Comparison of pathogenicity and gene expression profiles between adult Schistosoma japonicum isolated from hilly and marshland and lake regions of Anhui Province / 中国血吸虫病防治杂志

Objective To compare the differences in pathogenicity and gene expression profiles between adult Schistosoma japonicum isolated from hilly and marshland and lake regions of Anhui Province, so as to provide the scientific evidence for formulating the precise schistosomiasis control strategy in different endemic foci. Methods C57BL/6 mice were infected with cercariae of S. japonicum isolates from Shitai County (hilly regions) and Susong County (marshland and lake regions) of Anhui Province in 2021, and all mice were sacrificed 44 days post-infection and dissected. The worm burdens, number of S. japonicum eggs deposited in the liver, and the area of egg granulomas in the liver were measured to compare the difference in the pathogenicity between the two isolates. In addition, female and male adult S. japonicum worms were collected and subjected to transcriptome sequencing, and the gene expression profiles were compared between Shitai and Susong isolates of S. japonicum. The differentially expressed genes (DEGs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results The total worm burdens [(14.50 ± 3.96) worms/mouse vs. (16.10 ± 3.78) worms/mouse; t = 0.877, P = 0.392], number of female and male paired worms [(4.50 ± 0.67) worms/mouse vs. (5.10 ± 1.45) worms/mouse; t = 1.129, P = 0.280], number of unpaired male worms [(5.50 ± 4.01) worms/mouse vs. (5.60 ± 1.69) worms/mouse; t = 0.069, P = 0.946], number of eggs deposited in per gram liver [(12 116.70 ± 6 508.83) eggs vs. (16 696.70 ± 4 571.56) eggs; t = 1.821, P = 0.085], and area of a single egg granuloma in the liver [(74 359.40 ± 11 766.34) µm2 vs. (74 836.90 ± 13 086.12) µm2; t = 0.081, P = 0.936] were comparable between Shitai and Susong isolates of S. japonicum. Transcriptome sequencing identified 584 DEGs between adult female worms and 1 598 DEGs between adult male worms of Shitai and Susong isolates of S. japonicum. GO enrichment analysis showed that the DEGs between female adults were predominantly enriched in biological processes of stimulus response, cytotoxicity, multiple cell biological processes, metabolic processes, cellular processes and signaling pathways, cellular components of cell, organelles and cell membranes and molecular functions of binding and catalytic ability, and KEGG enrichment analysis showed that these DEGs were significantly enriched in pathways of vascular endothelial growth factor signaling, glutathione metabolism, arginine and proline metabolism. In addition, the DEGs between male adults were predominantly enriched in biological processes of signaling transduction, multiple cell biological processes, regulation of biological processes, metabolic processes, development processes and stimulus responses, cellular components of extracellular matrix and cell junction and molecular functions of binding and catalytic ability, and these DEGs were significantly enriched in pathways of Wnt signaling, Ras signaling, natural killer cells-mediated cytotoxicity, extracellular matrix-receptor interactions and arginine biosynthesis. Conclusions There is no significant difference in the pathogenicity between S. japonicum isolates from hilly and marshland and lake regions of Anhui Province; however, the gene expression profiles vary significantly between S. japonicum isolates.

Diagnostic criteria and research progress on heart allograft pathology / 器官移植

With the improvement of surgical technique of heart transplantation and clinical application of potent immunosuppressant, the quantity of heart transplantation and the survival time of heart allograft have been significantly improved. However, a series of complications, such as right ventricular failure, ischemia-reperfusion injury, acute rejection, "Quilty lesion", infection and chronic rejection characterized by transplant coronary artery disease (TCAD) may still occur at different stages after heart transplantation. The application of endomyocardial biopsy (EMB) makes it possible to observe and understand the pathological features of multiple complications of heart allograft including rejection, which has become the most accurate diagnostic tool for postoperative complications. In this article, the brief history of heart allograft pathology, main postoperative complications and pathological diagnostic criteria, and cutting edge research progress on diagnostic criteria of rejection were illustrated, aiming to bring clinical benefits to more recipients undergoing heart transplantation.

Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor

BACKGROUND: Gallbladder cancer (GBC) is the most common tumor of the biliary tract. The incidence of GBC shows a large geographic variability, being particularly frequent in Native American populations. In Chile, GBC represents the second cause of cancer-related death among women. We describe here the establishment of three novel cell lines derived from the ascitic fluid of a Chilean GBC patient, who presented 46% European, 36% Mapuche, 12% Aymara and 6% African ancestry. RESULTS: After immunocytochemical staining of the primary cell culture, we isolated and comprehensively characterized three independent clones (PUC-GBC1, PUC-GBC2 and PUC-GBC3) by short tandem repeat DNA profiling and RNA sequencing as well as karyotype, doubling time, chemosensitivity, in vitro migration capability and in vivo tumorigenicity assay. Primary culture cells showed high expression of CK7, CK19, CA 19-9, MUC1 and MUC16, and negative expression of mesothelial markers. The three isolated clones displayed an epithelial phenotype and an abnormal structure and number of chromosomes. RNA sequencing confirmed the increased expression of cytokeratin and mucin genes, and also of TP53 and ERBB2 with some differences among the three cells lines, and revealed a novel exonic mutation in NF1. The PUC-GBC3 clone was the most aggressive according to histopathological features and the tumorigenic capacity in NSG mice. CONCLUSIONS: The first cell lines established from a Chilean GBC patient represent a new model for studying GBC in patients of Native American descent.

Analysis on Gene Set Enrichment of Related Signaling Pathways and Immune Infiltration in Intracranial Aneurysm / 中国实验方剂学杂志

Objective::Based on gene array technology, gene set enrichment analysis (GSEA) and immune infiltration analysis were performed on chip data of intracranial aneurysm (IA) mRNA expression profile, in order to provide theoretical basis for understanding the formation mechanism of IA. Method::The GSE75436 raw data were obtained from the gene expression omnibus (GEO). GSEA of biological process (BP) in gene ontology (GO) and Kyoto gene and genome encyclopedia (KEGG) signaling pathways were analyzed for gene expression profile by R software. The CIBERSORT deconvolution method was used to analyze the infiltration ratio of 22 types of immune cells in the expression profile. And COREMINE database was used to predict traditional Chinese medicines (TCMs), which were significant correlation with the enrichment result. Result::The GSEA results showed that the changes in gene expression of IA samples mainly involved in the regulation of cytokines, activation and differentiation of leukocyte, inflammatory immune response and other processes. The infiltration matrix analysis of immune cells showed that mast cells resting and neutrophils were significantly reduced in IA samples. The comparison of paired samples showed that mast cells and natural killer cells (NK cells) were significantly activated in the IA samples of the same individual, while neutrophils and T cells CD4 naive were significantly reduced. Through COREMINE prediction, it was found that Stephaniae Tetrandrae Radix was correlated with the activation of granulocytes, Sapindi Mukorossi Semen and Pistaciae Chinensis Cortex were correlated with the activation of neutrophils, Trichosanthis Semen, Paeoniae Radix Alba and Ligustri Lucidi Fructus were correlated with the cytotoxicity mediated by NK cells. Conclusion::Activation of mast cells and NK cells are closely associated with the occurrence and development of IA. The inflammatory immune processes and pathways such as nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) signaling pathway and cytotoxicity mediated by NK cells may be important factors in the pathogenesis of IA, and TCMs such as Stephaniae Tetrandrae Radix may be the potential molecular drug sources.

Bioinformatics analysis of expression profiles of long noncoding RNA in endometrial cancer / 上海交通大学学报（医学版）

Objective • To analyze the differentially expressed profiles of long noncoding RNA (lncRNA) in endometrial cancer (EC) tissues and normal endometrial tissues. Methods • The RNA was extracted from 21 EC tissues and 5 normal endometrial tissues, respectively, and lncRNAs expression profiles were analyzed and screened by transcriptome sequencing technology. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out for the differentially expressed lncRNAs, and their expression differences between the transcriptome sequencing and TCGA database were analyzed. Results • There were 3 060 differentially expressed lncRNAs, of which 2 046 were upregulated and 1 014 were down-regulated. GO functional analysis showed that these lncRNAs were associated with cell adhesion, immune response, inflammatory response and cell proliferation. KEGG pathway analysis showed that these lncRNAs were mainly enriched on the pathways, such as PI3KAkt signaling pathway, cell adhesion and cytokine-cytokine receptor interaction. Intersection analysis showed that 57 lncRNAs were up-regulated or downregulated simultaneously in the sequencing results and TCGA database. Conclusion • The expression of lncRNAs in EC tissues and normal endometrial tissues are significantly different, suggesting that it may play an important role in the occurrence and development of EC.

Bioinformatic analysis on related genes of lung adenocarcinoma / 中国肿瘤生物治疗杂志

@# To indentify the candidate genes and signaling pathways in lung adenocarcinoma by analyzing gene profiles with bioinformatics. Methods: The expression profiles of GSE40791, GSE68571, GSE43458, and GSE18842 were down-loaded from the Gene Expression Omnibus (GEO) database. The four microarray datasets were integrated to obtain the differentially expressed genes related to lung adenocarcinoma. STRING database was used to construct the protein-protein interaction (PPI) network of differentially expressed genes, and to further explore the gene modules and the key genes. DAVID was used to perform the gene enrichment analysis of each gene module, and to explore the regulatory function of each gene module in adenocarcinoma cells, as well as the relationship between the key genes in the module and the prognosis of the patients. Results: Thirty-seven up-regulated genes and 120 down-regulated genes were obtained from the primary screen, and the protein-protein interaction(PPI) network was successfully constructed. According to MCODE algorithm, we constructed gene modules and calculated the core genes (KIF14, SEPP1, SPP1, RBP4) in the PPI network. Finally, four modules were proved to be involved in regulation of cell cycle, blood coagulation, cell adhesion and cell metabolism, and four key genes were proved to be differentially expressed between lung adenocarcinoma tissues and normal tissues (all P<0.05). Survival analysis showed that expressions of KIF14, SEPP1 and SPP1 had significant effect on the prognosis of lung adenocarcinoma (P<0.01 or P<0.05), while RBP4 exerted insignificant difference in the survival rate of lung adenocarcinoma patients (P>0.05). Conclusion: With bioinformatics, three differentially expressed genes between lung adenocarcinoma tissues and normal adjacent tissues were finally screened out and proved to be closely related to the prognosis of patients, which provided new thoughts in the diagnosis and prognosis prediction of lung adenocarcinoma and improved the study efficiency on the mechanism of lung adenocarcinoma.

Effects of Dendrobium officinale Polysaccharides on Gene Expression Profile of HUVEC / 中国药房

OBJECTIVE： To investigate the effects of Dendrobium officinale polysaccharides on gene expression profile of HUVEC. METHODS： HUVEC was selected as objects. MTS method was used to detect the effects of different doses of D. officinale polysaccharides （50， 100， 200， 400， 800 μg/mL） on the proliferation activity of HUVEC. The growth inhibitory concentration of 30％ cells （IC30） was calculated to screen the dose of follow-up tests. cDNA microarray assay was used to detect the changes of gene expression profile for HUVEC after treated with D. officinale polysaccharides for 24 h， so as to screen differentially expressed genes. GO enrichment analysis and KEGG pathway enrichment analysis were performed for top 5 differentially expressed genes by using DAVID bioinformatics resource database. Real-time fluorescence quantitative polymerase chain reaction （qRT-PCR） was used to validate the results of microarray detection with immunity-related differentially expressed genes as objects. RESULTS： After treated with 100， 200， 400， 800 μg/mL D. officinale polysaccharides， survival rate of HUVEC  were decreased significantly （P＜0.05 or P＜0.01）. IC30 value was 408 μg/mL. After treated with 400 μg/mL （by IC30） D. officinale polysaccharides， there were 91 differentially expressed genes in HUVEC cells， of which 84 were up-regulated and 7 were down-regulated. Top 5 genes of up-regulated and down- regulated expression were SELE， CCL2， CXCL6， IL8， ICAM1 as well as VWCE， CPT1A， CLU， CCL14， CINS4， which may be mainly associated with immune conditions and inflammatory responses. The differentially expressed genes mainly distributed in extracellular domain， and were enriched in biological processes such as production and response of cytokines and stimulus response， and played molecular functions such as chemokine and its receptor activity. The up-regulated genes as SELE， ICAM1 and CXCL2 were mainly enriched in TNF signaling pathway， influenza A （H1N1）， herpes simplex virus infection and other pathways. The down-regulated gene CCL14 was mainly enriched in chemokine signaling pathway. Results of qRT-PCR validation tests showed that relative expression of ICAM1 was increased significantly， while that of CCL14 was decreased significantly （P＜0.05）， which was in agreement with microarray detection results. CONCLUSIONS： After treated with D. officinale polysaccharides， the expression of 91 genes in HUVEC cells are different significantly， mainly being up-regulated. The differentially expressed genes may participate in immune regulation through TNF signaling pathway， influenza A （H1N1） and herpes simplex virus infection.

Application of multiple support vector machine recursive feature elimination model in cancer feature gene selection / 国际生物医学工程杂志

Objective To analyze the cancergene expression profile data using multi-support vector machine recursive feature elimination algorithm (MSVM-RFE) and calculate the genetic ranking score to obtain the optimal feature gene subset. Methods Gene expression profiles of bladder cancer, breast cancer, colon cancer and lung cancer were downloaded from GEO (Gene Expression Omnibus) database.The differentially expressed genes were obtained by differential expression analysis. The differential gene expressions were sequenced by MSVM-RFE algorithm and the average test errors of each gene subset were calculated. Then the optimal gene subsetsof four kinds of cancer were obtained according to the minimum average test errors. Based on the datasets of four kinds of cancer characteristic genes before and after screening, linear SVM classifiers were constructed and the classification efficiencies of the optimal feature gene subsets were verified. Results Using the optimal feature gene subsetobtained by MSVM-RFE algorithm, the classification accuracy was improved from (96.77±1.28)％to (99.85±0.46)％for the bladder cancer data, improved from (83.77±4.93)％to (88.30±3.85)％for the breast cancer data, and improved from (72.69±2.41)％to (90.21±3.31)％for the lung cancer data.Besides, theoptimal feature gene subsetkept the classification accuracy of colon cancer classifierat a high level (>99.5％). Conclusions The feature gene extraction based on MSVM-RFE algorithm can improve the classification efficiency of cancer.

Affymetrix gene sequencing technique used to analyze the mechanism of pituitary's regulation of CSA model in rats / 西安交通大学学报(医学版)

Objective To analyze differences in gene expression profile of pituitary tissue in cervical spondylosis of vertebral artery type(CSA)model rats and explore the mechanism of adrenal gland's regulation of CSA.Methods Ten SPF male Wistar rats were randomly divided into model group and blank group.The CSA model was established by compound modeling method.The total RNA was extracted from the pituitary;the gene expression profile was detected by whole gene chip,ontology(GO),and signal pathway analysis.Results Compared with the normal group,the differential genes'expression profile analysis showed that the total number of the differential genes was 321(fold change︱ ＞ 2,P＜0.05),with 203 up-regulated genes and 118 down-regulated genes.A total of 1 294 genes rich in GO function were involved in the regulation of intercellular signal activity and nerve cell function;the stress response to external stimuli;and the regulation of coagulation function,angiogenesis, endometrial system,and cell cycle;There were 145 signal transducers,including adipocytokine signaling pathway, TGF-β signal transduction,AMPK signaling pathway,PPAR signal pathway,Wnt signaling pathway,and MAPK signal transduction pathway.Conclusion The pituitary regulates CSA mainly through the inflammatory stimulation,immune regulation,regulation of vertebral artery function,and endometrial system.

Effect of rabdosia serra (maxim.) hara on gene expression profile of hepatocellular carcinoma HepG2 cells / 重庆医学

Objective To adopt the expression profile chip to investigate the effect of Rabdosia serra (Maxim.) hara water extract on related gene of human hepatocellular carcinoma(HCC) HepG2 cells for researching the possible mechanism of its water extract on HCC.Methods The human HCC HepG2 cells were cultured in vitro.After adding Rabdosia serra (Maxim.) hara water extract (9.54 mg/mL) for 24 h action,the expression profile chip was adopted to detect the HepG2 gene change after Rabdosia serra (Maxim.) hara action and then the chip results were verified by using RT-PCR and Western blot.Results The phase contrast microscope observation found that compared with the negative control group,the number of HepG2 cells was significantly reduced after Rabdosia serra (Maxim.) hara water extract action.The expression profile results showed that after Rabdosia serra (Maxim.)hara water extract action for 24 h,264 genes were risen to over twice folds compared with the negative control group and 194 genes were decreased by over twice folds compared with the negative control group.The gene ontology(GO) and KEGG analysis indicated that Rabdosia serra (Maxim.) hara could up-regulate multiple genes in DUSPs and IGFBPs family and down-regulate multiple genes in MCMs family.The RT-PCR detection found that compared with the negative control group,DUSP1 and IGFBP1 in the Rabdosia serra (Maxim.) hara treatment group were increased,while FXR and ALDH8A1 were decreased (P＜0.01),which were consistent with the results of expression profile chip.The Western blot results found that the protein expression level of DUSP1 in the Rabdosia serra (Maxim.) hara treatment group was also significantly higher than that in the negative control group (P＜ 0.01).Conclusion The expression profile chip shows that Rabdosia serra (Maxim.) hara can inhibit the proliferation of HCC cells by regulating multiple genes.

Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders / 神经科学通报·英文版

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 Cdh1, 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.

Regulatory effect of NOB1 on osteosarcoma cell-related genes detected by gene microarray technique / 吉林大学学报(医学版)

Objective; To screen the genes may be regulated by NOB1 by using gene microarray technique, and to clarify the regulatory effect of NOB1 on the expression of osteosarcoma cell-related genes. Methods: The U20S cells were treated with lentivirus-mediated RNA interference and to establish the osteosarcoma cells Lv-shN0Bl-U20S. Lv-shCon-U20S group and Lv-shN0Bl-U20S group were set up. The mRNA expressions of those cells were detected using expression pattern analysis. Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to predict the global functions of NOB1, including biological processes, cellular components, molecular functions, and signaling pathways. Results; After NOB1 interference in the U20S cells, there were 792 genes with up-regulated mRNA expression level and 1 059 genes with down-regulated mRNA expression level, with a total variation of 1 851 genes. The GO analysis results showed that from the enrichment degree of cell location entries, the differentially encoded product proteins were mainly distributed on the cell membrane as 56. 9% of the total difference genes, 39. 4% of the totally differential genes distributed in the extracellular region, and 20% of the totally differential genes in the extracellular space; from the enrichment degrees of the molecular function items, the main function of the differentially encoded product proteins was calciu mion binding-related function (22% of the totally differential genes), the second function was transporter activity (9. 2% of the totally differenital genes), and the third function was actin binding activity (8. 7% of the totally differential genes). In terms of the enrichment of biochemical process entries, the main participation process of differentially encoded product proteins was 18. 7% of the totally differential genes of signal transduction, the second involved process was 15. 6% of the totally differential genes produced by multiple organelles, and the third process was the cell adhesion process accounted for 10. 2% of the totally differential genes. The KEGG analysis results showed that their encoding proteins were involved in plasma membrane, calcium ion binding activity and signal transduction. Conclusion; Knockout of NOB1 can affect the expressions of osteosarcoma cell-related genes in an all-round way.

Establishment and Analysis for Differential Gene Expression Profile of Left Atrium in Permanent Atrial Fibrillation Patients / 中国循环杂志

Objective: To explore the relevant gene, signaling pathway for permanent atrial fibrillation (pAF) occurrence in order to provide the molecular basis of the pathogenesis of pAF. Methods: Our research included in 2 groups: pAF group, n=7 patients and Control group, n=4 healthy subjects with sinus rhythm. Agilent 4x44K microarray was used to analyze the mRNA in left atrium for differential gene expression profile. Based on Gene Ontology, KEGG and Biocarta databases, differentially expressed genes were studied for their relevant function and signaling pathway. Furthermore, the genes with significant differences were verified by quantitative real time PCR (qRT-PCR) in pathological specimen from 5 pAF patients and 5 normal heart donors. Results: The expression profile identified 987 abnormally expressed genes, 567 of them were down-regulated and 420 were up-regulated. 9 genes with significant differences were verified by qRT-PCR in pathological specimen and the changes were similar to microarray; those genes were closely related to pAF by involving left atrium fibrosis, electrical remodeling, inflammation, cellular stress response, metabolism and transcription regulation. GO and Pathway analysis indicated that down-regulated genes were mainly involved in metabolic processes; up-regulated genes had the effects on cellular stress response, immune response and platelet activation. Conclusion: Microarray technology identified some important genes related to pAF occurrence; such genes involved in left atrial structural and functional remodeling via affecting cellular metabolism, inflammation, immune response and thrombogenesis in relevant patients.

Digital gene expression profiling of dendritic cells treated with Seabuckthorn favones / 中华微生物学和免疫学杂志

Objective To study the changes in morphology , phenotypes and gene expression pro-files of dendritic cells (DCs) following treatment with Seabuckthorn flavones (SF).Methods DCs were treated with 200μg/ml of SF and then cultured for 7 days.Changes in the morphology of DCs were observed under light microscope .Flow cytometry was used to detect DC surface molecules .Total RNA was extracted to construct the library for digital gene expression profiling ( DGE ) .Differentially expressed genes were screened out and further analyzed by gene ontology ( GO) enrichment analysis and Kyoto encyclopedia of genes and genomes ( KEGG ) pathway enrichment analysis .Results Compared with control group , SF treatment significantly enhanced the expression of HLA-DR, CD80, CD83 and CD86 on DCs.A total of 355 differentially expressed genes were screened out by DGE , including 176 up-regulated genes and 179 down-regulated genes .GO enrichment was mainly involved in the regulation and development of the immune sys -tem and other biological processes .KEGG pathway analysis showed that the significantly enriched pathways were closely related to inflammation , the immune system, cancer and other diseases .Conclusion SF can promote the expression of DC co-stimulatory molecules and pro-mature molecules, and regulate the expres-sion of immunity-related genes such as CD11a, SLAMF6, LMCD1, TSC22D3 and IKZF3.

Visualization Study on the Disturbance of Aorta Gene Expression Profile in Acute Hyperglycemia Mice Model / 中国循环杂志

Objective:Based on the visualization function for gene network disturbance of Matlab platform,data mining method was used to directly observe transcriptonal changes in aorta vessel at short-time hyperglycemia condition.Methods:The information was down loaded from GEO database of NCBI.Using Matlab system to transfer the data set to a computer-readable structure,using data filter to obtain apparent gene expression disturbance profile after short-time hyperglycemia condition.Applying three clustering algorithms,based on DAVID platform to conduct gene ontology (GO) annotation and enrichment analysis in order to calibrate KEGG pathway and to form gene expression profile analysis.Results:Via data set screening,the pattern of gene expression was divided into 9 clusters by special algorithms.GO analysis indicated that obvious gene enrichments were found in acute inflammation reaction gene,myocardium remodeling gene,stabilizing intracellular calcium gene,cell cycle regulation gene,chemotactic effect gene;especially in mucopolysaccharide gene,glycoprotein structure related gene,fat catabolism gene and myofibril related gene.The above findings were identical to previous study.K-means clustering method presented that in hyperglycemia condition,up-regulated genes didn't return to normal level when blood glucose back to normal which mainly including cell cycle regulation gene,myocardium remodeling gene and stabilizing intracellular calcium gene.Conclusion:Our work provided a new explanation of diabetes metabolic memory;short-term hyperglycemia caused arterial damage was irreversible which incurred inefficient hypoglycemic therapy in coronary artery disease patients.

Visualization Study on the Disturbance of Aorta Gene Expression Profile in Acute Hyperglycemia Mice Model / 中国循环杂志

Objective:Based on the visualization function for gene network disturbance of Matlab platform,data mining method was used to directly observe transcriptonal changes in aorta vessel at short-time hyperglycemia condition.Methods:The information was down loaded from GEO database of NCBI.Using Matlab system to transfer the data set to a computer-readable structure,using data filter to obtain apparent gene expression disturbance profile after short-time hyperglycemia condition.Applying three clustering algorithms,based on DAVID platform to conduct gene ontology (GO) annotation and enrichment analysis in order to calibrate KEGG pathway and to form gene expression profile analysis.Results:Via data set screening,the pattern of gene expression was divided into 9 clusters by special algorithms.GO analysis indicated that obvious gene enrichments were found in acute inflammation reaction gene,myocardium remodeling gene,stabilizing intracellular calcium gene,cell cycle regulation gene,chemotactic effect gene;especially in mucopolysaccharide gene,glycoprotein structure related gene,fat catabolism gene and myofibril related gene.The above findings were identical to previous study.K-means clustering method presented that in hyperglycemia condition,up-regulated genes didn't return to normal level when blood glucose back to normal which mainly including cell cycle regulation gene,myocardium remodeling gene and stabilizing intracellular calcium gene.Conclusion:Our work provided a new explanation of diabetes metabolic memory;short-term hyperglycemia caused arterial damage was irreversible which incurred inefficient hypoglycemic therapy in coronary artery disease patients.

Differential analysis of gene expression profiles for lymphonode metastasis of colon cancer / 临床检验杂志

Objective To investigate the differences in the gene expression profiles between SW480 and SW620 cell lines.Methods A dataset of GDS756 containing the gene expression profiles of SW480 and SW620 was downloaded from the GEO database in NCBI.The differential expression genes between SW480 and SW620 were analyzed with gene set enrichment analysis (GSEA) and leading edge subset analysis.The genes in leading edge subset were re-annotated by FunRich software.The core genes of leading edge subset closely relating to SW480 or SW620 were analyzed with the STRING on-line analytical system.The functional core genes closely relating to SW480 or SW620 were obtained by the combined analysis of the core genes and high frequency genes from leading edge subset.Results GSEA identified 12 significantly enriched gene sets,491 leading edge genes and 7 highly overlapping genes from SW480 and 80 significantly enriched gene sets,870 leading edge genes and 6 highly overlapping genes from SW620.The STRING system identified 5 core genes from SW480 and 8 from SW620.The combined analysis of GSEA and bionetwork obtained 2 functional core genes,TOP2A and CDK1,from SW620.Conclusion The SW480 and SW620 cells with identical genetic background have different functional gene expression profiles,and the functional core genes TOP2A and CDK1 in SW620 cells may be related to the signal pathways of colon cancer metastasis.

Differences in gene expression profiles of hypoxic human embryonic retinal microvascular endothelial cells induced by cobalt chloride / 中华实用儿科临床杂志

Objective To study the differentially expressed genes and analyze its functional pathways of retinopathy of prematurity(ROP),in order to discover the pathogenesis and provide the theoretical basis for the prevention and treatment of ROP.Methods Fetal eyeballs of induced labor were obtained and retinal microvascular endothelial cells were isolated and cultured.The endothelial cells were divided into 7 groups according to the medium of cobalt chloride (CoC12) concentration (0 μ mol/L,100 μ mol/L,150 pμmol/L,200 μmol/L,250 pμmol/L,300 μmol/L,350 μmol/L),and 150 μmol/L CoCl2 was finally used to induce ROP model in vitro.Retinal microvascular endothelial cells were verified by adopting Ⅷ factor and CD31 antibody fluorescence staining.RNA purification,gene chip hybridization and signi-ficant analysis of microarrays were performed to screen differentially expressed genes.Genes functional pathways were studied by using gene ontology analysis software.Results (1) The proliferation activity of vascular endothelial cells decreased when CoCl2 ≥ 150 μmol/L(F =21,P ＜ 0.05).(2) In 150 μmol/L CoC]2 group,blue nucleus and green cytoplasm were visible in the second and the third generation vascular endothelial cells stained by factor Ⅷ antibody,and red fluorescence could also be observed in the cytoplasm by means of CD31 monoclonal antibody staining.However,only blue nucleus was detected in the group without CoCl2.(3)There were 326 genes differently expressed in retinal micro vascular endothelial cells induced by CoCl2 in vitro,among whom,198 genes were up-regulated and 128 genes were down-regulated.Up-regulated expression genes were 1.5 times more than those of the down-regulated genes.(4)Ten biological pathways including cell hypoxia,angiogenesis suppression and iron ion transport etc.may play important roles in ROP pathogenesis.Conclusions Hypoxic retinal microvascular endothelial cells induced by CoCl2 can successfully be used to induce cell model of ROP in vitro.Differentially expressed genes may play an important role in ROP development.Functional pathway such as hypoxic cells,inhibition of angiogenesis,iron ion transport may be associated with ROP pathogenesis.

An integrative bioinformatics study of gene expression profile in prostate cancer / 安徽医科大学学报

Objective To analyze gene expression profile for exploring the function and regulatory network of differ-entially expressed genes in prostate cancer by bioinformatics. Methods The data of gene expression profile in prostate cancer were obtained from GEO database. R software and affy, limma, pheatmap, ggplot2 and other R packages were applied for data mining and bioinformatics analysis. Combined with DAVID and GeneMANIA , dif-ferentially expressed genes and their regulatory networks were annotated. Results These differentially expressed genes with statistical significance were 56 genes, 15 upregulated genes, 41 downregulated genes;these genes were enriched into different subgroups. cav1, slc16a2, cav2, slc16a5, magi2, ptrf, pdlim5, lmod1 and abcc6 were en-riched into the cell membrane component subgroup ofcell component category. cav1, cav2 and ptrf regulated the function of caveolae, they may play an important role in the occurrence and development of prostate cancer. Conclusion Differentially expressed genes between prostate cancer and adjacent tissues assemble a complex regu-latory network. Bioinformatics is a tool for data mining of the regulatory network , which provides ideas and data for the molecular mechanisms in prostate cancer.

Differential gene expression profile of miRNAs in mouse models with renal ischemia-reperfusion injury / 器官移植

To screen the differentially-expressed microRNAs (miRNAs) in mouse models with renal ischemia-reperfusion injury (IRI),aiming to offer foundation for unraveling the molecular mechanism of the incidence and progression of IRI.Methods The mouse models with acute IRI were established by renal artery clamping.Fifteen mice were divided into the IRI group and sham surgery group (E group).The animals in the IRI group were subdivided into the A group (45 min ischemia followed by 24 h reperfusion),B group (25 min ischemia followed by 24 h reperfusion),C group (45 min ischemia followed by 4 h reperfusion) and D group (25 min ischemia followed by 4 h reperfusion) (n=3 for each group).The severity ofIRI was evaluated by histological changes and renal function.The differentially-expressed miRNAs in the IRI mouse models at different ischemia time (25 and 45 min) and reperfusion time (4 and 24 h) were screened by using cluster analysis of miRNAs microarray data.The differential expression of miR-695 and miR-145 was validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR).Results Both histological changes and renal function confirmed that the IRI mouse models were successfully established.Compared with the sham surgery group,71 differentially-expressed miRNAs were detected in the IRI group including 30 down-regulated miRNAs and 40 up-regulated miRNAs.The results of qRT-PCR demonstrated that if the standardized expression level of miRNAs in the E group was 1,the relative expression levels of miR-695 and miR-145 were 11.82 and 0.31 in the IRI group (both P＜0.05),which were consistent with the chip results.Conclusions After renal IRI,different changes occur in the gene expression profile of miRNAs.These differentially-expressed miRNAs act as molecular biomarkers for renal IRI with potential clinical and scientific research values.