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 resul...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.展开更多
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 emo...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.展开更多
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.Epithelia...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.展开更多
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 spe...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.展开更多
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 detaile...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.展开更多
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 ...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.展开更多
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 ...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.展开更多
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 l...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.展开更多
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 ...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.展开更多
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 ...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.展开更多
OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal inst...OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal instillation of ovalbumin in mouse.After administration of SCRT on asthma-induced mouse,the expression of genes in lung tissue was measured using whole genome microarray.The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed.RESULTS:Treatment of SCRT restored expression level of many up- or down-regulated genes in asthma model,and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites.CONCLUSION:In this study,we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.展开更多
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 mJcroa...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.展开更多
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 id...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.展开更多
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...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.展开更多
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...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.展开更多
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 ...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.展开更多
Because of their physiological similarity to humans, pigs provide an excellent model for the study of obesity. This study evaluated diet-induced adiposity in genetically lean pigs and found that body weight and energy...Because of their physiological similarity to humans, pigs provide an excellent model for the study of obesity. This study evaluated diet-induced adiposity in genetically lean pigs and found that body weight and energy intake did not differ between controls and pigs fed the high-fat （HF） diet for three months. However, fat mass percentage, adi- pocyte size, concentrations of total cholesterol （TC）, triglyceride （TG）, high-density lipoprotein cholesterol （HDL-C） and low-density lipoprotein cholesterol （LDL-C）, insulin, and leptin in plasma were significantly higher in HF pigs than in controls. The HF diet increased the expression in backfat tissue of genes responsible for cholesterol synthesis such as Insig-1 and Insig-2. Lipid metabolism-related genes including sterol regulatory element binding protein lc （SREBP-lc）, fatty acid synthase 1 （FASN1）, diacylglycerol O-acyltransferase 2 （DGAT2）, and fatty acid binding protein 4 （FABP4） were significantly up-regulated in backfat tissue, while the expression of proliferator-activated receptor-α（PPAR-α） and carnitine palmitoyl transferase 2 （CPT2）, both involved in fatty acid oxidation, was reduced. In liver tissue, HF feeding significantly elevated the expression of SREBP-lc, FASN1, DGAT2, and hepatocyte nuclear factor-4α （HNF-4α） mRNAs. Microarray analysis further showed that the HF diet had a significant effect on the expression of 576 genes. Among these, 108 genes were related to 21 pathways, with 20 genes involved in adiposity deposition and 26 related to immune response. Our results suggest that an HF diet can induce genetically lean pigs into obesity with body fat mass expansion and adipose-related inflammation.展开更多
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 character...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.展开更多
Recurrent genomic imbalances at 16p 11.2 are genetic risk factors of variable penetrance for developmental delay and autism.Recently, 16pl 1.2（chr16：29.5 Mb-30.1 Mb） deletion has also been detected in individuals w...Recurrent genomic imbalances at 16p 11.2 are genetic risk factors of variable penetrance for developmental delay and autism.Recently, 16pl 1.2（chr16：29.5 Mb-30.1 Mb） deletion has also been detected in individuals with early-onset severe obesity.The penetrance of 16p11.2 deletion as a genetic risk factor for obesity is unknown.We evaluated the growth and body mass characteristics of 28 individuals with 16p11.2 （chr16：29.5 Mb-30.1 Mb） deletion originally ascertained for their developmental disorders by reviewing their medical records.We found that nine individuals could be classified as obese and six as overweight.These individuals generally had early feeding and growth difficulties,and started to gain excessive weight around 5-6 years of age.Thirteen out of the 18 deletion carriers aged 5 years and older（72%） were overweight or obese,whereas only two of 10 deletion carriers（20%） younger than five were overweight or obese.Males exhibited more severe obesity than females.Thus,the obesity phenotype of 16p11.2 deletion carriers is of juvenile onset,exhibited an age- and gender-dependent penetrance. 16p11.2 deletion appears to predispose individuals to juvenile onset obesity and in this case are similar to the well-described Prader-Willi syndrome（PWS）.Early detection of this deletion will provide opportunity to prevent obesity.展开更多
Tetrabromobisphenol A（TBBPA） and its derivatives are now being highly concerned due to their emerging environmental occurrence and deleterious effects on non-target organisms.Considering the potential neurotoxicity ...Tetrabromobisphenol A（TBBPA） and its derivatives are now being highly concerned due to their emerging environmental occurrence and deleterious effects on non-target organisms.Considering the potential neurotoxicity of TBBPA derivatives which has been demonstrated in vitro, what could happen in vivo is worthy of being studied. Tetrabromobisphenol A bis（2-hydroxyethyl ether）（TBBPA-BHEE）, a representative TBBPA derivative, was selected for a21-day exposure experiment on neonatal Sprague Dawley（SD） rats through intranasal administration. The neurobehavioral, histopathological changes, and differentially expressed genes based on RNA microarray were investigated to evaluate the neurological effects of this chemical. The results indicated that TBBPA-BHEE exposure significantly compromised the motor co-ordination performance and the locomotor activities（p 〈 0.05）. The neurobehavioral phenotype could be attributed to the obvious histopathological changes in both cerebrum and cerebellum, such as neural cell swelling, microglial activation and proliferation. A total of 911 genes were up-regulated, whereas 433 genes were down-regulated. Gene set enrichment analysis showed multiple signaling pathways, including ubiquitin-mediated proteolysis and wingless-int（Wnt） signaling pathway etc. were involved due to TBBPA-BHEE exposure. The gene ontology enrichment analysis showed the basic cellular function and the neurological processes like synaptic transmission were influenced. The toxicological effects of TBBPA-BHEE observed in this study suggested the potential neuronal threaten from unintended exposure,which would be of great value in the biosafety evaluation of TBBPA derivatives.展开更多
基金supported by grants from the National Natural Science Foundation of China (81761128035 and 81781220701)the Shanghai Municipal Science and Technology Committee (17XD1403200 and 18dz2313505)+2 种基金the Research Physician Project of Shanghai Municipal Education Commission (20152234)the Shanghai Municipal Health and Family Planning Commission (GDEK201709, 2017ZZ02026, and 2017EKHWYX02)the Scientific Program of Shanghai Shenkang Hospital Development Center (16CR2025B) of China
文摘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.
基金supported by the National Natural Science Foundation of China(81371213,81070987,and30971531)the grants from the Ministry of Science and Technology of China(2010CB945600 and 2010CB945601)
文摘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.
基金supported by grants from the National Science Foundation of China (No.30801340No.30901586No.30770913)
文摘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.
基金Supported by a MeDDrive grant From the University of Dresden 2003by a grant from the Dr. Mildred Scheel Stiftung No. 70-2923
文摘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.
基金supported by grants from the Natural Science Foundation of Guangdong Province(No. 2016A030313796/2017B030311010)
文摘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.
基金Project supported by the National Natural Science Foundation of China (No 30771918)the National Basic Research Program (973) of China (No 2007CB512905)the State S & T Projects (11th Five Year) (No 2008ZX10002-007) of China
文摘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.
文摘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.
基金This study was supported by the grants from the Health Department Foundation of Heilongjiang Province （No. 2007-413） and the Natural Science Foundation of Heilongjiang Province （No. D200633）.
文摘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.
基金grants from the National Natural Science Foundation of China
文摘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.
基金This work was supported by the High Technology Project(Grant No.2001AA223011)the State Key Basic Research Program(Grant No.G1999054105).
文摘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.
文摘OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal instillation of ovalbumin in mouse.After administration of SCRT on asthma-induced mouse,the expression of genes in lung tissue was measured using whole genome microarray.The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed.RESULTS:Treatment of SCRT restored expression level of many up- or down-regulated genes in asthma model,and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites.CONCLUSION:In this study,we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.
基金supported by a grant from the National Natural Science Foundation of China(Grant No.61373057)a grant from the Zhejiang Provincial Natural Science Foundation of China(Grant No.Y1110763)
文摘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.
基金the National Natural Science Foundation of China （Grant No. 30470172）.
文摘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.
基金Supported by the National Natural Science Foundation of China,No.30971626 and No.81473512
文摘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.
基金a grant from the National Natural Sciences Foundation of China (No. 50477043)
文摘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.
文摘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.
基金Project supported by the National Key Research and Development Program of China(Nos.2018YFD0500400 and 2018YFD0501100)the National Basic Research Program(973)of China(No.2013CB127304)+1 种基金the China Agriculture Research System(No.CARS-36)and the National Natural Science Foundation of China(No.31402086)
文摘Because of their physiological similarity to humans, pigs provide an excellent model for the study of obesity. This study evaluated diet-induced adiposity in genetically lean pigs and found that body weight and energy intake did not differ between controls and pigs fed the high-fat （HF） diet for three months. However, fat mass percentage, adi- pocyte size, concentrations of total cholesterol （TC）, triglyceride （TG）, high-density lipoprotein cholesterol （HDL-C） and low-density lipoprotein cholesterol （LDL-C）, insulin, and leptin in plasma were significantly higher in HF pigs than in controls. The HF diet increased the expression in backfat tissue of genes responsible for cholesterol synthesis such as Insig-1 and Insig-2. Lipid metabolism-related genes including sterol regulatory element binding protein lc （SREBP-lc）, fatty acid synthase 1 （FASN1）, diacylglycerol O-acyltransferase 2 （DGAT2）, and fatty acid binding protein 4 （FABP4） were significantly up-regulated in backfat tissue, while the expression of proliferator-activated receptor-α（PPAR-α） and carnitine palmitoyl transferase 2 （CPT2）, both involved in fatty acid oxidation, was reduced. In liver tissue, HF feeding significantly elevated the expression of SREBP-lc, FASN1, DGAT2, and hepatocyte nuclear factor-4α （HNF-4α） mRNAs. Microarray analysis further showed that the HF diet had a significant effect on the expression of 576 genes. Among these, 108 genes were related to 21 pathways, with 20 genes involved in adiposity deposition and 26 related to immune response. Our results suggest that an HF diet can induce genetically lean pigs into obesity with body fat mass expansion and adipose-related inflammation.
基金Mongolian Medicine Food and Drug Source Protection and Utilization Innovation Team Construction Project,No.190301National Natural Science Foundation of China,No.81760765+2 种基金Inner Mongolia University for Nationalities Doctoral Start-up Grant,No.BS412 and No.BS413Mongolian Medicine Engineering Technology Research Centre Open Fund Project,No.MDK2017072Inner Mongolia Autonomous Region Talent Development Fund Project,No.RC201802.
文摘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.
基金the Chinese National Natural Science Foundation(No.8 1000346,Y.G.Y.)foundation grant from the Center for Clinical Nutrition Study(SCMC-YP-HOPE-KY-0905 for Y.G.Y)+5 种基金Health Science grant from the social development branch of Pudong New District(PW2009D-9 for Y.G.Y)the Simons Foundation(J.F.G.)Autism Speaks(J.F.G.)Developmental Genome Anatomy Project(P01 GM061354)Chinese National"973"Project on Population and Health(No.2010CB529601,B.-L.W.)Science and Technology Council of Shanghai(No.09JC1402400(B.-L.W.)
文摘Recurrent genomic imbalances at 16p 11.2 are genetic risk factors of variable penetrance for developmental delay and autism.Recently, 16pl 1.2（chr16：29.5 Mb-30.1 Mb） deletion has also been detected in individuals with early-onset severe obesity.The penetrance of 16p11.2 deletion as a genetic risk factor for obesity is unknown.We evaluated the growth and body mass characteristics of 28 individuals with 16p11.2 （chr16：29.5 Mb-30.1 Mb） deletion originally ascertained for their developmental disorders by reviewing their medical records.We found that nine individuals could be classified as obese and six as overweight.These individuals generally had early feeding and growth difficulties,and started to gain excessive weight around 5-6 years of age.Thirteen out of the 18 deletion carriers aged 5 years and older（72%） were overweight or obese,whereas only two of 10 deletion carriers（20%） younger than five were overweight or obese.Males exhibited more severe obesity than females.Thus,the obesity phenotype of 16p11.2 deletion carriers is of juvenile onset,exhibited an age- and gender-dependent penetrance. 16p11.2 deletion appears to predispose individuals to juvenile onset obesity and in this case are similar to the well-described Prader-Willi syndrome（PWS）.Early detection of this deletion will provide opportunity to prevent obesity.
基金supported by the Major International (Regional) Joint Project (No. 21461142001)the National Basic Research Program of China (No. 2015CB453102)+2 种基金the National Natural Science Foundation of China (Nos. 21621064, 21477153)the Strategic Priority Research Program of the Chinese Academy of Science (No. 14040302)the Chinese Academy of Sciences (No. QYZDJ-SSW-DQC017)
文摘Tetrabromobisphenol A（TBBPA） and its derivatives are now being highly concerned due to their emerging environmental occurrence and deleterious effects on non-target organisms.Considering the potential neurotoxicity of TBBPA derivatives which has been demonstrated in vitro, what could happen in vivo is worthy of being studied. Tetrabromobisphenol A bis（2-hydroxyethyl ether）（TBBPA-BHEE）, a representative TBBPA derivative, was selected for a21-day exposure experiment on neonatal Sprague Dawley（SD） rats through intranasal administration. The neurobehavioral, histopathological changes, and differentially expressed genes based on RNA microarray were investigated to evaluate the neurological effects of this chemical. The results indicated that TBBPA-BHEE exposure significantly compromised the motor co-ordination performance and the locomotor activities（p 〈 0.05）. The neurobehavioral phenotype could be attributed to the obvious histopathological changes in both cerebrum and cerebellum, such as neural cell swelling, microglial activation and proliferation. A total of 911 genes were up-regulated, whereas 433 genes were down-regulated. Gene set enrichment analysis showed multiple signaling pathways, including ubiquitin-mediated proteolysis and wingless-int（Wnt） signaling pathway etc. were involved due to TBBPA-BHEE exposure. The gene ontology enrichment analysis showed the basic cellular function and the neurological processes like synaptic transmission were influenced. The toxicological effects of TBBPA-BHEE observed in this study suggested the potential neuronal threaten from unintended exposure,which would be of great value in the biosafety evaluation of TBBPA derivatives.
