Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach  

作　　者：Abeer Babiker Idris Alaa B Idris Manal A Gumaa Mohammed Babiker Idris Amanda Elgoraish Mohamed Mansour Dalia Allam Bashir MO Arbab Nazar Beirag El-Amin M Ibrahim Mohamed A Hassan 

机构地区：[1]Department of Agricultural Science and Technology,Institute of Natural and Applied Sciences,Erciyes University,Kayseri 38039,Turkey [2]Department of Medical Microbiology,Faculty of Medical Laboratory Sciences,University of Khartoum,Khartoum 11111,Sudan [3]Department of Neurosurgery,Ribat University Hospital,Khartoum 11111,Sudan [4]BioMérieux Clinical and Application Advisor,Al-Jeel Medical Co.,Riyadh 11422,Saudi Arabia [5]Department of Epidemiology,Tropical Medicine Research Institute,Khartoum 11111,Sudan [6]Department of Gastroenterology,Ibn Sina Specialized Hospital,Khartoum 11111,Sudan [7]Department of Gastroenterology,Modern Medical Centre,Khartoum 11111,Sudan [8]Biosciences,College of Health,Medicine and Life Sciences,Brunel University,London UB83PH,Uxbridge,United Kingdom [9]Department of Translation Bioinformatics,Detavax Biotech,Kayseri 38350,Turkey

出　　处：《World Journal of Gastroenterology》2022年第2期242-262,共21页世界胃肠病学杂志（英文版）

摘　　要：BACKGROUND Helicobacter pylori(H.pylori)is a ubiquitous bacterium that affects nearly half of the world’s population with a high morbidity and mortality rate.Polymorphisms within the tumor necrosis factor-alpha(TNF-A)promoter region are considered a possible genetic basis for this disease.AIM To functionally characterize the genetic variations in the TNF-A 5’-region(-584 to+107)of Sudanese patients infected with H.pylori using in silico tools.METHODS An observational study was carried out in major public and private hospitals in Khartoum state.A total of 122 gastric biopsies were taken from patients who had been referred for endoscopy.Genomic DNA was extracted.Genotyping of the TNF-A-1030 polymorphism was performed using PCR with confronting two-pair primer to investigate its association with the susceptibility to H.pylori infection in the Sudanese population.Furthermore,Sanger sequencing was applied to detect single nucleotide polymorphisms in the 5’-region(-584 to+107)of TNF-A in H.pylori-infected patients.Bioinformatics analyses were used to predict whether these mutations would alter transcription factor binding sites or composite regulatory elements in this region.A comparative profiling analysis was conducted in 11 species using the ECR browser and multiple-sequence local alignment and visualization search engine to investigate the possible conservation.Also,a multivariate logistic regression model was constructed to estimate odds ratios and their 95%confidence intervals for the association between TNF-A-1030,sociodemographic characteristics and H.pylori infection.Differences were statistically significant if P<0.05.Statistical analyses were performed using Stata version 11 software.RESULTS A total of seven single nucleotide polymorphisms were observed in the TNF-A 5’-region of Sudanese patients infected with H.pylori.Only one of them(T>A,-76)was located at the in silico-predicted promoter region(-146 to+10),and it was predicted to alter transcription factor binding sites and composite regulatory el

关 键 词：5’-region PROMOTER TNF-A Helicobacter pylori In silico analysis SUDAN 

分 类 号：R573[医药卫生—消化系统]