Genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells in patients with systemic sclerosis with interstitial lung disease / 中南大学学报(医学版)

OBJECTIVES@#This study aims to investigate the genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with systemic sclerosis (SSc) with interstitial lung disease (ILD), and to analyze the effects of DNA methylation on Wnt/β-catenin and chemokine signaling pathways.@*METHODS@#PBMCs were collected from 19 patients with SSc (SSc group) and 18 healthy persons (control group). Among SSc patients, there were 10 patients with ILD (SSc with ILD subgroup) and 9 patients without ILD (SSc without ILD subgroup). The genome-wide DNA methylation and gene expression level were analyzed by using Illumina 450K methylation chip and Illumina HT-12 v4.0 gene expression profiling chip. The effect of DNA methylation on Wnt/β-catenin and chemokine signal pathways was investigated.@*RESULTS@#Genome-wide DNA methylation analysis identified 71 hypermethylated CpG sites and 98 hypomethylated CpG sites in the SSc with ILD subgroup compared with the SSc without ILD subgroup. Transcriptome analysis distinguished 164 upregulated genes and 191 downregulated genes in the SSc with ILD subgroup as compared with the SSc without ILD subgroup. In PBMCs of the SSc group, 35 genes in Wnt/β-catenin signaling pathway were hypomethylated, while frizzled-1 (FZD1), mitogen-activated protein kinase 9 (MAPK9), mothers against DPP homolog 2 (SMAD2), transcription factor 7-like 2 (TCF7L2), and wingless-type MMTV integration site family, member 5B (WNT5B) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of dickkopf homolog 2 (DKK2), FZD1, MAPK9 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05). In PBMCs of the SSc group, 38 genes in chemokine signaling pathway were hypomethylated, while β-arrestin 1 (ARRB1), C-X-C motif chemokine ligand 10 (CXCL10), C-X-C motif chemokine ligand 16 (CXCL16), FGR, and neutrophil cytosolic factor 1C (NCF1C) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of ARRB1, CXCL10, CXCL16 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05).@*CONCLUSIONS@#There are differences in DNA methylation and transcriptome profiles between SSc with ILD and SSc without ILD. The expression levels of multiple genes in Wnt/β- catenin and chemokine signaling pathways are upregulated, which might be associatea with the pathogenesis of SSc.

Identification of heat shock protein hsp70 family genes from Rana amurensis and its expression profiles upon infection / 生物工程学报

Heat shock proteins (HSPs) widely exist in all organisms, the structures of which are usually extraordinarily conservative. They are also well-known stress proteins that are involved in response to physical, chemical and biological stresses. HSP70 is an important member of the HSPs family. In order to study the roles of amphibians HSP70 during infection, the cDNA sequence of Rana amurensis hsp70 family genes were cloned by homologous cloning method. The sequence characteristics, three-dimensional structure and genetic relationship of Ra-hsp70s were analyzed by bioinformatics methods. The expression profiles under bacterial infection were also analyzed by real-time quantitative PCR (qRT-PCR). Expression and localization of HSP70 protein were tested by immunohistochemical techniques. The results showed that three conservative tag sequences of HSP70 family, HSPA5, HSPA8 and HSPA13, were found in HSP70. Phylogenetic tree analysis indicated four members are distributed in four different branches, and members with the same subcellular localization motif are distributed in the same branch. The relative expression levels of the mRNA of four members were all significantly upregulated (P < 0.01) upon infection, but the time for up-regulating the expression levels were diverse in different tissues. The immunohistochemical analysis showed that HSP70 was expressed to different degrees in the cytoplasm of liver, kidney, skin and stomach tissue. The four members of Ra-hsp70 family have ability to respond bacterial infection to varying degrees. Therefore, it was proposed that they are involved in biological processes against pathogen and play different biological functions. The study provides a theoretical basis for functional studies of HSP70 gene in amphibians.

Transcriptome-wide Identification and Expression Profiles of WRKY Transcription Factor in Prunella vulgaris / 中国实验方剂学杂志

Objective:To identify WRKY genes from the transcriptome dataset of Prunella vulgaris by bioinformatics method, and analyze the protein characteristics and expression level of these genes. Method:WRKY transcription factor were identified from the P. vulgaris transcriptome database，their motif，physical and chemical properties，functional annotations，family evolution and expression patterns were analyzed, and their functions were predicted. Result:A total of 23 WRKY transcription factors were identified from P. vulgaris in this study by computational prediction method.Structural analysis found that WRKY proteins contained a highly conserved motif WRKYGQK. Phylogenetic analysis of WRKYs together with the homologous genes from Arabidopsis thaliana could be divided into two groups（group Ⅰ-Ⅱ）. There were 7 members in group Ⅰ，and 16 members in group Ⅱ, group Ⅱ was subdivided into five subgroups，namely group Ⅱb （3 members），Ⅱc（5 members），Ⅱd（3 members），Ⅱe（5 members）. The physical and chemical properties of WRKY protein showed that the amino acid number was between 85 and 599，the molecular weight was between 9 527.5-66 438.45 Da，the theoretical isoelectric point was between 5.01-9.83.Among them, c13719.graph_c0，c32199.graph_c0，c24547.graph_c0，c37881.graph_c0 may play a role in the regulation of secondary metabolitessynthesis of P. vulgaris.And c32199.graph_c0，c26537.graph_c0，c23728.graph_c0 may has an effect in identifying and defensing pathogens in P. vulgaris.The transcriptional profiles of these 23 WRKY genes in various tissues were investigated using transcriptome dataset.The results showed that the expression level of WRKY genes varied significantly in different tissues. Conclusion:This study identifies the organization and transcriptional profiles of PmWRKY genes for the first time, so as to provide the helpful information for further studies of functions of WRKYs.

Emodin regulates microRNA expressions of ileum in sepsis mice model / 中华急诊医学杂志

Objective@#To investigate the regulation of emodin on microRNA expressions in mouse model with sepsis by GeneChip microRNA array.@*Methods@#Forty two c57 mice were randomly (random number) divided into 3 groups: sham operation group (sham group, n=14),sepsis group(n=14) and emodin group (n=14). The sepsis model of the mouse was subjected to cecal ligation and puncture (CLP). Mice in emodin group received intraperitoneal injection of emodin (40 mg/kg) half an hour before operation and every 12 hours after CLP. All mice were sacrificed 48 h after surgery and part of the ileum were removed for intestine tissue stained with hematoxylin eosin. The levels of tumor necrosis factor-α(TNF-α), interleukin-6 (IL-6) and intestinal fatty acid binding protein (I-FABP) in peripheral blood were measured by enzyme-linked immunosorbent assay (ELISA). Total RNA of ileum tissues was extracted from the sepsis group and emodin group, and then subjected to miRNA microarray. The results of microarray were further verified by quantitative real-time PCR (qRT-PCR). Target genes of differentially expressed miRNAs were predicted and subjected to gene ontology (GO) and KEGG pathway enrichment analysis. Data of multi-groups were analyzed by one way variance (ANOVA) and inter-group comparisons were made by SNK-q tests. Mann-Whitney U test was used when homogeneity of variance were not met. The value of P<0.05 was considered statistically significant.@*Results@#Compared to the sepsis group, the levels of serum TNF-α, IL-6 and I-FABP in the emodin group were decreased significantly. MiRNA microarray showed that 23 miRNAs were differentially expressed in the emodin group as compared to the sepsis group, among which 17 miRNAs were up-regulated and 6 miRNAs were down-regulated. qRT-PCR results were consistent with miRNA array data. Target genes of 10 selected miRNAs were predicted and subjected to bioinformatic analysis. A total of 3 410 target genes were significantly enriched in 2 072 GO biological process terms, 246 GO cellular component items and 277 GO molecular function terms. Moreover, KEGG pathway analysis showed that these differential miRNAs were involved in the regulation of PI3K-Akt signaling pathway, MAPK signaling pathway, and TNF signaling pathway.@*Conclusions@#Emodin can regulate the expression of multiple microRNAs, and play an important role in protecting the intestinal mucosal barrier via a variety of targets and pathways.

Emodin regulates microRNA expressions of ileum in sepsis mice model / 中华急诊医学杂志

Objective To investigate the regulation of emodin on microRNA expressions in mouse model with sepsis by GeneChip microRNA array.Methods Forty two c57 mice were randomly (random number) divided into 3 groups:sham operation group (sham group,n=14),sepsis group(n=14) and emodin group (n=14).The sepsis model of the mouse was subjected to cecal ligation and puncture (CLP).Mice in emodin group received intraperitoneal injection of emodin (40 mg/kg) half an hour before operation and every 12 hours after CLP.All mice were sacrificed 48 h after surgery and part of the ileum were removed for intestine tissue stained with hematoxylin eosin.The levels of tumor necrosis factor-α (TNF-α),interleukin-6 (IL-6) and intestinal fatty acid binding protein (I-FABP) in peripheral blood were measured by enzyme-linked immunosorbent assay (ELISA).Total RNA of ileum tissues was extracted from the sepsis group and emodin group,and thensubjected to miRNA microarray.The results of microarray were further verified by quantitative real-time PCR (qRT-PCR).Target genes of differentially expressed miRNAs were predicted and subjected to gene ontology (GO) and KEGG pathway enrichment analysis.Data of multi-groups were analyzed by one way variance (ANOVA) and inter-group comparisons were made by SNK-q tests.Mann-Whitney U test was used when homogeneity of variance were not met.The value of P＜0.05 was considered statistically significant.Results Compared to the sepsis group,the levels of serum TNF-α,IL-6 and I-FABP in the emodin group were decreased significantly.MiRNA microarray showed that 23 miRNAs were differentially expressed in the emodin group as compared to the sepsis group,among which 17 miRNAs were up-regulated and 6 miRNAs were down-regulated.qRT-PCR results were consistent with miRNA array data.Target genes of 10 selected miRNAs were predicted and subjected to bioinformatic analysis.A total of 3 410 target genes were significantly enriched in 2 072 GO biological process terms,246 GO cellular component items and 277 GO molecular function terms.Moreover,KEGG pathway analysis showed that these differential miRNAs were involved in the regulation of PI3K-Akt signaling pathway,MAPK signaling pathway,and TNF signaling pathway.Conclusions Emodin can regulate the expression of multiple microRNAs,and play an important role in protecting the intestinal mucosal barrier via a variety of targets and pathways.

Altered expression profile and function of microRNA-301a in gastric stromal tumor / 实用医学杂志

Objective The aim was to screen the expression profiles of microRNAs (miRNAs) in gastrointestinal stromal tumors (GIST) and explore the function of microRNA-301 a (miR-301 a). Methods Collected the tumor and adjacent normal tissues of 45 patients, who were diagnosed primary GIST. The expression profiles of tumor miRNAs in 5 of the 45 patients were obtained by microarray technology, and the abnormal expression levels of miRNAs in the remaining 40 patients were detected by Real Time-PCR as a validation experiment. Correlation analysis was analyzed between the significantly up-regulated expression of miR-301 a and the clinicopathological features of the patients. The MTT experiment was used to explore the effect of miR-301 a on the growth of GIST cell lines. Results Five kinds of miRNAs with high expression and five kinds of miRNAs with low expression were screened out from GIST, of which the expression of miR-301 a was up-regulated most obviously. The expression of miR-301 a was closely related to tumor risk grade, tumor size, mitosis and necrosis (P < 0.05). The overexpression of miR-301 a in GIST cell lines could significantly enhance the proliferation of cells. Conclusions MiR-301 a was up-regulated in GIST, which was closely related to malignant clinicopathological features and could affect the growth and proliferation of tumor cells in vitro. MiR-301 a might be a potential target for future treatment of GIST.

Differences in expression profiles of circular RNA between luminal breast cancer cells and normal breast cells / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the differences in the expression profiles of circular RNA (circRNA) between luminal breast cancer cells and normal breast cells.</p><p><b>METHODS</b>Total RNA extracted from luminal breast cancer cells MCF7 and normal breast cells MCF10A was digested with Rnase R to remove linear RNAs and enrich circRNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNAs using a random priming method, and were hybridized onto the circRNA hybridization array. The circRNA expression profiles of MCF7 and MCF10A cells were analyzed using Agilent Feature Extraction software. Quantile normalization and subsequent data processing were performed, and volcano plot filtering and hierarchical clustering were utilized to analyze the circRNA expression patterns. The expressions of 3 circRNAs with significant log fold changes were validated using qPCR.</p><p><b>RESULTS</b>The hybridization array data revealed significant differences in the circRNA expression profiles between MCF7 and MCF10A cells. Compared with those of MCF10A cells, the 12910 circRNAs expressed in MCF7 cells showed 5964 up-regulated, 81 consistently regulated, and 6865 down-regulated circRNAs; 343 circRNAs showed a log fold change by more than 2 folds, among which 213 circRNAs were up-regulated and 130 were down-regulated. Nine circRNAs showed differential expressions by more than 2 folds, including 8 up-regulated ones, namely hsa_circRNA_061260 (6.02 folds), hsa_circRNA_103933 (5.96 folds), hsa_circRNA_005239 (5.84 folds), hsa_circRNA_100689 (5.69 folds), hsa_circRNA_004087 (5.60 folds), hsa_circRNA_104420 (5.25 folds), hsa_circRNA_104421 (5.13 folds) and hsa_circRNA_101222 (5.03 folds); only one circRNA was down-regulated, namely hsa_circRNA_104864 (5.09 folds). The expressions of hsa_circRNA_100689, hsa_circRNA_005239 and hsa_circRNA_104864 were further validated by qPCR, which yielded consistent results with the microarray data.</p><p><b>CONCLUSIONS</b>The circRNA expression profiles differ significantly between luminal breast cancer cells and normal breast cells. These differentially expressed circRNAs may serve as potential novel targets for the diagnosis of luminal breast cancer.</p>

Cloning and expressing of a polyketide synthase gene in Antrodia camphorata / 中草药

Objective To obtained the gene AcPKS1 of Antrodia camphorata, analyze using bioinformatics, and detect the condition of expressing in the different medium. Methods Polyketide synthases gene was obtained from the genome of A. camphorata through analyzing the genome, and the full length of the gene was obtained through designed the special primers including initiation codon and termination codon and the template using cDNA of A. camphorata, which named the gene AcPKS1, and using the bioinformatics analysis and expression profiles analysis in the different medium. Results The full length of AcPKS1 gene was 6 348 bp, including six introns and seven exons, and the expression region encoded 2 115 amino acids; the bioinformatics analysis showed that AcPKS1 was a kind of nonreduced PKS of type in fungi, the domains was SAT-KS-PT-ACP-ACP-TE, and the enzyme catalyzed a new kind of cyclization in the process of polyketides biosynthesis; The expression profiles revealed that glucose was necessary during the expression of AcPKS protein, and the expression quantity of the AcPKS1 protein basically proportion to the content of glucose. Conclusion The result of this text has applied foundation to identify the polyketide synthase gene and take full advantage genomic resources of A. camphorata.

Leucemia linfoblástica aguda infantil: una aproximación genómica / Acute lymphoblastic leukemia: a genomic perspective

Resumen: En paralelo al proyecto de la secuenciación del genoma humano, se han desarrollado varias plataformas tecnológicas que están permitiendo ganar conocimiento sobre la estructura del genoma de las entidades humanas, así como evaluar su utilidad en el abordaje clínico del paciente. En la leucemia linfoblástica aguda (LLA), el cáncer infantil más común, las herramientas genómicas prometen ser útiles para detectar a los pacientes con alto riesgo de recaída, ya sea al diagnóstico o durante el tratamiento (enfermedad mínima residual), además de que permiten identificar los casos en riesgo de presentar reacciones adversas a los tratamientos antineoplásicos y ofrecer una medicina personalizada con esquemas terapéuticos diseñados a la medida del paciente. Un ejemplo claro de esto último es la identificación de polimorfismos de un solo nucleótido (SNPs) en el gen de la tiopurina metil transferasa (TPMT), donde la presencia de dos alelos nulos (homocigotos o heterocigotos compuestos) indica la necesidad de reducir la dosis de la mercaptopurina hasta en un 90% para evitar efectos tóxicos que pueden conducir a la muerte del paciente. En esta revisión se proporciona una visión global de la genómica de la LLA, describiendo algunas estrategias que contribuyen a la identificación de biomarcadores con potencial utilidad en la práctica clínica.

Abstract: In parallel to the human genome sequencing project, several technological platforms have been developed that let us gain insight into the genome structure of human entities, as well as evaluate their usefulness in the clinical approach of the patient. Thus, in acute lymphoblastic leukemia (ALL), the most common pediatric malignancy, genomic tools promise to be useful to detect patients at high risk of relapse, either at diagnosis or during treatment (minimal residual disease), and they also increase the possibility to identify cases at risk of adverse reactions to chemotherapy. Therefore, the physician could offer patient-tailored therapeutic schemes. A clear example of the useful genomic tools is the identification of single nucleotide polymorphisms (SNPs) in the thiopurine methyl transferase (TPMT) gene, where the presence of two null alleles (homozygous or compound heterozygous) indicates the need to reduce the dose of mercaptopurine by up to 90% to avoid toxic effects which could lead to the death of the patient. In this review, we provide an overview of the genomic perspective of ALL, describing some strategies that contribute to the identification of biomarkers with potential clinical application.

Expression profiles analysis of gene chip of salvianolatelyophilized injection in treatment of stroke in diabetic rats / 中国药理学通报

Aim To investigate the effect of salvianolate syophilized injection on brain tissue gene expression profiles in stroke of diabetic rats.Methods T1DM was induced in adult male Wistar rats by injecting streptozotocin.T1DM rats were then subjected to 90 minutes of middle cerebral artery occlusion(MCAO).The rats were randomly assigned to sham group(DM+Sham),ischemia-reperfusion group(DM+ MCAO/R),edaravone group(6 mg·kg-1,ED)and salvianolate lyophilized injection treatment group(5.25,10.5,21 mg·kg-1,SLI)with 13 rats in each group.Drugs were administered by tail vein injection 3 hours after MCAO/R,daily and lasting for 14 days.Infarct volume and gene expression in the brain tissue were detected by TTC staining and the gene chip technique.Results Compared with DM+Sham group,67 differential expressed genes were detected in the DM+MCAO/R group,among which 41 genes were up-regulated and 26 genes were down-regulated.Compared with DM+MCAO/R group,59 differential expressed genes were detected in the SLI(21 mg·kg-1)group,among which 45 genes were up-regulated and 14 genes were down-regulated.Hierarchical cluster results suggested that a number of genes were significantly changed in T1DM rats,such as Ly6i,Pax7 and Irx2.Effects of SLI on the stroke in T1DM rats were majorly related to coagulation and hemostasis system,inflammatory cytokines,oxidative stress,substance metabolism,angiogenesis and signal transduction.Conclusion Salvianolate lyophilized injection protects against focal cerebral ischemia/reperfusion injury in type 1 diabetic rats through regulation of the coagulation and hemostasis system,inflammatory cytokines,oxidative stress,substance metabolism,angiogenesis and signal transduction.

Gene expression profiles in response to ΔNp63α overexpression in human cervical cancer cell line SiHa / 安徽医科大学学报

Objective To analyze the gene expression profiles in response to ΔNp63α overexpression, and screen the potential target genes or signal pathways regulated by ΔNp63α. Methods To generate ΔNp63α overexpressed SiHa cells ( SiHa-ΔNp63α) and the control cells ( SiHa-NC) , recombinant lentivirus transfection was performed. Microarray was applied to detect the change of gene expression profiles, and the results were analyzed with bioinfor-matic software. Quantitative real-time PCR was used to validate the expression levels of selected genes. Results Among the 1405 differentially expressed genes which were statistically significant, >1. 5 fold increase or reduce of gene expression, 843 were up-regulated and 562 were down-regulated in SiHa cells with ΔNp63α overexpression. The genes were mostly involved in cell development,cycle regulation, signal transduction, communication, adhe-sion, metastasis and invasion, etc. The involved signal pathways consisted of antigen processing and presentation, cytokine-cytokine receptor interaction, cell adhesion, complement and coagulation cascades, and so on. Conclu-sion The research on the potential target genes or mediated signal pathways regulated by ΔNp63α could be helpful to explain the development of cervical cancer.

Differential expression profile of microRNAs in different types of uveal melanoma / 中华实验眼科杂志

Background Researches showed that microRNA (miRNA) is involved in the pathogenesis and development of many tumors and plays a cancer-suppressing-gene like role or cancer-gene like action.Uveal melanoma (UM) is a common ocular malignant tumor in aduh,and the mechanism of UM pathogenesis and metastasis is still not elucidated.Understanding the differential expression of miRNAs in UM is expected to provide a basis for targeting treatment of UM.Objective This study was to screen and compare the expression profiles of miRNAs in epithelial type and spindle type of UM.Methods The use of specimens of UM and donor eyes was approved by Ethic Commission of Capital Medical University.The specimens of epithelial type (4 specimens) and spindle type (4 specimens) of UM confirmed by histopathology and immunochemistry were collected in Beijing Tongren Hospital from March 2013 to October 2015.The expression profile of miRNA was assayed by miRNA array.Normal uveal specimens were obtained from 8 donors as controls.The differentially expressing miRNAs were screened by intergroup differential folds of ≥2.The genes targeting differentially expressed miRNAs were predicted using multiples online software and the potential signal pathway was further analyzed by bioinformatics method.The microarray outcomes were validated by real-time quantitative PCR.Results Spindle cell type and epithelial cell type of UMs were verified by hematoxylin and eosin staining.Immunochemistry showed that HMB45,melanin-A and S-100 were positively expressed in the two types of UM.Compared with the normal uveal tissue,109 differentially expressed miRNAs,including 29 up-regulated and 80 down-regulated miRNAs were seen in the spindle cell type of UM,and in the epithelial cell type of UM,50 differentially expressed miRNAs were found,including 23 up-regulated and 27 down-regulated miRNAs.In spindle cell type of UM,the up-regulated miRNAs were miR-146a-5p,miR-25-3p and miR-29b-l-5p,and down-regulated ones were miR-126-5p,miR-183-5p and miR-96-5p.In epithelial cell type of UM,the up-regulated miRNAs were miR-155-5p,miR-210 and miR-378a-5p,and down-regulated ones were miR-199a-5p,miR-143-3p and miR-143-5p.In addition,the mutual up-regulated miRNA in both spindle cell type of UM and epithelial cell type of UM were miR-132-3p,miR-21-5p,miR-34a-5p and miR-34b-5p,and mutual down-regulated ones were miR-125b-2-3p,miR-126-3p,miR-199a-3p and miR-214-3p.Bioinformatics analysis showed that the targeting genes predicted by differentially expressed miRNAs participated in a number of biological pathways,including cancer-related pathway,mitogenactivated protein kinase (MAPK) pathway,Wnt signal pathway and intercellular adhesion,endocytosis,prostatic cancer,colorectal cancer pathways.Conclusions Many differentially expressed miRNAs exist among spindle cell type of UM,epithelial cell type of UM and normal uveal tissue.These miRNAs participate in or regulate the biological behaviour of UM via different signal pathways.

Caracterización funcional y estructural de genes asociados a preeclampsia expresados en la placenta humana / Structural and functional characterization of genes associated with preeclampsia expressed in human placenta / Caracterização estrutural e funcional de genes associados à pré-eclâmpsia expressaram em humanos placenta

Introducción: La preeclampsia continúa siendo la primera causa de morbimortalidad perinatal. El conocimiento sobre su etiología molecular se ha incrementado en los últimos años debido al avance en la aplicación de las ciencias "ómicas". Ello ha llevado a identificar genes candidatos que participarían en su patogénesis. Objetivo: Identificar y caracterizar estructural y funcionalmente genes expresados en placenta que se asocian con preeclampsia. Métodos: A partir de una revisión de literatura de los últimos diez años, se identificaron 16 genes cuya expresión en placenta estaba asociada con la patología. Se realizó la minería de datos incluyendo las siguientes variables: número de genes, tamaño de los genes, número de exones codificantes, islas CpG y las familias de los diferentes elementos repetidos en una ventana de 100Kbp. Mediante un análisis bioinformático, usando los diferentes recursos del NCBI (www.ncbi.nlm.nih.gov) y del Genome Browser de UCSC (http://genome.ucsc.edu/). Adicionalmente se usó el portal BioGPS (http://biogps.gnf.org/#goto=welcome) se determinaron los niveles de expresión de cada gen por tejidos. Resultados: Se registraron diferencias en la cromatina que contiene las familias de elementos no codificantes de los genes asociados en comparación con los controles (Prueba de Kruskall-Wallis, P= 0.0341824). Los genes LEP, EBI3, PROCR, FSTL3, HEXB, INHBA y ENG fueron los que registraron el mayor puntaje z en placentas preeclámpsicas. Conclusión:La aplicación de las herramientas bioinformáticas se convierte en un instrumento potente para el análisis integrado de la expresión de genes y su papel en la patogénesis de la PE. Esto conllevaría a la identificación temprana de mujeres afectadas.

Introduction: Preeclampsia still is the main cause of perinatal morbi-mortality; due to the advance in the application of the omics sciences the knowledge about its molecular etiology has increased in the last years, this has led to the identification of candidate genes, which would be involved in its pathogenesis. Objective: To identify those genes, expressed in placenta that are associated with preeclampsia and compare their structural and functional characteristics. Methods: From a literature review, 16 genes were found, whose expression in placenta was associated to the pathology. Data mining was performed including the following genomic variables: number of genes, genomic size, coding exon count, CpG islands and repeat elements in a 100Kbp window. For the Bioinformatics analysis, we used different resources of the NCBI (www.ncbi.nlm.nih.gov) and the UCSC Genome Browser (http://genome.ucsc.edu/). Furthermore, the portal BioGPS (http://biogps.gnf.org/#goto=welcome) Was used to determine the expression levels of each gene per tissue. Results: Significant differences were found for the non-coding elements of the chromatin in that associated genes, in comparison with controls (Kruskall-Wallis test, P= 0.0341824). The genes LEP, EBI3, PROCR, FSTL3, HEXB, INHBA and ENG were the ones with the highest z- score values in preeclampsic placenta. Conclusion: The application of computational tools has become a powerful instrument for the integrated analysis of gene expression and its role in the pathogenesis of PE. This would lead to an early detection of affected women.

Introdução: A pré-eclâmpsia ainda é a principal causa perinatal Morbi-mortalidade; devido ao avanço na aplicação das ciências "ómicas" o conhecimento sobre sua etiologia molecular tem aumentado nos últimos anos, Isto levou à identificação de genes candidatos, que estariam envolvidos na sua Patogênese. Objetivo: Para identificar esses genes, Expresso em placenta que está associada à pré-eclâmpsia e comparar as suas características estruturais e funcionais. Métodos: A partir de uma revisão da literatura, foram encontrados 16 genes, cuja expressão na placenta foi asociada à patología. Extração de dados Foi realizada incluindo as seguintes variáveis genómicas: Número de genes, tamanho genômico, exon contagem de codificação, CpG ilhas e repetir elementos em uma janela de 100Kbp. Para a análise bioinformática, Utilizamos diferentes recursos do NCBI (www.ncbi.nlm.nih.gov) e do UCSC Genome Browser (http://genome.ucsc.edu/). Além disso, o portal BioGPS (http://biogps.gnf.org/#goto=welcome) foi utilizado para determinar os níveis de expressão de cada gene por tecido. Resultados: Se encontrou diferenças significativas para os elementos não codificantes da cromatina nos genes associados, Em comparação com os controlos (teste de Kruskall-Wallis, P = 0,0341824). Os genes LEP, EBI3, PROCR, FSTL3, HEXB, INHBA e ENG foram os que apresentaram os maiores valores de z-score na placenta pré-eclâmpsica. Conclusão: A aplicação de ferramentas computacionais tornou-se um poderoso instrumento para a análise integrada da expressão gênica e seu papel na patogênese da PE. Isso levaria a uma detecção precoce das mulheres afetadas.

Comparative proteomic analysis of Yersinia pestis 201 and 201△pCD1 strains / 军事医学

Objective To explore the potential pathogenesis of Yersinia pestis and provide new clues for vaccine development through comparative proteomic analysis of wild-type and pCD1 cured strain of Yersinia pestis 201.Methods Differentially expressed proteins at 26℃ and 37℃ were separated and identified using two-dimensional electrophoresis coupled with mass spectrometry .Results A total of 24 differently expressed proteins were successfully identified from the samples of bacteria grown at 26℃ and 25 proteins at 37℃.Among these, 7 proteins were encoded by pCD 1 plasmid. Conclusion Through comparative proteomic research, we have found that the abundance of several proteins can be dramatically changed when the large plasmid pCD 1 is missing,suggesting that the plasmid can regulate the expression of many genes located in the chromosome .

Relationship between the density difference of microRNA binding and the evolution-ary conservation of 3′UTRs in housekeeping and non-housekeeping human genes / 军事医学

Objective To study the microRNA ( miRNA) regulation on the expression of housekeeping and non-house-keeping human genes from the systemic level , and to reveal the influence of conservation at 3′UTRs region for the density difference of miRNA regulatory between the two classes of genes .Methods We obtained miRNA regulation informations for the two classes of genes through the integration analysis of three sequence-based target gene prediction softwares and the conjoint analysis based on gene expression profile data .We also used phastCons-score based evolution analysis to study the conservation of 3′UTRs regions between the two classes of genes .Results Our results showed that housekeeping genes have a significantly higher density of miRNA binding sites and their 3′UTR are relatively conservative .Conclusion These findings highlight the importance of miRNA regulation in housekeeping genes , suggesting that investigating the roles of miR-NAs on the robustness of housekeeping genes expression is highly necessary .

Gene-expression profiling of spleen in sepsis rat models / 中华急诊医学杂志

Objective To find out the differences in gene expression of spleen tissue in septic rats by using DNA microarrays.Methods Thirty male Wistar rats were randomly (random number) and equally divided into control group and sepsis group,and septic rat model was induced by cecal ligation puncture (CLP).The rats of control group were only subjected to a simulated operation without CLP.Gene expression profiles were studied by using RatRef-12 gene chip.Rat gene expression profile was showed by using microarray to detect the changes in gene expression pattern of rat spleen tissue after CLP.And subsequently,by using relevant computer software to screen and analyze,the comparison of differences in gene expression between the sepsis group and control group was made.Results Of 22 523 genes,205 differential genes were found between sepsis group and control group,accounting for 0.910％.Among them 98 genes showed up-regulation,with 48 known functional genes,and 107 genes showed down-regulation,with 64 known functional genes.The function of such different genes were associated mainly with apoptosis,inflammation and energy metabolism of spleen cells.Conclusions Splenic dysfunction may be attibuted to the abnormal expression of relevant genes subjected to apoptosis,inflammation and alteration of energy metabolism.It may be the cause of immunosuppression in the later stage of sepsis.

6 Paths of ERK5 signaling pathway regulate hepatocyte proliferation in rat liver regeneration.

Generally, extra-cellular-signal-regulated kinase 5 (ERK5) signaling pathway regulates many physiological activities, such as cell proliferation and cell differentiation. However, little is known about how ERK5 signaling pathway composed of 15 paths participates in regulating hepatocyte proliferation during liver regeneration (LR). In this study, to explore the influence ERK5 signaling pathway upon hepatocytes at gene transcription level, rat genome 230 2.0 array was used to detect expression changes of 75 related genes in isolated hepatocytes from rat regenerating liver. Bioinformatics and systems biology methods were applied to analyze the precise role of ERK5 signaling pathway in regulating hepatocyte proliferation during LR. Results showed that 62 genes were contained in the array and 22 genes were significantly changed. It was found that 6 paths were related to hepatocyte proliferation during rat LR. Among them, paths 3, 6 and 13 of ERK5 signaling pathway modulated cell cycle progression by decreasing the negative influence on ERK5 and paths 3, 4, 8 and 9 by reinforcing the positive influence on ERK5. In summary, the study shows that 22 genes and 6 paths of ERK5 signaling pathway participate in regulating proliferation of hepatocytes in rat LR.

Study on the diferences of gene expression of peripheral blood mononuclear cells between ACCPA+ and ACCPA patients with rheumatoid arthritis / 中华风湿病学杂志

Objective To explore the differences of gene expression of peripheral blood mononuclear cell (PBMC) between the anti-cyclic citrullinated peptide antibody (ACCPA) positive and ACCPA negative patients with rheumatoid arthritis (RA) by microarray analysis.Methods Total RNA was extracted from PBMC of 5 ACCPA positive and ACCPA negative patients with RA,and age-and sex-matched control subjects respectively.Ⅲumina oligonucleotide microarray was used to characterize 47231gene expression profile for each sample.Results Among the target genes,88 differentially expressed genes were identified in RA patients.Fifty-one up-regulated genes and 37 down-regulated genes were found in RA patients compared to those in control subjects (fold change＞1.5).The differential expression of genes were associated with apoptosis,cytokine,signal identification protein,chemotaxis factor etc.There were 20 differential expression genes between the ACCPA positive and ACCPA negative patients with RA,9 up-regulated genes and 11 downregulated genes were found.The differential expression genes were associated with protein biding,,translation control,signal identification protein,cell cycle,metabolism etc.Conclusion There are differential gene expression between the ACCPA positive and ACCPA negative patients with RA.Genes screened from the target such as IFI,KIR,CHI3L1 can provi-de important information for further study and treatment of RA.

Gene expression profiles of peripheral blood mononuclear cells in primary biliary cirrhosis patients / 中华风湿病学杂志

Objective To explore the differentially expressed genes in peripheral blood mononuclear cells of patients with primary biliary cirrhosis and compare it with healthy controls.Methods Peripheral blood mononuclear cells were isolated from 9 primary biliary cirrhosis patients and 9 age and sex matched healthy controls.Total RNA was extracted from peripheral blood mononuclear cells and analyzed by human genome oligonucleotide microarrays (22K).The differences of gene expression and signaling pathway of patients and healthy controls were compared.Results Seventy-nine genes differentially expressed in primary biliary cirrhosis were identified by microarray analysis,in which 21 were up-regulated and 58 were downregulated.The genes were further categorized into 27 signaling pathways,in which 6 pathways were involved in immune regulation and apoptosis:natural killer cell mediated cytotoxicity pathway,toll-like receptor signaling pathway,antigen processing and presentation pathway,cytokine-cytokine receptor interaction pathway,T cell receptor signaling pathway and apoptosis pathway.Conclusion This study has identified that some genes are different in transcription expression in the primary biliary cirrhosis patients.It may provide new clues for the pathogenesis and biomarker studies.

Mycoplasma hyorhinis and Mycoplasma fermentans induce cell apoptosis and changes in gene expression profiles of 32D cells

Infection of mycoplasmas has been linked to various human diseases including arthritis, pneumonia, infertility and cancer. While Mycoplasma hyorhinis and Mycoplasma fermentans have been detected in gastric adenocarcinomas, the mechanisms underlyine the pathogenesis are unknown. In this study, cell growth kinetics, Hoechst 33258 staining, DNA ladder assays, Western blotting analysis and cDNA microarray assays were performed to investigate the roles of M. hyorhinis and M. fermentans during infection of mammalian cells. Our data demonstrated that these mycoplasmas inhibid the growth of immortalised cell lines (32D and COS-7) ane tumor cell lines (HeLa and AGS). In addition, the infection of the 32D cell line with M. hyorhinis and M. fermentans induced compression of the nucleus, degradation of the cell genome and dysregulation of the expression of genes related to proliferation, apoptosis, tumorigenesis, signaling pathway and metabolism. Apoptosis related proteins Bcl-2, Bid and p53 were down-regulated, Fas was up-regulated and Bax was dysregulated in mycoplasma-infected 32D cells. Together, our data demonstrated that infection of mycoplasmas inhibitd cele growts through modification of gene expression profiles and post-translation modification of proliferation and apoptosis related proteins.