Transcriptional alteration of NF-κB-associated long noncoding RNAs in the stomach of Helicobacter pylori-infected and non-infected patients.

INTRODUCTION: Helicobacter pylori could colonize the gastric mucosa and cause gastritis, ulcers and cancer. Numerous virulence factors have been identified in this bacterium that play important roles in promoting gastric disorders. Although the interaction of long noncoding RNAs (lncRNAs) with transcription, processing, and translation of genes associated with different diseases are described, their interaction with the inflammatory genes and H. pylori infection in the gastric tissue is not well known. This study compared changes in common NF-κB-regulatory lncRNAs in the gastric tissue of H. pylori-infected and non-infected patients with gastritis. Moreover, a link between the virulence entity of the strains and the transcriptional changes was analyzed. METHODOLOGY: Two groups of infected and non-infected patients with chronic gastritis were included in the study. Genotyping of the H. pylori strains was done by PCR and relative changes in the expression of NF-κB and regulatory lncRNAs, lincRNA-p21, MALAT1, NKILA, were measured by relative quantitative real time-PCR. RESULTS: Transcriptional levels of MALAT1, lincRNA-p21, and NKILA genes decreased in the infected patients compared with the non-infected patients, which was significantly linked with increased NF-κB gene expression. Our results showed that a hypervirulent strain of H. pylori with oipA"on"/HP-NAP+/iceA1+/iceA2+/vacA s1m1/s1m2+/cagA+ genotype can promote a higher level of NF-κB transcription in the inflamed tissue. CONCLUSIONS: H. pylori infection could promote down-regulation of lincRNA-p21, MALAT1 and NKILA in the infected gastric tissue in correlation with NF-κB upregulation. More detailed studies are needed to show a link between the virulence genes and their impact on the regulation of lncRNAs in the stomach.

Microbiome analysis of bile samples in patients with choledocholithiasis and hepatobiliary disorders.

Introduction: The involvement of bacteria in the pathogenesis of biliary tract disease is largely unknown. In this study, we investigated the microbiota of the biliary tissue among adult patients with choledocholithiasis during endoscopic retrograde cholangiography (ERCP). Methods: 16S rDNA sequencing of bile samples, culture, and data of the medication history, underlying diseases, and liver function tests were used for the interpretation of differences in the composition of detected bacterial taxa. Results: The four most common phyla in the bile samples included Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Infection with anaerobic and microaerophilic bacteria showed host specificity, where Fusobacterium, Prevotella, Veillonella, Propionibacterium, Gemella, and Helicobacter coexist in the same patients. Clostridium and Peptoclostridium spp. were detected in 80% and 86% of the patients, where the highest relative abundance rates were detected in patients with elevated alkaline phosphatase (ALP) levels and leukocytosis, respectively. Higher diversity in the bacterial population was detected in patients with common bile duct (CBD) stone, in which the richness of an unclassified member of Alphaproteobacteria plus Helicobacter, Enterobacter/Cronobacter spp., Sphingomonas, Prevotella, Fusobacterium and Aeromonas were detected. Conclusions: Our findings suggested correlations between the presence and relative abundance of several bacterial taxa and CBD stone formation and the effect of medication and underlying diseases on the bile microbial communities. A study on a higher number of bile samples from patients compared with the control group could reveal the role of these bacteria in the pathogenesis of biliary tract disease.

Activation of the DNA damage response pathway in the infected gastric tissue with Helicobacter pylori: a case-control study.

INTRODUCTION: Gastritis is among the most common human diseases worldwide. Although the involvement of Helicobacter pylori infection as a class I human carcinogen for gastric cancer progression is accepted, it is not well known how gastritis progression to atrophy and stomach cancer occurs. In this case-control study, the potential link of H. pylori infection with alteration in the transcription of genes involved in DNA Damage Response pathways was investigated among the patients with gastritis. METHODOLOGY: To measure the difference in the relative mRNA expression level of ATM, CHEK2, TP53, DCLRE1C, POLM, and XRCC4 genes between H. pylori-infected and non-infected patients, gastric biopsies of 30 H. pylori infected patients with moderate chronic gastritis and 30 non-infected patients with mild chronic gastritis were analyzed. RESULTS: Up-regulation of genes linked to non-homologous end joining (NHEJ) pathway (DCLRE1C, POLM, and XRCC) was shown in 40% (8.44 fold ± 13.91), 63.33% (15.72 fold ± 33.08) and 50% (9.99 fold ± 21.55), respectively, and also to DDR pathway (ATM, CHEK2, and TP53) in 33% (2.42 fold ± 3.17), 40% (2.86 fold ± 3.61) and 50% (5.00 fold ± 6.52), respectively. No correlation was detected between alteration in the transcription level of the studied genes and age or gender. CONCLUSIONS: Our results provide new data that may support the potential involvement of H. pylori infection in the activation of genes involved in DNA damage response, mainly through a non-homologous end-joining DNA repair system that might be linked to mutagenesis in the pre-cancerous gastric tissue.

Transcriptional analysis of Helicobacter pylori cytotoxic-associated gene-pathogenicity island in response to different pH levels and proton pump inhibitor exposure.

BACKGROUND: Long-term use of proton pump inhibitors (PPIs) can increase the risk of gastric cancer in Helicobacter pylori-infected patients; nevertheless, there is no data about their impact on the pathogenicity of H. pylori. This study aimed at investigating the transcriptional alteration of key gene mediators of cytotoxin-associated gene-pathogenicity island (cag-PAI) among clinical H. pylori isolates in response to omeprazole at different pH levels. METHODS: Accordingly, H. pylori isolates with the same virulence genotypes selected from the gastric biopsies of patients and transcriptional alteration in the cag-PAI genes studied in the presence or absence of omeprazole (2 mg/mL) at pH 2.0, 4.0 and 7.0 after 30 and 90 minutes of the treatment. Relative changes in the transcriptional levels were recorded in each assay, separately. RESULTS: Of 18 H. pylori isolates, the cag-PAI empty site was detected in four strains, while the presence of cagA, cagL and cagY was characterized in 77.7%, 83.3% and 83.3% of the cag-PAI-positive strains, respectively. Transcriptional analysis of the selected strains showed up-regulation of cagA and cagL, mainly at pH 2.0 and 4.0 after 30 and 90-minute exposure. A diversity in the expression levels of cag-PAI genes was seen among the strains at the extent and time of induction. CONCLUSION: Our results showed that omeprazole could increase the expression of H. pylori cagA and cagL at acidic pH. Heterogeneity among the strains probably has an impact on the extent of their interplay with PPIs. Further studies are needed to establish this correlation.

Transcriptional alteration of genes linked to gastritis concerning Helicobacter pylori infection status and its virulence factors.

BACKGROUND: Helicobacter pylori infection and heterogeneity in its pathogenesis could describe diversity in the expression of inflammatory genes in the gastric tissue. We aimed to investigate transcriptional alteration of genes linked to gastritis concerning the H. pylori infection status and its virulence factors. METHODS AND RESULTS: Biopsy samples of 12 infected and 12 non-infected patients with H. pylori that showed moderate chronic gastritis were selected for transcriptional analysis. Genotyping of H. pylori strains was done using PCR and relative expression of inflammatory genes was compared between the infected and non-infected patients using relative quantitative real-time PCR. Positive correlations between transcriptional changes of IL8 with TNF-α and Noxo1 in the infected and TNF-α with Noxo1, MMP7, and Atp4A in the non-infected patients were detected. Six distinct genotypes of H. pylori were detected that showed no correlation with gender, ethnicity, age, endoscopic findings, and transcriptional levels of host genes. Irrespective of the characterized genotypes, our results showed overexpression of TNF-α, MMP7, Noxo1, and ATP4A in the infected and IL-8, Noxo1, and ATP4A in the non-infected patients. CONCLUSIONS: A complexity in transcription of genes respective to the characterized H. pylori genotypes in the infected patients was detected in our study. The observed difference in co-regulation of genes linked to gastritis in the infected and non-infected patients proposed involvement of different regulatory pathways in the inflammation of the gastric tissue in the studied groups.

Investigation of the rpoB Mutations Causing Rifampin Resistance by Rapid Screening in Mycobacterium Tuberculosis in North-East of Iran.

BACKGROUND AND OBJECTIVES: The incidence of rifampin-resistant strains of Mycobacterium tuberculosis has attracted more attention than the tuberculosis infection due to laborious treatment and control. Recognizing the Mycobacterium tuberculosis genotypes involving in drug resistance via multiplex PCR, a simple and rapid genotyping method, is an emergency for better treatment and control of tuberculosis. This study was designed to specify the frequency of rifampin-resistant strains of Mycobacterium tuberculosis isolated from patients by multiplex allele-specific Polymerase Chain Reaction assay (MAS-PCR). METHODS: In this study, 88 Mycobacterium tuberculosis positive samples were included from Qaem Hospital, Mashhad. MAS-PCR was used to detect the rifampin resistance associated mutations in rpoB gene. RESULTS: Mutations in three codons of rpoB gene causing rifampin resistance were detected in 51 isolates (58.96%). The detected mutations in codons 531, 526, and 516 were 55.68%, 38.63%, and 13.63%, respectively. The simultaneous mutations were detected in 11 isolates (12.50%) in codons 531, 526 and 516, in 21 isolates (23.86%) in codons 531 and 526, and in one isolate (1.13%) in codons 526 and 516. CONCLUSION: According to the results of this study, the frequency of rifampin-resistant strains of Mycobacterium tuberculosis isolated from Khorasan province patients (North-East of Iran) was high. The developed MAS-PCR assay can be used for rapid detection in clinical diagnostic laboratories in areas with high prevalence of multidrug-resistant Mycobacterium tuberculosis strains. In this respect, MAS-PCR is simple, rapid, and highly sensitive method for drug susceptibility tests for detecting multidrug-resistant Mycobacterium tuberculosis.