Helicobacter pylori (H. pylori) is a gram-negative, microaerophilic, spiral-shaped bacterium that infects approximately 50% of the global population and is classified as a Group I human carcinogen. The association between the gastric microbiome and H. pylori plays a significant role in the development and progression of gastric cancer (GC) (1, 2). H. pylori infection is closely associated with chronic gastritis, peptic ulcers, GC and mucosa-associated lymphoid tissue (MALT) lymphoma. H. pylori infection can cure chronic active gastritis and peptic ulcer disease, reduce the risk of peptic ulcer bleeding in aspirin users, and lower the risk of GC in infected individuals (3, 4). Research has shown that H. pylori infection increases the risk of developing colorectal cancer (CRC) (5, 6), and reduces the risk of inflammatory bowel disease (IBD) (7, 8). In conclusion, H. pylori may be related to IBD, and the specific mechanism needs to be further studied.

IBD is a chronic, recurrent inflammatory disease of the gastrointestinal tract that includes ulcerative colitis (UC) and Crohn’s disease (CD) (9). The main gastrointestinal symptoms of IBD include abdominal pain, diarrhea, bloody stools and weight loss (10). Currently, the aetiology and pathogenesis of IBD are not fully understood. Some studies have shown that genetic and environmental factors, gut microbiota imbalance, intestinal mucosal immune responses, and damage to the intestinal mucosal barrier play important roles in IBD (11–14). Multiple studies have shown that H. pylori infection is associated with IBD and that H. pylori may influence the immunoregulatory functions related to IBD (8, 15, 16). However, the specific molecular mechanism is still unclear.

In this study, we used bioinformatics methods to comprehensively analyze the relationship between H. pylori and IBD on the basis of sequencing data of the two diseases from databases. By analyzing the coexpression of DEGs via GO and KEGG analyses, identifying candidate Hub genes (core genes coexpressed between H. pylori and IBD), predicting small-molecule drugs and performing transcription factor analysis, we explored the potential pathogenic mechanisms common to the two diseases.

Studies have shown that IBD is an autoimmune disease and that H. pylori infection and colonization have a protective effect against IBD. The mechanisms involved include alterations in inflammatory responses and immune reactions, with improvements in living standards, decreases in H. pylori infection rates, and increases in H. pylori eradication rates, and the incidence of IBD has gradually increased in some regions (26, 27). Additionally, some animal experiments have confirmed a negative correlation between H. pylori infection and the onset of IBD (28, 29). Studies have shown that H. pylori activate Toll-like receptors (TLRs), triggering proinflammatory or anti-inflammatory effects, during the progression of H. pylori infection. Inflammatory factors (IL-6, IL-8, IL-18, IL-32, IL-1β, TNF-α, CCL2, CCL20, CXCL1 and CXCL10) and immune cells (dendritic cells, regulatory T cells, B cells and M2 macrophages) play key roles in the persistence, differentiation, malignant progression, immune infiltration, immune response and immune evasion associated with H. pylori-related diseases, involving various pathogenic mechanisms (30–36).

The pathogenesis of IBD is related to immune system impairment, where activation of the immune system promotes inflammatory responses, leading to tissue damage. Inflammatory factors play important regulatory roles in intestinal mucosal inflammation. Changes in the expression of IL-6, IL-12, IL-23, IL-32, TNF-α and IL-1β promote mucosal inflammation. Therapeutic antibodies and targeted drugs for these factors have been developed and are gradually being used in clinical IBD treatment (37–40). Furthermore, inflammation of the intestinal mucosa is exacerbated by the actions of immune cells, including neutrophils, T lymphocytes, B lymphocytes, macrophages, and dendritic cells (41–45). Therefore, inflammatory factors, immune cells and immune-related genes are key hubs linking H. pylori and IBD. This study identified the DEGs commonly expressed in both H. pylori-infected patients and IBD patients and explored potential targets to provide a theoretical basis for the management and treatment of patients with both H. pylori and IBD.

In this study, we utilized the H. pylori and IBD datasets to identify 151 overlapping DEGs. GO and KEGG enrichment analyses indicated that these DEGs were enriched primarily in response to chemokine signaling, the inflammatory response and the immune response. These findings suggest that these DEGs are involved in the regulation of immune and inflammatory responses. Therefore, disruption of the immune system and the inflammatory microenvironment may be major factors in the pathogenesis of H. pylori infection and IBD. Using the MCC and degree algorithms, 10 Hub genes were subsequently identified: TLR4, IL10, CXCL8, IL1B, TLR2, CXCR2, CCL2, IL6, CCR1 and MMP-9. GO and KEGG enrichment analyses were performed on these Hub genes, which focused mainly on responses to lipopolysaccharides, responses to molecules of bacterial origin, responses to biotic stimuli and leukocyte migration. These genes were identified as diagnostic markers for H. pylori and IBD. Validation using the H. pylori and IBD datasets revealed that the expression of Hub genes was upregulated in patients with H. pylori infection and IBD, with the expression of MMP-9 significantly upregulated.

Matrix metalloproteinases (MMPs) are a class of glycosylated endopeptidases that degrade extracellular matrix (ECM) molecules, including gelatinase A (MMP-2) and gelatinase B (MMP-9). These MMPs are involved in various inflammatory diseases, such as H. pylori-associated gastritis and gastric and duodenal ulcers. Initially, H. pylori was shown to activate MMP-9 expression in gastric epithelial cells, contributing to the development of H. pylori-related gastric diseases (46, 47). In clinical samples, MMP-9 mRNA expression was found to be significantly upregulated in H. pylori-positive patients, with a notable association with CagA status and peptic ulcer disease (PUD) (48). MMP-9 plays a critical role in gastric remodeling in children with H. pylori-related gastritis (49). Moreover, studies on single nucleotide polymorphisms (SNPs) of the MMP-9 gene revealed that the rs3918249-rs17576 CG haplotype increased the risk of H. pylori-positive PUD (50); SNPs in the MMP-9 gene were also associated with H. pylori-positive gastric ulcers (GU) (51). Mechanistically, H. pylori lipopolysaccharide (LPS)-induced gastric mucosal MMP-9 release is associated with the activation of the MAPK, ERK, and p38 pathways (52). H. pylori can promote the progression of H. pylori-related GC by upregulating semaphorin 5A (Sema5A) and regulating the ERK/MMP-9 signaling pathway (53). These studies are consistent with our findings, which demonstrate that MMP-9 is significantly upregulated in H. pylori infection in both the training and validation sets. These studies indicate that MMP-9 plays a crucial role in H. pylori-related gastric diseases, although the specific molecular mechanisms involved require further investigation.

In the intestinal mucosa of IBD patients, mice, and dogs, MMP-9 has been shown to promote the development of colitis (54–56). In children with UC, its expression increases with the severity of the disease (57). Fibroblasts in IBD continuously express IL-21, which enhances MMP-9 production (58). Some studies have suggested that in mouse models of acute and chronic dextran sulfate sodium (DSS)-induced colitis and acute 2,4,6-trinitrobenzene sulfonic acid-induced colitis, the parameters associated with chronic colitis in MMP-9 knockout mice are similar. Pharmacological inhibition of MMP-9 with bioactive peptides does not improve DSS-induced colitis, suggesting that the upregulation of MMP-9 may be a consequence of intestinal inflammation rather than a cause (59). Mechanistic studies have shown that MMP-9 increases intestinal tight junction (TJ) permeability via the upregulation of myosin light-chain kinase (MLCK) through the p38 kinase signaling pathway in both in vivo and in vitro models (60). Additionally, MMP-9 regulates intestinal epithelial tight junction barrier function through NF-κB pathway activation of MLCK (61). The long noncoding RNA (lncRNA) growth arrest-specific transcript 5 (GAS5) can regulate MMP-9 expression, mediating tissue damage in IBD patients. Inflammatory tissues show downregulation of GAS5 and upregulation of MMP-9 (62). Furthermore, a mutated CXCL8 protein (G31P) binds to CXCR1/2, rendering CXCL8 inactive, reducing MMP-9 expression, and alleviating colonic fibrosis (63). The upregulation of MMP-9 in IBD is consistent with our validation results, but MMP-9 affects the progression of IBD through multiple pathways. On the basis of the enrichment analysis results in this study, the current research is insufficient to fully explain the pathogenesis of IBD, and further studies are needed to provide a theoretical basis for clinical IBD treatment.

Therefore, MMP-9 may play a significant role in the pathogenesis and progression of both H. pylori infection and IBD, and modulating this enzyme could have important implications. The findings of this study provide key clues for further research into the connection between these two diseases and their potential therapeutic targets.

Moreover, MMP-9 is critically involved in a variety of diseases, particularly in cancer. In studies on lymphoma, EGR-1, an early growth response protein 1, is expressed by stromal cells within lymphoma tissues and inhibits the transcriptional activation of the MMP-9 gene in these stromal cells (64). MMP-9 inhibitors have been shown to enhance the functionality of TCR-T cells, which are suppressed by EBV-induced M2 macrophages. The combination of MMP-9 inhibitors with TCR-T-cell therapy has demonstrated effective treatment outcomes for EBV-positive solid tumours (65). Tumor necrosis factor alpha-induced protein 8 (TIPE) has been identified as a promoter of CRC metastasis through its regulatory effects on MMP-9 expression (66). Targeting mTORC1 can facilitate the progression from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) via the inhibition of MMP-9 (67). In oral squamous cell carcinoma (OSCC), MED1, a subunit of the Mediator complex, activates the transcription of MMP-9 while simultaneously inhibiting CD8+ T-cell antitumor immune responses (68).

Within the context of inflammation, injury repair mechanisms also highlight the significant role played by MMP-9. Recent studies have indicated that unbound bilirubin (UCB) and its derivative dimethyl ester bilirubin (BD1) effectively inhibit the neutrophil-mediated activity of MMP-9 while reducing proinflammatory cytokine gene expression and modulating MAPK pathway signaling to alleviate psoriasis-like skin inflammation in mice (69). Furthermore, the commensal bacterium Enterococcus faecalis activates the expression of MMP-9 in host intestinal tissue; pharmacological inhibition of this activation can prevent anastomotic leakage in rat models (70). In cases of ischemic stroke, MMP-9 inhibitors have been shown to specifically reduce the levels of MMP-9, inflammation, and activation while improving neurological function (71). Research on tissue damage and regeneration indicates that liver-specific inhibition of MMP-9 accelerates liver regeneration by 40% following partial hepatectomy; it also prevents proteolytic cleavage of vascular endothelial growth factor-mesenchymal stem cell-derived factor in hepatic tissue, thereby mitigating damage and enhancing regenerative capacity (72). In hydrogel studies, cinnamaldehyde (CA), a specific TRPA1 agonist, is incorporated into a dual-layer hybrid hydrogel (CA@HA-Gel) designed to respond to matrix MMP-9, which inhibits ferroptosis in wound endothelial cells and significantly promotes healing in diabetic wounds (73). In conclusion, MMP-9 plays a critical role in various biological processes, including inflammation, the injury response, tissue regeneration, tumor progression and immune regulation.

In the pathogenesis of H. pylori infection and IBD, immune cell infiltration plays an important role. Immune infiltration analysis revealed the relationships between immune cells and cellular molecules in H. pylori infection and IBD, which may affect the immune response and inflammatory processes in these diseases. We utilized CIBERSORT to analyze the immune cell infiltration patterns of DEGs in both diseases, and the immune infiltration results were similar. In IBD, immune cell infiltration is increased in CD8+ T cells, monocytes, M0 macrophages, activated mast cells, and neutrophils, whereas memory B cells, resting NK cells, and resting mast cells are decreased. Studies have shown that specific infiltration is dominated by intraganglionic B cells and monocytes in CD, whereas the myenteric plexus (MP) in UC is infiltrated by CD8+ T cells, leading to neuronal apoptosis. In a DSS-induced colitis model, monocyte, B cell, and CD8+ T-cell infiltration also occurs (74). Different clinical outcomes of CD are related to the exhaustion of CD8+ T cells. In active CD, activated CD39+ and CD39+PD-1+ CD8+ T-cell subsets are enriched at low frequencies, whereas during remission, exhaustion-related transcriptional characteristics are upregulated in these subsets (75). Monocytes and macrophages play important roles in regulating the immune response of the intestinal mucosa in IBD. Macrophages produce proinflammatory and anti-inflammatory cytokines, chemokines, toxic mediators, and macrophage extracellular traps (METs), regulating processes such as epithelial cell proliferation, angiogenesis, fibrosis, and the immune response. Additionally, several IBD susceptibility genes related to the maturation and function of macrophages, such as RUNX3, IL21R, GTF2I, and LILRB3, play key roles in the pathogenesis of IBD (76). Synbindin, a classical membrane tethering factor, regulates TLR4 signaling and suppresses the proinflammatory activation of macrophages in response to the microbiota during colitis (77). Moreover, IL-10 is a key regulator of monocyte IL-23 production, providing the basis for targeted therapies such as IL-23p19 and/or IL-1α/IL-1β in IBD patient subgroups (78–80). Our findings, which are consistent with those of other studies, show that the intestinal mucosa in IBD patients contains many activated memory CD4 T cells, M1 macrophages, M2 macrophages, activated mast cells, and neutrophils (81–84). Thus, immune cells play an essential role in regulating immune responses in the intestinal mucosa and provide strategies for the treatment of IBD.

In exploring the relationship between core genes and immune cell infiltration, we emphasize a comprehensive discussion and literature review concerning the association between MMP-9 and the aforementioned significant immune cells. In OSCC, MED1 activates MMP-9 transcription and inhibits the antitumor immune response of CD8+ T cells (68). MMP-9 suppresses the infiltration and cytotoxic activity of CD8+ T cells, thereby providing support for the existence of an inhibitory tumor immune microenvironment (TIME) and resistance to PD-1 inhibitors associated with gain-of-function mutations in CTNNB1 (85). In chronic hepatitis B (CHB), MMP-9 plays an important role in regulating the intrahepatic anti-HBV CD8 T-cell response by mediating the release of soluble CD100 (86). Patients with prostate cancer can increase the expression of MMP-9 in their peripheral blood NK cells and secrete factors that recruit and polarize monocytes (87). Following surgery for acute aortic dissection, platelets release MMP-9 to reprogram monocytes, thereby contributing to postoperative recovery (88). MMP-9 is a central protein related to the immune system and is associated with immune cell infiltration in patients with spinal tuberculosis (STB) (89). In glioblastoma patients, the release of MMP-9 by tumor-infiltrating neutrophils contributes to the efficacy of bevacizumab (90). Therefore, MMP-9 is associated not only with CD8+ T cells, monocytes, and neutrophils but also with other immune cells.

In the analysis of immune infiltration related to H. pylori infection, the small sample size of H. pylori infection data from the GEO datasets resulted in fewer immune infiltrates than did the results of CIBERSORT. In the future, we plan to conduct transcriptomic sequencing on a large number of H. pylori-infected gastric mucosa samples to address the limitations of small sample sizes and perform effective immune infiltration analysis. According to studies on H. pylori and immune cell infiltration, H. pylori infection induces the infiltration of T lymphocytes and enhances apoptosis through inflammatory responses (91–95). H. pylori can induce the expression of cystathionine γ-lyase (CTH) in macrophages, promoting persistent inflammation (96). H. pylori infection impacts the TIME, leading to a poorer prognosis in de novo gastric diffuse large B-cell lymphoma (gDLBCL) (97, 98). Immune cells play crucial roles in the pathogenesis of H. pylori-related diseases.

In addition, this study identified potential small-molecule compounds from the CMap database by screening DEGs in H. pylori and IBD and revealed that alpha-linolenic acid, dexamethasone, and phentolamine interact with several Hub genes. We further used the PubChem tool to predict the unique chemical and 3D structures of these three drugs. These small-molecule drugs may improve the pathological conditions of H. pylori infection and IBD, providing potential directions for the treatment of these diseases and their associated complications.

The Hub genes were closely related to small molecule drugs and transcription factors. As shown in Figure 7B , dexamethasone was closely associated with the Hub genes; however, there was no direct correlation between MMP-9 and dexamethasone, as depicted in Figure 7B , although indirect relationships were present. Dexamethasone has been shown to downregulate both MMP-9 expression and oxidative stress levels in mice suffering from eosinophilic meningitis induced by Angiostrongylus cantonensis infection (99). MMP-9 is correlated with the selected small-molecule drugs. Dexamethasone induces the secretion of MMP-9 both in vitro and in vivo, thereby enhancing the production of mature brain-derived neurotrophic factor (mBDNF), which is essential for synaptic plasticity in adults (100). As shown in Figure 8 , several transcription factors identified through the selection of Hub genes revealed that in IBD, several transcription factors were significantly downregulated (NFKB1, REL and RELA), whereas STAT1 expression was upregulated. RELA may play an important role in coronary artery disease (CAD) by targeting MMP-9 (101). Additionally, MMP-9 may participate in the development of various diseases through the STAT1-related signaling pathway (89, 102–104). Dexamethasone plays a pivotal role in the clinical management of IBD. Through our bioinformatics exploration, we identified common Hub genes associated with H. pylori infection and IBD, particularly MMP-9, which was significantly upregulated under both conditions. On the basis of our literature review informed by bioinformatics, we hypothesize that the activation of this pathway increases the expression of transcription factors, activates MMP-9, and promotes inflammatory responses as well as immune cell activation. Furthermore, the small-molecule drugs we identified may modulate the expression of MMP-9 through various pathways, indicating a need for further investigation.

MMP-9 is a common diagnostic marker for both H. pylori and IBD, and although some relevant studies exist in these two diseases, the underlying mechanisms remain unclear. Due to funding limitations, further validation and in-depth exploration of these mechanisms were not conducted. In the future, our research group will further investigate the pathogenesis of these two diseases to provide a theoretical basis and direction for disease prevention and treatment.

In this study, we revealed that the inflammatory response and immune response may be the common pathogenic mechanisms of H. pylori infection and IBD. Additionally, we identified 10 Hub genes (TLR4, IL10, CXCL8, IL1B, TLR2, CXCR2, CCL2, IL6, CCR1 and MMP-9) with significant diagnostic relevance, among which MMP-9 was significantly upregulated in both the training and validation sets for these two diseases. MMP-9 may modulate target genes associated with inflammation and immune responses via transcription factor activation, and the small-molecule drugs identified could serve as a significant strategy for inhibiting MMP-9, thereby providing a scientific rationale for clinical interventions in H. pylori and IBD.