OBJECTIVETo examine the micro-RNA (mirna) expression profile in tissues of early gastric cancer and to screen the specific mirna associated with gastric cancer.

METHODSGene chip technology was used to detect the expression of mirna in early gastric cancer tissues and adjacent normal tissues.

RESULTSCompared to adjacent normal tissues, a total of 36 mirnas were down-regulated, such as mir-9-1, mir-103 and mir-141, while 12 mirnas were up-regulated, such as mir-196a, mir-142-3p and mir-25, etc.

CONCLUSIONAbnormal mirna expression level in early gastric cancer tissues may be associated to the development of gastric cancer.

Down-Regulation ; Gene Expression Regulation, Neoplastic ; Humans ; MicroRNAs ; genetics ; Oligonucleotide Array Sequence Analysis ; Stomach Neoplasms ; genetics ; Up-Regulation

In order to understand the role of the upstream region of the Mycobacterium leprae 18-kDa gene on the gene regulation, the region was divided into two at the -50 position from the first start codon of the gene and their effect on transcription was examined by using a LacZ transcriptional reporter gene assay. The presence of each of these two regions conferred transcription repression not only on its cognate M. lepraerae 18-kDa gene promoter, but also on a heterologous promoter such as the Mycobacterium bovis BCG hsp65 gene promoter. Moreover, it was found that these regions could confer transcription repression activity in both cases in an orientation-independent manner. Thus, these results indicate that the upstream region of the M. leprae 18-kDa gene harbors transcription repression responsive element(s) acting as an operator and can be further divided into two separately functional regions, suggesting a bipartite structure of the element(s). The identification of transcription repression activity of the upstream region in the M. leprae 18-kDa gene will contribute greatly for the understanding of the 18-kDa gene regulation mechanism, and provide also useful information for the manipulation of mycobacterium gene expression.
Bacterial Proteins/*genetics ; Down-Regulation/*genetics ; *Gene Expression Regulation, Bacterial ; Mycobacterium leprae/*genetics ; Response Elements/*genetics ; Transcription, Genetic

OBJECTIVETo detect and analyze the characteristic miRNAs profile of anal fistula and explore their possible target genes and potential clinical significance.

METHODSThe anal mucosa close to the hemorrhoids were collected from three patients undergoing fistulectomy and hemorrhoidectomy (fistula group) as well as three patients receiving only hemorroidectomy(hemorrhoids group), matching with fistula group in age, gender and body weight. miRNA microarray was used to compare the expression of 1 285 human miRNAs of the anal mucosa between two groups. Cluster analysis was adopted to analyze the accumulation of the differentially expressed miRNAs(P<0.05, fold≥2.0 or ≤0.5) and their target genes were predicted with 10 softwares such as DIANAmT, miRanda, miRDB, miRWalk etc. Comprehensive scoring was performed to identify genes with highest predictive score. Gene ontology (GO) concentration technique was used to analyze the target gene-associated biological process. Immunohistochemistry was used to examine protein expression of genes with the highest score.

RESULTSAmong 1285 miRNAs in fistula group, 13 miRNAs were differentially expressed with those in hemorrhoid group, including 2 of up-regulation and 11 of down-regulation. Paired t test showed that in fistula group, miRNA-3609 up-regulation was 5.98 folds(P=0.0231) and miR-181a-2-3p down-regulation was 0.13 folds(P=0.0067) compared to those in hemorrhoid group, which had the greatest differential expression. Cluster analysis suggested that up-regulated miR-3609 and miR-6086 had similar change trend in both groups. Among 11 down-regulated miRNAs, miR-125bp-1-3p and miR-548q had similar expression and other 9 miRNAs had similar expression as well, including miR-1185-1-3p, miR-532-3p, miR-1233-5p, miR-769-5p, miR-149-5p, miR-99b-3p, miR-141-3p, miR-138-5p, and miR-181a-2-3p. Target gene prediction analysis of above 13 genes showed that 7 miRNAs(53.8%) were eligible to predict their potential target genes, yielding totally 104 possible target genes. The rest of 6 miRNAs(46.2%) failed to predict any target gene. The highest score in prediction of target gene was chitinase 1(ChIT1) and its corresponding differential miRNA was miR-769-5p(r=-0.94286, P=0.0167). Gene ontology analysis showed that the most associated biological process related with these 104 target genes was keratinization, immune response and signal transduction. Immunohistochemistry revealed ChiT1 expression of anal mucosa in fistula group was significantly higher compared to hemorrhoid group(P<0.01).

CONCLUSIONSThere is a characteristic miRNAs profile in anal fistula patients, which may play a role in the occurrence and development of anal fistula.

Cluster Analysis ; Down-Regulation ; Humans ; MicroRNAs ; Rectal Fistula ; genetics ; Signal Transduction ; Up-Regulation

OBJECTIVE: To isolate the collagen phagocytic subpopulation of fibroblast (CPSF) and non-collagen phagocytic subpopulation of fibroblast (nCPSF) and to identify their differentially expressed genes.
 METHODS: The CPSF and nCPSF was isolated by using collagen-fluorescein-isothiocynate-latex bead (COL-FITC-LB) phagocytosis technique and FCM sorting method. Microarray analysis was used to screen the differentially expressed genes, which were verified by real-time PCR. 
 RESULTS: CPSF and nCPSF was successfully isolated. Seventeen differentially expressed genes were identified. Compared with nCPSF, the expression of 12 or 5 genes was up-regulated or down-regulated in CPSF. Three of the 12 up-regulated genes were urokinase plasminogen activator receptor-associated protein (uPARAP), cytochrome b-245, beta polypeptide (CYBB) and Hook homolog 1 (HOOK1), which were confirmed by real-time PCR. uPARAP mRNA expression level in CPSF was 2788 times of that in nCPSF. CYBB mRNA expression in CPSF was only 0.85 times of that in nCPSF. HOOK1 mRNA expression in CPSF was 1.96 times of that in nCPSF (P<0.05). 
 CONCLUSION A novel method is successfully established to isolate CPSF and nCPSF. uPARAP is the main differentially expressed gene in CPSF and nCPSF, which is obviously involved in the fibroblast collagen phagocytosis. It might be a potential biomarker for treatment of collagen diseases.
Collagen ; genetics ; Down-Regulation ; Fibroblasts ; cytology ; Humans ; Microarray Analysis ; Phagocytosis ; Up-Regulation

OBJECTIVE: Circular RNAs (circRNAs) participate in several important pathological processes and have been used in the diagnosis and treatment of various diseases. This study aimed to investigate the role of circRNAs in neural tube defects (NTDs). METHOD: We characterized circRNA-associated competitive endogenous RNA (ceRNA) networks in brain tissue of low folate -induced NTDs mouse at embryonic day 13.5 by high-throughput sequencing. The expression levels of Circzfp644, miR-20-5p and Gas7 were detected by RT-PCR. Gas7 and Circzfp644 functions were determined by miRNA-mimics and inhibitors in mouse teratocarcinoma cells (F9 cells), and luciferase gene reporter assay was assessed in the F9 cells. In addition, the expression levels of Circzfp644, miR-20-5p and Gas7 were determined by Nanostring in human NTDs tissues. RESULTS: We detected 57 circRNA transcripts, 16 miRNAs, and 148 mRNAs that were significantly dysregulated in NTDs brain tissues compared with their expression levels in control (normal) tissues. Circzfp644 shared miRNA response elements with the growth arrest specific 7 ( Gas7) gene and competitively bound with miR-20-5p to increase the expression of Gas7. Downregulation of Circzfp644 and Gas7 and upregulation of miR-20-5p were found in human NTD tissue. CONCLUSION This study provides new perspectives on the role of circRNAs in nervous system development and the pathogenesis of NTDs.
Humans ; Animals ; Mice ; RNA, Circular/genetics* ; MicroRNAs/metabolism* ; Down-Regulation ; Neural Tube Defects/genetics* ; Folic Acid

OBJECTIVE: To study the effect of down-regulating miR-488 targeting Jag1 on the injury of hypoxia-reoxygenation myocardial H9c2 cells. METHODS: A hypoxic-reoxygenated myocardial H9c2 cell injury model was constructed. miR-488 inhibitor was used to transfect the cells. CCK-8 method and flow cytometry were used to detect cell proliferation and apoptosis in each group. Lactate dehydrogenase (LDH), superoxide dismutase (SOD), malonaldehyde (MDA), catalase (CAT) levels were detected. Western blotting was used to detect the expression of Bcl-2 associated X Protein (Bax) and B cell lymphoma/lewkmia-2 (Bcl-2). Target genes of miR-488 were predicted, and a luciferase reporter system was used to verify the targeting relationship between the two. Myocardial H9c2 cells were co-transfected with miR-488 inhibitor and Jag1 siRNA, and treated with hypoxia and reoxygenation, cell proliferation, apoptosis, LDH, SOD, MDA, CAT levels, and Bax, Bcl-2 protein expression were detected. RESULTS: The expression of miR-488 in the hypoxia-reoxygenated myocardial H9c2 cells was increased, along with reduced cell proliferation, increased apoptosis, increased Bax protein expression, decreased Bcl-2 protein expression, increased MDA, decreased CAT and SOD, and increased LDH level in the supernatant of cell culture. When myocardial H9c2 cells were transfected with miR-488 inhibitor and treated with hypoxia and reoxygenation, the expression of miR-488 was decreased, along with increased cell proliferation, decreased apoptosis, decreased Bax protein expression, increased Bcl-2 protein expression, decreased MDA, increased CAT and SOD, and decreased LDH level in the supernatant of cell culture. Down-regulation of miR-488 could target and down-regulate Jag1 expression. And Jag1 siRNA could reverse the effect of miR-488 inhibitor on the proliferation, apoptosis, LDH, SOD, MDA, CAT levels and the expression of Bax and Bcl-2 of hypoxic-reoxygenated myocardial H9c2 cells. CONCLUSION Down-regulating miR-488 targeted Jag1 can attenuate hypoxia-reoxygenation induced myocardial H9c2 cell injury.
Apoptosis/genetics* ; Down-Regulation ; Humans ; Hypoxia/genetics* ; Jagged-1 Protein/genetics* ; MicroRNAs/genetics* ; Myocardial Reperfusion Injury ; Myocytes, Cardiac

OBJECTIVETo investigate the relationship between UNC5b gene expression and angiogenesis of hepatocellular carcinoma (HCC).

METHODSIn situ hybridization was performed to detect the expression of UNC5b mRNA in HCC samples, paracarcinomatous liver tissues samples and normal liver samples. The relationship between UNC5b mRNA expression and the HCC clinicopathological features were also analyzed. Human umbilical artery endothelial cells were isolated and stimulated with HCC tissues homogenate, vascular endothelial growth factor and basic fibroblast growth factor. Then RT-PCR was employed to detect the expression of UNC5b mRNA in normal HUAEC as well as activated HUAEC.

RESULTSIn situ hybridization results showed that UNC5b mRNA expression was detected majorly in endothelial cells of all normal liver tissues, and partial PCLTs but was weak or even undetectable in endothelial cells of the corresponding HCC tissues. The expression levels of UNC5b gene in PCLTs were significantly correlated with capsular formation of HCC. Furthermore, RT-PCR results showed that the expression levels of UNC5b mRNA in activated HUAEC were significantly higher than those in normal HUAEC.

CONCLUSIONSDown-regulation of UNC5b gene expression is related to angiogenesis of HCC, which may be associated with the progression of HCC.

Carcinoma, Hepatocellular ; blood supply ; genetics ; Down-Regulation ; Gene Expression Regulation, Neoplastic ; Humans ; Liver Neoplasms ; blood supply ; genetics ; Neovascularization, Pathologic ; genetics ; RNA, Messenger ; genetics ; Receptors, Cell Surface ; genetics

Although heterologous biosynthesis of polyketide erythromycin has been successfully achieved in Escherichia coli, the titer remains at a very low level (-10 mg/L). In this study, based on genome-scale metabolic model of E. coli, in silico method flux distribution comparison analysis was used to discover novel potential targets for heterologous 6-dEB biosynthesis. Synthetic small regulatory RNAs (sRNAs) was used to experimentally test 12 down-regulated targets. The results showed that repression of each of these target genes e.g. lsrC and ackA led to significantly improve heterologous 6-dEB biosynthesis. Using co-repression of lsrC and ackA, 6-dEB titer was improved by 59.9% in shake-flask with a maximum yield of 22.8 mg/L. This study indicates that combined flux distribution comparison analysis and synthetic small regulatory RNAs is an effective strategy to improve 6-dEB production in E. coli.
Down-Regulation ; Erythromycin ; biosynthesis ; Escherichia coli ; genetics ; metabolism ; Industrial Microbiology ; methods ; RNA

BACKGROUNDBrain hypoplasia and mental retardation in Down syndrome (DS) can be attributed to a severe and selective disruption of neurogenesis. Secondary disruption of the transcriptome, as well as primary gene dosage imbalance, is responsible for the phenotype. MicroRNA (miRNA) expression is relatively abundant in brain tissue. Perturbed miRNA expression might contribute to the cellular events underlying the pathology in DS.

METHODSMiRNA expression profiles in the cerebrum of Ts65Dn mice, a DS model, were examined with a real-time RT-PCR array. MiRNA target gene expression was detected by real-time quantitative PCR and Western blotting. Based on the prediction of their cerebrum-specific targets, the functions of the misregulated miRNAs were annotated by Gene Ontology (GO) enrichment analysis.

RESULTSA total of 342 miRNAs were examined. Among them, 20 miRNAs showed decreased expression in the brains of Ts65Dn mice, and some of these belonged to the same family. Two known targets of the miR-200 family, Lfng and Zeb2, were specifically selected to compare their expression in the cerebrum of Ts65Dn mice with those of euploids. However, no significant difference was found in terms of mRNA and protein expression levels of these genes. By enrichment analysis of the cerebrum-specific targets of each miRNA, we found that 15 of the differential miRNAs could significantly affect target genes that were enriched in the GO biological processes related to nervous system development.

CONCLUSIONPerturbed expression of multiple functionally cooperative miRNAs contributes to the cellular events underlying the pathogenesis of DS.

Animals ; Brain ; metabolism ; Disease Models, Animal ; Down Syndrome ; etiology ; genetics ; Gene Expression Regulation ; Mice ; MicroRNAs ; physiology

OBJECTIVETo identify methylation profiles in myelodysplastic syndrome (MDS) and to provide the biomarkers for the early diagnosis and differential diagnosis of MDS.

METHODSGenes were screened for hypermethylation by genome-wide DNA methylation profiles. Transcription down-regulation was determined with a gene expression microarray. Methylation-specific, real-time, and bisulfite-sequencing PCR cloning and sequencing were performed to validate selected genes in MDS cases and non-malignant hematologic diseases (controls). Diagnostic test, such as sensitivity and specificity, was used to evaluate the value of methylation patterns.

RESULTSA draft of methylation patterns was established and refined to 6 genes after validation in 211 patients and 60 controls. The hypermethylated genes were ABAT (97%), DAPP1 (98%), FADD (89%), LRRFIP1 (96%), PLBD1 (89%), and SMPD3 (85%). A combination of 5 or more than 5 genes showed a specificity of 95% and sensitivity of 91.4% for the diagnosis of MDS. The accuracy of diagnosis was 92.3%.

CONCLUSIONWe demonstrated here that the ABAT, DAPP1, FADD, LRRFIP1, PLBD1 and SMPD3 genes are hypermethylated and downregulated in MDS. The six genes could be the markers of the methylation patterns in MDS, as a noninvasive approach for the diagnosis of MDS.

DNA Methylation ; Down-Regulation ; Gene Expression ; Genome, Human ; Humans ; Myelodysplastic Syndromes ; diagnosis ; genetics