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Objective:To investigate the expression and related signaling pathways of reduced folate carrier 1 (RFC1) in colorectal cancer (CRC) and its relationship with the prognosis of patients.Methods:The expression of RFC1 gene in various solid tumors and CRC was analyzed in the Cancer Genome Atlas(TCGA) database. The RFC1 protein-protein interaction network was established using the search tool for the retrieval of interacting genes (STRING). The differences in survival rate between patients with high and low expression of RFC1 were compared using the Gene Expression Profile Interaction Analysis (GEPIA) database. Differentially expressed genes were subjected to Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis using the Annotation, Visualization and Integrated Discovery (DAVID) database. The immunohistochemical expression level and location of RFC1 in CRC tissues and adjacent normal tissues were analyzed.Results:The expression difference of RFC1 mRNA in various human solid tumors was not obvious. In CRC tissues, the expression level of RFC1 was higher than that in adjacent normal tissues, but the expression level of RFC1 was not related to the tumor stage of the CRC patients. The correlation index between RFC1 proteins was 119, and the average inter-protein region clustering coefficient was 0.836. There was significant protein network enrichment between RFC1 and its interacting genes ( P<0.05). The biological processes of RFC1 are mainly enriched in DNA replication, semi-conservative replication to maintain telomere activity, DNA metabolism, error-free translation synthesis, DNA synthesis involved in DNA repair, etc. The cellular components are mainly enriched in replication forks, chromosomes, nucleoplasm, DNA replication factor C complex, Ctf18 RFC complex, etc. The molecular functions are mainly enriched in DNA binding nucleic acid binding, impaired DNA binding, DNA activity, catalytic activity, etc. For the KEGG signaling pathway, RFC1 is mainly enriched in DNA replication, nucleotide excision repair, mismatch repair, and malignant tumorigenesis. The disease-free survival rate and overall survival rate of CRC patients with high expression of RFC1 were lower than those of low expression group, and the difference in overall survival rate between the two was statistically significant ( P<0.05). The RFC1 protein was mainly expressed in the cytoplasm, and the positive expression was yellow-brown granular and evenly distributed in the cells. Most of the RFC1 proteins were highly or moderately expressed in colorectal cancer tissues, but low in normal intestinal epithelium. Conclusions:The expression of RFC1 is increased in CRC tissues, and its high expression is related to the decreased overall survival rate of CRC patients. RFC1 can be used as a molecular marker of poor prognosis in CRC and may become a potential target for CRC therapy.
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Objective: Microarray chip was used to detect the differentially expressed microRNA (miRNA) in kidney tissues of rats with kidney-Yang deficiency induced by adenine,and its significance was analyzed by bioinformatics method. Method: Rats with kidney-Yang deficiency were induced by intragastric administration of 150 mg·kg-1 adenine in model group, while rats in normal group were given the same amount of saline.Kidney tissues were taken for hematoxylin-eosin (HE) staining pathological sections after anesthesia and blood urea nitrogen (BUN), creatinine (SCr) in blood and 24-hour urinary protein (24U-TP) in urine were measured. μParaflo microfluidic chip technology was used to investigate differential expression miRNA in kidney tissues, and microarray results were verified by Real-time PCR. Bioinformatics database was used to analyze the target genes and functions of differential expression miRNAs. Result: Gene chip results showed that there were 50 differentially expressed microRNAs after modeling. Compared with control group, only 9 miRNAs were highly expressed in kidney tissues with significant difference were detected in model group. Compared with the normal group, the expression of rno-miR-21-5p, rno-let-7i-5p, rno-miR-146b-5p and rno-miR-15b-5p in model group increased significantly(PPPPPConclusion: This experiment found 4 miRNAs involved in the regulation of renal interstitial fibrosis (RIF) and 2miRNAs with unknown functions, which provided a new clue for further analysis of the regulatory network of kidney-yang deficiency.
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Objective@#To fully investigate the roles of gene variations associated with lipid metabolism in pediatric non-alcoholic fatty liver disease(NAFLD).@*Methods@#One hundred obese children who were admitted to the gastroenterology department of Shenzhen Children′s Hospital from September 2017 to September 2018 meeting the inclusion criteria were collected.There were 66 males and 34 females aged 8-18 years.Exon sequencing was performed on blood samples from 100 subjects including 39 children with NAFLD(NAFLD group) and 61 healthy obese children(control group). The mutations of genes in lipid metabolism were investigated, and the functions of the variants were further evaluated through PPI analysis and Go term enrichment analysis and software tools which could predicts possible impact on the structure and function of proteins.@*Results@#There were no significant differences between NAFLD and control group in gender and age(all P>0.05). Body mass index(BMI) and waist in the control group were significantly lower than those of NAFLD group(all P<0.000 1). PPI showed that protein microsomal triglyceride transfer protein microsomal triglyceride transfer protein (MTTP), apolipoprotein B (APOB) and Hepatic lipase C (LIPC) were directly interacted.Go analysis showed that the most enriched pathway were triacylglycerol, acylglycerol, neutral lipids, glycerol ether and organo ether (P<0.001). Two variants (chr4: 100504575: G>C, chr4: 100510903: A>G) located in MTTP were significantly differently distributed between 2 groups(all P=0.002), and a potential pathogenic mutation could exist in rs2306986 site.@*Conclusions@#The findings of this study indicate that lipid metabolism plays an important role in NAFLD and rs2306986 in MTTP was associated with higher susceptibility to NAFLD.
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To explore the medication rules of herbal prescriptions for nonalcoholic fatty liver disease,and analyze the possible drug targets and interactions,in order to explore the mechanisms of the herbs. Randomized controlled trials of herbal prescriptions for treating nonalcoholic fatty liver disease were collected from CNKI,Wan Fang,VIP,Sino Med and PubMed databases. The properties,flavors and meridian tropism of herbs were analyzed by using systematic cluster analysis method with SPSS 19. 0 software. Subsequently,the association rules of herbs were analyzed by using Clementine 12. 0 software. Finally,the interactions between targets and relevant signaling pathways were analyzed by Traditional Chinese Medicine Systems Pharmacology Database(TCMSP),Search Tool for the Retrieval of Interacting Genes/Proteins(STRING) and Kyoto Encyclopedia of Genes and Genomes(KEGG). In the 88 prescriptions screened out,the commonly used herbs were Salvia miltiorrhiza,Bupleurum chinense,Alisma orientale,and Crataegus pinnatifida,and the potential signaling pathways were PPAR signaling pathway and calcium signaling pathway. The results showed that the main effects of herbal prescriptions were to improve blood flow/clear blood stasis,clear heatiness/dampness,promote digestion and strengthen spleen. And its mechanism of action may be achieved through the regulation of PPAR signaling pathway and calcium signaling pathway.
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Humans , Data Mining , Drugs, Chinese Herbal , Therapeutic Uses , Medicine, Chinese Traditional , Meridians , Non-alcoholic Fatty Liver Disease , Drug Therapy , Randomized Controlled Trials as Topic , Signal TransductionABSTRACT
This study was aimed to detect the expression of miR-665 in the hippocampal of depression rat model treated with Kai-Xin Jie-Yu (KXJY) decoction and bioinformatic analysis of target genes of miR-665,in order to investigate the role of miR-665 in the pathogenesis of depression and the antidepressant mechanism of KXJY decoction.The rat model of chronic stress depression was established and then treated with KXJY decoction for 42 days.The total RNA from hippocampus tissues was extracted.And the relative expression of miR-665 in hippocampus of rats in each group was detected by RT-qPCR.TargetScan and microRNAorg databases were used to predict target genes for miR-665.DAVID database was used to classify GO function and to analyze KEGG signaling pathway of target genes.The results showed that compared with the normal group,the expression level of miR-665 in hippocampus of the model group was significantly higher with significant difference (P ＜ 0.01).Compared with the model group,the expression level of miR-665 in hippocampus of Chinese medicine group and western medicine group decreased significantly with significant difference (P ＜ 0.01).The biological functions of miR-665 target genes were mainly concentrated in the response to organic substance.The signal pathway was mainly concentrated in N-Glycan biosynthesis.It was concluded that miR-665 may be involved in the pathological process of depression,by correcting the abnormal expression of miR-665,which may be one of the antidepressant mechanisms of KXJY decoction.Through the analysis and prediction of the target genes,it provided a certain direction and theoretical basis for further study on the specific mechanism of KXJY decoction intervention on miR-665.
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Objective The sequence characteristics and polymorphism of the UL141 gene may help find the pathogenesis of human cytomegalovirus (HCMV) infection.This study was to charac-terize the sequences of HCMV UL141 in low-passage clinical isolates in Guangzhou . Methods We collected urine samples from 10 in-fants with clinically confirmed HCMV infection in the Guangzhou are-a, isolated low-passage clinical virus strains and identified them by multiplex PCR.We performed amplification, cloning, identification and sequencing of the HCMV UL141 gene and searched the GenBank for its homologous sequences followed by sequence analysis . Results The HCMV UL141 gene was found to have 2 open reading frames( ORF) , UL141a and UL141b, composed of 315 and 1017 nucleotides and included in the GenBank with the sequence numbers of DQ180372 and DQ180371, respectively.The full length of the UL141 gene in the low-passage HCMV clinical strain (D3) was 1277 bp, the coding protein consisting of 338 amino acid residues , and the full lengths of the ORFs UL 141a and UL141b were 315 bp and 1017 bp, respectively, with relatively conservative DNA sequences .Mutations were identified in 46 sites with base substitution but no insertion or deletion .The modification sites in all the isolated strains were relatively conservative after translation of the HCMV UL 141 coding protein.The isoelectric points of the UL141 protein were 8.36-8.68 for all the clinical isolates. Conclusion Polymorphism exists in the UL141 gene and its amino acid sequences of the HCMV low-passage clinical strains isolated from infants in Guangzhou , which has shed some light on the function of the ULl 41 protein and pathogenesis of HCMV infection .
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Objective The sequence characteristics and polymorphism of the UL141 gene may help find the pathogenesis of human cytomegalovirus (HCMV) infection.This study was to charac-terize the sequences of HCMV UL141 in low-passage clinical isolates in Guangzhou . Methods We collected urine samples from 10 in-fants with clinically confirmed HCMV infection in the Guangzhou are-a, isolated low-passage clinical virus strains and identified them by multiplex PCR.We performed amplification, cloning, identification and sequencing of the HCMV UL141 gene and searched the GenBank for its homologous sequences followed by sequence analysis . Results The HCMV UL141 gene was found to have 2 open reading frames( ORF) , UL141a and UL141b, composed of 315 and 1017 nucleotides and included in the GenBank with the sequence numbers of DQ180372 and DQ180371, respectively.The full length of the UL141 gene in the low-passage HCMV clinical strain (D3) was 1277 bp, the coding protein consisting of 338 amino acid residues , and the full lengths of the ORFs UL 141a and UL141b were 315 bp and 1017 bp, respectively, with relatively conservative DNA sequences .Mutations were identified in 46 sites with base substitution but no insertion or deletion .The modification sites in all the isolated strains were relatively conservative after translation of the HCMV UL 141 coding protein.The isoelectric points of the UL141 protein were 8.36-8.68 for all the clinical isolates. Conclusion Polymorphism exists in the UL141 gene and its amino acid sequences of the HCMV low-passage clinical strains isolated from infants in Guangzhou , which has shed some light on the function of the ULl 41 protein and pathogenesis of HCMV infection .
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Objective:To clone the outer membrane protein hopX gene of Helicobacter pylori(Hp)and to perform sequencing and analysis of biological information.Methods:Polymerase chain reaction(PCR)was used to amplify the hopX gene from Hp chromosomal DNA.Then the target gene was digested by restricted endonuclease enzyme of BamH I,and inserted into the prokaryotic expression vector pQE30 digested by corresponding restricted endonuclease enzyme.The recombinant vector was used to select and transform for nucleotide sequence analysis.The biological property at the amino acid level was analyzed by Omiga 2.0 and Antheprot v 5.0.The transformant colony was induced with IPTG and the fusion protein was analyzed by SDS-PAGE and Western blot.Results:The recombinant plasmid was constructed.DNA sequence analysis showed the sequence of hopX was 1 284 bp.The homology of the strains in nucleotide acid was 96%～97%.Their homogeneity in the amino acids was 97%～99%.We get a GeneBank accession number EF208122.Omiga 2.0 software predicted its relative molecular mass(Mr.)was 47 kD and possessed good antigencity.The expressed product contained about 37% of total somatic proteins and Western blot method showed good antigenicity of the recombinant protein.Conclusion:A confirmed gene hopX has been obtained,providing a good foundation for recombination,expression and related study.The corresponding peptide of the gene performed the structural characteristics of some typical antigen molecules,which suggest that it might be a novel vaccine candidate.