Journal Description
Journal of Molecular Pathology
Journal of Molecular Pathology
is an international, peer-reviewed, open access journal on every topic related to modern histopathology and cytopathology, predictive pathology and molecular cytopathology, published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), CAPlus / SciFinder, and other databases.
- Journal Rank: CiteScore - Q1 (Health Professions (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 28.2 days after submission; acceptance to publication is undertaken in 6.8 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Impact Factor:
1.1 (2024);
5-Year Impact Factor:
1.1 (2024)
Latest Articles
The Current Landscape of Molecular Pathology for the Diagnosis and Treatment of Ependymoma
J. Mol. Pathol. 2025, 6(3), 23; https://doi.org/10.3390/jmp6030023 - 4 Sep 2025
Abstract
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
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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.
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(This article belongs to the Collection Feature Papers in Journal of Molecular Pathology)
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Open AccessArticle
Evaluation of a New Ethanol-Based Preservative Medium for Liquid-Based Cervical Cytology: A Performance Pilot Study for Molecular Applications
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Floriana Conticelli, Pasquale Pisapia, Antonino Iaccarino, Maria Salatiello, Alessandro Venuta, Gianluca Gragnano, Luca Vallefuoco, Rosanna Sorrentino, Giuseppe Portella, Nadia Casatta, Carmelo Lupo, Dario Bruzzese, Giancarlo Troncone and Caterina De Luca
J. Mol. Pathol. 2025, 6(3), 22; https://doi.org/10.3390/jmp6030022 - 2 Sep 2025
Abstract
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
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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.
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(This article belongs to the Collection Feature Papers in Journal of Molecular Pathology)
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Open AccessCommunication
Ethylenediaminetetraacetic Acid (EDTA)-Decalcified, Formalin-Fixed Paraffin-Embedded (FFPE) Tumor Tissue Shows Comparable Quality and Quantity of DNA to Non-Decalcified Tissue in Next-Generation Sequencing (NGS)
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Francis Hong Xin Yap, Jen-Hwei Sng, Jeremy Wee Kiat Ng, Hanis Abdul Kadir, Pei Yi Chan and Timothy Kwang Yong Tay
J. Mol. Pathol. 2025, 6(3), 21; https://doi.org/10.3390/jmp6030021 - 2 Sep 2025
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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:
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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.
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Open AccessReview
The Future of Cancer Diagnosis and Treatment: Unlocking the Power of Biomarkers and Personalized Molecular-Targeted Therapies
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Getnet Molla and Molalegne Bitew
J. Mol. Pathol. 2025, 6(3), 20; https://doi.org/10.3390/jmp6030020 - 28 Aug 2025
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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
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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.
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Open AccessBrief Report
ERBB2 Mutation Testing in NSCLC: A Pan-European Real-World Evaluation of the Oncomine Precision Assay
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Ilaria Alborelli, Melanie Demes, Peter Wild, Susana Hernandez, Fernando Lopez-Rios, Olivier Bordone, Christophe Bontoux, Paul Hofman, Caterina De Luca, Giancarlo Troncone, Luisella Righi, Umberto Malapelle, Ricella Souza da Silva, Luis Cirnes, Fernando Schmitt, Eveline Keller, Philip M. Jermann, John Longshore and Lukas Bubendorf
J. Mol. Pathol. 2025, 6(3), 19; https://doi.org/10.3390/jmp6030019 - 14 Aug 2025
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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,
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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.
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Open AccessReview
Mechanism of Sepsis
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Hideaki Yamamoto, Muhammad Usman, Aristides Koutrouvelis and Satoshi Yamamoto
J. Mol. Pathol. 2025, 6(3), 18; https://doi.org/10.3390/jmp6030018 - 7 Aug 2025
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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
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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.
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Open AccessReview
The Current Landscape of Molecular Pathology for the Diagnosis and Treatment of Pediatric High-Grade Glioma
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Emma Vallee, Alyssa Steller, Ashley Childress, Alayna Koch and Scott Raskin
J. Mol. Pathol. 2025, 6(3), 17; https://doi.org/10.3390/jmp6030017 - 1 Aug 2025
Abstract
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
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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.
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(This article belongs to the Collection Feature Papers in Journal of Molecular Pathology)
Open AccessArticle
Methylene Blue Increases Active Mitochondria and Cellular Survival Through Modulation of miR16–UPR Signaling Axis
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Carlos Garcia-Padilla, David García-Serrano and Diego Franco
J. Mol. Pathol. 2025, 6(3), 16; https://doi.org/10.3390/jmp6030016 - 23 Jul 2025
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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
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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.
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Open AccessArticle
Impact of hMLH1 −93G>A (rs1800734) and hMSH2 1032G>A (rs4987188) Polymorphisms on Colorectal Cancer Susceptibility
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Bayram Bayramov, Nigar Karimova, Nigar Mehdiyeva, Hagigat Valiyeva, Rena Karimova, Royal Shirinov, Hazi Aslanov, Zumrud Safarzade, Orkhan Isayev and Nuru Bayramov
J. Mol. Pathol. 2025, 6(3), 15; https://doi.org/10.3390/jmp6030015 - 8 Jul 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Beyond Genomics: Epigenetic and Transcriptomic Dynamics in Tumor Progression)
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Open AccessArticle
Exploring the Interplay of TGF-β and Body Weight in Thyroid Cancer: A Comparative Analysis of Cytokine Levels Before and After Surgery in Differentiated Thyroid Cancer and Obese Patients with Nodular Goiter
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Adam Bednarczyk, Grzegorz Kowalski, Agata Gawrychowska, Joanna Bronikowska, Zenon P. Czuba and Jacek Gawrychowski
J. Mol. Pathol. 2025, 6(3), 14; https://doi.org/10.3390/jmp6030014 - 1 Jul 2025
Abstract
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
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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.
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Open AccessReview
The Current Landscape of Molecular Pathology for the Diagnosis and Treatment of Atypical Teratoid Rhabdoid Tumor
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Ashley Childress, Alayna Koch, Emma Vallee, Alyssa Steller and Scott Raskin
J. Mol. Pathol. 2025, 6(2), 13; https://doi.org/10.3390/jmp6020013 - 14 Jun 2025
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a rare, aggressive pediatric central nervous system (CNS) tumor that predominantly affects children under the age of 3. It is defined by the inactivation of the SMARCB1 gene, leading to the loss of INI1, a protein essential
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Atypical teratoid rhabdoid tumor (ATRT) is a rare, aggressive pediatric central nervous system (CNS) tumor that predominantly affects children under the age of 3. It is defined by the inactivation of the SMARCB1 gene, leading to the loss of INI1, a protein essential for cell lineage determination and cell differentiation. Current standard of care treatment requires aggressive multimodal therapy with maximal safe resection, high-dose chemotherapy with autologous stem cell rescue, and radiation, yet overall survival remains < 50%. These intensive regimens have improved overall survival but are associated with significant morbidity and long-term effects. Molecular profiling has significantly advanced the understanding of ATRTs, revealing four molecular subgroups, ATRT-TYR, ATRT-MYC, ATRT-SHH, and ATRT-SMARCA4, each with distinct clinical presentations, oncogenic pathways, and prognoses. Molecular characterization enables better prognostic stratification, guiding treatment decisions and allowing for more personalized therapeutic approaches. Targeted therapies based on these molecular insights remain experimental, and continued exploration of molecular mechanisms and how they differ amongst subgroups is pivotal for the development of less toxic, more effective targeted treatments.
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(This article belongs to the Collection Feature Papers in Journal of Molecular Pathology)
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Open AccessReview
Dysfunctional Astrocyte Metabolism: A Driver of Imbalanced Excitatory/Inhibitory Tone and Support for Therapeutic Intervention Targets
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Uchechukwu G. Joseph, Mega O. Oyovwi, Ejayeta Jeroh, Daniel T. Esuku and Benneth Ben-Azu
J. Mol. Pathol. 2025, 6(2), 12; https://doi.org/10.3390/jmp6020012 - 11 Jun 2025
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A balanced excitatory/inhibitory (E/I) tone is crucial for proper brain function, and disruptions can lead to neurological disorders. This review explores the role of astrocytes in maintaining a balanced E/I tone in the brain, which is crucial for proper functioning. It highlights the
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A balanced excitatory/inhibitory (E/I) tone is crucial for proper brain function, and disruptions can lead to neurological disorders. This review explores the role of astrocytes in maintaining a balanced E/I tone in the brain, which is crucial for proper functioning. It highlights the potential for dysfunctional astrocyte metabolism to disrupt E/I balance, leading to neuronal dysfunction and potentially causing neurological disease pathogenesis. The review focuses on glucose, lactate shuttling, and glutamate metabolism. This review synthesizes findings from in vitro, in vivo, and human studies examining the interplay between astrocyte metabolism, neuronal activity, and E/I balance. Literature searches were conducted using keywords including “astrocyte metabolism”, “excitatory/inhibitory balance”, “glutamate”, “lactate shuttle”, “neurometabolic coupling”, and “neurological disorders” in databases such as PubMed and Web of Science. Disruptions in astrocyte glucose uptake or glycolysis can impair lactate production, reducing neuronal energy supply and affecting neuronal excitability. Impaired glutamate uptake and conversion to glutamine within astrocytes leads to elevated extracellular glutamate, promoting excitotoxicity. Altered glycogen metabolism and other metabolic impairments within astrocytes can also affect neuronal health and contribute to imbalances between excitation and inhibition. Dysfunctional astrocyte metabolism represents a significant contributor to E/I imbalance in the brain. Understanding the specific metabolic vulnerabilities of astrocytes and their impact on neuronal function provides potential therapeutic targets for neurological disorders characterized by E/I dysregulation. Targeting astrocyte metabolism may offer a novel approach to restoring E/I balance and improving neurological outcomes.
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Open AccessReview
The Current Landscape of Molecular Pathology for the Diagnosis and Treatment of Pediatric Medulloblastoma
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Alayna Koch, Ashley Childress, Emma Vallee, Alyssa Steller and Scott Raskin
J. Mol. Pathol. 2025, 6(2), 11; https://doi.org/10.3390/jmp6020011 - 11 Jun 2025
Abstract
Medulloblastoma (MB) is a malignant brain tumor that requires intense multimodal treatment. There is significant treatment-related morbidity associated with MB, and overall prognosis varies between the subgroups of the disease. These tumors were previously risk-stratified based solely on histopathological features. However, advancements in
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Medulloblastoma (MB) is a malignant brain tumor that requires intense multimodal treatment. There is significant treatment-related morbidity associated with MB, and overall prognosis varies between the subgroups of the disease. These tumors were previously risk-stratified based solely on histopathological features. However, advancements in oncologic molecular research have led to novel changes to MB tumor classification, which also affects the prognosis and treatment strategies for individual patients. The WHO CNS5 now recognizes four main molecular subgroups of MB. Each subgroup contains its own genomic heterogeneity that correlates with a unique way to risk stratify patients, determine overall prognosis, and inform treatment. These discoveries have already impacted the implications and outcomes of current treatments based on the subgroup of patients. Ongoing research to better understand this classification system has paved the way for the development of molecular targeted therapy.
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(This article belongs to the Collection Feature Papers in Journal of Molecular Pathology)
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Open AccessCase Report
Surgical Management of Intrathoracic Triton Tumors: Insights into Emerging Molecular and Epigenetic Mechanisms with a Case Series of Three Patients
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Alessandro Bonis, Alberto Busetto, Federica Pezzuto, Giulia Pagliarini, Vincenzo Verzeletti, Mario Pezzella, Giorgio Cannone, Eleonora Faccioli, Marco Mammana, Giovanni Maria Comacchio, Alessandro Rebusso, Marco Schiavon, Chiara Giraudo, Fiorella Calabrese, Andrea Dell’Amore, Samuele Nicotra, Angelo Paolo Dei Tos and Federico Rea
J. Mol. Pathol. 2025, 6(2), 10; https://doi.org/10.3390/jmp6020010 - 30 May 2025
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Malignant Triton Tumors (MTTs) are rare, high-grade malignant peripheral nerve sheath tumors (MPNSTs) frequently associated with Type 1 Neurofibromatosis (NF1). NF1, an autosomal dominant disorder, predisposes approximately 10% of affected individuals to developing MPNSTs, with 50% of these tumors occurring in NF1 patients,
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Malignant Triton Tumors (MTTs) are rare, high-grade malignant peripheral nerve sheath tumors (MPNSTs) frequently associated with Type 1 Neurofibromatosis (NF1). NF1, an autosomal dominant disorder, predisposes approximately 10% of affected individuals to developing MPNSTs, with 50% of these tumors occurring in NF1 patients, while others arise sporadically or in association with radiation exposure. MTTs predominantly affect anatomical regions rich in large nerves, such as the limbs, spinal root, and cranial nerves. Mediastinal presentations are exceedingly rare, posing significant diagnostic and therapeutic challenges. Current treatment strategies include surgical resection, chemotherapy, radiotherapy, and lung-sparing procedures for metastatic disease. Molecular studies of MPNSTs have revealed that NF1 mutations lead to dysregulation of the RAS signalling pathway, while epigenetic alterations (e.g., SUZ12/EED mutations) further contribute to tumor progression. Dysregulated phylogenetically conserved pathways, including Wnt/beta-catenin and non-canonical SHH signalling, play a role in sarcoma progression and Schwann cell transformation. Recent advances in miRNA research highlight their involvement in tumor invasion and progression, with dysregulated miRNA expression and chromatin remodeling contributing to the pathogenesis of these neoplasms. However, the distinct molecular profiles for MTTs remain incompletely understood. Further investigation of the genetic and epigenetic landscape is essential for improving our understanding and identifying potential therapies. Herein, we present a single-center retrospective case series of three patients with an intrathoracic triton tumor treated at our University Hospital between 2000 and 2024, serving as a starting point for future insights into MPNST pathobiology.
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Open AccessArticle
Evaluation of Navify Mutation Profiler Tertiary Analysis Software Assessing for Hematologic Malignancies
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Ruby Singhrao, Michael J. Clark, Shikha Chugh, Lisha Capucion, Shuba Krishna, Ranga Yerram, Lili Niu, Adama Parham, Amy Harrell, John Duncan, Kristina Clark and Manana Javey
J. Mol. Pathol. 2025, 6(2), 9; https://doi.org/10.3390/jmp6020009 - 22 May 2025
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Background: Navify® Mutation Profiler (Navify MP) is a cloud-based, tertiary analysis software that provides curation, annotation, and reporting of somatic genomic alterations and biomarker signatures identified by next-generation sequencing. The Navify MP software leverages Association for Molecular Pathology/American Society of Clinical Oncology/College
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Background: Navify® Mutation Profiler (Navify MP) is a cloud-based, tertiary analysis software that provides curation, annotation, and reporting of somatic genomic alterations and biomarker signatures identified by next-generation sequencing. The Navify MP software leverages Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (AMP/ASCO/CAP) Somatic Variant Classification Guidelines to provide information on detected somatic genomic variants and associated therapies according to region-specific approvals. Methods: This validation study assessed the accuracy of the Navify MP software and curation process for hematologic malignancies as compared to expert opinion. A total of 86 variants derived from hematologic malignancies (including myeloid and lymphoid leukemias, B cell lymphomas, and multiple myeloma) were used to contrive 12 VCF files. The VCFs were made up of the following classes of genomic alterations: single nucleotide variants, small insertions and deletions, fusions, and copy number alterations. Of the 86 variants, 42 were Tier IA, and 44 were non-Tier IA, based on AMP/ASCO/CAP classification. The study was performed at four sites with seven software users (molecular genetics experts). Results: Tier classification agreement between Navify MP and expert user assignment was 91.34% for Tier IA and 95.02% across all hematologic variants. The agreement on associated therapies for the Navify MP-classified Tier IA hematologic variants was 99.08%. Conclusions: Navify MP is a robust automated solution for genomic variant reporting of hematologic malignancies and remains up to date with evolving regional approvals and medical guidelines.
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Open AccessBrief Report
Association of SEPT9 Gene Methylation with the Clinicopathologic Features and Fusobacterium nucleatum Infection in Colorectal Cancer Patients
by
Siew-Wai Pang, Subasri Armon, Jack-Bee Chook, Kaik-Boo Peh, Suat-Cheng Peh and Sin-Yeang Teow
J. Mol. Pathol. 2025, 6(2), 8; https://doi.org/10.3390/jmp6020008 - 23 Apr 2025
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Background/Objectives: Colorectal cancer (CRC) is a significant global health issue. The identification of methylated Septin 9 (mSEPT9) as a biomarker for CRC represents a significant advancement in cancer diagnostics. On the other hand, Fusobacterium nucleatum (FN) is one of the
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Background/Objectives: Colorectal cancer (CRC) is a significant global health issue. The identification of methylated Septin 9 (mSEPT9) as a biomarker for CRC represents a significant advancement in cancer diagnostics. On the other hand, Fusobacterium nucleatum (FN) is one of the most studied cancer-related microbes in CRC. This study provided cohort evidence on the association of mSEPT9 with clinicopathologic characteristics and FN infection in CRC patients. Methods: Paired formalin-fixed paraffin-embedded (FFPE) tissue DNA (cancerous and adjacent non-cancer tissues) of eighty-three CRC patients was collected. Methylation-specific qPCR targeting the v2 promoter region of mSEPT9 was carried out on bisulfite-converted FFPE DNA. For FN detection, a TaqMan probe-based method targeting the 16S rRNA gene was used. The differences in mSEPT9 levels and FN expression between cancer and non-cancer tissues were evaluated. Association studies between mSEPT9 in the tumor and relative mSEPT9 levels with FN infection and available clinical data were conducted. Results: Higher mSEPT9 levels were found in the cancerous tissue compared to non-cancerous tissue (p < 0.0001). High mSEPT9 levels in the tumor were significantly associated with older patients (p < 0.001) and larger tumor size (p = 0.048) but not with other clinicopathologic variables. In double-positive patients where mSEPT9 was detected in both cancerous and non-cancerous tissue, the expression fold-change in mSEPT9, calculated using the 2−ΔΔCT formula, was significantly higher in patients with tumor size equal to or greater than 5 cm (p = 0.042). High levels of mSEPT9 in tumor were not associated with FN infection. However, high levels of FN infection were associated with mSEPT9 (p < 0.021). Conclusions: High levels of mSEPT9 are found in CRC tumor tissue and are associated with older age and larger tumor size, while high levels of FN infection are associated with mSEPT9 in this single-center cohort study.
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Open AccessReview
Current Topics on the Integration of Artificial Intelligence in the Histopathological and Molecular Diagnosis of Uveal Melanoma
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Serena Salzano, Giuseppe Broggi, Andrea Russo, Teresio Avitabile, Antonio Longo, Rosario Caltabiano and Manuel Mazzucchelli
J. Mol. Pathol. 2025, 6(2), 7; https://doi.org/10.3390/jmp6020007 - 17 Apr 2025
Abstract
Background: This review examines the expanding influence of artificial intelligence (AI) in the detection and management of uveal melanoma (UM). Methods: This work delves into the application of AI technologies such as machine learning (ML), deep learning (DL), and convolutional neural networks (CNNs)
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Background: This review examines the expanding influence of artificial intelligence (AI) in the detection and management of uveal melanoma (UM). Methods: This work delves into the application of AI technologies such as machine learning (ML), deep learning (DL), and convolutional neural networks (CNNs) in various diagnostic procedures, molecular profiling, and predictive analysis. Results: The discussion underscores AI’s potential to enhance diagnostic precision and efficiency. Particular focus is placed on its role in histopathological assessments of UM, where algorithms facilitate the analysis of whole-slide images (WSIs). AI contributes to more accurate tumor classification, assists in planning treatments, and improves the prediction of the prognostic indicators and molecular characteristics of the tumor. Conclusions: Despite these promising developments, this review acknowledges existing hurdles to AI implementation, including issues with data standardization and the interpretability of AI models. It emphasizes the need for further research to fully integrate AI into clinical workflows, ultimately aiming to improve patient care and outcomes.
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(This article belongs to the Special Issue Automation in the Pathology Laboratory)
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Open AccessArticle
Kolmogorov–Arnold Networks for Automated Diagnosis of Urinary Tract Infections
by
Anurag Dutta, A. Ramamoorthy, M. Gayathri Lakshmi and Pijush Kanti Kumar
J. Mol. Pathol. 2025, 6(1), 6; https://doi.org/10.3390/jmp6010006 - 5 Mar 2025
Abstract
Medical diagnostics is an important step in the identification and detection of any disease. Generally, diagnosis requires expert supervision, but in recent times, the evolving emergence of machine intelligence and its widespread applications has necessitated the integration of machine intelligence with pathological expert
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Medical diagnostics is an important step in the identification and detection of any disease. Generally, diagnosis requires expert supervision, but in recent times, the evolving emergence of machine intelligence and its widespread applications has necessitated the integration of machine intelligence with pathological expert supervision. This research aims to mitigate the diagnostics of urinary tract infections (UTIs) by visual recognition of Colony-Forming Units (CFUs) in urine culture. Recognizing the patterns specific to positive, negative, or uncertain UTI suspicion has been complemented with several neural networks inheriting the Multi-Layered Perceptron (MLP) architecture, like Vision Transformer, Class-Attention in Vision Transformers, etc., to name a few. In contrast to the fixed model edge weights of MLPs, the novel Kolmogorov–Arnold Network (KAN) architecture considers a set of trainable activation functions on the edges, therefore enabling better extraction of features. Inheriting the novel KAN architecture, this research proposes a set of three deep learning models, namely, K2AN, KAN-C-Norm, and KAN-C-MLP. These models, experimented on an open-source pathological dataset, outperforms the state-of-the-art deep learning models (particularly those inheriting the MLP architecture) by nearly . By rapid UTI detection, the proposed methodology reduces diagnostic delays, minimizes human error, and streamlines laboratory workflows. Further, preliminary results can complement (expert-supervised) molecular testing by enabling them to focus only on clinically important cases, reducing stress on traditional approaches.
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(This article belongs to the Special Issue Automation in the Pathology Laboratory)
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Open AccessArticle
Challenges in Amplicon-Based DNA NGS Identification of MET Exon 14 Skipping Events in Non-Small Cell Lung Cancers
by
Magdalena Jurkiewicz, Raymond Yeh, Catherine A. Shu, Susan J. Hsiao, Mahesh M. Mansukhani, Anjali Saqi and Helen Fernandes
J. Mol. Pathol. 2025, 6(1), 5; https://doi.org/10.3390/jmp6010005 - 26 Feb 2025
Cited by 2
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Introduction: MET Exon 14 skipping alterations are drivers of non-small cell lung carcinoma (NSCLC) with responses to tyrosine kinase inhibitors. Amplicon-based DNA NGS assays (DNA NGSs) for the detection of METex14 skipping can yield false-negative results. We examined the efficacy of
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Introduction: MET Exon 14 skipping alterations are drivers of non-small cell lung carcinoma (NSCLC) with responses to tyrosine kinase inhibitors. Amplicon-based DNA NGS assays (DNA NGSs) for the detection of METex14 skipping can yield false-negative results. We examined the efficacy of METex14 skipping with a DNA NGS and reflex RNA-based NGS (RNA NGS) strategy. Materials and Methods: Clinical cases with definitive or suspected lung adenocarcinoma (LungCa), lacking driver mutations with targeted DNA NGS, underwent the RNA NGS to identify oncogenic drivers. Samples with METex14 skipping identified on reflex RNA NGSs were confirmed with Sanger sequencing. Results:METex14 skipping events were detected in 22/762 (2.9%) samples by DNA NGS. RNA NGS identified 10 additional samples, for an overall frequency of 32/762 (4.1%). All 22 METex14 DNA variants affected the donor splice site. Sanger sequencing revealed that missed METex14 variants were largely deletions spanning the ~30 bp intronic region upstream of the splice acceptor site. The failure of DNA NGS to detect all METex14 mutants was due to a lack of coverage of the 3′ splice acceptor site of intron 13, branch point, and polypyrimidine tract. Conclusions: Modification of amplicon-based DNA hotspot assays, with primers that cover both donor and acceptor splice sites, can identify a larger number of METex14 skipping events. Clinical data show that patients with advanced NSCLC and METex14 variants responded to targeted therapy.
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Open AccessArticle
Discovery of Novel Small-Molecule Immunomodulators for Cancer Immunotherapy Using OB2C Technology
by
Hsiao-Chi Wang and Tsung-Chieh Shih
J. Mol. Pathol. 2025, 6(1), 4; https://doi.org/10.3390/jmp6010004 - 8 Feb 2025
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Background/Objective: Immunomodulators play a critical role in regulating immune responses, with immunostimulatory agents enhancing cancer therapy by activating immune cells such as T cells. While immune checkpoint inhibitors (ICIs) targeting PD-1 and CTLA-4 have shown clinical success, the availability of small-molecule immunomodulators remains
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Background/Objective: Immunomodulators play a critical role in regulating immune responses, with immunostimulatory agents enhancing cancer therapy by activating immune cells such as T cells. While immune checkpoint inhibitors (ICIs) targeting PD-1 and CTLA-4 have shown clinical success, the availability of small-molecule immunomodulators remains limited. This study aimed to identify novel small-molecule immunomodulators using the One-Bead-Two-Compound (OB2C) library approach for potential cancer immunotherapy. Methods: A OB2C library consisting of 1,764 compounds was screened to identify small-molecule immunomodulators capable of enhancing immune responses. The bead library was incubated with Jurkat cells, which express high levels of α4β1 integrin, each and every compound-bead was uniformly covered with cells. IFN-γ production was measured as a marker of immune activation. The most potent compound was further evaluated for its effects on PBMC activation and cytolytic activity against prostate cancer cells. Tumor cell viability assays were performed to evaluate its effect on immune-mediated tumor suppression. Results: Two immunomodulators, Kib-IM-1 and Kib-IM-4, were identified from a 1764-compound OB2C library. However, only Kib-IM-4 was confirmed to induce PBMC clustering and significantly enhance IFN-γ production. In addition, Kib-IM-4 promoted immune cell activation and enhanced the cytolytic activity of PBMCs against prostate cancer cells, leading to a reduction in tumor cell viability. Conclusions: These findings highlighted Kib-IM-4’s potential as a novel small-molecule immunomodulator for cancer immunotherapy. By enhancing immune cell activation and promoting tumor cell cytolysis, Kib-IM-4 represents a promising candidate for further development in cancer treatment.
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