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Objective To evaluate the feasibility of the combination of amplification refractory mutation system (ARMS) and quantitative real-time polymerase chain reaction (PCR) method in fast detection of clarithromycin resistance of Helicobacter pylori (H.pylori) in gastric mucosa.Methods A total of 150 gastric mucosal specimens with positive H.pylori culture were collected from the H.pylori positive patients who failed in H.pylori eradication from January to August in 2013.The drug resistant gene mutation types of H.pylori in these samples were detected by quantitative real-time PCR based on ARMS.And the accuracy was confirmed by sequencing.The clarithromycin resistance of H.pylori was determined by E-assay.Chi-square test was used for statistical analysis.Results Among 149 gastric mucosal specimens (one specimens without wild type or mutation type had been eliminated),the results of quantitative real-time PCR based on ARMS of two samples were not consistent with the results of sequencing;the consistent rate was 98.7％ (147/149).Among 149 specimens with positive H.pylori culture,104 samples (69.8％) were clarithromycin resistance.In 101 samples the clarithromycin resistance was detected by quantitative real-time PCR based on ARMS;the consistent rate was 97.1％ (101/104).Both E-assay and clarithromycin resistant rate detected by E-assay or quantitative real-time PCR based on ARMS was 69.8％ (104/149) and 67.8％ (101/149),respectively,and the difference was not significant (x2 =0.141,P=0.932).Conclusion The combination of ARMS and quantitative real-time PCR method in fast detection of clarithromycin resistance of H.pylori in gastric mucosa is strongly feasible and highly consistent has high consistent rate with sequencing and E-assay.
ABSTRACT
Objective To evaluate the feasibility of the combination of amplification refractory mutation system (ARMS) and quantitative real-time polymerase chain reaction (PCR) method in fast detection of clarithromycin resistance of Helicobacter pylori (H.pylori) in gastric mucosa.Methods A total of 150 gastric mucosal specimens with positive H.pylori culture were collected from the H.pylori positive patients who failed in H.pylori eradication from January to August in 2013.The drug resistant gene mutation types of H.pylori in these samples were detected by quantitative real-time PCR based on ARMS.And the accuracy was confirmed by sequencing.The clarithromycin resistance of H.pylori was determined by E-assay.Chi-square test was used for statistical analysis.Results Among 149 gastric mucosal specimens (one specimens without wild type or mutation type had been eliminated),the results of quantitative real-time PCR based on ARMS of two samples were not consistent with the results of sequencing;the consistent rate was 98.7％ (147/149).Among 149 specimens with positive H.pylori culture,104 samples (69.8％) were clarithromycin resistance.In 101 samples the clarithromycin resistance was detected by quantitative real-time PCR based on ARMS;the consistent rate was 97.1％ (101/104).Both E-assay and clarithromycin resistant rate detected by E-assay or quantitative real-time PCR based on ARMS was 69.8％ (104/149) and 67.8％ (101/149),respectively,and the difference was not significant (x2 =0.141,P=0.932).Conclusion The combination of ARMS and quantitative real-time PCR method in fast detection of clarithromycin resistance of H.pylori in gastric mucosa is strongly feasible and highly consistent has high consistent rate with sequencing and E-assay.
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Objective To investigate the whole genomic expression profiles of chronic atrophic gastritis with interleukin(IL)-1β-31CC/-511TT genotype as measured by oligonucleotide microarray technique.Methods Genomic RNA was extracted from gastric biopsies of 12 patients with chronic atrophic gastritis(6 with IL-1β-31CC/-511TT and 6 with IL-1β-31TT/-511CC).The genomic profiles of IL-1β gene polymorphisms 31CC/-511TT and 31TT/-511CC were compared and tested for differential expressed genes associated with 31CC/-511TT using Agilent human whole genomic oligonucleotide microarrays.The results were further analyzed in terms of gene ontology(GO).Results There were 200 differentially expressed genes associated with IL-1β-31CC/-511TT,159 of which were up-regulated and 41 were down-regulated.These genes mainly involved in macromolecule metabolic process,post-translational protein modification,ubiquitin cycle,and protein kinase cascade.Five genes had biological activities,one of which was down-regulated gene(PCSK5)and 4 were upregulated genes(PRKCA,NPLOC4,TRIB3 and MAPKAPK3).Conclusions The chronic atrophic gastritis with IL-1β-31CC/-511TT genotype has molecular phenotypes which is associated with malignance and inflammation.These individuals are needed more intensive preemptive treatment and dynamic surveillance.
ABSTRACT
BACKGROUND: Angiotensinogen (AGT) gene is the firstly discovered candidate gene for essential hypertension, both the T174M and M235T polymorphisms locate at the second exons of AGT gene, and there is existence of linkage disequilibrium. The polymorphism at A-6G and G-217A sites in promotor region plays an important role in regulating the gene expression, and the products of keep close correlation with the level of blood pressure. OBJECTIVE: To investigate the association between the polymorphism of AGT gene at A-6G, T174M and G-217A sites and the risk for the attack of essential hypertension in Chinese Han population, DESIGN: A cluster sampling and case-control analysis. SETTINGS: Department of Geriatrics and Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University; Southern Research Center of National Human genome; Department of Cardiology, Dongtai People's Hospital of Jiangsu Province. PARTICIPANTS: The experiment was carried out in the countryside of Dongtai county, Yancheng city, Jiangsu province. All the subjects were selected from the countryside of Dongtai county, Yancheng city, Jiangsu province. Totally 177 patients with essential hypertension who had never accepted any drug treatment, were taken as the essential hypertension group, and hypertension was diagnosed according to the diagnostic standard of hypertension set by WHO/ISH in 1999 (systolic blood pressure ≥ 140 mm Hg and/or diastolic blood pressure ≥ 90 mm Hg); Another 86 normal person were taken as the normal control group. ② Inclusive criteria: The enrolled subjects should be Han nationality; long-term local residents but not from other places; able to answer questions clearly; diagnosed by disease history, clinical symptoms, physical signs and assistant examinations; have complete data of investigation of uniform questionnaires by face-to-face interview (including demographic information, profession history, family history and life styles of smoking, drinking, drinking tea, etc.). ③ Exclusive criteria: The patients with secondary hypertension in the essential hypertension group, subjects having family hisory of hypertension in the normal control group, and those with chronic diseases of liver and kidney, and diabetes mellitus in both groups were excluded. METHODS: Peripheral venous blood samples (3 mL) were collected, and DNA was extracted from human peripheral blood with FlexiGene DNA Kit (250). The Primer3 software was applied to design primers, and the polymorphism sites in the primer sequence were excluded. After multiplex polymerase chain reaction (PCR), 3 μL products were selected to detected the amplified results by agarose gel electrophoresis. The successfully amplified PCR products were purified with the QIAquick PCR Purification Kit, and the purified products were fragmentized with Dnase Ⅰ . The fragmentized products of enzyme digestion were labeled with fluorescein by deoxynucleotide terminal transferase. Two allele specific probes and one mismatched probe were designed respectively for each single nucleotide polymorphism. The chips were prepared with the OmniGridTM 100 TLC samler, each probe was repeated for three times to form three matrix. The hyridization solution was degenerated at 95 ℃ for 10 minutes, and then immediately cut on ice. 10 μL hybridization solution was added onto the chip matrix, hybridized at 50 ℃ for 2 hours, then washed and dried. The chips were scanned with the GenePix 4000B laser confocal scanner (Figure 2),and the intensity of the fluorescent signal for each probe was extracted with GenePix Pro, and the allele score of each single nucleotide polymorphism was calculated to judge the genotype. MAIN OUTCOME MEASURES: ① Comparison of the frequencies of genotype distribution at each polymorphism site of AGT gene in both groups; ② Correlation analysis of the polymorphism of AGT gene at A-6G and T-174M sites with the risk for the attack of essential hypertension; ③ Effects of the polymorphism of AGT gene at A-6G, T-174M and G-217A sites on blood pressure.RESULTS: According to the intention-to-treat analysis,all the 263 subjects were involved in the analysis of results. ① At the A-6G site of AGT gene, the frequencies of AA, AG and GG genotypes (P=0.014) and A and G alleles (P=0.004, OR=0.44) had significant differences between the essential hypertension group and normal control group; At the T174M site, the frequencies of CC, CT and TT genotypes (P=0.031) and A and G alleles (P=0.014, OR=0.55) were significantly different; At the G-217A site, no obvious differences were found in the GG, AG and AA genotypes (P=0.722) and G and A alleles (P=0.403, OR=0.80). ② The risk of essential hypertension in the individuals carrying AA genotype of A-6G polymorphism and CC genotype of T174M polymorphism was reduced by 57% (95%CI= 0.23-0.82, P= 0.010) and 56% (95%CI= 0.25-0.79, P= 0.006) respectively. ③ There were no significant differences in the systolic blood pressure, diastolic blood pressure and mean arterial pressure among different genotypes at the A-6G, T174M sites and G-217A sites (F=0.100- 2.911, P ＞ 0.05). CONCLUSION: The AA genope at A-6G and the CC genotype at T174M site of AGT gene may reduce the risk for the attack of essential hypertension in Chinese Hun population, and no significant correlation was found between the genotype of G-217A polymorphism and the attack of essential hypertension.