Application of proteomics to the study of Helicobacter pylori and implications for the clinic

Effects of Lactobacillus spp. on Helicobacter pylori: A Promising Frontier in the Era of Antibiotic Resistance

Helicobacter pylori, a pathogenic bacterium responsible for multiple gastrointestinal disorders, has emerged as a major global concern due to rise in antibiotic resistance. Unwanted side effects of antibiotics therapy are further complicating the treatment strategies. Consequently, an alternative approach, using probiotics has emerged as a promising solution for treating H. pylori infections. Probiotics have shown considerable potential in increasing the cure rate and reducing the side effects through diverse mechanisms. Among the widely employed probiotics, Lactobacillus spp. has garnered particular attention in this review. After reviewing the studies on effects of Lactobacillus spp. on H. pylori, it is evident that several Lactobacillus spp. have demonstrated their potential efficacy against H. pylori infection, when administered alone or in conjunction with antibiotics, in a strain-specific manner. Furthermore, the inclusion of Lactobacillus spp. in the treatment regimen has also been associated with a reduction in the side effects related to antibiotic-based therapies. Future research may focus on identifying optimal strains and treatment regimens, understanding the long-term impacts of use, and determining their role in preventing H. pylori infection in various populations.

Helicobacter pylori regulated microRNA map of human gastric cells

BACKGROUND

Helicobacter pylori is an infection of concern for its chronic colonization leading to peptic ulcers and gastric cancer. In recent times, microRNAs have been extensively studied to understand their role in the pathogenesis of this bacteria in diverse contexts of gastric diseases. The current analysis reports the microRNA-mRNA interactions that are associated with effective survival and virulence of this pathogen.

MATERIALS AND METHODS

We convened differentially regulated human microRNAs responsive to H. pylori infection (HP-hDEmiRs) at different multiplicity of infection and time points in human gastric cell lines through retrospective data mining of experimental studies. In view of the molecular disparity of clinical samples and animal models, data from tissue, serum/plasma, urine, and ascites were excluded. Further, we utilized diverse bioinformatics approaches to retrieve experimentally validated, high-confidence targets of the HP-hDEmiRs to analyze the microRNA-mRNA interactions that are relevant to H. pylori pathogenesis.

RESULTS

A total of 39 HP-hDEmiRs that showed unidirectional expression of either overexpression or downregulation were identified to modulate 23 targets explicitly studied under this infection. We also identified 476 experimentally validated targets regulated by at least 4 of the HP-hDEmiRs. In addition to the pathways prior-associated with H. pylori infection, the microRNA-mRNA interactome analysis identified several cellular processes and pathways highly associated with cell cycle, cell division, migration, and carcinogenesis.

CONCLUSION

This study generated a platform to study the mechanisms utilized by this pathogen using microRNAs as surrogate.

Are pro- and/or synbiotics beneficial in Helicobacter pylori eradication therapy in children? A narrative review

To assess the effect of pro- and synbiotics in the eradication therapy of Helicobacter pylori (Hp), as well as their effect on adverse effects and therapy compliance in children, a review was performed. We searched for relevant studies published in the English language in PubMed in the last 5 years. Articles were extracted using subject heading and keywords of interest to the topic. There is low-quality evidence that Lactobacillus casei, Bifidobacterium infantis, and Clostridium butyricum (only one RCT for all three) and Saccharomyces boulardii (more than 1 RCT) increase the eradication rate and decrease the adverse effects. Data with synbiotics report only a trend towards a better eradication. Heterogeneity in study designs and outcomes is a major limitation to propose evidence-based recommendations. A reduced incidence of antibiotic-associated diarrhoea is reported. Therapy compliance has been poorly studied.   Conclusion: Due to study heterogeneity, there is very low evidence that some specific probiotics strains increase the eradication rate of Hp when added to standard eradication therapy in children. Whether this is related to immunological effects of the strain or a decrease of adverse effects is not known. More studies, especially comparative trials, are needed before the addition of pro- or synbiotics to Hp eradication treatment can be recommended in daily routine. What is Known: • Eradication treatment of Helicobacter pylori in children has a low success rate and induces frequently adverse effects. • The addition of probiotics might improve eradication and decrease adverse effects, but no paediatric guideline does recommend probiotics as part of the eradication treatment. What is New: • There is low-quality evidence that Lactobacillus casei, Bifidobacteria infantis, and Clostridium butyricum (only one randomized controlled trial (RCT) for all three) and Saccharomyces boulardii (more than 1 RCT) increase the eradication rate and decrease the adverse effects. • Data with synbiotics report only a trend towards a better eradication.

Emerging techniques of western blotting for purification and analysis of protein

Background

Western blotting is frequently employed in molecular techniques like Proteomics and Biology. Because it is a sequential framework, differences and inaccuracies could even take place at any stage, decreasing this particular method's reproducibility and reliability.

Main text

New approaches, like automated microfluid western blotting, DigiWest, single cell resolution, microchip electrophoresis, and capillary electrophoresis, were all implemented to reduce the future conflicts linked with the western blot analysis approach. Discovery of new in devices and higher susceptibility for western blots gives innovative opportunities to expand Western blot’s clinical relevance. The advancements in various region of west blotting included in this analysis of transfer of protein and validation of antibody are described.

Conclusion

This paper describes another very developed strategy available as well as demonstrated the correlation among Western blotting techniques of the next generation and their clinical implications. In this review, the different techniques of western blotting and their improvement in different stages have been discussed.

Complement factors and alpha-fetoprotein as biomarkers for noninvasive prenatal diagnosis of neural tube defects

Neural tube defects (NTDs) are serious congenital malformations. In this study, we aimed to identify more specific and sensitive maternal serum biomarkers for noninvasive NTD screenings. We collected serum from 37 pregnant women carrying fetuses with NTDs and 38 pregnant women carrying normal fetuses. Isobaric tags for relative and absolute quantitation were conducted for differential proteomic analysis, and an enzyme-linked immunosorbent assay was used to validate the results. We then used a support vector machine (SVM) classifier to establish a disease prediction model for NTD diagnosis. We identified 113 differentially expressed proteins; of these, 23 were either up- or downregulated 1.5-fold or more, including five complement proteins (C1QA, C1S, C1R, C9, and C3); C3 and C9 were downregulated significantly in NTD groups. The accuracy rate of the SVM model of the complement factors (including C1QA, C1S, and C3) was 62.5%, with 60% sensitivity and 67% specificity, while the accuracy rate of the SVM model of alpha-fetoprotein (AFP, an established biomarker for NTDs) was 62.5%, with 75% sensitivity and 50% specificity. Combination of the complement factor and AFP data resulted in the SVM model accuracy of 75%, and receiver operating characteristic curve analysis showed 75% sensitivity and 75% specificity. These data suggest that a disease prediction model based on combined complement factor and AFP data could serve as a more accurate method of noninvasive prenatal NTD diagnosis.

Using Probiotics as Supplementation for Helicobacter pylori Antibiotic Therapy

Helicobacter pylori is a well-known pathogen that is highly prevalent in the world population, and H. pylori infection is potentially hazardous to humans because of its relationship to various gastrointestinal diseases, such as gastric ulcers, chronic gastritis, and gastric carcinoma. Therefore, the clinical guidelines recommend taking antibiotic therapy to eradicate the pathogen, which usually leads to the desired therapeutic effect. However, some failure cases of this therapy indicate that the increasing antibiotic resistance and side effects may affect the therapeutic effect. Here we propose that using probiotics as supplementation for antibiotic therapy may provide an extra help. Recent studies have shown that probiotic supplementation therapy has promising application prospects; it can enhance the antibiotic effect to achieve a better therapeutic result and maintain the balance of the host gastrointestinal microbiota. In summary, under global conditions of increasing H. pylori prevalence, probiotic supplementation therapy is worthy of further studies for future clinical application.

Helicobacter pylori Infection and Autoimmune Thyroid Diseases: The Role of Virulent Strains

Aim: To verify a possible association between overall H. pylori and CagA+ H. pylori infection and autoimmune thyroid diseases (AITDs). Methods: Consecutive patients with AITDs admitted to one single centre of Endocrinology during one solar year were examined. The diagnoses were Hashimoto thyroiditis (HT) in 76, Graves’ Disease (GD) in 39, and aspecific thyroiditis (AT) in 44 patients. Controls were 136 individuals without AITDs. Median values of fT3, fT4, anti-thyreoglobulin (Tg) antibodies, IL-1β, IL-6, and TNF-α in patients were compared with those in controls. H. pylori infection and CagA status were determined serologically. Structural homology of some thyroid proteins with H. pylori antigens was investigated. Results: H. pylori infection prevalence was significantly increased in GD (66.6%) and HT (64.4%) patients, vs. 29.4% of controls and 34.0% of AT. CagA seropositivity was significantly more frequent in GD (46.1%) and HT (46.9%) infected patients, vs. infected controls (20%). fT3 and fT4 median values were significantly decreased in infected CagA+ GD patients vs. uninfected GD patients. IL-1β median values were increased in patients respect to controls, independently of the clinical form of AITD. Median values of IL-6, TNF-α and anti-Tg autoantibodies in CagA infected patients were significantly higher than those measured in infected CagA− and uninfected patients and in infected CagA+ controls. The examined thyroid proteins shared putative conserved domains with numerous bacterial antigens. Conclusions: Overall H. pylori and CagA+ H. pylori infection were associated with GD and HT, putatively through an increased inflammatory status and molecular mimicry.

Differential Helicobacter pylori Plasticity in the Gastric Niche of Subjects at Increased Gastric Cancer Risk

Helicobacter pylori (H. pylori) represents an independent risk factor for Gastric Cancer (GC). First Degree Relatives (FDR) of GC subjects and Autoimmune Gastritis (AG) patients are both at increased risk for GC. H. pylori genetic heterogeneity within the gastric niche of FDR and AG individuals has been little explored. To understand whether they exploit an increased H. pylori stability and virulence, 14 AG, 25 FDR, 39 GC and 13 dyspeptic patients (D) were investigated by a cultural PCR-based approach characterizing single colonies-forming-units. We chose three loci within the Cytotoxin-associated gene-A Pathogenicity Island (CagPAI) (cagA,cagE,virB11), vacA, homA and homB as markers of virulence with reported association to GC. Inflammatory/precancerous lesions were staged according to Sydney System. When compared to D, FDR, similarly to GC patients, were associated to higher atrophy (OR = 6.29; 95% CI:1.23-31.96 in FDR; OR = 7.50; 95% CI:1.67-33.72 in GC) and a lower frequency of mixed infections (OR = 0.16; 95% CI:0.03-0.81 in FDR; OR = 0.10; 95% CI:0.02-0.48 in GC). FDR presented also an increased neutrophil infiltration (OR = 7.19; 95% CI:1.16-44.65). Both FDR and GC carried a higher proportion of CagPAI⁺vacAs1i1mx⁺homB⁺ profiles (OR = 2.71; 95% CI: 1.66-4.41 and OR = 3.43; 95% CI: 2.16-5.44, respectively). Conversely, AG patients presented a lower frequency of subtypes carrying a stable CagPAI and vacAs1i1mx. These results underline different H. pylori plasticity in FDR and AG individuals, and thus, a different host-bacterium interaction capacity that should be considered in the context of eradication therapies.

Protein purification and analysis: next generation Western blotting techniques

INTRODUCTION

Western blotting is one of the most commonly used techniques in molecular biology and proteomics. Since western blotting is a multistep protocol, variations and errors can occur at any step reducing the reliability and reproducibility of this technique. Recent reports suggest that a few key steps, such as the sample preparation method, the amount and source of primary antibody used, as well as the normalization method utilized, are critical for reproducible western blot results. Areas covered: In this review, improvements in different areas of western blotting, including protein transfer and antibody validation, are summarized. The review discusses the most advanced western blotting techniques available and highlights the relationship between next generation western blotting techniques and its clinical relevance. Expert commentary: Over the last decade significant improvements have been made in creating more sensitive, automated, and advanced techniques by optimizing various aspects of the western blot protocol. New methods such as single cell-resolution western blot, capillary electrophoresis, DigiWest, automated microfluid western blotting and microchip electrophoresis have all been developed to reduce potential problems associated with the western blotting technique. Innovative developments in instrumentation and increased sensitivity for western blots offer novel possibilities for increasing the clinical implications of western blot.