ABSTRACT
Objective:To investigate the effect of metformin on the microRNA (miRNA) expression and screen potential target with network pharmacology analysis in patients with type 2 diabetes.Methods:Fifteen patients with new diagnosed type 2 diabetes admitted to our hospital were selected, who received metformin during hospitalization and after discharge. The expression of serum matrix metalloproteinase (MMP)-9, transforming growth factor (TGF)-β1, and myocardial fibrosis related miRNAs were compared before and 6 month after metformin treatment. In addition, gene ontology (GO) and KEGG pathway enrichment analysis were applied to analyze differential expression miRNAs showing statistical significance. Meanwhile, the network figure was established to reflect the target gene messenger RNA (mRNA) corresponding to differentially expressed miRNA.Results:Compared with pre-medication, the serum level of MMP-9 was significantly decreased after treatment ( P<0.05). Besides, the expression of homo sapiens microRNA (hsa-miR)29a-3p, hsa-miR133a-5p, hsa-miR21-5p, hsa-miR30c-5p, and hsa-miR1-3p in patients with type 2 diabetes were dramatically down-regulated by metformin ( P<0.05 or P<0.01). Results of GO analysis and KEGG pathway enrichment analysis showed that differentially expressed miRNAs were mainly concentrated in endoplasmic reticulum lumen, synapse, basement membrane and other cell components. The molecular functions such as Rho GTPase binding and participation in extracellular matrix structural constituent were exerted through biological processes such as collagen catabolic process, regulation of short-term neuronal synaptic plasticity, and axon extension, which were mainly enriched in advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathway in diabetic complications, tumor necrosis factor (TNF) signaling pathway, and Wnt signaling pathway, etc. The outcome of miRNA-mRNA network analysis demonstrated that there were 230 target genes mRNAs corresponding to differentially expressed miRNA. Conclusion:Metformin could play its role in the treatment of type 2 diabetes by down regulating the expression of miRNA, participating in the transduction of related cellular signaling pathways, regulating chromatin, nucleic acid binding, and enzyme activities.
ABSTRACT
To explore the mechanism of Shouhui Tongbian Capsules in treating constipation by means of network pharmacology and molecular docking approach. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) and Bioinfoematics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine(BATMAN) were applied to obtain chemical components and potential targets of eight herbs in Shouhui Tongbian Capsules according to the screening principles of oral availability(OB)≥30% and drug-like property(DL)≥0.18. Disease targets relating to constipation were screened out through GeneCards, PharmGkb and other databases, drug targets were integrated with disease targets, and intersection targets were exactly the potential action targets of Shouhui Tongbian Capsules for treating constipation; PPI network of potential targets was constructed using STRING platform, and GO(gene ontology) analysis and KEGG(Kyoto encyclopedia of genes and genomes) pathway data were obtained to conduct enrichment analysis and predict its mechanism of action. Cytoscape 3.6.1 was used to construct a network of "medicinal materials-chemical components-drug targets", and the network topology analysis was carried out on the PPI network to obtain its main components and key targets. Molecular docking between components and key targets of Shouhui Tongbian Capsules verified the accuracy of network pharmacological analysis results. The PPI network analysis showed 92 chemical components, including quercetin, stigmaste-rol, aloe-emodin, rhein, and key targets for instance AKT1, MAPK1, IL6, JUN, TNF and TP53. The enrichment analysis of KEGG screened out 157 signal pathways(P<0.01), mainly involving interleukin 17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, thyroid hormone signaling pathway. Quercetin, resveratrol and lysine with top degree value had a rational conformation in docking site of protein crystal complexes. This study preliminarily showed that various active ingredients in Shouhui Tongbian Capsules could regulate multiple signaling pathways, increase intestinal smoothness and peristalsis function, ensure smooth intestinal lumen, and play a role in treating constipation by acting on key targets, such as AKT1, MAPK1, IL6 and JUN.
Subject(s)
Humans , Capsules , Constipation/genetics , Drugs, Chinese Herbal , Medicine, Chinese Traditional , Molecular Docking SimulationABSTRACT
@#Objective: To explore the genes that may be regulated by cell division cycle 25A (CDC25A) with gene chip technology, and to elucidate and verify that CDC25A has a regulatory effect on the expression of liver cancer related genes. Methods: CDC25A expression in human liver cancer HepG2 cells was silenced by siRNA interference technology and a nude mouse xenograft model of liver cancer was successfully constructed in our previous research. Affymetrix human gene expression profiling microarray was used to further screen differentially expressed genes (DEGs) after silencing CDC25A in liver cancer xenografts, and GO analysis and KEGG analysis were performed. Some of the DEGs were verified by qPCR. Results: The chip screened 188 DEGs in liver cancer xenograft tissues after CDC25A silence, including 78 up-regulated genes and 110 down-regulated genes. These DEGs mainly involved in cell proliferation, apoptosis, protein complex binding, extracellular space, etc., and associated with the changes in pathways such as focal adhesions and extracellular matrix (ECM) receptor interactions. qPCR showed that the expression of HIPK2 mRNA was up-regulated and the mRNA expressions of (microfibrillar-associated protein 5(MFAP5) and cyclin D1 (CCND1) were down-regulated, which were consistent with the results of microarray detection. Conclusion: Using human gene expression profiling chip, the DEGs in liver cancer xenograft tissues in nude mice after silencing CDC25Awere successfully screened, providing effective clues for exploring the effect of CDC25Aon the growth of liver cancer.
ABSTRACT
BACKGROUND: Whole-genome expression profiling is a technical method for gene expression research, with high sensitivity and specificity. This technique can be used to detect differential genes related to chronic periodontitis in the whole genome, therefore efficiently and quickly finding chronic periodontitis-related factors. OBJECTIVE: To screen genes related to chronic periodontitis by using the whole-genome expression profiling. METHODS: Normal periodontal ligament tissue of 15 patients with orthodontic extraction was selected as control group, and periodontal tissue of 21 patients with chronic periodontitis was selected as experimental group. To screen up-regulated and down-regulated genes. the genome-wide expression profile chips of four chronic periodontitis tissues and four healthy tissues were compared. The expression of the differential gene PI3K-Akt signal pathway was verified by real-time PCR (7 normal cases and 13 cases of chronic periodontitis) and western blot (4 normal cases and 4 cases of chronic periodontitis). The experimental protocol was approved by the Ethics Committee of the First Affiliated Hospital of Hainan Medical University (approval No. HNM20180034) and informed consent was obtained from each patient. RESULTS AND CONCLUSION: Analysis of the whole genome expression profile chip revealed that 1 565 up-regulated genes and 1 849 down-regulated genes were significantly differentially expressed in chronic periodontitis samples. The enrichment analysis revealed that the expression of PI3K-Akt signaling pathway was significantly different in chronic periodontitis (P < 0.001). Real-time PCR and western blot assay results indicated that PI3K and Akt expression was higher in the experimental group than in the control group (P < 0.05). All the findings indicate that the genome-wide expression profile chip is fast and highly sensitive to screen the changes in chronic periodontitis-related genes. Significantly differential expression of PI3K-Akt signal pathway in chronic periodontitis provides an experimental basis for the treatment of chronic periodontitis.
ABSTRACT
Objective To analyze and identify the protein of patients with IgA nephropathy for identification and quantitative a-nalysis using the combination of liquid chromatography and mass spectrometry which combined isobaric tags for relative and abso-lute quantification .Methods Proteomic analysis of renal tissue in patients with IgA nephropathy and normal controls was per-formed to identify different expressed proteins .Results A total of 1860 proteins were identified ,287 proteins were upregulated in renal tissue of IgA nephropathy patients ,287 proteins were downregulated significantly ,finally 9 upregulated proteins and 8 down regulated proteins were identified(protein fold difference greater than 1 .5) .Conclusion Quantitative proteomic technology is effi-ciently applicable for identification and relative quantitation of proteome in renal tissue ,which could get all the information of differ-ent protein .This is useful for us to better understand the relationship of protein and the pathogenesis of IGA nephropathy .
ABSTRACT
Objective To explore the difference of gene expression profiling between normal basilar arteries and basilar arteries of cerebral vasospasm (CVS) after subarachnoid hemorrhage (SAH) in rabbits. Methods cDNA chip of normal basilar arteries and basilar arteries of CVS after SAH in rabbits were downloaded from GEO database. The chip was analyzed and screened by Bioconductor software, and function enrichment and pathway analysis of the differentially expressed genes were analyzed by Cytoscape software. Then 6 adult male Japanese rabbits were used, and randomly divided into normal control group (n=3) and SAH model group (n=3). Rabbit SAH models were established by cisterna secondary-blood-injection method. RNA data of normal basilar artery specimens on the 0 day and basilar artery specimens after SAH on the 5-day were used to validate the parts of differentially expressed genes by qRT-PCR. Results A total of 4356 differentially expressed genes were found in normal basilar arteries and basilar arteries of CVS after SAH in rabbits. Among them, 920 genes were considered to be significant with P-value<0.05, such as GRIK1, MYH13, ZNF45, SAA3, RLN1, MSR1 and others. Function enrichment analysis indicated that the differentially expressed genes were involved in regulation of Ca2+transmembrane transporter activity, negative regulation of ion transmembrane transport, regulation of potassium ion transport, positive regulation of JAK-STAT signaling cascades and other biological processes. Pathway analysis showed that calcium signaling pathway, cGMP-PKG signaling pathway, HIF-1 signaling pathway, PI3K-Akt signaling pathway and other signaling pathways maybe related with the differentially expressed genes. qRT-PCR verification showed that the expression of MSR1 in SAH model group was consistent with that of the chip result. Conclusion The gene expressions of basilar arteries of CVS after SAH in rabbits are significantly different, and MSR1 gene can be used as a potential target for studying the pathological mechanism of CVS.
ABSTRACT
Objective To analyze and identify the protein of patients with IgA nephropathy for identification and quantitative a-nalysis using the combination of liquid chromatography and mass spectrometry which combined isobaric tags for relative and abso-lute quantification .Methods Proteomic analysis of renal tissue in patients with IgA nephropathy and normal controls was per-formed to identify different expressed proteins .Results A total of 1860 proteins were identified ,287 proteins were upregulated in renal tissue of IgA nephropathy patients ,287 proteins were downregulated significantly ,finally 9 upregulated proteins and 8 down regulated proteins were identified(protein fold difference greater than 1 .5) .Conclusion Quantitative proteomic technology is effi-ciently applicable for identification and relative quantitation of proteome in renal tissue ,which could get all the information of differ-ent protein .This is useful for us to better understand the relationship of protein and the pathogenesis of IGA nephropathy .
ABSTRACT
Objective To study the effects of anti -cancer drug NSC319726 on the gene expression of ovarian cancer.Methods The data that NSC319726 acted on the ovarian cancer cell lines TOV112D was down-loaded from the GEO database and then the bioinformatical analysis was conducted .Results NSC319726 in-creased 246 genes including MMP3,CXCR4 et al and decreased 198 genes such as PBX1 in ovarian cancer cell lines.GO analysis indicated that six GO items were related to metabolism .Pathway analysis revealed that NSC319726 could affect the circadian clock and MMP signaling pathway .Conclusion NSC319726 could affect the expression of multiple functional genes in ovarian cancer cell lines and might be a potential drug targeting to the precursor-B cell acute lymphoblastic leukemia .Meanwhile , it should be noted that NSC 319726 may have effects on the tumor metastasis and human sleep .Therefore,further research needs to be conducted before the clinical use .
ABSTRACT
Background and purpose:Inlfammatory bowel diseases (IBD) are a group of chronic intestinal diseases, including ulcerative colitis (UC) and Crohn’s disease (CD). This study identified differentially expressed miRNAs in UC, CD and colitis-associated colorectal cancers (CAC) to explore their potential as novel molecular biomarkers. Methods:Tissue samples were taken from 13 UC patients, 3 CD patients, 12 CAC patients, and 8 age-and gender-matched healthy controls. The miRNA expressions were detected by real-time fluorescent quantitative polymerase chain reaction (RTFQ-PCR) assay. Known targets of deregulated miRNAs were utilized using miRWalk 2.0 database, and subsequent bioinformatics analysis of these target genes was performed by DAVID software (GO-analysis, KEGG-analysis and BIOCARTA-analysis). Results:The data showed that miR-146a, miR-27a, miR-29a, miR-20a and miR-21 were upregulated in UC, CD and CAC tissues compared with normal control. Moreover, the target genes of these miRNAs were enriched in several key signal transduction pathways including cancer-related pathway and immu-nity-associated pathway. Conclusion:miR-146a, miR-27a, miR-29a, miR-20a and miR-21 may play important roles in the switching from IBD to CAC.
ABSTRACT
Background Isothiocyanates (ITCs) are natural products obtained from plants of the Brassicas family. They represent an environmentally friendly alternative for the control of phytopathogenic fungi. However, as it has been observed with synthetic fungicides, the possibility of inducing ITC-resistant strains is a major concern. It is, therefore, essential to understanding the molecular mechanisms of fungal resistance to ITCs. We analyzed a subtractive library containing 180 clones of an Alternaria alternata strain resistant to 2-propenyl ITC (2-pITC). After their sequencing, 141 expressed sequence tags (ESTs) were identified using the BlastX algorithm. The sequence assembly was carried out using CAP3 software; the functional annotation and metabolic pathways identification were performed using the Blast2GO program. Results The bioinformatics analysis revealed 124 reads with similarities to proteins involved in transcriptional control, defense and stress pathways, cell wall integrity maintenance, detoxification, organization and cytoskeleton destabilization; exocytosis, transport, DNA damage control, ribosome maintenance, and RNA processing. In addition, transcripts corresponding to enzymes as oxidoreductases, transferases, hydrolases, lyases, and ligases, were detected. Degradation pathways for styrene, aminobenzoate, and toluene were induced, as well as the biosynthesis of phenylpropanoid and several types of N-glycan. Conclusions The fungal response showed that natural compounds could induce tolerance/resistance mechanisms in organisms in the same manner as synthetic chemical products. The response of A. alternata to the toxicity of 2-pITC is a sophisticated phenomenon including the induction of signaling cascades targeting a broad set of cellular processes. Whole-transcriptome approaches are needed to elucidate completely the fungal response to 2-pITC.
Subject(s)
Isothiocyanates , Drug Resistance, Fungal , Alternaria/genetics , Alternaria/metabolism , Fungicides, Industrial , Computational Biology , Subtractive Hybridization Techniques , Hybridization, GeneticABSTRACT
Eichhornia crassipes is an aquatic plant native to the Amazon River Basin. It has become a serious weed in freshwater habitats in rivers, lakes and reservoirs both in tropical and warm temperate areas worldwide. Some research has stated that it can be used for water phytoremediation, due to its strong assimilation of nitro- gen and phosphorus, and the accumulation of heavy metals, and its growth and spread may play an important role in environmental ecology. In order to explore the molecular mechanism of E. crassipes to responses to nitrogen deficiency, we constructed forward and reversed subtracted cDNA libraries for E. crassipes roots under nitrogen deficient condition using a suppressive subtractive hybridization (SSH) method. The forward subtraction included 2 100 clones, and the reversed included 2 650 clones. One thousand clones were randomly selected from each library for sequencing. About 737 (527 unigenes) clones from the forward library and 757 (483 unigenes) clones from the reversed library were informative. Sequence BlastX analysis showed that there were more transporters and adenosylhomocysteinase-like proteins in E. crassipes cultured in nitrogen deficient medium; while, those cultured in nitrogen replete medium had more proteins such as UBR4-like e3 ubiquitin- protein ligase and fasciclin-like arabinogalactan protein 8-like, as well as more cytoskeletal proteins, including actin and tubulin. Cluster of Orthologous Group (COG) analysis also demonstrated that in the forward library, the most ESTs were involved in coenzyme transportation and metabolism. In the reversed library, cytoskeletal ESTs were the most abundant. Gene Ontology (GO) analysis categories demonstrated that unigenes involved in binding, cellular process and electron carrier were the most differentially expressed unigenes between the forward and reversed libraries. All these results suggest that E. crassipes can respond to different nitrogen status by efficiently regulating and controlling some transporter gene expressions, certain metabolism processes, specific signal transduction pathways and cytoskeletal construction.
Se ha convertido en una maleza importante en hábitats de agua dulce en ríos, lagos y embalses, tanto en zonas tropicales como templadas de todo el mundo. Algunas investigaciones han indicado que se puede utilizar para la fitorremediación de agua, debido a su fuerte asimilación de nitrógeno y fósforo, y la acumulación de metales pesados, su crecimiento y propagación puede desempeñar un papel importante en la ecología ambiental. Con el fin de explorar el mecanismo molecular de respuesta a la deficiencia de nitrógeno en E. crassipes, se construyeron bibliotecas de cDNA mediante síntesis adelantada y retrasada para raíces de E. crassipes en condiciones de deficiencia de nitrógeno mediante el método de hibridación supresiva sustractiva (SSH). Para este estudio se utilizaron 2 100 clones de síntesis adelantada y 2 650 de síntesis retrasada. De la biblioteca se escogieron al azar mil clones, 737 (527 unigenes) de síntesis adelanta- da y 757 (483 unigenes) de síntesis retrasada que fueron informativos. El análisis BLASTX mostró que había más transportadores y proteínas adenosilhomocisteinasa en E. crassipes cultivadas en un medio deficiente de nitrógeno; mientras que las cultivadas en un medio repleto de nitróge- no tenían más proteínas como UBR4 e3 ubiquitina-proteína ligasa y la proteína arabinogalactano 8 tipo fasciclina, así como otras proteínas del citoesqueleto, incluyendo la actina y la tubulina. Clúster del Grupo Ortológico (COG) también demostró que en la biblioteca de síntesis adelan- tada, la mayoría de los marcadores de secuencia expresada (ESTs) estaban involucrados en el transporte de coenzimas y el metabolismo.
Subject(s)
Environmental Restoration and Remediation , Expressed Sequence Tags , Eichhornia/genetics , Genes, Plant , Nitrogen/metabolism , Phosphorus/metabolism , Eichhornia/classification , Eichhornia/metabolism , Gene Library , Nitrogen/deficiency , Polymerase Chain ReactionABSTRACT
Objective To explore the differential expression of microRNAs (miRNAs) in Burkitt lymphoma (BL) and their potential use as biomarkers for BL diagnosis.Methods The different miRNAs in BL from reactive hyperplasia of lymph node cases were screened by miRNA chip.The potential targets of miRNAs were predicted using miRWALK.MAS3 program was used to determine the putative functions of potential miRNA target genes by annotation using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.Results A total of 46 miRNAs (36 upregulated and 21 downregulated) were dysregulated in BL compared with reactive hyperplasia of lymph node.Interestingly,members of the let-7 family (let-7f-1-3p) was downregulated in BL.The target genes of let-7f-1-3p were predicted,and the GO enrichment analysis revealed their functions were mainly related with multicellular organismal development and regulation of transcription from RNA polymerase Ⅱ promote.KEGG pathway analysis was also carried out among the predicted target genes,which showed that they were mainly involved in TGF-beta signaling pathway and related with chronic myeloid leukemia.Conclusions The set of differentially expressed miRNAs identified here expands the range of potential diagnostic markers for BL.
ABSTRACT
Objective To compare the gene expression difference between 0.1 and 5 Gy X-ray irradiated cells,and to explore its possible mechanism.Methods A cDNA microarray corresponding to 45033 human genes was used to analyze the transcriptional profiles of normal human lymphoblastoid AHH-1 cells at 4 h after 0.1 or 5 Gy irradiation.The genes with a fold change ≥ 2.0 were identified as the differentially expressed genes.real-lime PCR and Western blot were used to confirm the expression of PERP.Results The microarray assay showed that there were 760 up-regulated genes and 1222 down-regulated genes in the cells at 0.1 Gy,while there were 744 genes down-regulated and 457 genes up-regulated in the cells at 5 Gy.In addition,55 genes were commonly up-regulated and 339 genes commonly down-regulated at 0.1 and 5 Gy.The predominant biological processes of the differential genes responding to low-dose radiation include cell-cell signaling transduction and DNA damage response,and the altered genes after 5 Gy irradiation were related to cell proliferation,differentiation,and apoptosis.Moreover,the expression of PERP gene was down regulated,which was consistent with the data of microarrey assay.Conclusions The quantitative and qualitative differences in the gene expressions may contribute to the diversed biological effects induced by low or high doses of ionizina radiation.