and -10 expression in cells treated with AM extracts. MMP-1,-2,-3 and-9 were almost the same or slightly increased and NF-kappaB, I kappaB kinase alpha, integrin-alpha1 and -alpha10, and MAP kinase were increased in cells with AM extracts. CONCLUSIONS: When cultured corneal fibroblasts were insulted by TNF-alpha, AM extracts seemed to protect the cells, by down-regulating various inflammation - and cell death- related genes, and by increasing the expression of genes enhancing cell proliferation and differentiation.
Subject(s)
Humans , Amnion , Cell Proliferation , Fibroblasts , Gene Expression , Inflammation , Interleukin-1 , NF-kappa B , Nitrogen , Oligonucleotide Array Sequence Analysis , Phosphotransferases , Tumor Necrosis Factor-alphaABSTRACT
When deprived of combined nitrogen, aerobically-grown filaments of Anabaena sp. strain PCC7120 differentiate specialized cells called the heterocysts. The differentiation process is an elaborate and well orchestrated programme involving sensing of environmental and developmental signals, commitment of cells to development, gene rearrangements, intricate DNA-protein interactions, and differential expression of several genes. It culminates in a physiological division of labour between heterocysts, which become the sole sites of aerobic nitrogen fixation, and vegetative cells, that provide photosynthate to the heterocysts in return for nitrogen supplies. We propose a model, to describe the chronology of the important events and to explain how cell type-specific differential gene expression is facilitated by DNA-protein interactions leading to the development of heterocysts and constitution of nitrogen-fixing apparatus in Anabaena.