Role of matrix metalloproteinase,tissue inhibitor of metalloproteinase and tumor necrosis factor-α single nucleotide gene polymorphisms in inflammatory bowel disease

AIM:To study the (functional) relevance of single nucleotide polymorphisms (SNPs) in genes encoding matrix metalloproteinases (MMP)-1,-2,-3,-9,tissue inhibitors of metalloproteinases (TIMP)-1,-2 and tumor necrosis factor (TNF)-α in the etiopathogenesis of inflammatory bowel diseases (IBD),that may enhance susceptibility and/or disease severity. METHODS:Genomic DNA from 134 Crohn's disease (CD),111 ulcerative colitis (UC) patients and 248 control subjects was isolated from resected intestinal tissue or blood. Allelic composition at SNP loci was determined by PCR-RFLP or tetra primer ARMS PCR. RESULTS:The TIMP-1 genotype TT in women and T in men at SNP +372 T/C was found to increase CD susceptibility (39% vs 23.8%,P=0.018 and 67.9% vs 51.6%,P=0.055,respectively),while women with this genotype were less prone to development of fistulae during follow-up (41.4% vs 68.3%,P=0.025). Male IBD or CD patients carrying the TIMP-1 +372 T-allele expressed lower levels of TIMP-1 in surgically resected macroscopically inflamed tissue (0.065 < P < 0.01). The 5T5T genotype at MMP-3 SNP -1613 5T/6T increased the chance of stenotic complications in CD during follow-up (91.2% vs 71.8%,P = 0.022) but seemed to protect against colonic involvement of this disease at first endoscopic/radiologic examination (35.3% vs 59.5%,P=0.017). CONCLUSION:Allelic composition at the examinedSNPs in genes coding for TIMP-1 and MMP-3 affect CD susceptibility and/or phenotype,i.e.,fistulizing disease,stricture pathogenesis and first disease localisation. These findings reinforce the important role of these proteins in IBD.

Single and Mitochondrial Gene Inheritance Disorder Prediction Using Machine Learning

One of the most difficult jobs in the post-genomic age is identifying a genetic disease from a massive amount of genetic data.Furthermore,the complicated genetic disease has a very diverse genotype,making it challenging to find genetic markers.This is a challenging process since it must be completed effectively and efficiently.This research article focuses largely on which patients are more likely to have a genetic disorder based on numerous medical parameters.Using the patient’s medical history,we used a genetic disease prediction algorithm that predicts if the patient is likely to be diagnosed with a genetic disorder.To predict and categorize the patient with a genetic disease,we utilize several deep and machine learning techniques such as Artificial neural network(ANN),K-nearest neighbors(KNN),and Support vector machine(SVM).To enhance the accuracy of predicting the genetic disease in any patient,a highly efficient approach was utilized to control how the model can be used.To predict genetic disease,deep and machine learning approaches are performed.The most productive tool model provides more precise efficiency.The simulation results demonstrate that by using the proposed model with the ANN,we achieve the highest model performance of 85.7%,84.9%,84.3%accuracy of training,testing and validation respectively.This approach will undoubtedly transform genetic disorder prediction and give a real competitive strategy to save patients’lives.

Relation of cytochrome P450 2C19 gene 681G>A single nucleotide polynmrphism to clopidogrel resistance after PCI in Chinese

Objectives Clopidogrel is a prodrug that has to be converted to an active metabolite by hepatic cytochrome P450(CYP) isoenzymes to inhibit platelet aggregation.Individualvariability of platelet inhibition by clopidogrel suggests a possibility for genetic factors having a significant influence on clopidogrel responsiveness.In this study,we sought to determine the association between the single nucleotide polymorphism of CYP 2C19 681G】A and the occurrence of clopidogrel resistance(CR) in Chinese.Methods The study enrolled 614 hospitalized patients who underwentsuccessful percutaneouscoronary intervention with drug-eluting stents were received the treatmentwith dual antiplatelet regimen(aspirin plus clopidogrel).All patients received loading doses of 600 mg clopidogrel and 300 mg aspirin.20μmol/L ADP-induced platelet aggregation ratio(PAR ) was assessed 24 h after clopi- dogrel administration.The maximum residual PAR≥70%was defined as CR.Genomic DNA was extracted from whole blood samples according to standard protocols,the single nucleotide polymorphism of the CYP2C19 681G】A was genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in all the patients.Results CR was found in 126 patients(20.5%).There was CYP2C19 681G】A polymorphism in the study population.The frequencies of the three kinds of genotypes(GG,GA,A A) in CR group and non-CR (NCR)group were 32.5%,47.6%,19.8%and 48.0%, 45.0%,7.0%,respectively.The frequency of AA genotype was significantly higher in NCR group than that in CR group (OR =3.03,95%CI:1.889～5.784,P=0.003).The A allele carriers were more likely to develop clopidogrel resistance compared with that of G allele carriers(OR=1.85,95%CI: 1.392～2.459,P=0.002).Conclusions CYP2C19 681G/A polymorphism is associated with the risk of CR,and the A allele carriers may be a possible genetic susceptibility factor for patients with CR.

Association of polymorphism of tumor necrosis factor-alpha gene promoter region with outcome of hepatitis B virus infection

AIM： To determine whether -238G/A and -857C/T polymorphisms of tumor necrosis factor-alpha （TNF-α）, gene promoter and hepatitis B （HB） viral genotypes were associated with outcomes of HBV infection. METHODS： A total of 244 HBV self-limited infected subjects, 208 asymptomatic carriers, and 443 chronic HB patients were recruited to conduct a case-control study. TNF-α -238G/A and -857C/T gene promoter polymorphisms were examined by polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）, and HBV genotypes were examined by nested PCR. RESULTS： The positive rate of HBV DNA in asymptomatic carder group and chronic HB group was 46.6% and 49.9%, respectively. HBV genotype proportion among the asymptomatic carriers was 2.1% for genotype A, 25.8% for genotype B, 68.0% for genotype C, and 4.1% for genotype B＋C mixed infection, and 0.9% for genotype A, 21.7% for genotype B, 71.5% for genotype C, 5.9% for genotype B＋C mixed infection in chronic HB group. There was no significant difference in genotype distribution between the asymptomatic carrier group and chronic HB group （X^2 = 1.66, P = 0.647）. The frequency of -238GG genotype in self-limited group was 95.1%, significantly higher than 90.7% in chronic HB group and 89.0% in asymptomatic carrier group （P = 0.041 and P = 0.016, respectively）.The frequency of TNF-α-857 CC in chronic HB group was 79.7%, significantly higher than 64.4% in asymptomatic carrier group and 70.9% in self-limited group （P〈0.001 and P = 0.023, respectively）. A multiple logistic regression analysis revealed that TNF-α-238GA and -857CC were independently associated with chronic HB after gender and age were adjusted.CONCLUSION： TNF-α promoter variants are likely to play a substantial role in the outcome of HBV infection.

The Study on the Gene Expression of Preimplantation IVF Bovine Embryos

The cattle different stage embryos obtained from in vitro was studied using the technology of single preimplantation embryo mRNA different display:single 8-cell and blastocyst stage embryos were studied using technology of mRNA different display and one different fragment was found. The result suggested that this fragment displayed high homology (99%) to cattle mRNA for ribosomal protein L31. Then to detect the expression of RPL31mRNA in 8 cell and blastocyst stage embryos by real-time quantitative PCR,the result showed the relative amount of 8 cells was 3.2 times of blastocyst's.

Association of Connexin Gene Polymorphism with Essential Hypertension in Kazak and Han Chinese in Xinjiang,China

Essential hypertension（EH） is affected by both genetic and environmental factors.The polymorphism of connexin（Cx） genes is found associated with the development of hypertension.However,the association of the polymorphism of Cxs with EH has not been investigated.This study aimed to investigate the association of the polymorphism of connexin（Cx） genes Cx37,Cx40,and Cx43 with EH in Kazak and Han Chinese in Xinjiang,China.Polymerase chain reaction-restriction fragment length polymorphism（PCR-RFLP） method and matrix-assisted laser desorption ionization time-of-flight mass spectrometry（MALDI-TOF-MS） were used to analyze the polymorphism of Cx genes in Kazak and Han EH patients as well as their normotensive controls.The results showed that there were no significant differences in the frequencies of different three genotypes（A/A,A/G,and G/G） and A and G alleles of Cx40 rs35594137 and rs11552588 between EH patients and normotensive controls.However,in Kazak EH patients,the frequencies of three genotypes（A/A,A/G,and G/G） of Cx37 rs1630310 were 24.8%,47.2% and 28.0%,respectively,which were significantly different from those in Han EH patients.In Han EH patients,the frequencies of the three genotypes（C/C,C/G and G/G） of Cx43 rs1925223 were 6.4%,35.6% and 58.0%,respectively.Frequencies of the other four genotypes had no statistical differences among Kazak and Han EH patients and their normotensive controls.These results suggest polymorphisms of Cx37 rs1630310 and Cx43 rs1925223 genes may be associated with the pathogenesis of EH.Carrying Cx37 rs1630310-A or Cx43 rs1925223-G genotypes may protect against the development of EH.

Apolipoprotein A-V gene therapy for disease prevention/treatment:a critical analysis

Apolipoprotein（apo） A-V is a novel member of the class of exchangeable apo＇s involved in triacylglycerol（TG）homeostasis.Whereas a portion of hepatic-derived apoA-V is secreted into plasma and functions to facilitate lipoprotein Iipase-mediated TG hydrolysis,another portion is recovered intracellularly,in association with cytosolic lipid droplets.Loss of apo A-V function is positively correlated with elevated plasma TG and increased risk of cardiovascular disease.Single nucleotide polymorphisms（SNP） in the APOA5 locus can affect transcription efficiency or introduce deleterious amino acid substitutions.Likewise,rare mutations in APOA5 that compromise functionality are associated with increased plasma TG and premature myocardial infarction.Genetically engineered mouse models and human population studies suggest that,in certain instances,supplementation with wild type（WT） apoA-V may have therapeutic benefit.It is hypothesized that individuals that manifest elevated plasma TG owing to deleterious APOA5 SNPs or rare mutations would respond to WT apoA-V supplementation with improved plasma TG clearance.On the other hand,subjects with hypertriglyceridemia of independent origin（unrelated to apoA-V function） may not respond to apoA-V augmentation in this manner.Improvement in the ability to identify individuals predicted to benefit,advances in gene transfer technology and the strong connection between HTG and heart disease,point to apoA-V supplementation as a viable disease prevention / therapeutic strategy.Candidates would include individuals that manifest chronic TG elevation,have low plasma apoA-V due to an APOA5 mutation/polymorphism and not have deleterious mutations/polymorphisms in other genes known to influence plasma TG levels.

Differential gene network analysis from single cell RNA-seq

Study of gene expression has been arguably the most active research field in functional genomics.Over the last two decades,various high-throughput technologies,from gene expression microarray to RNA-seq,have been widely applied to the wholegenome profiling of gene expression.The commonality of these experiments is that they measure the gene expression levels of"bulk"sample,which pools a large number(often in the scale of millions)of cells,and thus the measurements reflect the average expression

Association of ADIPOQ and ADIPOR Variants with Risk of Colorectal Cancer：A Meta-analysis

Numerous epidemiological studies have studied the association of adiponectin（ADIPOQ） gene and adiponectin receptor（ADIPOR） gene polymorphisms with risk of colorectal cancer（CRC）,but the outcomes were incomplete and inconsistent.Therefore,we conducted a meta-analysis to assess the associations systematically.All eligible case-control studies published up to Jan.2015 were searched from Pub Med,the Cochrane library,Elsevier,Wiley Online library,China National Knowledge Infrastructure,Wan Fang data and Chongqing VIP.Effect sizes of odds ratio（OR） and 95% confidence interval（95%CI） were calculated by using a fixed-or random-effect model.Twelve case-control studies including 6141 cases and 7398 controls were selected.Significant differences in the distributions of allele frequency with CRC risk were directly present in ADIPOQ variants rs2241766,rs1501299 and ADIPOR variant rs1342387.In stratified analysis for different populations,significant differences were present in ADIPOQ variant rs822396 for Ashkenazi Jewish,in ADIPOQ variant rs1501299 and ADIPOR variant rs1342387 for Chinese and in ADIPOQ variant rs 2241766 for Ashkenazi Jewish and Chinese.In addition,the factors correlated with insulin resistance had synergistic effect with ADIPOQ variants rs2241766 T/G and rs1501299 G/T on risk of CRC.ADIPOQ variants rs2241766 T/G,rs1501299 G/T and ADIPOR variant ADIPOR rs1342387 G/A had a population specific correlation with CRC risk,which may be mediated by insulin resistance.And large well-designed studies are still needed for further evaluation of rs822396 and rs1063538,especially for their interaction and combined effect in the correlation with CRC risk.

New insights into the role of intra-tumor genetic heterogeneity in carcinogenesis: identification of complex single gene variance within tumors

Aim:Present cancer hypotheses are almost all based on the concept that accumulation of specific driver gene mutations cause carcinogenesis.The discovery of intra-tumor genetic heterogeneity(ITGH),has resulted in this hypothesis being modified by assuming that most of these ITGH mutations are in passenger genes.In addition,accumulating ITGH data on driver gene mutations have revealed considerable genotype/phenotype disconnects.This study proposes to investigate this disconnect by examining the nature and degree of ITGH in breast tumors.Methods:ITGH was examined in tumors using next generation sequencing of up to 68,000 reads and analysis tools that allowed for identification of distinct minority variants within single genes,i.e.,complex single gene variance(CSGV).Results:CSGV was identified in the androgen receptor genes in all breast tumors examined.Conclusion:Evidence of CSGV suggests that a selection-as opposed to a mutation-centric hypothesis could better explain carcinogenesis.Our hypothesis proposes that tumors develop by the selection of preexisting de novo mutations rather than just the accumulation of de novo mutations.Thus,the role of selection pressures,such as changes in tissue microenvironments will likely be critical to our understanding of tumor resistance as well as the development of more effective treatment protocols.

Analysis of two single nucleotide polymorphisms and loss of heterozygosity detection in the VHL gene in Chinese patients with sporadic renal cell carcinoma

Renal cell carcinoma （RCC） is the most common malignant tumour in the adult kidney. Recent studies have shown that inactivation of the tumour suppressor gene VHL located in chromosome 3p25-26 region is responsible for sporadic RCCs. According to Kundson＇s two hit theory, the mechanism of inactivation of a tumour suppressor gene involves mutation, hypermethylation and loss of heterozygosity （LOH）.

Relation between connective tissue growth factor rs9399005 gene single nucleotide polymorphism and coronary heart disease

Objective To investigate the relationship between connective tissue growth factor(CTGF)rs9399005 gene polymorphism and serum CTGF level,coronary heart disease(CHD).Methods The serum CTGF levels were de-tected by enzyme linked immunosorbent assay in 214 cases of CHD and 64 cases of normal control group.CTGF gene rs9399005 single nucleotide polymorphism(SNP)was analyzed by Sanger method.Baseline clinical data,serum CTGF and genotype distribution frequencies

The precise regulation of different COR genes by individual CBF transcription factors in Arabidopsis thaliana

The transcription factors CBF1/2/3 are reported to play a dominant role in the cold responsive network of Arabidopsis by directly regulating the expression levels of cold responsive （COR） genes. In this study, we obtained CRISPR/Casg-mediated loss-of-function mutants of cbf1-3. Over 3,ooo COR genes identified by RNA-seq analysis showed a slight but significant change in their expression levels in the mutants compared to the wild- type plants after being treated at 4 ℃ for 12 h. The C-repeat （CRT） motif （5＇-CCGAC-3＇） was enriched in promoters of genes that were up-regulated by CBF2 and CBF3 but not in promoters of genes up-regulated by CBFI. These data suggest that CBF2 and CBF3 play a more important role in directing the cold response by regulating different sets of downstream COR genes. More than 2/3 of COR genes were co-regulated by two or three CBFs and were involved mainly in cellular signal transduction and metabolic processes; less than 1[3 of the genes were regulated by one CBF, and those genes up-regulated were enriched in cold-related abiotic stress responses. Our results indicate that CBFs play an important role in the trade-off between cold tolerance and plant growth through the precise regulation of COR genes in the complicated transcriptional network.