Observational Study
Copyright ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Jan 14, 2022; 28(2): 242-262
Published online Jan 14, 2022. doi: 10.3748/wjg.v28.i2.242
Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach
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
Abeer Babiker Idris, Department of Agricultural Science and Technology, Institute of Natural and Applied Sciences, Erciyes University, Kayseri 38039, Turkey
Abeer Babiker Idris, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum 11111, Sudan. abeer.babiker89@gmail.com
Alaa B Idris, Department of Neurosurgery, Ribat University Hospital, Khartoum 11111, Sudan
Manal A Gumaa, El-Amin M Ibrahim, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum 11111, Sudan
Mohammed Babiker Idris, BioMérieux Clinical and Application Advisor, Al-Jeel Medical Co., Riyadh 11422, Saudi Arabia
Amanda Elgoraish, Department of Epidemiology, Tropical Medicine Research Institute, Khartoum 11111, Sudan
Mohamed Mansour, Dalia Allam, Department of Gastroenterology, Ibn Sina Specialized Hospital, Khartoum 11111, Sudan
Bashir MO Arbab, Department of Gastroenterology, Modern Medical Centre, Khartoum 11111, Sudan
Nazar Beirag, Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London UB8 3PH, Uxbridge, United Kingdom
Mohamed A Hassan, Department of Bioinformatics, Africa city of technology, Khartoum 11111, Sudan
Mohamed A Hassan, Department of Bioinformatics, DETAGEN Genetic Diagnostics Center, Kayseri 38350, Turkey
Mohamed A Hassan, Department of Translation Bioinformatics, Detavax Biotech, Kayseri 38350, Turkey
Author contributions: Idris AB and Hassan MA conceptualized and designed the study; Idris AB, Idris A, Gumaa MA, Idris MB, Mansour M, Allam D and Arbab MOB participated in sample collection and analysis of the data; Idris AB and Elgoraish A statistically analyzed the data; Idris AB performed the bioinformatics analysis, interpretation of the data and drafting the article; Idris AB, Beirag N, Mansour M, Hassan MA and Ibrahim EM revised the manuscript’s language and critically assessed the intellectual content; all authors approved the final version of the article to be published.
Institutional review board statement: The study was reviewed and approved by the Khartoum Ministry of Health research department, University of Khartoum, Faculty of Medical Laboratory Sciences review board, and Research Ethics Committees of hospitals.
Informed consent statement: Written informed consent was taken from participants before they enrolled in the study.
Conflict-of-interest statement: The authors declare that there are no conflicts of interest.
Data sharing statement: The data regarding TNF-A-1030 T>C genotypes and alleles distributions among participants and the in silico results of the software that used to support the findings of this study are available from the corresponding author at abeer.babiker89@gmail.com on a reasonable request.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Corresponding author: Abeer Babiker Idris, DSc, Academic Research, Department of Agricultural Science and Technology, Institute of Natural and Applied Sciences, Erciyes University, Merkez Kampüs Talas Yolu Melikgazi, Kayseri 38039, Turkey. abeer.babiker89@gmail.com
Received: April 29, 2021
Peer-review started: April 29, 2021
First decision: June 17, 2021
Revised: July 13, 2021
Accepted: December 31, 2021
Article in press: December 31, 2021
Published online: January 14, 2022
Abstract
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 elements. A novel mutation (A > T, +27) was detected in the 5’ untranslated region, and it could affect the post-transcriptional regulatory pathways. Genotyping of TNF-A-1030 showed a lack of significant association between -1030T and susceptibility to H. pylori and gastric cancer in the studied population (P = 0.1756) and (P = 0.8116), respectively. However, a significant association was detected between T/C genotype and H. pylori infection (39.34% vs 19.67%, odds ratio = 2.69, 95% confidence interval: 1.17-6.17, P = 0.020). Mammalian conservation was observed for the (-146 to +10) region in chimpanzee (99.4%), rhesus monkey (95.6%), cow (91.8%), domesticated dog (89.3%), mouse (84.3%), rat (82.4%) and opossum (78%).

CONCLUSION

Computational analysis was a valuable method for understanding TNF-A gene expression patterns and guiding further in vitro and in vivo experimental validation.

Keywords: 5’-region, Promoter, TNF-A, Helicobacter pylori, In silico analysis, Sudan

Core Tip: According to the literature, a considerable number of polymorphisms have been discovered in the tumor necrosis factor-alpha (TNF-A) promoter. A crucial question is whether these polymorphisms have any significant functional impact on disease incidence or severity. Seven single nucleotide polymorphisms were detected in the TNF-A 5’-region; only one of them, TNF-A-76, was located at the in silico-predicted promoter region (-146 to +10). This single nucleotide polymorphism may lead to the modification of the transcriptional regulation of TNF-A in Helicobacter pylori infection. Nevertheless, this conclusion cannot substitute for the experimental proofs, but it can provide direction or insight for them.