Comprehensive analysis of the function of helicobacter-associated ferroptosis gene YWHAE in gastric cancer through multi-omics integration, molecular docking, and machine learning

Gastric cancer is strongly associated with Helicobacter pylori (H. pylori) infection. However, the molecular mechanisms underlying the development of gastric cancer in the context of H. pylori infection, particularly in relation to ferroptosis, remain poorly understood. In this study, we investigated the role of the Helicobacter-associated ferroptosis gene YWHAE in gastric cancer. We analyzed multi-omics data, performed molecular docking, and employed machine learning to comprehensively evaluate the expression, function, and potential implications in gastric cancer, including its influence on drug sensitivity, mutation, immune microenvironment, immunotherapy, and prognosis. Our findings demonstrated that the YWHAE gene exhibits high expression in both H. pylori-associated gastritis and gastric cancer. Pan-cancer analysis revealed elevated expression of YWHAE in several cancer types compared to normal tissues. We also examined the methylation, single nucleotide variations (SNVs), and copy number variations (CNVs) associated with YWHAE. Single-cell analysis indicated that the YWHAE gene is expressed in various cell types, with its expression level potentially influenced by H. pylori infection. Functionally, we observed a positive correlation between YWHAE gene expression and ferroptosis in gastric cancer and associated with multiple cancer-related signaling pathways, including MAPK, NF-κB, and PI3K. Furthermore, we predicted five small molecule compounds that show promise for treating gastric cancer patients and screened five drugs with the highest correlation with YWHAE and validated them by molecular docking. Additionally, significant differences were observed in various immune cell types and immunotherapeutic response between the high and low YWHAE gene expression groups. Moreover, we found a positive correlation between YWHAE gene expression and the tumour mutation burden (TMB). By applying 10 machine learning algorithms and 101 integration combinations, we developed a prognostic model for YWHAE-related genes. Finally, qRT-PCR and immunohistochemistry (IHC) consistently demonstrated the upregulation of YWHAE in gastric cancer. In conclusion, we conducted a comprehensive analysis of YWHAE gene in gastric cancer. Our findings provided novel insights into the role of YWHAE as a gene associated with H. pylori infection and ferroptosis in gastric cancer and expanded our understanding of the molecular mechanisms underlying gastric carcinogenesis.

Helicobacter pylori-activated fibroblasts as a silent partner in gastric cancer development

The discovery of Helicobacter pylori (Hp) infection of gastric mucosa leading to active chronic gastritis, gastroduodenal ulcers, and MALT lymphoma laid the groundwork for understanding of the general relationship between chronic infection, inflammation, and cancer. Nevertheless, this sequence of events is still far from full understanding with new players and mediators being constantly identified. Originally, the Hp virulence factors affecting mainly gastric epithelium were proposed to contribute considerably to gastric inflammation, ulceration, and cancer. Furthermore, it has been shown that Hp possesses the ability to penetrate the mucus layer and directly interact with stroma components including fibroblasts and myofibroblasts. These cells, which are the source of biophysical and biochemical signals providing the proper balance between cell proliferation and differentiation within gastric epithelial stem cell compartment, when exposed to Hp, can convert into cancer-associated fibroblast (CAF) phenotype. The crosstalk between fibroblasts and myofibroblasts with gastric epithelial cells including stem/progenitor cell niche involves several pathways mediated by non-coding RNAs, Wnt, BMP, TGF-β, and Notch signaling ligands. The current review concentrates on the consequences of Hp-induced increase in gastric fibroblast and myofibroblast number, and their activation towards CAFs with the emphasis to the altered communication between mesenchymal and epithelial cell compartment, which may lead to inflammation, epithelial stem cell overproliferation, disturbed differentiation, and gradual gastric cancer development. Thus, Hp-activated fibroblasts may constitute the target for anti-cancer treatment and, importantly, for the pharmacotherapies diminishing their activation particularly at the early stages of Hp infection.

Mechanisms of the Epithelial-Mesenchymal Transition and Tumor Microenvironment in Helicobacter pylori-Induced Gastric Cancer

Helicobacter pylori (H. pylori) is one of the most common human pathogens, affecting half of the world’s population. Approximately 20% of the infected patients develop gastric ulcers or neoplastic changes in the gastric stroma. An infection also leads to the progression of epithelial–mesenchymal transition within gastric tissue, increasing the probability of gastric cancer development. This paper aims to review the role of H. pylori and its virulence factors in epithelial–mesenchymal transition associated with malignant transformation within the gastric stroma. The reviewed factors included: CagA (cytotoxin-associated gene A) along with induction of cancer stem-cell properties and interaction with YAP (Yes-associated protein pathway), tumor necrosis factor α-inducing protein, Lpp20 lipoprotein, Afadin protein, penicillin-binding protein 1A, microRNA-29a-3p, programmed cell death protein 4, lysosomal-associated protein transmembrane 4β, cancer-associated fibroblasts, heparin-binding epidermal growth factor (HB-EGF), matrix metalloproteinase-7 (MMP-7), and cancer stem cells (CSCs). The review summarizes the most recent findings, providing insight into potential molecular targets and new treatment strategies for gastric cancer.

Atractylodes lancea volatile oils attenuated helicobacter pylori NCTC11637 growth and biofilm

Atractylodes lancea is a traditional Chinese perennial herb, which has been used for treating gastrointestinal diseases in traditional medicine. The aim of this study was to investigate the effect of Atractylodes lancea volatile oils on the planktonic growth and biofilm formation of Helicobacter pylori (H. pylori). Firstly, the minimal inhibitory concentration (MIC) of the volatile oils against H. pylori were determined using broth dilution method. SPSS17.0 was used to account 50% inhibiting concentration (IC50). Moreover, the anti-biofilm activity of the volatile oils was determined by crystal violet measurement and fluorescence microscope. Finally, gastric epithelial cells (GES-1 cells) were co-incubated with H. pylori with or without volatile oils treated. Real-time PCR and western blot were performed to detect the translocation of virulence factor Cag A. We found that Atractylodes lancea volatile oils inhibited the growth of H. pylori in a concentration dependent manner. The MIC and IC50 of volatile oils against H. pylori were 7.5 mg/mL and 2.181 mg/mL respectively. Fluorescence microscopy and crystal violet measurement indicated that volatile oils at sub-MIC concentration could reduce biofilm formation of H. pylori. In addition, volatile oils decreased the translocation of Cag A and reduced inflammatory cytokine IL-8 in GES-1 cells. Our results suggested that Atractylodes lancea volatile oils could be a potential compound of a novel class of H. pylori inhibitors with anti-H. pylori effects.

Helicobacter pylori infection and gastric cancer biology: tempering a double-edged sword

Helicobacter pylori (H. pylori) infection affects an estimated 4.4 billion people globally. Moreover, H. pylori presents the most significant risk factor for gastric cancer and low-grade mucosa-associated lymphoid tissue (MALT) lymphoma, and it is the first example of bacterial infection linked to carcinogenesis. Here, we contend that H. pylori research, which focuses on a cancer-causing pathogen resident in a relatively accessible organ, the stomach, could constitute an exemplar for microbial-related carcinogenesis in less tractable organs, such as the pancreas and lung. In this context, molecular biological approaches that could reap rewards are reviewed, including: (1) gastric cancer dynamics, particularly the role of stem cells and the heterogeneity of neoplastic cells, which are currently being investigated at the single-cell sequencing level; (2) mechanobiology, and the role of three-dimensional organoids and matrix metalloproteases; and (3) the connection between H. pylori and host pathophysiology and the gut microbiome. In the context of H. pylori's contribution to gastric cancer, several important conundrums remain to be fully elucidated. From among them, this article discusses (1) why H. pylori infection, which causes both gastric and duodenal inflammation, is only linked to gastric cancer; (2) whether a "precision oncomicrobiology" approach could enable a fine-tuning of the expression of only cancer-implicated H. pylori genes while maintaining beneficial H. pylori-mediated factors in extra-gastric tissues; and (3) the feasibility of using antibiotics targeting the microbial DNA damage system, which shares commonalities with mechanisms for human cell replication, as chemopreventives. Additional therapeutic perspectives are also discussed.

Pathogenesis of Helicobacter pylori infection

In this review, we highlight progress in the last year in characterizing known virulence factors like flagella and the Cag type IV secretion system with sophisticated structural and biochemical approaches to yield new insight on the assembly and functions of these critical virulence determinants. Several aspects of Helicobacter pylori physiology were newly explored this year and evaluated for their functions during stomach colonization, including a fascinating role for the essential protease HtrA in allowing access of H. pylori to the basolateral side of the gastric epithelium through cleavage of the tight junction protein E-cadherin to facilitate CagA delivery. Molecular biology tools standard in model bacteria, including regulated gene expression during animal infection and fluorescent reporter gene fusions, were newly applied to H. pylori to explore functions for urease beyond initial colonization and establish high salt consumption as a mediator of gene expression changes. New sequencing technologies enabled validation of long postulated roles for DNA methylation in regulating H. pylori gene expression. On the cell biology side, elegant work using lineage tracing in the murine model and organoid primary cell culture systems has provided new insights into how H. pylori manipulates gastric tissue functions, locally and at a distance, to promote its survival in the stomach and induce pathologic changes. Finally, new work has bolstered the case for genomic variation as an important mechanism to generate phenotypic diversity during changing environmental conditions in the context of diet manipulation in animal infection models and during human experimental infection after vaccination.