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Objective:To mining differential expression genes (DEGs) and establish a regulatory network of dysregulated microRNAs (miRNAs) and messenger RNAs (mRNAs) in biliary atresia (BA) spectrum via bioinforma-tics analysis, and to explore the pathogenesis of BA.Methods:GSE46960 dataset was download from gene expression omnibus (GEO). DEGs between normal liver tissues and BA tissues were analyzed using the GEO2R analysis tool.The functional and pathway enrichment analyses of DEGs were performed utilizing the Database for Annotation, Visualization and Integrated Discovery (DAVID6.8). A protein-protein interaction (PPI) network was constructed using the PPI database (STRING11.0) and Cytoscape_v3.7.1 software, and thus key genes were analyzed.BA-related miRNAs were obtained using the human miRNA disease database (HMDD_V3.0) and target mRNAs were predicted by the miRNA target prediction database (miRDB). The intersection between the predicted target mRNAs and DEGs from the GSE46960 dataset was selected.The regulatory network of miRNA-mRNA was constructed using Cytoscape software.Results:A total of 565 DEGs, including 352 up-regulated ones and 213 down-regulated ones were identified.Among them, up-regulated DEGs were enriched in extracellular matrix(ECM)-receptor interaction, focal adhesion kinase (FAK), Amoebiasis, and the phosphoinositide 3 kinase/protein kinase B(PI3K/Akt) pathway.Down-regulated DEGs were enriched in metabolic signaling, biosynthesis of antibiotics and steroid biosynthesis pathway.From the PPI network, 10 key genes were screened out.A complex miRNA-mRNA regulatory network was constructed based on screened DEGs.Conclusions:Identified DEGs and miRNA-mRNA regulatory network constructed in this study may help clarify the molecular mechanisms of BA.This study provides a new direction to explore promising molecular targets for the diagnosis and treatment of BA.
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Objective To investigate the dynamic changes of gene expressions in mouse jejunum after lethal dose abdomen irradiation (ABI).Methods RNA was extracted from mouse jejunum at 0 and 6 h,3.5 and 5 d after 14 Gy 137Cs γ-ray ABI and then subjected to RNA-sequence analysis.Gene with expressions changed more than 2-fold of control were identified as differentially expressed ones.The selected genes were subsequently analyzed using IPA,Funrich,GO and KEGG software.Results Gene analysis of mouse jejunum samples showed that radiation activated p53 pathway at 6 h and 3.5 d after ABI.Interaction network analysis of genes suggested that Lck,Cdkl and Fyn,genes could play an important role in jejunum damage at 3.5 d after ABI.The gene expression profiles demonstrated that ABI up-regulated DNA damage repair pathways and down-regulated cell adhesion molecules,focal adhesion and IgA production pathways.Conclusions The p53 signaling pathway and some key genes such as Lck,Cdkl,and Fyn may contribute to the radiation-induced intestinal injury.
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Objective To isolate and identify differential expression genes associated with multidrug resistance of leukemia . Methods Differential expression genes between leukemia cell line K 562 and resistant cell lines K562/DOX were isolated by using suppression subtractive hybridization (SSH) technique .Total RNA were extracted .cDNA were synthesized and digested by restric-tion enzyme Rsa Ⅰ ,then connected with adopter1 and adopter2R ,and linked with pMD19-T vector .Constructed vectors were trans-ferred into E .coli .Subtracted cDNA library was constructed ,and the positive clones were screened according to base sequences and homologous sequences .The differential expression genes were indentified by comparison analysis of Gene Bank database .Results A total of 220 differential expression genes were sequenced ,including hemoglobin ,ribosomes and mitochondria related genes ,and heat shock factor binding protein 1 (HSPB1) gene and other genes .Conclusion SSH method and molecular cloning technique could be used to construct subtracted cDNA library of differential expression genes between drug resistant and not -resistant leukemia cells , which might be useful for further screening and cloning of differential expression genes of multidrug resistant tumor cells .
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Objective To obtain differential expression genes from colorectal cancer cells derived from colo205 for further research. Methods RNA from colo205 cells,CD133+cells and CD133-cells were sequenced and analyzed by bioinformatics software. Results One hundred and twenty four differential expression genes were obtained, which involves 32 metabolic pathways. Conclusions Large quantities of differential genes can be found among different groups of cells derived from colo205 cells , which can provide epigenetic evidence for colorectal cancer research.
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Objective: To screen for the differentially expressed genes during irradiation-induced malignant transformation of human bronchus epithelium cells (BEAS-2B). Methods: Suppression subtraction hybridization (SSH) was used to construct a subtracted cDNA library of differentially expressed genes during irradiation-induced malignant transformation of BEAS-2B cells. Then the subtracted library was screened by PCR and the differential fragments were sequenced and analyzed with BLAST. Fluorescent real-time quantitative PCR was used to investigate some of the differentially expressed genes. The new EST was registered in GenBank. Results: Then 40 clones were chosen to be sequenced from the library of increased expression and decreased expression respectively according to the length of insertion element. Totally 73 sequences were obtained from the 80 sequenced clones. Forty-one sequences were decreased in the transformed cells; BLAST analysis indicated that there were 6 known sequences, 20 unknown sequences, 7 void sequences and 8 repeated sequences. Thirty-two sequences were increased in the transformed cells; Blast analysis indicated that there were 14 known sequences, 9 unknown sequences, and 9 repeated sequences. Fluorescent quantitative PCR revealed that, compared with control group, the expression of MY06, HACE1, ZNF143, and HNRPH1 were significantly increased in the radiation transforming group, with their mRNAs increased by 3.49, 29.38, 12.99 and 5.00 folds, respectively. Compared with control group, the expression of PCBP2, RPL15, and TCERG1 in the radiation transforming group was significantly decreased, with their mRNAs decreased by 1.89,48.77 and 11.95 folds, respectively. The 29 unknown sequences were registered in the GenBank (ID: EB643220-EB643248). Conclusion: The cDNA library has been successfully established for malignant transformation cellular model by suppression subtractive hybridization; the library includes a number of unknown genes. The increased gene ZNF143 is associated with cell proliferation and cell division. TCERG1, as an assistant transcription activation factor, plays an important role in the mRNA transcription and later modification. PCBP2, a Polyc connection protein, plays a modulating role in protein translation. These genes have not been reported in the radiation carcinogenicity.
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Objective To screen and identify the differential expression genes on peripheral blood cells of mice based on the experimental animal model of radon exposure. Methods BALB/c mice were exposed in a type HD-3 multifunctional radon-room, with the accumulative doses of radon-exposure group at 105 WLM and control group at 1 WLM. Total RNA was extracted from peripheral blood cells and the methods of SMART for dscDNA synthesis and SSH for gene screening was applied. With the construction of the cDNA library enriched with differentially expressed genes, the pMD 18-T plasmid containing LacZ operator at the multiple cloning site was used to allow a blue-white screening. The TA clones were amplified by nested PCR and the reverse Northern blot was used to identify up and down regulation of the clones. The differently expressed cDNA was then sequenced and analyzed. Results The subtracted cDNA libraries were successfully constructed. A total of 390 recombinant white colonies were randomly selected. Among the 312 cDNA monoelones selected from bath forward- and reverse-subtracted libraries,41 clones were chosen to sequence for their differential expressions based on reverse Northern blot. Among the 41 sequenced clones, 10 clones with known function/annotation and 3 new ESTs with the GenBank accession numbers were obtained. Most of the known function/annotation genes were revealed to be related with cell proliferation, metabolism, cellular apoptosis and carcinogenesis. Conclusions The animal model of radon exposure was established and the cDNA library of peripheral blood cells was suceessfully constructed. Radon exposure could up- and down-regulate a series of genes. Differentially expressed genes could be identified by using SSH technique and the results may help exploring mechanisms of random exposure.