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

Abstract

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.

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

“…For histological investigation, the biopsies were preserved in 10% formalin. DNA extraction was performed by using innuPREP DNA Mini Kit (analytikjena AG, Germany) and followed the protocol that was given by the manufacturer, as previously described in[ 30 ].…”

“…Two sets of primers were used in PCR with confronting two-pair primer to detect the TNF-A -1030 C/T polymorphism as follow: for allele T, the sequences of the primers were F: 5'-AAGGCTCTGAAAGCCAGCTG-3' and R: 5'-CCAGACCCTGACTTTTCCTTCA-3'; and for allele C, F: 5'-GAAGCAAAGGAGAAGCTGAGAAGAC-3' and R: 5'-CTTCCATAGCCCTGGACATTCT-3'[ 54 ]. The PCR mixture components were the same as in[ 30 ]. The amplification conditions were initial denaturation at 95 °C for 10 min, followed by 30 cycles of denaturation at 95 °C for 1 min, annealing at 66 °C for 1 min, extension at 72 °C for 1 min and final extension at 72 °C for 5 min.…”

Old and New Aspects of H. pylori-Associated Inflammation and Gastric Cancer

“…The complex interrelationship between these cytokines, H. pylori infection and IL-1β was emphasized by a study performed on acute coronary syndrome patients, where it was shown that the coexistence of H. pylori -seropositivity and certain IL-1β polymorphisms is associated with higher levels of high-sensitivity CRP, resulting in an increased risk of ST-segment elevation myocardial infarction [ 81 ]. In addition, genetic variants in the promoter regions of the IL-1β gene were recently shown to alter cytokine expression, creating a hypoacidity environment involved in enabling the long-term persistence and colonization of H. pylori [ 82 ]. Nevertheless, the influence of IL-1β gene polymorphisms on H. pylori infection might be closely related to ethnicity or geographical area [ 83 ].…”

“…Genetic variants in the promoter regions of the IL-1β gene → alter cytokine expression → a hypoacidity environment involved in enabling long-term persistence and colonization of H. pylori [ 82 ]…”

Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study

“…1,2 It has been associated with the development of various clinical disorders of the upper gastrointestinal tract, such as aseptic ulcers, chronic gastritis, gastric adenocarcinoma and gastric mucosa-associated lymphoid tissue (MALT) lymphoma, which is classified as type I cancer-causing agent by the World Health Organization (WHO). [3][4][5] Its distribution is worldwide and affects more than 90% of the world population, but it is more common in developing countries with the highest prevalence found in Africa, 6,7 probably due to the possible transmission through the fecal-oral route and the unsafe sanitation conditions in these countries. 1,8 Clinically, a variety of various invasive techniques (requiring endoscopy and biopsy which include, culture, histological examination, and rapid urease test, CLO (Campylobacter like organism) test, smear examination, and molecular studies) or noninvasive techniques (including serology, respiratory urea breath test, or the detection of fecal antigen) are often performed to detect H. pylori infection.…”