Molecular Biomarkers in Peptic Ulcer Disease: Bridging Pathophysiology and Personalized Management

I. Introduction: The Evolving Landscape of Peptic Ulcer Disease

A. Brief Overview of Peptic Ulcer Disease (PUD)

Peptic Ulcer Disease (PUD) is a prevalent gastrointestinal disorder defined by a mucosal discontinuity, characterized by breaks that extend through the entire thickness of the mucosa, penetrating into the submucosa or deeper layers of the stomach or duodenum.¹ Pathophysiologically, PUD results from a critical breakdown in the delicate balance between aggressive factors (primarily hydrochloric acid and pepsin) and the stomach’s robust mucosal protective factors (mucus, bicarbonate, and adequate blood flow).²

B. Global Prevalence and Clinical Importance

PUD remains a significant burden on global healthcare, although its etiology and prognosis have undergone notable transformations in recent decades. Analysis of global epidemiological data reveals that the overall case burden continues to rise. The worldwide incidence of PUD increased, with cases reaching 2,854,370 in 2021, representing an 11.05% cumulative growth since 1990.⁴ Concurrently, global prevalence cases reached 6,567,782 in 2021, marking an 8.77% cumulative growth over the same period.⁴ Incidence and prevalence rates remain consistently higher in males, though the age-standardized mortality rate (ASMR) has been noted to be higher in women.⁴ Critically, while the number of PUD cases has grown, the global age-standardized mortality rate (ASMR) has decreased dramatically, falling from 7.14 per 100,000 population in 1990 to 2.75 per 100,000 in 2021.⁴ This decoupling suggests that while acute treatment and management of severe complications (like bleeding or perforation) have improved significantly, the underlying factors initiating ulcer formation remain inadequately controlled, driving the overall rise in incidence. This shift in the clinical challenge—from managing high mortality to mitigating rising case numbers—points directly to the changing dominant etiologies, particularly the increasing reliance on nonsteroidal anti-inflammatory drugs (NSAIDs) among the aging global population, requiring diagnostic tools (biomarkers) capable of identifying non-infectious damage.

C. Role of Biomarkers in Understanding Disease Mechanisms and Management

Biomarkers—measurable indicators of a biological state—are indispensable in modern clinical practice, offering a non-invasive window into disease progression and response to therapy. In PUD, they provide essential capabilities for early non-invasive diagnosis, identifying individuals at high risk for complications or recurrence, and tailoring specific therapies based on molecular profiles.⁶ The evaluation of biomarkers moves diagnosis beyond simple symptom reporting or expensive endoscopy, enabling precision medicine approaches that optimize clinical outcomes.⁶

D. Purpose and Scope of the Review

This expert review systematically evaluates the established, emerging, and future molecular biomarkers relevant to PUD. The scope encompasses markers of inflammation, oxidative stress, mucosal integrity, infection status, and genetic predisposition, assessed for their roles in diagnosis, prognosis, and personalized therapeutic prediction.

II. Pathophysiology of Peptic Ulcer Disease: Mechanistic Detail

A. Mechanisms of Mucosal Injury: The Homeostatic Balance

The integrity of the gastric mucosa is maintained by a complex, multi-layered defensive barrier involving pre-epithelial mucus and bicarbonate secretion, epithelial cell function (rapid turnover and tight junctions), and sub-epithelial blood flow regulated by local mediators. PUD develops when aggressive factors overcome these defenses. Historically, the two primary drivers of PUD are infection with Helicobacter pylori and the use of NSAIDs.²

B. Role of Helicobacter pylori Infection

H. pylori infection facilitates mucosal injury through several mechanisms, including the direct action of cytotoxins (such as VacA and CagA) and the induction of chronic, deep-seated inflammation. The resulting gastritis weakens the mucosal barrier, compromises epithelial integrity, and often leads to mucosal atrophy, making the lining vulnerable to acid and pepsin.²

C. NSAID-Induced Ulcers: The Dual Pathogenicity Model

The clinical significance of NSAID-induced PUD has grown substantially, particularly with the aging population, and the mechanisms involved are distinct and profound. NSAID damage operates via two critical pathways ²:

1. Systemic Mechanism (COX-1 Inhibition):

 NSAIDs inhibit cyclooxygenase (COX) enzymes. The primary pathogenic mechanism involves the inhibition of the constitutively expressed COX-1 enzyme. This blockage dramatically reduces the synthesis of protective prostaglandins, which are essential for maintaining mucosal integrity. The decrease in prostaglandins leads to three critical defects: diminished mucus and bicarbonate secretion, impaired cell proliferation, and a reduction in mucosal blood flow. The resulting systemic compromise fundamentally weakens the entire defensive apparatus.

2. Direct Mucosal Injury (Topical/Cellular Mechanism):

 Separate from COX inhibition, NSAIDs also cause direct, topical damage to the gastric epithelium. As weak acids, they disrupt mucus phospholipids and cell membranes, initiating cellular damage. A highly specific consequence of this process is the uncoupling of mitochondrial oxidative phosphorylation within the epithelial cells.³ This mechanism is crucial because it immediately generates reactive oxygen species (ROS), providing a direct mechanistic link to the biomarkers discussed in Section 4.2.

D. Imbalance and Synergistic Interactions

The rising prevalence of NSAID use, especially among the elderly population being treated for chronic conditions, has resulted in a considerable healthcare burden.³ Retrospective studies have clearly demonstrated this risk: elderly NSAID users experience a substantially higher ulcer hospitalization rate (16.7 per 1,000 person-years) compared to nonusers (4.2 per 1,000 person-years).³ Furthermore, the simultaneous presence of H. pylori and chronic NSAID use exhibits a powerful synergistic effect. H. pylori weakens the mucosa through chronic inflammation, while NSAIDs compromise protection through prostaglandin depletion and direct cellular injury. Patients with both risk factors face a 3.53-fold higher risk of peptic ulcers and associated complications, such as bleeding, compared to those with either factor alone.³ It is essential to recognize that even after successful H. pylori eradication, chronic NSAID users remain at high risk of ulcer recurrence due to persistent prostaglandin depletion and impaired mucosal integrity.³ This necessitates a diagnostic strategy that can monitor for the molecular damage inflicted by NSAIDs independently of the infection status, making non-infectious biomarkers critical for ongoing management.

III. Concept of Biomarkers

A. Definition and Classification

A biomarker is formally defined as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. Biomarkers are classified based on their clinical utility:

1. Diagnostic Biomarkers: Used to identify the presence of a disease (e.g., detecting H. pylori infection).⁷
2. Prognostic Biomarkers: Used to predict the natural course or outcome of the disease, regardless of treatment (e.g., predicting gastric cancer risk).⁶
3. Predictive Biomarkers: Used to forecast the likelihood of a specific therapeutic response (e.g., predicting antibiotic resistance).⁶
4. Therapeutic Biomarkers: Used to monitor drug efficacy and measure overall treatment response.

B. Importance of Biomarkers in Gastrointestinal Diseases

The integration of robust and specific biomarkers is fundamental to the movement toward precision medicine in gastroenterology. They enable clinicians to identify patients with the greatest risk for severe disease, allowing for aggressive and individualized therapies.⁶ Furthermore, novel non-invasive methodologies, such as liquid biopsy (initially developed for GI cancers), offer the potential for high-sensitivity early detection and prognosis in conditions like PUD and its pre-malignant precursors, overcoming the limitations and invasiveness of conventional tissue biopsy.⁷

IV. Biomarkers in Peptic Ulcer Disease (PUD)

4.1 Inflammatory Biomarkers

Inflammatory biomarkers reflect the systemic response mounted by the body against localized mucosal injury, providing insight into disease severity and potential complications.

• C-reactive protein (CRP): CRP is a widely used acute phase reactant. Studies indicate that while plasma CRP shows low sensitivity (26.42%) and serum CRP slightly higher (35.85%), its high specificity (96.30% in both plasma and serum) suggests that an elevated level is highly confirmatory of significant systemic inflammation or complication in a patient with suspected PUD.¹⁰
• Interleukins (IL-1β, IL-6, IL-8): Interleukins are key mediators of the inflammatory cascade. Serum IL-6 demonstrated a comparatively higher sensitivity (56.60%) combined with excellent specificity (96.30%) in diagnostic panels, making it a robust systemic marker for active disease and general inflammatory burden.¹⁰ IL-8, a potent chemokine responsible for neutrophil recruitment, maintains a high specificity (92.59%) in plasma.¹⁰
• Tumor necrosis factor-alpha (TNF-α): TNF-α, a powerful pro-inflammatory cytokine, similarly shows high specificity (ranging from 88.89% to 96.15%) but low sensitivity (21.15% to 37.74%).¹⁰ The consistent finding of high specificity across these inflammatory markers confirms their value in confirming the severity of an existing PUD or its acute complications, but their low sensitivity limits their utility as initial screening tools for mild, localized ulcers.

4.2 Oxidative Stress Biomarkers

Given the mechanistic understanding that NSAIDs uncouple mitochondrial phosphorylation and that inflammation generates reactive oxygen species (ROS), oxidative stress biomarkers provide direct evidence of cellular injury in PUD pathogenesis.³

• Malondialdehyde (MDA): MDA is a critical end-product of lipid peroxidation, which occurs when ROS attack cellular membranes. Elevated MDA levels are a direct measure of the magnitude of ongoing oxidative injury and subsequent membrane damage.¹²
• Superoxide dismutase (SOD) and Glutathione peroxidase (GPx): These enzymes constitute the body’s crucial first line of enzymatic defense against ROS.¹¹ SOD catalyzes the dismutation of superoxide radicals, while GPx reduces damaging hydrogen peroxide.¹¹ In PUD, especially chronic or NSAID-driven ulcers, reduced activity or concentration of SOD and GPx indicates that the mucosal cells are overwhelmed by oxidative stress.¹² Because MDA levels reflect the actual molecular damage, monitoring the normalization of MDA levels and the recovery of antioxidant enzyme activity (SOD/GPx) provides a powerful, quantifiable metric for molecular mucosal healing following therapeutic intervention.¹²

4.3 Gastric Mucosal and Enzymatic Biomarkers

These markers primarily reflect the functional status and integrity of the gastric lining, offering both diagnostic and crucial prognostic value, particularly regarding the risk of gastric malignancy.

• Pepsinogen I/II Ratio (PGI/PGII): Pepsinogen I (PGI) is predominantly secreted by the fundic glands (acid-secreting mucosa), while Pepsinogen II (PGII) is secreted across the stomach. A low PGI concentration, coupled with a low PGI/PGII ratio, is a highly reliable marker for severe atrophic gastritis (AG), a well-known precancerous lesion.¹⁴ Serum pepsinogen testing is an invaluable non-invasive biomarker for screening AG. The optimal critical value established in various studies is PGI/PGII $\le$ 4.6 (or $\le$ 4.0), yielding detection sensitivities up to 82.6% and specificities up to 91.7% for AG.¹⁴ The utility of this marker lies in its ability to stratify patients who require intensive endoscopic surveillance to detect early gastric cancer.¹⁵

Table 4.3.A: Utility and Stratification Value of Gastric Enzymatic Biomarkers

• Gastrin Levels: While not a primary PUD marker, gastrin measurement is essential for identifying rare hypersecretory states, such as Zollinger-Ellison Syndrome, which cause severe and refractory ulcer disease.
• Mucins (MUC1, MUC5AC): Mucins are critical for the pre-epithelial barrier. MUC5AC is a secreted mucin forming the protective gel, while MUC1 is a membrane-tethered mucin involved in cytoprotection and regulating inflammation.¹² Alterations in mucin expression patterns (e.g., increased MUC1 expression observed in idiopathic ulcers) are linked to defects in epithelial cytoprotection and play a role in ulcer pathogenesis.¹⁷

4.4 Infection-Related Biomarkers

Accurate identification and monitoring of H. pylori infection remain fundamental to PUD management.

• H. pylori Antibodies (IgG, IgA): Serologic antibody tests are convenient for initial diagnosis, reflecting exposure to the pathogen, but they are not accurate for confirming eradication success, as antibodies may persist long after the infection is cured.⁸
• Urease Activity (Urea Breath Test - UBT): The UBT is a highly accurate, non-invasive functional test that detects the active presence of H. pylori by measuring the ${}^{13}\text{C}$ or ${}^{14}\text{C}$ carbon released after ingesting urea.⁸ This test is essential for both initial diagnosis and confirmation of cure.⁸
• Stool Antigen Tests (SAT): SATs look for specific H. pylori antigens in the stool sample and are considered highly accurate and non-invasive, widely recommended for diagnosis and confirmation of eradication.⁸
• Stool PCR Tests: Molecular polymerase chain reaction (PCR) testing provides an advanced diagnostic capability. In addition to confirming the presence of H. pylori, the PCR test can simultaneously detect gene changes that confer resistance to common antibiotic medicines.⁴ This ability to function as a predictive biomarker for antibiotic resistance is crucial for guiding targeted initial therapeutic strategy, moving treatment away from unreliable empirical "test-and-treat" approaches toward individualized regimens (e.g., quadruple therapy).⁸

4.5 Genetic and Molecular Biomarkers

Molecular markers are emerging as key players in predicting healing and recurrence susceptibility.

• COX-2 Expression: While systemic NSAID inhibition of COX-1 causes initial damage, the enzyme COX-2 is known to play an important role in the healing phase by generating prostaglandins necessary for cell migration, angiogenesis, and tissue repair.¹⁸ Studies show that selective COX-2 inhibitors can delay the healing of experimental gastric ulcers.¹⁸ Therefore, COX-2 status and genetic polymorphisms affecting its expression or function can act as a crucial predictive biomarker regarding the trajectory of ulcer healing under different therapeutic regimens.
• Nitric Oxide Synthase (NOS): Nitric Oxide (NO) is a vital mediator of gastric mucosal blood flow, which is a key component of mucosal defense. Genetic polymorphisms in NOS can influence susceptibility to PUD and the rate of healing.
• MicroRNAs (miRNAs): MiRNAs are a class of small, non-coding RNAs (17–25 nucleotides) that regulate gene expression post-transcriptionally.⁷ They are actively involved in gastric inflammation, epithelial repair, and malignant transformation.¹⁹ MiRNAs meet most of the criteria for ideal biomarkers, possessing high accessibility, specificity, and sensitivity ⁷, and their dysregulation is associated with various gastrointestinal pathologies, including gastric cancer (e.g., miR-21, miR-155).²⁰ Ongoing research into specific miRNA signatures promises to provide therapeutic targets and highly specific, non-invasive diagnostic panels for PUD.¹⁹

V. Clinical Applications of Biomarkers in PUD

Biomarkers are essential tools that enable stratified and personalized care in PUD management, extending their utility beyond simple diagnosis.

A. Early Diagnosis and Risk Stratification

Biomarkers facilitate the early and mechanism-specific identification of PUD risk factors. For infection, highly accurate non-invasive tests like UBT and SAT confirm active H. pylori presence, informing the immediate need for eradication therapy.⁸ For prognostic risk stratification, the PGI/PGII ratio allows for the identification of severe atrophic gastritis, directing high-risk patients toward necessary intensive endoscopic surveillance to preemptively detect early gastric cancer.¹⁵

B. Monitoring Disease Progression and Healing

Monitoring the resolution of PUD requires more than just endoscopic visualization. Tracking the decrease in systemic inflammatory markers such as IL-6, which possesses high specificity, provides evidence of reduced systemic involvement.¹⁰ Furthermore, monitoring the reduction in cellular injury markers, specifically Malondialdehyde (MDA), and the recovery of antioxidant capacity (SOD/GPx) provides a quantifiable molecular metric of mucosal integrity restoration and healing at the cellular level, confirming the efficacy of cytoprotective therapies.¹²

C. Evaluating Treatment Response (Predictive and Therapeutic Biomarkers)

Effective PUD management hinges on evaluating treatment success. Confirmation of H. pylori eradication is mandatory and best achieved using UBT or SAT, which reliably confirm cure.⁸ Furthermore, molecular testing (Stool PCR) can provide critical predictive information by identifying gene changes associated with antibiotic resistance prior to treatment initiation.⁴ This predictive capacity ensures the selection of the most effective, mechanism-based therapeutic strategy, moving care toward precision medicine and minimizing the need for failed empirical regimens.⁸

D. Risk Prediction for Recurrence and Complications

Biomarkers are key to identifying patients who require long-term risk reduction strategies. Patients stratified as high-risk based on chronic NSAID use ⁸, advanced age, or a low PGI/PGII ratio (indicating underlying mucosal atrophy) require prophylactic acid suppression and ongoing surveillance. Systemic inflammatory markers (like IL-6 or CRP) can also be utilized to predict the risk of severe complications, such as acute ulcer bleeding, allowing for proactive, individualized risk management.¹⁰

VI. Limitations and Challenges: Bridging the Gap to Clinical Practice

Despite the enormous promise of molecular diagnostics, several critical translational challenges impede the widespread adoption of many emerging PUD biomarkers.

A. Variability in Biomarker Levels

The complexity of biological systems introduces significant variability, particularly for advanced markers like miRNAs. MiRNA expression is highly dynamic, fluctuating based on the specific disease stage, heterogeneity between patients, and even influenced by environmental factors such as the complex interplay with the gut microbiota.¹⁹ This inherent biological dynamism complicates the establishment of universal, reliable reference ranges necessary for routine clinical decision-making.

B. Lack of Standardization and Validation

A major hurdle for molecular diagnostics is the lack of standardized protocols. Significant variability exists in the collection, processing, and measurement of molecular markers such as miRNAs and circulating tumor DNA (ctDNA). This absence of uniformity undermines the reproducibility of research findings and clinical results across different laboratories, thereby stalling the integration of these promising tools into routine clinical practice.⁷

C. Cost and Accessibility Issues

Advanced molecular diagnostics, including liquid biopsy and omics-based assays, often require specialized equipment and complex bioinformatics analysis, leading to high associated costs.¹ This lack of cost-effectiveness, compared to established, inexpensive tests, prevents these new methods from serving as the new standard of care, especially in low-resource settings. Consequently, high-cost diagnostics must currently be reserved for specialized clinics and specific high-risk populations where the potential benefit (e.g., cancer prevention or personalized therapy) outweighs the economic burden.¹

Table 6.A: Translational Challenges Facing Emerging Molecular Biomarkers (MiRNAs/Liquid Biopsy)

VII. Future Perspectives: Personalization through Omics and AI

A. Emerging Molecular and Omics-Based Biomarkers

The future of PUD management lies in the integration of omics technology. This involves the continued development of advanced liquid biopsy panels combining circulating molecular markers (ctDNA, exosomes, and miRNAs) to provide non-invasive, high-sensitivity detection of early gastric pathology.¹ Focused research on identifying specific miRNA signatures that regulate gastric epithelial stem cell repair pathways holds the potential for novel therapeutic interventions aimed at treating refractory ulcers.⁷

B. Personalized Medicine Approaches

Personalized PUD management will be achieved through pharmacogenomics. By identifying genetic variants that predict an individual’s high susceptibility to NSAID-induced PUD (e.g., in genes related to mucosal repair or prostaglandin synthesis), clinicians can accurately guide prophylactic strategies, such as the appropriate use of proton pump inhibitors. Furthermore, biomarker-guided acid suppression will employ tools like the PGI/PGII status to tailor the dosage and duration of anti-secretory therapy post-ulcer healing, ensuring optimal mucosal recovery while avoiding unnecessary long-term medication use.

C. Integration of Biomarkers with Imaging and AI Tools

To manage the high dimensionality and biological variability associated with multi-omics data, integration with artificial intelligence (AI) and machine learning tools is essential.¹ AI can process complex, multi-marker profiles (combining transcriptomics, clinical markers, and imaging data) to generate automated, sophisticated risk scores. This integration will enhance surveillance strategies, allowing clinicians to combine specific biomarker signatures (e.g., low PGI/PGII status plus high-risk miRNA markers) with endoscopic imaging findings to accurately prioritize surveillance resources for those at greatest risk of developing gastric cancer.¹⁵

CONCLUSION

A. Summary of Key Findings

The clinical imperative in PUD has shifted from merely reducing mortality to mitigating a rising case burden driven by persistent non-infectious factors, namely NSAID use in an aging population.³ Foundational management relies on highly accurate infection markers (H. pylori UBT/SAT).⁸ However, the critical advance in PUD management comes from prognostic biomarkers like the PGI/PGII ratio, which is indispensable for identifying high-risk atrophy and guiding gastric cancer surveillance.¹⁴ Furthermore, measuring active disease and healing success is facilitated by emerging inflammatory (IL-6) ¹⁰ and oxidative stress (MDA) markers ¹², which reflect molecular activity beyond gross mucosal appearance. While advanced molecular diagnostics (miRNAs) offer immense potential for high-specificity, non-invasive detection ⁷, their clinical translation is currently hampered by lack of standardization and high cost.¹

B. Clinical Relevance of Biomarkers in Improving Diagnosis and Management of PUD

The strategic implementation of established and emerging biomarkers enables clinicians to transition decisively from empirical, symptom-based treatment to mechanism-based, predictive, and prognostic care. Biomarkers provide the foundation for molecular stratification, allowing for targeted H. pylori therapy based on resistance prediction ⁴, tailored acid suppression based on atrophy status, and personalized prophylaxis for NSAID users.⁸ This systematic approach, informed by molecular profiling, is essential for reducing complication rates, preventing recurrence, and ultimately improving the long-term gastric health outcomes for PUD patients.