Identification of Novel Epithelial Ovarian Cancer Biomarkers by Cross-laboratory Microarray Analysis

The purpose of this study was to pool information in epithelial ovarian cancer by combining studies using Affymetrix expression microarray datasets made at different laboratories to identify novel biomarkers.Epithelial microarray expression information across laboratories was screened and combined after preprocessing raw microarray data,then ANOVA and unpaired T test statistical analysis was performed for identifying differentially expressed genes(DEGs),followed by clustering and pathway analysis for these DEGs.In this work,we performed a combination analysis on microarrays from three different laboratories using gene expression data on ovarian cancer and obtained a list of differential expression profiles identified as potential candidate in aggressiveness of ovarian cancer.The clustering and pathway analysis explored the different molecular basis of different ovarian cancer stages and potential important regulatory pathways in ovarian cancer development.Our results showed that combination of microarray data from different laboratories in the same platforms may overcome biases derived from probe design and technical features,thereby accelerating the identification of trustworthy DEGs,and demonstrating the advantage of integrative analysis in gene expression studies on epithelial ovarian cancer research.

Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability

AIM： Gene expression profiling provides an unique opportunity to gain insight into the development of different types of gastric cancer. Tumor sample heterogeneity is thought to decrease the sensitivity and tumor specificity of microarray analysis. Thus, microdissection and preamplification of RNA is frequently performed. However, this technique may also induce considerable changes to the expression profile. To assess the effect of gastric tumor heterogeneity on expression profiling results, we measured the variation in gene expression within the same gasbic cancer sample by performing a gene chip analysis with two RNA preparations extracted from the same tumor specimen. METHODS： Tumor samples from six intestinal T2 gastric tumors were dissected under liquid nitrogen and RNA was prepared from two separate tumor fragments. Each extraction was individually processed and hybridized to an Affymetrix U133A gene chip covering approximately 18 000 human gene transcripts. Expression profiles were analyzed using Microarray Suite 5.0 （Affymetrix） and GeneSpring 6.0 （Silicon Genetics）. RESULTS： All gastric cancers showed little variance in expression profiles between different regions of the same tumor sample. In this case, gene chips displayed mean pair wise correlation coefficients of 0.94±0.02 （mean±SD）, compared to values of 0.61±0.1 for different tumor samples. Expression of the variance between the two expression profiles as a percentage of “total change” （Affymetrix） revealed a remarkably low average value of 1.18±0.78 for comparing fragments of the same tumor sample. In contrast, comparison of fragments from different tumors revealed a percentage of 24.4±4.5. CONCLUSION： Our study indicates a low degree of expression profile variability within gastric tumor samples isolated from one patient. These data suggest that tumor tissue heterogeneity is not a dominant source of error for microarray analysis of larger tumor samples, making total RNA extraction an appropriate strategy for performing gene chip expression profiling of gastric cancer.

Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders

Chromosome microarray analysis(CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon.We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6%(59 out of 434). This gave a detection rate of 14.7%for developmental delay/intellectual disability(DD/ID,38/259) and 12% for autism spectrum disorders(ASDs,21/175). Thirty-three recurrent(n≥2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes(such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes).The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results(94.9%) had benefits, allowing earlier diagnosis(36/59), prioritized full clinical management(28/59), medication changes(7/59), a changed prognosis(30/59), and prenatal genetic counseling(15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential.We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility.

Chromosomal microarray analysis vs.karyotyping for fetal ventriculomegaly:a meta-analysis

Background:Chromosomal abnormalities are important causes of ventriculomegaly(VM).In mild and isolated cases of fetal VM,obstetricians rarely give clear indications for pregnancy termination.We aimed to calculate the incidence of chromosomal abnormalities and incremental yield of chromosomal microarray analysis(CMA)in VM,providing more information on genetic counseling and prognostic evaluation for fetuses with VM.Methods:The Chinese language databases Wanfang Data,China National Knowledge Infrastructure,and China Biomedical Literature Database(from January 1,1991 to April 29,2020)and English language databases PubMed,Embase,and Cochrane Library(from January 1,1945 to April 29,2020)were systematically searched for articles on fetal VM.Diagnostic criteria were based on ultrasonographic or magnetic resonance imaging(MRI)assessment of lateral ventricular atrium width:≥10 to<15 mm for mild VM,and≥15 mm for severe VM.Isolated VM was defined by the absence of structural abnormalities other than VM detected by ultrasonography or MRI.R software was used for the meta-analysis to determine the incidence of chromosomal abnormalities and incremental yield of CMA in VM,and the combined rate and 95%confidence interval(CI)were calculated.Results:Twenty-three articles involving 1635 patients were included.The incidence of chromosomal abnormalities in VM was 9%(95%CI:5%-12%)and incremental yield of CMA in VM was 11%(95%CI:7%-16%).The incidences of chromosomal abnormalities in mild,severe,isolated,and non-isolated VM were 9%(95%CI:4%-16%),5%(95%CI:1%-11%),3%(95%CI:1%-6%),and 13%(95%CI:4%-25%),respectively.Conclusions:Applying CMA in VM improved the detection rate of abnormalities.When VM is confirmed by ultrasound or MRI,obstetricians should recommend fetal karyotype analysis to exclude chromosomal abnormalities.Moreover,CMA should be recommended preferentially in pregnant women with fetal VM who are undergoing invasive prenatal diagnosis.CMA cannot completely replace chromosome karyotype analysis.

Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders

Neuroplastin 65 （Np65） is an immunoglobulin superfamily cell adhesion molecule involved in synaptic formation and plasticity. Our recent study showed that Np65-knockout （KO） mice exhibit abnormal cognition and emotional disorders. However, the underlying mechanisms remain unclear. In this study, we found 588 differentially- expressed genes in Np65-KO mice by microarray analysis. RT-PCR analysis also revealed the altered expression of genes associated with development and synaptic structure, such as Cdhl, Htr3a, and Kcnj9. In addition, the expression of Wnt-3, a Wnt protein involved in development, was decreased in Np65-KO mice as evidenced by western blotting. Surprisingly, MRI and DAPI staining showed a significant reduction in the lateral ventricular volume of Np65-KO mice. Together, these findings suggest that ablation of Np65 influences gene expression, which may contribute to abnormal brain development. These results provide clues to the mechanisms underlying the altered brain functions of Np65-deficient mice.

Differentially expressed genes identified by microarray analysis Following leptin treatment of hepatic stellate cells

Background Liver fibrosis is the process through which numerous chronic liver diseases develop into liver cirrhosis. Leptin can activate hepatic stellate cells （HSCs） and play an important role in the formation of liver fibrosis. However, the process by which leptin activates HSCs is complicated, and research on this process is limited. The aim of this study was to explore the related changes in gene expression and the control mechanisms involved in leptin activated HSCs to understand the overall mechanism of liver fibrosis development. Methods We cultivate rat HSCs, with and without stimulation by leptin, and extracted mRNA. Differentially expressed genes were detected by microarray analysis. Results The differentially expressed genes identified included six upregulated genes and six downregulated genes. The representative upregulated genes included short chain dehydrogenase （CY5/CY3=2.265） and pulmonary surfactant protein A1 （CY5/CY3=2.036）. The significant downregulated gene encoded hepatic stearoyl coenzyme A desaturase 1 （SCD-1） （CY5/CY3=0.351）.Conclusion Leptin might mediate the molecular biological mechanisms of liver fibrosis.

Microarray analysis of gene expression after electrical stimulation of the dura mater surrounding the superior sagittal sinus in conscious adult rats

Background The molecular and cellular origins of migraine headache are among the most complex problems in contemporary neurology.Up to now the pathogenesis of migraine still remains unclearly defined.The objective of this study was to explore new factors that may be related to the mechanism of migraine.Methods The present study performed a comprehensive analysis of gene expression in the trigeminal nucleus caudalis induced by electrical stimulation of dura mater surrounding the superior sagittal sinus in conscious rats using microarray analysis followed by quantitative real-time reverse-transcribed polymerase chain reaction （qRT-PCR） verification.Student＆#39;s two sample t-test was employed when two groups were compared.A P value 〈0.05 was considered to be statistically significant.Results Comparing the placebo and the electrical stimulation groups,40 genes were determined to be significantly differentially expressed.These significantly differentially expressed genes were involved in many pathways,including transporter activity,tryptophan metabolism,G protein signaling,kinase activity,actin binding,signal transducer activity,anion transport,protein folding,enzyme inhibitor activity,coenzyme metabolism,binding,ion transport,cell adhesion,metal ion transport,oxidoreductase activity,mitochondrion function,and others.Most of the genes were involved in more than 2 pathways.Of particular interest is the up-regulation of Phactr3 and Akap5 and the down-regulation of Kdr.Conclusion These findings may provide important clues for a better understanding of the molecular mechanism of migraine.

Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant

In order to overcome the defects of difficult gene operations in low-copy suicide plasmid pCVD442,Gateway technology was applied in the construction process of recombinant plasmid for gene knockout in this study.With this improved knockout system,we inactivated sitC gene,which is associated with iron transport in Shigella flexneri 2a strain 301,to yield the mutant,MTS.The functional detection of the mutant was performed at the level of culture medium,cell and animal experiment,respectively.The gene expression profiles were compared with DNA microarray between the mutant and the wild type under iron-restricted conditions.The results showed that MTS grew obviously less well than the wild-type strains in L broth containing 150μmol/L iron chelator DIP(2,2′-dipyridyl).Addition of iron or manganese to the cultures stimulated the growth of MTS to wild-type levels in rich culture medium.In either the experiment on the ability of intracellular multiplication and cell-to-cell spread in HeLa and U937 cell lines,or the experiment on keratoconjunctivitis in guinea pigs,MTS showed no obvious changes in virulence compared with the parental strain Sf301.When 65μmol/L DIP was added to the cultured HeLa cells,the ability of intracellular multiplication of MTS reduced about 51.6%as compared with that of Sf301.The analysis of expression profiles under iron-limited condition showed that MTS was more sensitive for the change of iron deficiency than Sf301.There are 106 more up-regulated genes in MTS than in wild-type strains,which are involved in membrane transportation,amino acid metabolism and uncategorized function genes,while down-regulated genes are mainly in-volved in energy and carbohydrate metabolism.Under low iron conditions,the expression levels of known iron-transport associated genes generally increased.Additionally,the number of these genes and their increase amplitude in MTS are more than those in Sf301.Together,these results confirmed that Sit iron-transport system is important for the growth of Shigella.

Microarray analysis of genes involved in mice heart tissues of cardiac hypertrophy

Background Cardiac hypertrophy(CH)is a pathological state of heart which could lead to arrhythmias,cardiac failure,and sudden cardiac death.Pathology of cardiac hypertrophy has been acknowledged widely,but the detailed molecular mechanism has not been explored thoroughly.Our study was designed to identify differentially expressed genes(DEGs),and to explore the molecular mechanism and core genes that may be involved in the progression of cardiac hypertrophy.Methods Microarray data of cardiac hypertrophy(GSE76)was downloaded from the Gene Expression Omnibus(GEO)database.The DEGs were identified by R.Then Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis and protein-protein interaction(PPI)network analyses were performed by DAVID,STRING and Cytoscape.Results 1014 DEGs in GSE76 were identified,970 were downregulated genes and 44 were upregulated genes in cardiac hypertrophic tissues.The biological process(BP)analysis revealed that DEGs mainly included genes for inflammatory response,cell adhesion,and cell proliferation.The core genes were associated with cardiac remodeling and fibrosis,cell growth,inflammatory reaction,and cell adhesion.Conclusions This study indicated the potential significance of immune injury and cardiac fibrosis in the progression of cardiac hypertrophy.Meanwhile,the core genes may provide molecular targets for the disease diagnosis or drug treatment of cardiac hypertrophy in the future.

A microarray analysis of early activated pathways in concanavalin A-induced hepatitis

Objective:To explore the mechanisms of fulminant hepatitis(FH) in the early stages,and to determine the critical pathways in its initiation and progression.Methods:Twelve BALB/c mice were divided into four groups:one group left as negative control and sacrificed immediately after injection of phosphate-buffered saline(PBS),and another three groups with concanavalin A(Con A) administration sacrificed at 1,3,and 6 h after injection.Affymetrix GeneChip Mouse 430 2.0 Array was employed to evaluate the expression profile of each of the 12 samples.Further analysis was done on the microarray data to extract the genes that were differentially expressed.Enrichment analysis was carried out to determine relevant pathways within which regulated genes were significantly enriched.Results:A total of 393,8354 and 11 344 differentially expressed genes were found,respectively,at three time points.During 0-1 h and 1-3 h,most of the pathways enriched with regulated genes were related to immune response and inflammation,among which Toll-like receptor(TLR) signaling and mitogen-activated protein kinase(MAPK) signaling appeared during both phases,while cytokine-cytokine receptor interaction,apoptosis,T cell receptor signaling,and natural killer(NK) cell-mediated cytotoxicity pathways emerged during the second phase.Pathways found to be significant during 3-6 h were mostly related to metabolic processes.Conclusion:The TLR signaling pathway dominates the early responses of Con A-induced FH in mice.It stimulates the production of type I cytokines,therefore recruiting and activating T/NK cells.Activated T/NK cells exert their cytotoxicity on hepatocytes through inducing death receptorintermediated apoptosis,resulting in liver injury.

Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis

Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroarray data was presented, by combined with evidence acquired from comparative genornic hybridization （CGH） data. Methods： Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus （GEO） website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray （SAM） was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery （DAVID）. Finally, SVM-T-RFE gene selection algorithm was applied to identify ted genes in CRC. Results： A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy （100%） in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions- Our results demonstrated that integration analysis is an effective strategy for mining cancer- associated genes.

Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis

Carotenoids play an important role in many physiological processes in plants and the phytoene desaturase gene （PDS3） encodes one of the important enzymes in the carotenoid biosynthesis pathway. Here we report the identification and analysis of a T-DNA insertion mutant of PDS3 gene. Functional complementation confirmed that both the albino and dwarfphenotypes ofthepds3 mutant resulted from functional disruption of the PDS3 gene. Chloroplast development was arrested at the proplastid stage in thepds3 mutant. Further analysis showed that high level ofphytoene was accumulated in the pds3 mutant. Addition of exogenous GA3 could partially rescue the dwarf phenotype, suggesting that the dwarf phenotype ofthepds3 mutant might be due to GA deficiency. Microarray and RT-PCR analysis showed that disrupting PDS3 gene resulted in gene expression changes involved in at least 20 metabolic pathways, including the inhibition of many genes in carotenoid, chlorophyll, and GA biosynthesis pathways. Our data suggest that the accumulated phytoene in the pds3 mutant might play an important role in certain negative feedbacks to affect gene expression of diverse cellular pathways.

Circulating miRNAs as biomarkers for severe acute pancreatitis associated with acute lung injury

AIM To identify circulating micro(mi)RNAs as biological markers for prediction of severe acute pancreatitis(SAP) with acute lung injury(ALI).METHODS Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the mi RNA expression profiles were determined by microarray analysis. These mi RNAs were validated by quantitative reverse transcriptionpolymerase chain reaction, and their putative targets were predicted by the online software Target Scan, mi Randa and Pic Tar database. Gene ontology(GO) and Kyoto encyclopedia of genes and genomes(commonly known as KEGG) were used to predict their possible functions and pathways involved.RESULTS We investigated 287 mi RNAs based on microarray data analysis. Twelve mi RNAs were differentially expressed in the patients with SAP with ALI and those with SAP without ALI. Hsa-mi R-1260 b, 762, 22-3 p, 23 b and 23 a were differently up-regulated and hsa-mi R-550 a*, 324-5 p, 484, 331-3 p, 140-3 p, 342-3 p and 150 were differently down-regulated in patients with SAP with ALI compared to those with SAP without ALI. In addition, 85 putative target genes of the significantly dysregulated mi RNAs were found by Target Scan, mi Randa and Pic Tar. Finally, GO and pathway network analysis showed that they were mainly enriched in signal transduction, metabolic processes, cytoplasm and cell membranes.CONCLUSION This is the first study to identify 12 circulating mi RNAs in patients with SAP with ALI, which may be biomarkers for prediction of ALI after SAP.

Electromagnetic Field Change the Expression of Osteogenesis Genes in Murine Bone Marrow Mesenchymal Stem Cells

In order to identify the differentially expressing gene of bone marrow mesenchymal stem cells （MSCs） stimulated by electromagnetic field （EMF） with osteogenesis microarray analysis, the bone marrow MSCs of SD rats were isolated and cultured in vitro. The third-passage cells were stimulated by EMFs and total RNA was extracted, purified and then used for the synthesis of cDNA and cRNA. The cRNA of stimulated group and the control group was hybridized with the rat oligo osteogenesis microarray respectively. The hybridization signals were acquired by using X-ray film after chemiluminescent detection and the data obtained were analyzed by employing the web-based completely integrated GEArray Expression Analysis Suite. RT-PCR was used to identify the target genes： Bmp1, Bmp7, Egf and Egfr. The results showed that 19 differentially expressing genes were found between the stimulated group and the control group. There were 6 up-regulated genes and 13 down-regulated genes in the stimulated group. Semi-quantitative RT-PCR confirmed that the expressions of Bmpl, Bmp7 mRNA of the stimulated group were up-regulated （P〈0.05） and those of Egf, Egfr were down-regulated （P〈0.05）. It was suggested that the gene expression profiles of osteogenesis of the bone marrow MSCs were changed after EMF treatment. It is concluded that the genes are involved in skeletal development, bone mineral metabolism, cell growth and differentiation, cell adhesion etc.

The involvement of XPC protein in the cisplatin DNA damaging treatment-mediated cellular response

Recognition of DNA damage is a critical step for DNA damage-mediated cellular response. XPC is an important DNA damage recognition protein involved in nucleotide excision repair (NER). We have studied the XPC protein in cisplatin DNA damaging treatment-mediated cellular response. Comparison of the microarray data from both normal and XPCdefective human fibroblasts identified 861 XPC-responsive genes in the cisplatin treatment (with minimum fold change≥1.5).The cell cycle and cell proliferation-related genes are the most affected genes by the XPC defect in the treatment. Many other cellular function genes, especially the DNA repair and signal transduction-related genes, were also affected by the XPC defect in the treatment. To validate the microarray data, the transcription levels of some microarray-identified genes were also determined by an RT-PCR based real time PCR assay. The real time PCR results are consistent with the microarray data for most of the tested genes, indicating the reliability of the microarray data. To further validate the microarray data, the cisplatin treatment-mediated caspase-3 activation was also determined. The Western blot hybridization results indicate that the XPC defect greatly attenuates the cisplatin treatment-mediated Caspase-3 activation. We elucidated the role of p53 protein in the XPC protein DNA damage recognition-mediated signaling process. The XPC defect reduces the cisplatin treatment-mediated p53 response. These results suggest that the XPC protein plays an important role in the cisplatin treatment-mediated cellular response. It may also suggest a possible mechanism of cancer cell drug resistance.

Protective effect and mechanisms of action of Mongolian medicine Sulongga-4 on pyloric ligation-induced gastroduodenal ulcer in rats

BACKGROUND Sulongga-4(SL-4)is a herbal formula used in traditional Mongolian medical clinics for the treatment of peptic ulcers and gastroenteritis,even though its pharmacological mechanism has not been well characterized.AIM To evaluate the protective effect and identify the mechanisms of action of SL-4 on gastroduodenal ulcer induced by pyloric ligation(PL)in rats.METHODS PL was performed to induce gastric and duodenal ulcers in rats,which were then treated with oral SL-4(1.3,2.6,or 3.9 g/kg per day)for 15 d.PL-induced gastroduodenal ulceration.Therapeutic effects were characterized by pathological and histological evaluations and inflammatory indicators were analyzed by enzyme-linked immunosorbent assay.Microarray analyses were conducted to identify gene expression profiles of gastroduodenal tissue in PL rats with or without SL-4 treatment.The candidate target genes were selected and verified by quantitative reverse transcription polymerase chain reaction(qRT-PCR).RESULTS SL-4 decreased histopathological features in the PL-induced ulcerated rats.SL-4 significantly (P < 0.05) decreased expression of tumor necrosis factor-α,interleukin (IL)-1β, IL-6, endotoxin, platelet-activating factor, and increasedprostaglandin E2 and epidermal growth factor in ulcer tissue. Microarray analysiswas used to identify a panel of candidate target genes for SL-4 acting on PLinducedulceration. Genes included some complement and coagulation cascadeand retinol metabolism pathways that are closely associated with inflammatoryresponses and gastric mucosal protective mechanisms. qRT-PCR showed thataltered expression of the selected genes, such as CYP2b2, UGT2b1, A2m, andMASP1 was consistent with the microarray results.CONCLUSIONSL-4 exerts protective effects against PL-induced gastroduodenal ulcers viareducing inflammatory cytokines and elevating expression of gastric acidinhibitory factors. Downregulation of CYP2b2 and UGT2b1 genes in retinolmetabolism and upregulation of A2m and MASP1 genes in the complement andcoagulation cascades pathways are possibly involved in SL-4-mediated protectionagainst gastroduodenal ulcer.

Gene modulation associated with inhibition of liver regeneration in hepatitis B virus X transgenic mice

AIM： To analyze the modulation of gene expression profile associated with inhibition of liver regeneration in hepatitis B X （HBx）-expressing transgenic mice. METHODS： Microarray technology was performed on liver tissue obtained from 4 control （LacZ） and 4 transgenic mice （HBx-LacZ）, 48 h after partial hepatectomy. The significance of the normalized logratios was assessed for each gene, using robust t-tests under an empirical Bayes approach. Microarray hybridization data was verified on selected genes by quantitative PCR. RESULTS： The comparison of gene expression patterns showed a consistent modulation of the expression of 26 genes, most of which are implicated in liver regeneration. Up-regulated genes included DNA repair proteins （Rad-52, MSH6） and transmembrane proteins （syndecan 4, tetraspanin）, while down-regulated genes were connected to the regulation of transcription （histone deacetylase, Zfp90, MyoDl） and were involved in the cholesterol metabolic pathway and isoprenoidbiosynthesis （farnesyl diphosphate synthase, Cyp7b1, geranylgeranyl diphosphate synthase, SAA3）. CONCLUSION： Our results provide a novel insight into the biological activities of HBx, implicated in the inhibition of liver regeneration,

Profiles of metabolic gene expression in the white adipose tissue, liver and hypothalamus in leptin knockout(Lep^(△I14/△I14)) rats

Leptin deficiency is principally linked to metabolic disorders. Leptin knockout（Lep△I14/△I14 Sprague Dawley rats created by CRISPR/Cas9 is a new model to study metabolic disorders. We used a whole rat genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of the white adipose tissue, liver and hypothalamus in Lep△I14/△I14）and wild-type（WT） rats. We found 1,651 differentially expressed（enriched） genes in white adipose tissue,916 in the liver, and 306 in the hypothalamus in the Lep△I14/△I14 rats compared to WT. Gene ontology category and KEGG pathway analysis of the relationships among differentially expressed genes showed that these genes were represented in a variety of functional categories, including fatty acid metabolism, molecular transducers and cellular processes. The reliability of the data obtained from microarray was verified by quantitative real-time PCR on 14 representative genes. These data will contribute to a greater understanding of different metabolic disorders, such as obesity and diabetes.

NF-κB and ERK-signaling pathways contribute to the gene expression induced by cag PAI-positive-Helicobacter pylori infection

AIM： To elucidate the sequential gene expression profile in AGS cells co-cultured with wild-type Helicobacter pylori （H pylon） as a model of Hpylori-infected gastric epithelium, and to further examine the contribution of cag-pathogenicity islands （cagPAI）-coding type IV secretion system and the two pathways, nuclear factor kappa B （NF-κB） and extracellular signal-regulated kinases （ERK） on wild-type Hpylori-induced gene expression. METHODS： Gene expression profiles induced by Hpylori were evaluated in AGS gastric epithelial cells using cDNA microarray, which were present in the 4600 independent clones picked up from the human gastric tissue. We also analyzed the contribution of NF-κB and ERK signaling on H pylori-induced gene expression by using inhibitors of specific signal pathways. The isogenic mutant with disrupted cagE （△cagE） was used to elucidate the role of cagPAI-encoding type IV secretion system in the gene expression profile. RESULTS： According to the expression profile, the genes were classified into four clusters. Among them, the clusters characterized by continuous upregulation were most conspicuous, and it contained many signal transducer activity-associated genes. The role of cagPAI on cultured cells was also investigated using isogenic mutant cagE, which carries non-functional cagPAI. Then the upregulation of more than 80% of the induced genes （476/566） was found to depend on cagPAI. Signal transducer pathway through NF-κB or ERK are the major pathways which are known to be activated by cagPAI-positive H pylori. The role of these pathways in the whole signal activation by cagPAI-positive H pyloriwas analyzed. The specific inhibitors against NF-κB or ERK pathway blocked the activation of gene expression in 65% （367/566） or 76% （429/566） of the genes whose activation appealed to depend on cagPAI. CONCLUSION： These results suggest that more than half of the genes induced by cayPAI-positive H pylori depend on NF-κB and ERK signaling activation, and these pathways may play a role in the gene expression induced by hostbacterial interaction which may associate with H pylorirelated gastro-duodenal diseases.

Genomics of hepatitis B virus-related hepatocellular carcinoma and adjacent noncancerous tissues with cDNA microarray

Background Hepatocellular carcinoma （HCC） is a common primary cancer frequently associated with hepatitis B virus （HBV） infection. However, whether these identified genes are particularly associated with HBV-related HCC remains unknown. The aim of this study was to investigate the differential gene expression between HBV-related HCC tissues and adjacent noncancerous tissues. Methods cDNA microarray was used to detect the differential gene expression profile in the HBV-related HCC tissues and adjacent noncancerous tissues, and reverse transcription-polymerase chain reaction （RT-PCR） was performed to verify the differential expression of candidate genes obtained from cDNA microarray experiment. Results In this study, 1369 genes or expressed sequence tags （ESTs） including 121 genes or ESTs with at least two-fold expression alterations between cancerous and noncancerous tissues were identified. Special AT-rich sequence binding protein 1 （SATB-1） expression was positive in 73% （16/22） of cancerous tissues and negative （0/22） in all noncancerous tissues of HBV-related HCC patients. Transmembrane 4 superfamily member 1 （TM4SF-1） expression was positive in 86% （19/22） of cancerous tissues and negative （0/22） in all noncancerous tissues. Suppression of tumorigenicity 14 （ST-14） expression was positive in 73% （16/22） of noncancerous tissues in patients with HBV-related HCC and negative in all HCC tissues （0/22）. Conclusion This study provided the gene expression profile of HBV-related HCC and presented differential expression patterns of SATB-1, TM4SF-1 and ST-14 between cancerous and noncancerous tissues in patients with HBV-related HCC.