Published online Jan 14, 2022. doi: 10.3748/wjg.v28.i2.242
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
Processing time: 257 Days and 7.5 Hours
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.
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.
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.
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%).
Computational analysis was a valuable method for understanding TNF-A gene expression patterns and guiding further in vitro and in vivo experimental validation.
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.