Independently Carriage of IL-1RN*2 Allele Associated with Increased Risk of Gastric Cancer in The Sudanese Population

Hassan

Ali

et al. 2019

Preprint

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Background: H. pylori is ubiquitous among humans, and one of the best studied examples of an intimate association between bacteria and humans. Under several diverse socio-demographic factors in Sudan, a continuous increase in the prevalence rate of H. pylori infection has been noticed which represents a major public health challenge. In this study, we analyzed the molecular evolution of H. pylori Strains detected from different ethnic and regions of Sudan using 16S rRNA gene and phylogenetic approach. Materials and methods:A total of 75 gastric biopsies taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was done by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was performed; then Blast these sequences with those available in the NCBI nucleotide database. The evolutionary aspects were analyzed using a MEGA7 software.Result: Molecular detection of H. pylori has shown that 28 (37.33%) of patients were positive for H. pylori. Bivariate analysis has found no significant differences exhibited across sociodemographic, endoscopy series and H. pylori infection. Nucleotide variations were found at five nucleotide positions (positions 219, 305, 578, 741 and 763-764) and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. The phylogenetic tree diverged into two lineages. Conclusion:The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. Sex mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites. 66.67% of them were located in the central domain of 16S rRNA. Studying the effect of these mutations on the functions of 16S rRNA molecules in protein synthesis and antibiotic resistance is of great importance.

“…(primers: F:5'-GCGCAATCAGCGTCAGGTAATG-3') (R:5'-GCTAAGAGAGCAGCCTATGTCC-3'). A PCR reaction was carried out using a previously described method by Abeer et al (43)…”

Section: S Rrna Gene Amplificationmentioning

confidence: 99%

Molecular Phylogenetic Analysis of16S rRNASequences Identified Two lineages ofH. pyloriStrains Detected from Different Regions in Sudan Suggestive of Differential Evolution

Hassan

Ali

et al. 2019

Preprint

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“…For histological examination, the biopsies were transported in formalin. DNA extraction was carried out by using innuPREP DNA Mini Kit (analytikjena AG, Germany) according to the protocol given by the manufacturer, as previously described in [67].…”

Section: Dna Extractionmentioning

confidence: 99%

First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach

Idris²,

Ataelmanan

et al. 2021

BMC Microbiol

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Background Helicobacter pylori (H. pylori) infects nearly half of the world’s population with a variation in incidence among different geographic regions. Genetic variants in the promoter regions of the IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Therefore, the aim of this study was to characterize the polymorphic sites in the 5′- region [−687_ + 297] of IL1B in H. pylori infection using in silico tools. Results A total of five nucleotide variations were detected in the 5′-regulatory region [−687_ + 297] of IL1B which led to the addition or alteration of transcription factor binding sites (TFBSs) or composite regulatory elements (CEs). Genotyping of IL1B − 31 C > T revealed a significant association between -31 T and susceptibility to H. pylori infection in the studied population (P = 0.0363). Comparative analysis showed conservation rates of IL1B upstream [−368_ + 10] region above 70% in chimpanzee, rhesus monkey, a domesticated dog, cow and rat. Conclusions In H. pylori-infected patients, three detected SNPs (− 338, − 155 and − 31) located in the IL1B promoter were predicted to alter TFBSs and CE, which might affect the gene expression. These in silico predictions provide insight for further experimental in vitro and in vivo studies of the regulation of IL1B expression and its relationship to H. pylori infection. However, the recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.

Section: Study Sitting and Study Populationmentioning

confidence: 99%

First Insights Into the Molecular Basis Association Between Promoter Polymorphisms of the Il1b Gene and Helicobacter Pylori Infection in the Sudanese Population: Computational Approach

Ataelmanan

et al. 2020

Preprint

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Background:Helicobacter pylori (H. pylori) infects nearly half of the world’s population with a variation in incidence among different geographic regions. Genetic variants in the promoter regions of IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori.Aim: To characterize the polymorphic sites in the 5’- region [-687_+297] of IL1B in H. pylori infection using in silico tools.Methods: Genomic DNA was extracted from 121 gastric biopsies and genotyping of IL1B-31 polymorphism was performed using PCR-CTPP to investigate its association with the susceptibility to H. pylori infection in the Sudanese population. In addition, Sanger sequencing was applied to detect SNPs in the 5’-region [-687_+297] of IL1B in 14 H. pylori-infected patients; and bioinformatics analyses were used to predict whether these mutations would alter TFBSs or CEs in this region. Also, comparative analysis was conducted for this region in 11 species using ECR browser and Mulan search engine.Results: A total of five nucleotide variations were detected in the 5’-regulatory region which led to the addition or alteration of the TFBSs and CEs. Genotyping of IL1B-31 C>T revealed a significant association between -31T and susceptibility to H. pylori infection in the studied population (P=0.0280). Comparative analysis showed conservation rates of IL1B upstream [−368_+10] region above 70% in chimpanzee, rhesus monkey, a domesticated dog, cow and rat.Conclusion: In H. pylori-infected patients, three detected SNPs (-338, -155 and -31) located in the IL1B promoter were predicted to alter TFBSs and CE, thereby might affecting gene expression. These in silico predictions provide insight for further experimental in vitro and in vivo studies of the regulation of IL1B expression and its relationship to H. pylori infection. However, recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.