J. Mol. Pathol., Volume 6, Issue 3 (September 2025) – 11 articles

This research delves into the complex relationship between progenitor cells and the differentiated cell types that make up the stomach. It highlights the need for further investigation into the mechanisms governing stomach development and how these mechanisms relate to the maintenance of the stomach in a healthy state. The transition from normal gastric mucosa to metaplasia involves significant alterations in the phenotype and function of gastric epithelial cells, including stem cells, mucous neck cells, chief cells, and parietal cells. The presented literature review provides an in-depth analysis of pyloric and pseudopyloric metaplasia, along with spasmolytic polypeptide-expressing metaplasia, focusing on their biological significance, underlying pathogenesis, diagnostic features, and prognostic implications. It explores the role of various gastric epithelial cell types in the pathogenesis of metaplasia, highlighting recent advances in cellular plasticity, molecular pathways, and the implications for gastric carcinogenesis. Full article

Ependymomas are a heterogeneous group of central nervous system tumors originating from ependymal cells, exhibiting significant variability in clinical behavior, prognosis, and treatment response based on anatomical location and molecular profile. Historically, diagnosis and grading relied on histopathological features, often failing to predict outcomes accurately across tumor subtypes. With the integration of molecular and epigenetic profiling, the classification and management of ependymomas have undergone a significant transformation, culminating in the updated 2021 World Health Organization Classification of Tumors of the Central Nervous System. This molecularly driven system emphasizes the relevance of DNA methylation patterns and fusion oncogenes, offering a more biologically accurate stratification of disease. These insights enhanced diagnostic accuracy and informed prognostic assessments, paving the way for new targeted therapies. Although conventional treatment primarily consists of surgical resection and radiotherapy, emerging preclinical and early-phase clinical studies suggest a potential for molecularly guided interventions targeting specific oncogenic pathways. Despite these advances, effective targeted therapies remain limited, highlighting the need for further research and molecular stratification in clinical trial design. Additionally, the practical implementation of molecular diagnostics in standard-of-care settings is challenged by cost, accessibility, and institutional variability, which may impede equitable integration. This review summarizes the evolution of ependymoma classification, current molecular subtypes, gaps in clinical application and their implications for personalized therapy and future clinical research. Full article

Background: Since liquid-based cytology (LBC) has replaced the conventional Papanicolaou test in cervical cancer screening programs, pre-analytical procedures—particularly the choice of LBC collection media—have become crucial to ensure the accuracy of high-risk (HR) HPV DNA testing. This study aims to evaluate whether the newly developed CytoPath^® LBC medium can serve as a reliable alternative to standard solutions. Methods: This study exploited cell lines to evaluate the stability, integrity, and recovery rate of genomic DNA at different fixation time points (1, 7, 14 and 40 days) and serial dilutions (1:5, 1:10 and 1:20) extracted from cell lines. These samples have also undergone quantitative Real-Time PCR (qPCR) based HR-HPV test to assess the relative performance of the new preservative solution in detecting viral DNA with respect to the standard reference. Results: Cervical cell lines preserved in both media demonstrated consistent DNA stability over time. DNA yields were comparable between the two media. Notably, the DNA Integrity Number (DIN) was higher in samples fixed with the CytoPath^® solution. HR-HPV detection by qPCR showed equivalent performance, regardless of the fixative used. Conclusions: The CytoPath^® fixative solution represents a valid alternative to standard preservation media, offering improved DNA integrity while maintaining equivalent performance in HR-HPV qPCR testing. Full article

Background: Bone tissue decalcification is essential for histopathological evaluation, but conventional methods using inorganic acids degrade nucleic acids, limiting molecular testing. EDTA is known to better preserve DNA, but its suitability for next-generation sequencing (NGS) in clinical settings remains to be validated. Methods: This retrospective study evaluated 752 formalin-fixed paraffin-embedded (FFPE) tissue samples undergoing NGS between January 2022 and October 2024. Of these, 31 were decalcified using EDTA (Osteosoft, Merck, Germany). DNA was extracted using the Qiagen AllPrep^® kit and quantified using Qubit and NanoDrop. Libraries were prepared with a custom 30-gene Ampliseq panel and sequenced on the Ion Torrent platform. Sequencing was deemed suboptimal if <95% of target regions reached ≥250X depth. Results were compared to 721 non-decalcified FFPE samples. Results: Suboptimal sequencing occurred in 9.7% of EDTA-decalcified and 9.0% of non-decalcified cases (p = 0.9). DNA concentration (Qubit) and NanoDrop 260/280 ratios were not significantly different (p = 0.4 and p = 0.8, respectively), though EDTA cases had lower DNA concentrations (NanoDrop, p = 0.006) and 260/230 ratios (p = 0.002). Mutation detection in decalcified samples was consistent with known mutation profiles for respective tumor types. Conclusions: EDTA-decalcified FFPE bone tissues produce NGS results comparable to non-decalcified specimens, with similar sequencing success rates and acceptable DNA quality. These findings support the use of EDTA as a suitable decalcification method for molecular diagnostics, enabling broader inclusion of bone specimens in clinical testing. Full article

Cancer remains a leading global health challenge, with conventional diagnostic and treatment methods often lacking precision and adaptability. This review explores transformative advancements that are reshaping oncology by addressing these limitations. It begins with an overview of cancer’s complexity, emphasizing the shortcomings of conventional tools such as imaging and chemotherapy, which frequently fail to deliver targeted care. The discussion then shifts to biomarkers, which represent a groundbreaking frontier in early detection, enabling the identification of unique biological signatures that signal the presence of cancer with heightened sensitivity. Building on this foundation, the review examines personalized molecular therapies, which target the specific genetic and molecular vulnerabilities of tumors. These therapies not only enhance treatment efficacy but also minimize adverse effects, offering patients improved outcomes and quality of life. By integrating biomarker-driven diagnostics with tailored therapeutic strategies, a new paradigm of precision oncology emerges, bridging the gap between early detection and effective intervention. Real-world case studies highlight both successes, such as significantly improved survival rates, and persistent challenges, including accessibility and cost barriers. Looking ahead, the review outlines pathways by which to scale these innovations, emphasizing the critical need for robust infrastructure, sustained research investment, and equitable healthcare policies. It concludes by envisioning a future where biomarkers and personalized therapies converge to redefine cancer care, offering earlier detection, precise interventions, and better patient experiences. This work underscores the urgency of adopting cutting-edge approaches to overcome cancer’s persistent threats, paving the way for a more effective and humane era in oncology. Full article

Background/Objectives: The non-small-cell lung cancer (NSCLC) therapeutic landscape has undergone a profound transformation with the introduction of multiple personalized treatment options. Mutations in ERBB2 (HER2) have recently emerged as promising novel targets for the treatment of non-squamous NSCLC (nsNSCLC). Accurate, rapid, and efficient molecular profiling is crucial for identifying patients who may benefit from targeted therapies, including HER2-directed agents. Materials and Methods: Here, we aimed to retrospectively assess the performance of the Oncomine™ Precision Assay* (OPA) in combination with the Ion Torrent Genexus™ Integrated Sequencer* (Thermo Fisher Scientific. Waltham, MA, USA) for detecting ERBB2 mutations in nsNSCLC. A total of 108 archived nsNSCLC samples, consisting of biopsies, resections, and cytological specimens, were used to assess concordance with in-house-validated orthogonal tests. Results: The OPA showed high sensitivity and specificity with an overall accuracy of 100% for single-nucleotide variants (SNVs) and insertions and deletions (Indels). SNVs and Indels with allele frequencies as low as 5% were correctly identified across samples with a tumor cell content ranging from 5% to 95%. Additionally, the assay demonstrated high reproducibility across the six participating laboratories. The turnaround time of the OPA was notably shorter compared to traditional orthogonal methods, facilitating rapid molecular report generation. Conclusions: The OPA in combination with the Ion Torrent Genexus™ System allows for highly sensitive and specific detection of relevant ERBB2 mutations. The assay’s streamlined workflow, coupled with its automated data analysis pipeline, enables a fast turnaround time for testing across a range of sample types. This includes samples with reduced tumor cell content and limited available input. This study demonstrates the future potential of using this assay in a clinical setting. Full article

Sepsis is a complex and life-threatening syndrome arising from a dysregulated immune response to infection that can lead to severe organ dysfunction and increased mortality. This multifactorial condition is marked by intricate interactions between immune, inflammatory, and coagulation pathways, which together contribute to systemic effects and multiorgan damage. The aberrant immune activation seen in sepsis includes profound leukocyte activation, endothelial dysfunction, imbalanced coagulation leading to disseminated intravascular coagulation (DIC), and the production of both pro-inflammatory and anti-inflammatory mediators. These events culminate in pathological alterations that extend beyond the initial site of infection, adversely impacting distant tissues and organs. Early recognition and timely intervention are crucial to mitigate the progression of sepsis and its associated complications. This review aims to explore the underlying biological mechanisms, including host–pathogen interactions, immune dysregulation, and the cascade of systemic and organ-specific effects that define sepsis. By delving into the pathophysiological processes, we intend to provide insights into the determinants of multiorgan failure and inform strategies for therapeutic intervention. Understanding these mechanisms is pivotal for advancing clinical outcomes and reducing mortality rates associated with this critical condition. Full article

Pediatric high-grade glioma (pHGG) is a devastating group of childhood cancers associated with poor outcomes. Traditionally, diagnosis was based on histologic and immunohistochemical characteristics, including high mitotic activity, presence of necrosis, and presence of glial cell markers (e.g., GFAP). With advances in molecular tumor profiling, these tumors have been recategorized based on specific molecular findings that better lend themselves to prediction of treatment response and prognosis. pHGG is now categorized into four subtypes: H3K27-altered, H3G34-mutant, H3/IDH-WT, and infant-type high-grade glioma (iHGG). Molecular profiling has not only increased the specificity of diagnosis but also improved prognostication. Additionally, these molecular findings provide novel targets for individual tumor-directed therapy. While these therapies are largely still under investigation, continued investigation of distinct molecular markers in these tumors is imperative to extending event-free survival (EFS) and overall survival (OS) for patients with pHGG. Full article

Background: Methylene blue (MB), a versatile redox agent, is emerging as a promising therapeutic in diseases associated with mitochondrial dysfunction. Its ability to optimize the electron transport chain increases ATP synthesis (30–40%) and reduces oxidative stress, protecting cellular components such as mitochondrial DNA. The protective role of this compound has been described in several neurodegenerative disease such as Alzheimer’s and Parkinson’s diseases. However, its role in cardiovascular disease has been poorly explored. Methods: In this study, we explored the impact of MB on murine (HL1) and human (AC16) cardiomyocyte redox signaling and cellular survival using RT-Qpcr analysis and immunochemistry assays. Results: Our results revealed that MB increased functional mitochondria, reversed H₂O₂-induced oxidative damage, and modulated antioxidant gene expression. Furthermore, it regulated the microRNA16–UPR signaling axis, reducing CHOP expression and promoting cell survival. Conclusions: These findings underscore its potential in cardioprotective therapy; however, its putative use as a drug requires in vivo validation in preclinical animal models. Full article

Background: This study is the first to investigate the association between colorectal cancer (CRC) risk and the hMLH1 −93G>A and hMSH2 1032G>A polymorphisms of mismatch repair (MMR) genes in the Azerbaijani population. Methods: Peripheral blood samples containing EDTA were collected from the study subjects (134 patients and 137 controls), and genomic DNA was extracted using the non-enzymatic salting-out method. Genotypes were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), and the results were visualized through agarose gel electrophoresis. Results: Overall, no statistically significant correlation was observed between CRC risk and the hMLH1 −93G>A polymorphism in the heterozygous GA (OR = 0.760; 95% CI = 0.374–1.542; p = 0.446), the mutant AA (OR = 1.474; 95% CI = 0.738–2.945; p = 0.270), or the A allele (OR = 1.400; 95% CI = 0.984–1.995; p = 0.062). However, in contrast to the dominant model, a statistically significant association was found between the recessive model and an increased CRC risk, with an odds ratio of 1.788 (95% CI = 1.102–2.900; p = 0.018). The hMLH1 −93G>A polymorphism was identified at a significantly higher frequency across the TNM stages, with the distribution showing statistical significance (p < 0.05). Additionally, no statistically significant association was observed between the hMSH2 1032G>A polymorphism and CRC risk. Conclusions: Although no overall association was observed for hMLH1 −93G>A, our findings suggest a potential link with increased colorectal cancer risk under the recessive model in the Azerbaijani population. Further studies are warranted to confirm this model-specific association and investigate the underlying biological mechanisms. Full article

Introduction: Thyroid cancer and obesity are prevalent conditions with significant global health implications. Differentiated thyroid cancer (DTC) is influenced by various molecular pathways, including those involving Transforming Growth Factor-Beta (TGF-β), a cytokine implicated in cell proliferation, differentiation, immune regulation, and fibrosis. Obesity (BMI > 30) has been associated with thyroid dysfunction and an increased incidence of nodular goiter. However, the relationship between TGF-β levels, thyroid malignancies, and metabolic disturbances remains unclear. This study aimed to analyze TGF-β1, -2, and -3 concentrations in blood serum before and after thyroidectomy in patients with DTC and obese individuals with nodular goiter to evaluate their potential role in thyroid pathology and obesity-related metabolic changes. Methods: A prospective study was conducted at a high-volume surgical center where over 700 thyroidectomy procedures are performed annually. Seventy-six consecutive patients (aged 26–79 years) were included: 21 with DTC and 55 with euthyroid nodular goiter. The latter group was subdivided based on BMI into obese (BMI > 30, n = 26) and non-obese (BMI < 30, n = 29) cohorts. Blood samples were collected preoperatively and on the first postoperative day for TGF-β quantification using the Bio-Plex Pro™ Human Cytokine Assay. Statistical analysis was performed using the Student’s t-test. Results: Postoperatively, patients with DTC exhibited significantly higher TGF-β1 (210,000 pg/mL), TGF-β2 (360 pg/mL), and TGF-β3 (170 pg/mL) levels compared to obese patients with nodular goiter (p < 0.05). In the nodular goiter group, BMI did not significantly influence preoperative TGF-β levels (p > 0.05). However, postoperatively, obese patients showed lower TGF-β1 (100,000 pg/mL) and TGF-β2 (30 pg/mL) levels compared to normal-weight individuals (p = 0.03), while no significant difference was observed for TGF-β3 (p > 0.05). Conclusions: The study highlights distinct alterations in TGF-β isoform levels in thyroid cancer and obesity. Elevated postoperative TGF-β levels in DTC patients suggest a role in tumor progression and response to surgical intervention. In contrast, the reduction of TGF-β1 and TGF-β2 levels in obese patients postoperatively may indicate a complex interplay between obesity, surgical stress, and cytokine regulation. These findings underscore the need for further research into the molecular mechanisms governing TGF-β dynamics in thyroid disorders and obesity, with potential implications for therapeutic interventions. Full article