Clinical application of gene chip technology in diagnosis and treatment of silicosis complicated with mycobacterial infection / 环境与职业医学

Background Gene chip technology has been increasingly used in the diagnosis and treatment of common tuberculosis. However, its role in the diagnosis and treatment of silicosis complicated with mycobacterial infection remains unclear. Objective To evaluate the application value of gene chip technology in the diagnosis and treatment of silicosis complicated with mycobacterial infection. Methods From January 2019 to June 2021, 197 silicosis patients suspected to be complicated with mycobacterial infection in Quanzhou First Hospital Affiliated to Fujian Medical University were enrolled in this study. The etiology evaluation for the 197 patients was conducted by acid-fast staining of sputum smear (sputum smear method), culture of Mycobacterium tuberculosis of sputum (sputum culture method), and gene chip technology of bronchoalveolar lavage fluid (BALF); and for 80 patients among them, acid-fast staining of BALF (BALF smear method) and culture of Mycobacterium tuberculosis of BALF (BALF culture method) were additionally performed. The positive rates and consistency were assessed using intraclass correlation coefficient (ICC). Test for Mycobacterium tuberculosis drug resistance mutation gene was added for patients with Mycobacterium tuberculosis complex by BALF gene chip technology. Results The average age of the 197 patients was (53.1±9.1) years, and the average dust exposure time was (21.1±9.4) years, including 192 males and 5 females. There were 8 cases with stage I silicosis, 17 cases with stage II silicosis, and 172 cases with stage III silicosis. Among them, 11.2% were positive for sputum smear; 24.4% were positive for sputum culture, and 36.0% were positive by gene chip of BALF. The difference between the three methods was statistically significant (P<0.05). The result of consistency test for the three methods showed that the ICC was 0.539 (P<0.001). Among the 80 patients, there was a significant difference in the positive rates of the five methods (χ2=25.23, P<0.001). The results of Bonferroni test showed statistically significant pair-wise differences between BALF culture method and sputum smear method, BALF culture method and BALF smear method, BALF gene chip method and sputum smear method, BALF gene chip method and BALF smear method (P<0.05), while there were no statistically significant differences between the other pairs (P>0.05). The result of consistency test for the five methods showed that the ICC was 0.586 (P<0.001). Among the 71 BALF gene chip positive cases, 59 cases reported positive Mycobacterium tuberculosis complex (17 cases were positive in the first-line anti-tuberculosis resistance test, and 2 cases were found positive quinolone resistance gene in the second-line anti-tuberculosis resistance test), and received regular anti-tuberculosis treatment, among them 45 cases improved and 14 cases were stable; 12 cases reported non-tuberculous mycobacteria cases, among them 5 cases received anti-non-tuberculous mycobacteria treatment (4 cases improved and 1 case was stable), and 7 cases with mild symptoms did not receive anti-non-tuberculous mycobacteria treatment. Conclusion Compared with sputum smear, sputum culture, and other traditional methods, gene chip technology of BALF can improve the positive rate of pathogenic diagnosis of silicosis complicated with mycobacterial infection, and can also quickly identify whether it is non-tuberculous mycobacteria infection or drug-resistant Mycobacterium tuberculosis infection, which is helpful to adjust treatment as soon as possible.

Mechanism of Proteoglycan TPG-1 from Trametes robiniophila Inhibiting Growth of Human Hepatoma SK-HEP-1 Cells / 中国实验方剂学杂志

ObjectiveProteoglycan TPG-1 isolated from Trametes robiniophila（Huaier） has proved to have anti-hepatoma activity， and this paper aims to explore the molecular mechanism. MethodHuman hepatoma SK-HEP-1 cells were treated with TPG-1 （0， 0.05， 0.1， 0.25， 0.5， 1 g·L-1）. Then cell survival was detected by methyl thiazolyl tetrazolium （MTT） and apoptosis by flow cytometry. In addition， expression of genes in SK-HEP-1 cells treated with or without TPG-1 was examined by DNA microarray to preliminarily explore the anti-hepatoma molecular mechanism of TPG-1. ResultTPG-1 inhibited the proliferation of SK-HEP-1 cells as compared with the blank group （P<0.01）. After treatment with 1 g·L-1 TPG-1 for 48 h， the apoptosis rate of SK-HEP-1 cells increased （P<0.01）， and TPG-1 promoted the cleavage of cysteinyl aspartate specific proteinase （Caspase）-3 and Caspase-7， the key mediators of apoptosis （P<0.01）. Additionally， TPG-1 （1 g·L-1） suppressed the migration of SK-HEP-1 cells （P<0.05）. A total of 971 differentially expressed genes （DEGs） were identified in SK-HEP-1 cells after treatment with TPG-1， with 486 up-regulated and 485 down-regulated. These DEGs were mainly involved in the Gene Ontology （GO） terms of interleukin-6 （IL-6） biosynthesis， antigen processing and presentation， superoxide dismutase activity， positive regulation of mitogen-activated protein kinase kinase kinase （MAPKKK） cascade， nature killer （NK） cell chemotaxis， and chemokine biosynthesis， and the Kyoto Encyclopedia of Genes and Genomes （KEGG） pathways of nucleotide-binding oligomerization domain （NOD）-like receptor signaling pathway， apoptosis， Toll-like receptor signaling pathway， retinoic acid-inducible gene-Ⅰ （RIG-Ⅰ）-like receptor signaling pathway， T-cell receptor signaling pathway， and chemokine signaling pathway. Western blot results showed that TPG-1 （1 g·L-1） activated mitogen-activated protein kinase （MAPK） signaling pathway in SK-HEP-1 cells （P<0.01）. ConclusionProteoglycan TPG-1 inhibited the proliferation and migration， and induced apoptosis of human hepatoma SK-HEP-1 cells. Up-regulation of MAPK signaling pathway may be responsible for the growth inhibition of human hepatoma SK-HEP-1 cells by TPG-1.

Bioinformatics Analysis of Microarray Data in Myelodysplastic Syndrome Based on Gene Expression Omnibus Database / 中国实验血液学杂志

OBJECTIVE@#To identify the key genes and explore mechanisms in the development of myelodysplastic syndrome (MDS) by bioinformatics analysis.@*METHODS@#Two cohorts profile datasets of MDS were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed gene (DEG) was screened by GEO2R, functional annotation of DEG was gained from GO database, gene ontology (GO) enrichment analysis was performed via Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key genes were screened by Matthews correlation coefficient (MCC) based on STRING database.@*RESULTS@#There were 112 DEGs identified, including 85 up-regulated genes and 27 down-regulated genes. GO enrichment analysis showed that biological processes were mainly enriched in immune response, etc, cellular component in cell membrane, etc, and molecular function in protein binding, etc. KEGG signaling pathway analysis showed that main gene enrichment pathways were primary immunodeficiency, hematopoietic cell lineage, B cell receptor signaling pathway, Hippo signaling pathway, and asthma. Three significant modules were screened by Cytoscape software MCODE plug-in, while 10 key node genes (CD19, CD79A, CD79B, EBF1, VPREB1, IRF4, BLNK, RAG1, POU2AF1, IRF8) in protein-protein interaction (PPI) network were screened based on STRING database.@*CONCLUSION@#These screened key genes and signaling pathways are helpful to better understand molecular mechanism of MDS, and provide theoretical basis for clinical targeted therapy.

Molecular Mechanism of Modified Guizhi Fulingwan Intervention on Uterine Fibroids in Rats Based on micRNA Expression Profiling / 中国实验方剂学杂志

Objective:To explore the molecular mechanism of modified Guizhi Fulingwan in rats with uterine fibroids. Method:Seventy-two female adult SD rats of SPF grade were randomly divided into a model group， a normal group， and a preventive administration group. The model group and preventive administration group were established by estrogen and progestin loading method. After successful modeling， the rats in the model group were randomly divided into a western medicine group （mifepristone）， the high-dose traditional Chinese medicine（TCM） group， and a low-dose TCM group. All the rats were dosing as required once a day for 28 consecutive days. Hematoxylin-eosin（HE）staining was used to observe the morphological changes of the uterus. The micRNA gene chip was used to detect the expression profile of uterine micRNA gene. Differential expressions of micRNA were screened by bioinformatics methods. Gene function enrichment was used to predict the possible signaling pathways in rats with uterine fibroids by modified Guizhi Fulingwan. Result:Compared with the normal group， microRNA of the model group was 1 up-regulated and 9 down-regulated. Compared with the model group， microRNA of the high-dose group of TCM group was 2 up-regulated and 1 down-regulated， in the preventive administration group， 9 was up-regulated and 2 was down-regulated. Gene function enrichment analysis indicated that four signaling pathways were closely related to uterine fibroids. They were mitogen-activated protein kinase （MAPK） signaling pathway， Wnt signaling pathway， mammalian rapamycin target protein （mTOR） signaling pathway and vascular endothelial cell growth factor （VEGF） signaling pathway. Conclusion:Modified Guizhi Fulingwan affected the expression profile of micRNA in rat model of uterine fibroids induced by estrogen and progesterone， suggesting that modified Guizhi Fulingwan may involve in a variety of biological processes such as signal transduction and gene regulation in the treatment of uterine fibroids.

Screening and identifying genes associated with malignant pleural mesothelioma based on public database / 中国职业医学

OBJECTIVE: To explore the related signaling pathways, biomarkers and prognostic genes of malignant pleural mesothelioma(MPM) based on the gene chip and second-generation sequencing datasets in public database by bioinformatics-related method. METHODS: MPM microarray expression datasets GSE51024 and GSE2549, with 82 and 49 MPM patients, respectively, were downloaded from the Gene Expression Omnibus database. The RNA sequencing data of 86 MPM patients were downloaded from the The Cancer Genome Atlas(TCGA). The weighted gene co-expression network analysis(WGCNA) and differentially expressed genes(DEGs) screening were used to screen and identify hub genes in the GSE51024 dataset by RStudio 4.0 software. The gene set enrichment analysis(GSEA) was used to explore relevant signaling pathways. Finally, a total of 135 MPM gene expression data from GSE2549 dataset and TCGA database were used to verify the hub genes. RESULTS: The green key gene module identified by the WGCNA was highly correlated with MPM, with a correlation coefficient of 0.83(P<0.01). A total of 3 245 DEGs were screened by DEGs analysis. Among them, 1 229 genes were up-regulated and 2 016 genes were down-regulated. GSEA results showed that the genes were significantly enriched in the areas of G2/M cell cycle checkpoint, epithelial-mesenchymal transition, E2 F target gene, and mitotic spindle pathways. Three hub genes were screened, including the proliferating cell nuclear antigen-associated factor(PCLAF), nucleolar and spindle-associated protein 1(NUSAP1) and topoisomerase Ⅱ-α(TOP2 A). Compared with para-cancerous tissues, normal pleural tissues or lung tissues, the relative expression of PCLAF, NUSAP1 and TOP2 A were increased in the MPM tissues(all P<0.05). Downregulation of these three genes was correlated with good prognosis, and upregulation of these three genes was correlated with poor prognosis in the patients. CONCLUSION: G2/M checkpoint, epithelial-mesenchymal transition, E2 F target gene and mitotic spindle pathway are the key signaling pathways in the occurrence and development of MPM. PCLAF, TOP2 A and NUSAP1 genes could be the biomarkers for the prognosis of MPM.

Expression of CHPF modulates cell proliferation and invasion in lung cancer

Lung cancer is the most common malignancy worldwide and is characterized by rapid progression, aggressive behavior, frequent recurrence, and poor prognosis. The TCGA database indicates that chondroitin polymerizing factor (CHPF) is overexpressed in human lung cancer tissues compared with normal tissues and this overexpression corresponds to shorter overall survival in lung cancer patients. In this study, to investigate the function of CHPF in lung cancer, lentiviral vectors expressing CHPF shRNA were stably transduced into A549 and H1299 cells. Compared to shCtrl cells, CHPF knockdown cells had significantly reduced proliferation. Furthermore, the silencing of CHPF in A549 and H1299 cells resulted in apoptotic induction, which led to decreased colony formation. Wound healing and transwell invasion assays revealed that CHPF could positively regulate the migration of lung cancer cells. The tumorigenic role of CHPF was also validated in nude mouse xenograft models. Affymetrix gene chip analysis indicated that CHPF regulated the proliferation and invasion of lung cancer cells through CDH1, RRM2, MKI67, and TNFRSF10B. We thus highlight CHPF as a novel target for lung cancer treatment.

Screening for Differentially Expressed Genes in Pancreatitis Cell Model Transfected With Ghrelin MiRNA by Gene Chip / 胃肠病学

Background: Previous studies suggest that ghrelin plays an important role in the pathogenesis of acute pancreatitis, but the mechanism is still unclear. Aims: To screen the differentially expressed genes in pancreatitis pancreatic acinar cells transfected with ghrelin miRNA by gene chip. Methods: Pancreatitis was induced by caerulin. AR42J cells were divided into ghrelin miRNA+caerulin group and negative control+caerulin group. AR42J cells were collected to extract RNA and synthesize ds-DNA, and was then hybridized with rat whole genome microarray for scanning and analyzing. Differentially expressed genes related to inflammation and calcium pathways were screened, and expressions of Bcl-2, caspase-8, caspase-12 were verified by RT-PCR. Results: For AR42J cells after intervention with ghrelin miRNA+caerulin, 2 938 differentially expressed genes were screened, including 1 435 up-regulated genes and 1 503 down-regulated genes. There were 60 differentially expressed genes involved in CAMP/Ca2+ signaling pathway and 199 differentially expressed genes involved in inflammation pathway. RT-PCR results showed that expressions of Bcl-2, caspase-12 were down-regulated and expression of caspase-8 was up-regulated in ghrelin miRNA+caerulin group, consistent with the results of gene chip. Conclusions: Gene chip can be used to screen the genes that play a key role in the process of pancreatitis pancreatic acinar cells transfected with ghrelin miRNA, and provide a theoretical basis and reference for the study of mechanism of endogenous ghrelin on pancreatitis pancreatic acinar cells.

Development and evaluation of thrombosis susceptibility gene chip / 吉林大学学报(医学版)

Objective: To explore the development methods and prelimnary clinical validation of thrombos susceptibility gene chip, and to illustrate a rapid and high-throughput method for detecting the thrombos susceptibility gene mutation. Methods: According to the published gene sequences of thrombotic susceptibility genes in GenBank, the reference probes and special probes were pointed on the glass slide. After ultraviolet crosslinking, thrombois susceptibility gene chip was eatablished. The validity of gene chip was tested by potive reference (mutant gene and normal gene at each detection site) and negative reference (distilled water) as templates, thereby performing PCR reaction. The specificity and sensitivity of gene chip were detected by using the human genome DNA of target sequence proven by sequencing as templates, thereby performng PCR reaction. Meanwhile 150 healthy subjects and 24 thrombosis patients with family hstory of unexplained thrombotic dsease from Jilin province, Henan provnce and Yunnan province were carried out the clinical verification of gene chip. The analyss index was the hybridization signal trength of the correspondng ite. Results: The hybridization results of postive reference and negative reference as templates showed that the specific hybridization signals appeared at the corresponding ites, which indicated that the detection sites of gene chip are effective. The gene chip used to detect the selected mutation sites had specific hybridization signals, suggesng there were good specificity of gene chip. The senstivity of gene chip was 50 - 100 mg · L-1 by testng genomic DNA with stepwise dilution. Eight individuals with thrombosis susceptibility gene mutations were found in 150 healthy subjects. Twenty ndividuals with thrombosis susceptibility gene mutations were found in 24 thrombosis patients with family hstory of unexplaned thrombotic dsease. The statistcs results showed that the detection rate of thrombosis susceptibility gene mutations in the thromboss patients with unexplaned thrombotic disease family history was significantly higher than that of the healthy subjects (P<0.05). Conclusion: The developed thrombosis susceptibility gene chip has great specificity, senstivity, and high detection rate of thromboss susceptibility genes. It has potental values in the early dagnosis and susceptibility sk assessment of thrombotic dseases.

Application potential of CD146 positive subpopulation as seed cells for cartilage tissue engineering / 中国组织工程研究

BACKGROUND: The development of regenerative medicine and the appearance of tissue engineering technology provide a new solution for cartilage defect reconstruction. In tissue engineering, mesenchymal stem cells are widely used seed cells. However, as a heterogeneous cell group, stem cells play different roles in different subsets. Therefore, the application of key functional subsets of mesenchymal stem cells in cartilage repair has a broad application prospect. OBJECTIVE: To sort CD146 positive subpopulation cells from human adipose-derived mesenchymal stem cells to verify their biological characteristics and potential as seed cells in cartilage tissue engineering. METHODS: Human adipose-derived mesenchymal stem cells were provided by Zhejiang Jinshidai Biotechnology Co., Ltd. Surface markers of human adipose-derived mesenchymal stem cells were identified by flow cytometry. CD146 positive subpopulation cells were sorted from human adipose-derived mesenchymal stem cells using magnetic-activated cell sorting. Molecular characteristics of two kinds of cells were analyzed by gene chip detection technology and bioinformatics analysis technology. Two kinds of cells were induced to chondrocytes in vitro and histologically examined. Cell viability and apoptosis of two kinds of cells were detected before and after cryopreservation. RESULTS AND CONCLUSION: Human adipose-derived mesenchymal stem cells highly expressed stem cell-associated markers CD73 and CD90, but did not express hematopoietic stem cell-associated markers CD34, CD45, and HLA-DR. Bioinformatics analysis results showed that CD146 positive subpopulation had different functions in inflammatory pathways and musculoskeletal diseases compared with human adipose-derived mesenchymal stem cells. CD146 positive subpopulation could differentiate into cartilage, and its chondrogenic differentiation ability was better than that of human adipose-derived mesenchymal stem cells. CD146 positive subpopulation had better apoptosis and activity than human adipose-derived mesenchymal stem cells after resuscitation. These results suggest that CD146 positive subpopulation has good chondrogenic differentiation potential and is a promising seed cell for cartilage tissue engineering.

Screening for differential genes of the esophageal squamous cell carcinoma after DDX46 knockdown and bioinformatics analysis of their interaction / 中国胸心血管外科临床杂志

@#Objective    To explore the mechanism of DDX46 regulation of esophageal squamous cell carcinoma. Methods    Picture signals of fluorescence in gene array were scanned and differential expression of gene in two groups (a DDX46-shRNA-LV group and a control-LV group) were compared by GCOSvL.4 software. These differential expressed genes were analyzed by bioinformatics methods finally, and validated by quantitative real time polymerase chain reaction (qRT-PCR) analysis. Results    According to the screening criteria of fold change ≥2 and P<0.05, 1 006 genes were differentially expressed after DDX46 knockdown, including 362 up-regulated and 644 down-regulated genes. Bioinformatics analysis and gene co-expression network building identified that these differentially expressed genes were mainly involved in cell cycle, proliferation, apoptosis, adhesion, energy metabolism, immune response, etc. Phosphatidylinositol 3-kinase (PI3K) was the key molecule in the network. The results of RT-qPCR were completely consistent with the results of gene microarra. Conclusion    Bioinformatics can effectively exploit the microarray data of esophageal squamous cell carcinoma after DDX46 knockdown, which provides a valuable clue for further exploration of DDX46 tumorigenesis mechanism and helps to find potential drug therapy.

Analysis of Gene Variation in Thymoma by Microarray / 中国肺癌杂志

BACKGROUND@#Thymoma is the most common malignant tumor in anterior mediastinum, and its specific pathogenesis is still unclear. This limits the study of targeted drugs for thymoma. The aim of the study is to investigate the genes and signal pathways of thymoma, and provide help for the research of thymic tumor pathogenesis using the technology of second-generation genechip to analyze thymoma.@*METHODS@#From January 2015 to December 2017, we analyzed 31 cases of thymoma by CapitaBio mRNA expression profile genechip technology, and then confirmed the genes by reverse transcription-polymerase chain reaction (RT-PCR).@*RESULTS@#We found some genes with different expression levels between thymoma and surrounding thymus tissue. Among them, six driving genes (FANCI, CAPD3, NCAPG, OXCT1, EPHA1 and MCM2) were significantly abnormal in thymoma. Some specific genes affected by copy-number variation were detected: E2F2, EphA1, CCL25 and MCM2 were significantly up-regulated, while IL-6, CD36, FABP4, SH2D1A and MYOC genes were significantly down-regulated. KEGG database analysis showed that the expression of 10 signaling pathway genes was generally up-regulated or down-regulated, such as systemic lupus erythematosus, viral oncogenes, primary immunodeficiency, cell cycle genes and p53 signaling pathway, which may be related to occurrence of thymoma.@*CONCLUSIONS@#We found a variety of genes abnormally expressed in thymoma, which will provide reference for the study of pathogenesis and biomarkers of thymoma in the future.

Effect of nano-silica dust exposure on gene expression of macrophages / 中国职业医学

OBJECTIVE: To detect the expression of differential expression genes(DEGs) on microarray chips of macrophages exposed to nano-silicon dioxide(SiO_2) dust, and to screen the leading signaling pathway of nano-SiO_2 dust exposure-related diseases. METHODS: The gene chip GSE13005 of RAW264.7 macrophage intervened by nano-SiO_2 dust was obtained from the public gene chip database developed by the National Center for Biotechnology Information. The macrophages in the control group were cultured in complete medium without adding SiO_2 dust, whereas the macrophages in the exposure group were treated with SiO_2 dust with the final concentrations of 5, 20, and 50 mg/L. The gene expression data of macrophages was analyzed by RMA Express 1.2.0 software and R language 3.5.1. The Kyoto Encyclopedia of Genes and Genomes(KEGG) was used to screen DEGs and perform gene ontology(GO) enrichment analysis on related genes and signaling pathways. RESULTS: A total of 67 DEGs of macrophages were screened after SiO_2 dust treatment, of which 48 genes were up-regulated and 19 genes were down-regulated. GO enrichment analysis results showed that the main functional items of participating DEGs were reaction of amine, regulation of viral genome replication,negative regulation of amino acid transport, ovulation, bronchodilator response, chemokine activity, negative regulation of muscle cell differentiation, response to lack of amino acid, positive regulation of glomerular mesangial cell proliferation, and positive regulation of vascular smooth muscle cell proliferation. KEGG signaling pathway analysis results suggested that DEGs could function through 7 signaling pathways including nuclear transcription factor-κB(NF-κB) signaling pathway, p53 signaling pathway, glioma, melanoma, toll-like receptor signaling pathway, renal cell carcinoma and salmonella infection. Further functional enrichment revealed that NF-κB signaling pathway changed most significantly after macrophages were exposed to nano-SiO_2 dust. CONCLUSION: Exposure to nano-SiO_2 could induce the abnormal expression of 67 genes in macrophages. The genes that participated in macrophage activation process induced by nano-SiO_2 dust exposure are related to NF kappa B signaling pathway.

Effects of zinc on placental gene expression in pregnant rats with fetal growth restriction / 西安交通大学学报(医学版)

Objective: To explore the effects of zinc on placental gene expression in pregnant rats with fetal growth restriction (FGR). Methods: FGR rat model was created, and then 36 pregnant rats were evenly divided into zinc group and control group. From the first day of pregnancy, rats in zinc group were fed on food with zinc supplementation, while those in control group were fed on tradational food. When pups were born 1 month later, Morris maze test and passive avoidance test were used. Gene chips were used to compare placental gene expression. Based on different genes detected by gene chip, we used Western blot to verify protein expression in placental tissues. Results: After training, the scores of Morris maze test and passive avoidance test both improved in both groups. From day 3, the scores in zinc group were significantly better than those in the control group (P of latent period of Morris maze test was 0.013, 0.024, 0.017; P of scores of passive avoidance test was 0.019 0, 0.003 7, and 0.004 3). Totally 346 different mRNAs were detected from the placental tissues by gene chips (P<0.01; 1

Study on the Effects of Danhong Injection on Gene Expression Profile of Acute Myocardial Infarction Model Rats by Gene Chip Technique / 中国药房

OBJECTIVE： To investigate the effects of Danhong injection （DHI） on gene expression profile of acute myocardial infarction （AMI） model rats. METHODS： Male SD rats were randomly divided into sham operation group， model group and DHI group （0.76 mL/kg）， with 10 rats in each group. AMI model was established by ligation of left anterior descending coronary artery in model group and DHI group. After modeling， sham operation group and model group were given constant volume of normal saline intramuscularly， and DHI group was given relevant medicine intramuscularly， once a day， for consecutive 14 days. After last administration， myocardial tissue in the marginal zone of infarction was separated. The change of gene expression profile was detected by gene chip technique. Using fold-change of relative expression as index， differentially expressed microRNA （miRNA） were screened. On the basis of retrieving their corresponding genes， gene ontology （GO） and KEGG pathway enrichment analysis were carried out by using DAVID bioinformatics resource database and KEGG pathway database， respectively. TargetScan database was used to predict the target gene messenger RNA （mRNA） corresponding to differentially expressed miRNA. Cytoscape 3.6.1 software was used to construct and analyze the miRNA-mRNA network. Agilent GeneSpring GX v11.5 software was used to screen target genes and miRNA related to inflammation in the above networks. RESULTS： Compared with sham operation group， there were 22 differentially expressed miRNAs in model group， 5 up-regulated and 17 down-regulated. Compared with model group， there were 26 differentially expressed miRNAs in DHI group， and all of them were up-regulated. The differentially expressed miRNAs related to DHI therapy for AMI included rno-let-7a-5p， rno-let-7d-5p， rno-let-7f-5p， rno-miR-26b-5p， rno-miR-29b-3p， cel-miR-39-3p， cel-miR-39-5p， rno-miR-142-5p， rno-miR-191a-5p， rno-miR-409a-3p. Results of GO analysis and KEGG pathway enrichment analysis showed that differentially expressed miRNAs were mainly concentrated in membrane-bound organelles， cytoplasm， endometrial system and other cell components. The molecular functions such as protein binding and ion binding were exerted through biological processes such as anatomical structure development， multicellular tissue development and development process，which were mainly enriched in calcium signaling pathway， PPAR signaling pathway， VEGF signaling pathway， cell apoptosis， glycosylphosphatidylinositol anchored biosynthesis， valine， leucine and isoleucine degradation， etc. miRNA-mRNA network analysis showed that there were 25 target gene mRNAs corresponding to differentially expressed miRNA and 24 miRNAs related to it. There were 6 inflammation-related target genes （IL6， IL1b， TNF， TLR4， CRP， CXCL12） in this network， involving 19 differentially expressed miRNAs. CONCLUSIONS： The therapeutic effect of DHI on AMI may be related to regulating the expression of related miRNA， affecting signal transduction of calcium ion， PPAR and VEGF pathways， and regulating the secretion of inflammatory markers such as interleukin， chemokine and C-reactive protein.

Characteristic bioanalysis of skeletal muscle cells gene markers in septic patients / 中华危重病急救医学

Objective To analyze the characteristics of skeletal muscle cells gene markers in septic patients by using bioinformatics. Methods The differential gene expression of marker microarrays (GSE13205) in skeletal muscle tissue of patients with sepsis was obtained from gene expression omnibus (GEO) database of National Center for Biotechnology Information (NCBI). Gene differential expression analysis was carried out using online GEO2R provided by NCBI. Data processing, analysis and mapping were carried out using online bioinformatics array research tool (BART) and Cytoscpe software, the software of the national resource for network biology. Functional annotation and pathway analysis of differential expression genes were performed using Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) provided by the database for annotation, visualization and integrated discovery (DAVID), and protein interaction analysis was further performed in search tool for the retrieve of interacting genes/proteins (STRING-DB). Results The TOP250 genes were extracted from the GSE13205 dataset. A total of 242 differentially expressed genes were included in the analysis. Among them, 78 up-regulated genes and 164 down-regulated genes were identified. After extensive data analysis, these differentially expressed genes were enriched into different biological processes or subsets of molecular functions, mainly enriched in the positive and negative regulation of growth, mineral absorption and other pathways. The 14 most closely related genes among differentially expressed genes were identified from the protein interaction network. Conclusion The differential expression genes in patients with sepsis were mainly concentrated on cell growth and apoptosis and mediating tumor-related immune function regulation.

Shenxiong Glucose Injection inhibits H_2O_2-induced apoptosis of H9c2 cells by activating PI3K/AKT pathway / 中国中药杂志

The aim of this paper was to explore the mechanism of Shenxiong Glucose Injection antagonizing apoptosis of H9 c2 cells induced by H_2O_2. H9 c2 cells were pretreated with 1. 7%,3. 4% and 6. 8% Shenxiong Glucose Injection,and then H_2O_2 was introduced to induce apoptosis in vitro. Cell viability was detected by MTS assay,morphological changes of apoptosis were observed by AO/EB fluorescence staining,apoptosis rate was detected by Annexin/PI method,cell expression profile was detected by gene chip technology,the mRNA of PIK3 CA,Bcl-2,Bax,caspase-3 and GAPDH were detected by qRT-PCR,the protein expression levels of PIK3 CA,AKT,P-AKT,Bcl-2,Bax and caspase-3 were detected by Western blot,and the contents of LDH and MDA were detected by kit. The results showed that Shenxiong Glucose Injection of different concentrations significantly increased the viability of H9 c2 cells treated with H_2O_2( P<0. 01),and reversed H_2O_2-induced apoptosis( P< 0. 01). The microarray experiments showed that 138 genes were altered in H9 c2 cells after treatment with Shenxiong Glucose Injection. The differential expression fold of PIK3 CA associated with PI3 K/AKT pathway was 3. 59. The results of qRT-PCR and Western blot showed that Shenxiong Glucose Injection could down-regulate the mRNA and protein expression levels of caspase-3( P<0. 01),up-regulate the mRNA and protein expression level of PIK3 CA and Bcl-2( P<0. 01),and up-regulate the phosphorylation levels of AKT( P<0. 01) in H_2O_2-treated H9 c2 cells. The protective effect of Shenxiong Glucose Injection on H_2O_2 cells injury was significantly inhibited by LY294002,a PI3 K/AKT pathway inhibitor. The results suggested that Shenxiong Glucose Injection may inhibit H_2O_2-induced H9 c2 cells apoptosis by regulating PI3 K/AKT signaling pathway.

Effect of midkine on expression of non-coding RNA in ovarian cancer / 临床检验杂志

Objective@#To explore the correlation of non-coding RNA and the tumor-associated antigen midkine (MK) in SKOV3cells and the clinical significance for diagnosis of ovarian cancer. @*Methods@#The Agilent′s gene chips (miRNAs chip and lncRNAs chip) were used to analyze the differential expression of miRNAs and lncRNAs in both MK-overexpressing SKOV3-MK cells and the control SKOV3-Con cells to screen the potential biomarkers in ovarian cancer. The clinical significance of midkine in the serum and tissues samples was analyzed for the patients with ovarian cancer by quantitative PCR combined with clinical data. @*Results@#Compared with control SKOV3-con cells, MK overexpression significantly promoted the expressions of 11 miRNAs and 7 lncRNAs in SKOV3 cells (P＜0.01, ratio＞3 fold), reduced the expressions of 8 miRNAs and 13 lncRNAs (P＜0.01, ratio＜0.3). Results of qPCR showed that the expression level of miR489 was significantly lower in ovarian cancer tissues than that of the contralateral normal ovarian tissues, while HOTAIR was significantly elevated (P＜0.05). The expression level of HOTAIR in the serum of ovarian cancer patients was significantly higher than that in healthy controls group with same age (0.036±0.024 vs 0.019±0.020, P=0.002). ROC curve analysis of HOTAIR showed that the specificity was 66.7%, the sensitivity was 75.6% and the AUC value was 0.749 as a marker for serum detection of ovarian cancer when the cutoff value was 0.017 6. @*Conclusion@#Long-chain non-coding RNA HOTAIR may be served as a potential biomarker in serum of ovarian cancer patients.

Differential expression analysis of circRNA in peripheral blood of tuberculosis patients in Xinjiang / 临床检验杂志

Objective@#To find the differential expression profiles of circRNA in whole blood and predict its target genes in blood of patients with tuberculosis in Xinjiang, and explore the relationship between circRNA and the development of tuberculosis. @*Methods@#The circRNAs expression in peripheral blood from 3 pulmonary tuberculosis patients and 3 healthy individuals were tested by using circRNA microarray assay. The whole blood from 43 patients with tuberculosis, 40 healthy individuals and 43 patients with pneumonia were collected to verify the results by real-time quantitative PCR system. The possibility of differentially expressed circRNA target genes were predicted by circRNA target gene prediction database. @*Results@#In the results of microarray assay 835 circRNAs were found to be expressed differentially in whole blood between the tuberculosis patients and healthy controls of Xinjiang area, of which 249 circRNAs were up-regulated and 586 circRNAs were down-regulated in the patients. The expressions of four significantly different circRNA were verified by real time quantitative PCR and the results showed that hsa_circ_0008276, hsa_circ_0003452, hsa_circ_0001846 and hsa_circ_0090508 were down-regulated (P＜0.05), and hsa_circ_0090508 was the more specific than the other three circRNAs. The results of circRNA target genes prediction suggested that has-miR-1294, has-miR-604, has-miR-616, has-miR-663b and has-miR-486-3p may be the potential target genes of hsa_circ_0090508. @*Conclusion@#The differentially expressed circRNA hsa_circ_0090508 was significantly downregulated in the patients with tuberculosis and may affect the regulation mechanism of tuberculosis through target genes.

Differential expression analysis of circRNA in peripheral blood of tuberculosis patients in Xinjiang / 临床检验杂志

Objective@#To find the differential expression profiles of circRNA in whole blood and predict its target genes in blood of patients with tuberculosis in Xinjiang, and explore the relationship between circRNA and the development of tuberculosis. @*Methods@#The circRNAs expression in peripheral blood from 3 pulmonary tuberculosis patients and 3 healthy individuals were tested by using circRNA microarray assay. The whole blood from 43 patients with tuberculosis, 40 healthy individuals and 43 patients with pneumonia were collected to verify the results by real-time quantitative PCR system. The possibility of differentially expressed circRNA target genes were predicted by circRNA target gene prediction database. @*Results@#In the results of microarray assay 835 circRNAs were found to be expressed differentially in whole blood between the tuberculosis patients and healthy controls of Xinjiang area, of which 249 circRNAs were up-regulated and 586 circRNAs were down-regulated in the patients. The expressions of four significantly different circRNA were verified by real time quantitative PCR and the results showed that hsa_circ_0008276, hsa_circ_0003452, hsa_circ_0001846 and hsa_circ_0090508 were down-regulated (P＜0.05), and hsa_circ_0090508 was the more specific than the other three circRNAs. The results of circRNA target genes prediction suggested that has-miR-1294, has-miR-604, has-miR-616, has-miR-663b and has-miR-486-3p may be the potential target genes of hsa_circ_0090508. @*Conclusion@#The differentially expressed circRNA hsa_circ_0090508 was significantly downregulated in the patients with tuberculosis and may affect the regulation mechanism of tuberculosis through target genes.

Genetic Screening of Deaf Mutation for 2545 Newborn / 中国康复理论与实践

Objective:To investigate the mutative rate and spectrum of common hereditary deafness genes in Chinese. Methods:Heel blood samples from 2545 infants born from January to October, 2018, were collected, and screened with microarray chip. Results:There were 119 children with mutation of deafness gene, including 60 cases (2.36%) with GJB2 mutation, male/female = 1∶1 (30/30); 48 (1.88%) with SLC26A4 mutation, male/female nearly 1∶1 (26/22); five (0.20%) with mutation of mitochondrial 12S rRNA gene; five (0.20%) with GJB3 mutation; one (0.04%) with heterozygosis in GJB2 235 and SLC26A4 IVS7-2 mutation. Other more, mutations of 1174A > T, 1229C > T and 15+5G>A of SLC26A4 were found in one child, respectively. Conclusion:The distribution of deafness gene loci has been investigated, which can be reference for prevention and control of hereditary deafness in Chinese.