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 30.6 days after submission; acceptance to publication is undertaken in 5.2 days (median values for papers published in this journal in the second 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
Peptide-Based Therapeutics in Autoimmune Diseases: Restoring Immune Balance Through Precision
J. Mol. Pathol. 2026, 7(1), 3; https://doi.org/10.3390/jmp7010003 - 8 Jan 2026
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Autoimmune diseases arise from the loss of antigen-specific tolerance, leading to chronic inflammation and tissue damage. Peptide-based therapeutics provide a precise strategy to restore immune balance by targeting autoreactive lymphocytes and antigen-presenting cells in tolerogenic contexts. These therapies induce regulatory T cells, modulate
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Autoimmune diseases arise from the loss of antigen-specific tolerance, leading to chronic inflammation and tissue damage. Peptide-based therapeutics provide a precise strategy to restore immune balance by targeting autoreactive lymphocytes and antigen-presenting cells in tolerogenic contexts. These therapies induce regulatory T cells, modulate APC phenotypes, and can interfere with proinflammatory signaling. Advances in delivery technologies, including nanoparticles, lipid nanoparticles, hydrogels, and conjugates, improve peptide stability, co-deliver tolerogenic cues, and enable targeted antigen presentation. mRNA lipid nanoparticle platforms permit in situ expression of peptides or immunomodulatory molecules. Preclinical studies in models of type 1 diabetes, multiple sclerosis, and lupus demonstrate robust antigen-specific tolerance, while early-phase clinical trials show safety and mechanistic engagement. Insights from approved peptide therapies in allergy and other fields underscore the importance of epitope selection, delivery context, and biomarker-guided development. Collectively, these strategies suggest that rationally formulated, precisely targeted peptide therapeutics hold promise for achieving durable immune tolerance in autoimmune disease.
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Open AccessReview
The Role of Whole Slide Imaging in AI-Based Digital Pathology: Current Challenges and Future Directions—An Updated Literature Review
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Samya A. Omoush, Jihad A. M. Alzyoud, Nidhal Kamel Taha El-Omari and Ahmad J. A. Alzyoud
J. Mol. Pathol. 2026, 7(1), 2; https://doi.org/10.3390/jmp7010002 - 1 Jan 2026
Cited by 1
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Background/Objectives: Combining Whole Slide Imaging (WSI) and Artificial Intelligence (AI) in digital pathology (DP) is accelerating the field of diagnostic pathology by improving analysis metrics accuracy, reproducibility, and speed. AI applications in pathology include automated image capture, assessment and analysis, risk stratification, and
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Background/Objectives: Combining Whole Slide Imaging (WSI) and Artificial Intelligence (AI) in digital pathology (DP) is accelerating the field of diagnostic pathology by improving analysis metrics accuracy, reproducibility, and speed. AI applications in pathology include automated image capture, assessment and analysis, risk stratification, and prognostic prediction. This integration introduces significant challenges, including data quality, high computational demands, the ability to generalize across different settings, and a range of ethical considerations. This review provides an end-to-end roadmap covering WSI acquisition, preprocessing, and deep learning (DL) channels through tumor recognition, biomarker prediction, and evolving computational methods such as original models and combined learning, highlighting the specific challenges and opportunities of WSI-attached AI in pathology. Methods: This review provides a WSI-centric analysis that examines AI and DL applications specifically as they overlap with the acquisition, processing, and computational analysis of WSI. Therefore, this review aims to comprehensively examine the challenges and pitfalls associated with the use of WSI in AI-Based Digital Pathology. Results: Pre-analytical factors like how the tissue is prepared, staining, and scanning artifacts affect AI and contain possible post-analytical barriers such as the range of colors used, color standardization, and algorithm transparency. Furthermore, there may be bias found in the training datasets that can blur the ethical and legal boundaries alongside regulatory uncertainty. Conclusions: Even though there is an array of challenges, AI applied in DP can enhance the accuracy of medical diagnosis, encourage workflow efficiency, facilitate cross-collaboration for pediatric research, and enable research into rare diseases. Further development on the topic needs to focus on defining standard operating procedures and guidelines alongside dependable datasets through teamwork from various scientific fields.
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Circulating miR-1246 as a Diagnostic and Prognostic Biomarker in Dengue Infection: A Case–Control Study
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Vishesh Rajbhandari, Frienson Pradhan, Kriti Rajbhandari, Rasika Ghulu, Ashna Dhakal and Amol Dahal
J. Mol. Pathol. 2026, 7(1), 1; https://doi.org/10.3390/jmp7010001 - 1 Jan 2026
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Background: Dengue is a growing mosquito-borne viral infection of global concern. It remains a major public health challenge in Nepal, where reliable biomarkers for disease staging and prognosis are lacking. In this study, we investigated circulating microRNA-1246 (miR-1246) as a potential diagnostic and
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Background: Dengue is a growing mosquito-borne viral infection of global concern. It remains a major public health challenge in Nepal, where reliable biomarkers for disease staging and prognosis are lacking. In this study, we investigated circulating microRNA-1246 (miR-1246) as a potential diagnostic and prognostic marker in dengue infection. Methods: Serum samples from 21 dengue-positive patients and 20 healthy controls were analyzed by quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR), with RNU6 as an internal control. Results: Dengue patients showed markedly elevated miR-1246 levels, with a mean 47-fold increase compared to controls (p = 0.001). Expression varied by disease stage, peaking in IgM positive cases, declining in weakly positive IgM patients, and reaching the lowest levels in IgG positive convalescent cases, a pattern consistent with clinical parameters such as platelet recovery. Receiver Operating Characteristic (ROC) analysis further highlighted diagnostic potential, yielding an Area Under the Curve (AUC) of 0.79, sensitivity of 95.24%, and specificity of 60.00%. Conclusions: These findings imply that miR-1246 is drastically dysregulated during dengue infection and could be a useful biomarker for tracking the intensity and course of the illness.
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Open AccessArticle
Prevalence and Clinical Significance of miR-155-5p and miR-221-3p in Colorectal and Thyroid Cancer: A Study in Sulaymaniyah Province
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Hersh Abdul Ham-Karim
J. Mol. Pathol. 2025, 6(4), 33; https://doi.org/10.3390/jmp6040033 - 18 Dec 2025
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Background: MicroRNAs (miRNAs) such as miR-155-5p and miR-221-3p are key regulators of gene expression in cancer. Although both have been implicated in colorectal cancer (CRC) and papillary thyroid carcinoma (PTC), data on their regional expression profiles and clinical associations remain scarce, particularly in
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Background: MicroRNAs (miRNAs) such as miR-155-5p and miR-221-3p are key regulators of gene expression in cancer. Although both have been implicated in colorectal cancer (CRC) and papillary thyroid carcinoma (PTC), data on their regional expression profiles and clinical associations remain scarce, particularly in the Middle East. This study assessed the expression patterns and clinical relevance of miR-155-5p and miR-221-3p in CRC and PTC patients from Sulaymaniyah Province, Iraq. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor and adjacent normal tissue samples were collected from 60 CRC patients and 50 PTC patients. miRNA expression levels were quantified using real-time quantitative PCR (RT-qPCR) and analyzed by the ΔΔCt method, adjusted for tumor cellularity. Statistical analyses were conducted to evaluate associations between miRNA expression and clinicopathological parameters. Results: miR-155-5p and miR-221-3p were frequently overexpressed in both CRC (65%) and PTC (72% and 68%, respectively). In CRC, miR-155-5p expression correlated significantly with histological grade, tumor location, and TNM stage (p < 0.05), while miR-221-3p did not show significant associations with clinicopathological features. In PTC, miR-155-5p exhibited a trend toward association with TNM stage (p = 0.02). No significant differences in expression levels of these miRNAs were observed between CRC and PTC samples. Conclusions: Overall, miR-155-5p and miR-221-3p are consistently overexpressed in CRC and PTC, indicating their potential as diagnostic biomarkers. miR-155-5p, in particular, shows promise as a marker of disease progression in CRC. These findings underscore the importance of region-specific studies in advancing our understanding of the molecular landscape of cancer.
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Open AccessReview
Molecular Perspective on Proteases: Regulation of Programmed Cell Death Signaling, Inflammation and Pathological Outcomes
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Aafreen Ansari, Kishu Ranjan, Ashish Kumar and Chandramani Pathak
J. Mol. Pathol. 2025, 6(4), 32; https://doi.org/10.3390/jmp6040032 - 12 Dec 2025
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Proteases are essential enzymes that regulate numerous physiological processes and cellular signaling networks to maintain homeostasis and cellular fate. This regulation is mediated by a group of proteases with the primary function of cleaving peptide bonds, thereby modulating the activity of proteins for
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Proteases are essential enzymes that regulate numerous physiological processes and cellular signaling networks to maintain homeostasis and cellular fate. This regulation is mediated by a group of proteases with the primary function of cleaving peptide bonds, thereby modulating the activity of proteins for vital functions and influencing various cellular and physiological functions including digestion, absorption, cellular signaling, apoptosis, inflammation, immune response, cell growth, differentiation, cell death, and reproduction. Proteases define the fate of cells by modulating the downstream signal transduction pathways for modalities of cell death known as apoptosis, necroptosis, pyroptosis, and autophagy. Similarly, during inflammatory stimulation, proteases orchestrate a cascade of pathways that optimize the immune response to pathogens. Proteases play a crucial role in the pathogenesis of various human diseases, including cancer, metabolic, inflammatory, and neurological disorders. The activation of specific proteases determines the outcomes of different forms of cell death inflammation and imbalance may cause various pathological manifestations highlighted in this review. Understanding protease-mediated signaling mechanisms is therefore vital for elucidating disease pathogenesis and identifying potential therapeutic targets.
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Open AccessReview
Cancer-Associated Fibroblasts and Epithelial–Mesenchymal Transition as Critical Contributors to Renal Cell Carcinoma Progression
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Sergii Vernygorodskyi, Anton B. Tonchev, Nikolai T. Evtimov and Kameliya Zhechkova Bratoeva
J. Mol. Pathol. 2025, 6(4), 31; https://doi.org/10.3390/jmp6040031 - 9 Dec 2025
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Renal cell carcinoma (RCC) features a complex tumor microenvironment, where cancer-associated fibroblasts (CAFs) play key roles in tumor progression, epithelial–mesenchymal transition (EMT), immune evasion, and resistance to treatment. This article updates our understanding of CAF origins, diversity, and functions in RCC, incorporating recent
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Renal cell carcinoma (RCC) features a complex tumor microenvironment, where cancer-associated fibroblasts (CAFs) play key roles in tumor progression, epithelial–mesenchymal transition (EMT), immune evasion, and resistance to treatment. This article updates our understanding of CAF origins, diversity, and functions in RCC, incorporating recent single-cell RNA sequencing (scRNA-seq) data that refine CAF subtypes. The paper explores the mechanistic interactions between CAFs and EMT, focusing on CAF-derived signaling pathways like TGF-β, IL-6/STAT3, HGF/c-MET, and Wnt/β-catenin, as well as extracellular-vesicle-mediated transfer of miRNAs and lncRNAs that promote metastatic behavior in RCC. It also addresses how CAF-driven remodeling of the extracellular matrix, metabolic changes, and activation of YAP/TAZ contribute to invasion and resistance to therapies, particularly in relation to tyrosine kinase inhibitors, mTOR inhibitors, and immune checkpoint blockade. The review highlights emerging therapeutic strategies targeting CAFs, such as inhibiting specific signaling pathways, disrupting CAF–tumor cell communication, and selectively depleting CAFs. In conclusion, it identifies limitations in current CAF classification systems and proposes future research avenues to improve RCC-specific CAF profiling and exploit the CAF–EMT axis for therapeutic gain.
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Open AccessArticle
Incorporation of Microsatellite Instability and Tumor-Infiltrating Lymphocytes in Opisthorchis viverrini-Associated Cholangiocarcinoma: Predicting Patient Outcomes
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Natcha Khuntikeo, Apiwat Jareanrat, Vasin Thanasukarn, Tharatip Srisuk, Vor Luvira, Watcharin Loilome, Poramate Klanrit, Anchalee Techasen, Jarin Chindaprasirt, Prakasit Sa-Ngiamwibool, Chaiwat Aphivatanasiri, Sureerat Padthaisong, Piya Prajumwongs and Attapol Titapun
J. Mol. Pathol. 2025, 6(4), 30; https://doi.org/10.3390/jmp6040030 - 1 Dec 2025
Abstract
Background: Cholangiocarcinoma (CCA) has the highest incidence in Northeastern Thailand, where patients generally present with late diagnosis and poor prognosis. Opisthorchis viverrini (OV) infection is the major cause of CCA, with oxidative stress driving DNA mutations and genetic instability. Microsatellite instability (MSI) is
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Background: Cholangiocarcinoma (CCA) has the highest incidence in Northeastern Thailand, where patients generally present with late diagnosis and poor prognosis. Opisthorchis viverrini (OV) infection is the major cause of CCA, with oxidative stress driving DNA mutations and genetic instability. Microsatellite instability (MSI) is a predictive biomarker in several cancers. This study aimed to investigate MSI status and its association with clinicopathological features and survival of CCA patients. Methods: Tissue and serum samples were collected from 25 surgical CCA patients. MSI status and mismatch repair (MMR) proteins were evaluated using an MSI scanner and immunohistochemistry (IHC). Serum OV IgG was assessed by ELISA, while tumor-infiltrating lymphocytes (TILs) were evaluated by two pathologists. Associations of MSI with clinicopathological features, OV status, MMR, and survival were analyzed. Results: Among CCA patients, 66.7% were MSI-high and 33.3% were MSI-low. MSI-high significantly correlated with age < 57 years, intraductal growth pattern, OV positivity, and early-stage disease. Patients with MSI-high and high TILs showed markedly improved median survival compared to MSI-low with low TILs (94.0 vs. 16.8 and 3.0 months; HR = 6.82 and 14.10; p = 0.004 and 0.001). Incorporation of MSI and TILs remained an independent prognostic factor in multivariate analysis (p < 0.05). Conclusions: MSI-high is highly prevalent in OV-associated CCA and is associated with intraductal growth, OV infection, and early-stage disease. Combined MSI and TIL status may serve as an independent prognostic factor, warranting validation in larger cohorts.
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(This article belongs to the Special Issue Advancing Cancer Diagnosis: Integrating Molecular Pathology into Histopathology for Solid Tumors)
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Open AccessCommentary
Mpox Insights: From Structure to Human Cell Interaction
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Md S. Zaman, Robert C. Sizemore, Draven Rodriguez, Emilio Lopez, S. M. Golam Alam, Suleyman Tufa, Juan C. Lopez-Alvarenga, Nuraly S. Akimbekov and Mohammed S. Razzaque
J. Mol. Pathol. 2025, 6(4), 29; https://doi.org/10.3390/jmp6040029 - 21 Nov 2025
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Mpox, a zoonotic viral disease, has emerged as a global concern due to outbreaks in both endemic and non-endemic regions in 2022. Rodents, including African squirrels and Gambian pouched rats, are suspected key reservoirs, with human infections occurring through direct contact with infected
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Mpox, a zoonotic viral disease, has emerged as a global concern due to outbreaks in both endemic and non-endemic regions in 2022. Rodents, including African squirrels and Gambian pouched rats, are suspected key reservoirs, with human infections occurring through direct contact with infected animals or bushmeat consumption. Previously confined to rural Africa, mpox has spread via international travel and the exotic pet trade. Human-to-human transmission occurs mainly via respiratory droplets and direct contact with bodily fluids or lesions. The virus has a double-stranded DNA genome within a lipid envelope. Despite lower mutation rates in DNA viruses, mpox has developed mutations, particularly in genes like F8L, G9R, and F13L, facilitating viral replication and immune evasion. The virus targets immune cells such as monocytes and macrophages, weakening host defenses and prolonging infection. Immunocompromised individuals are at higher risk of severe complications. Although generally self-limiting, severe cases may require antiviral treatment. This article briefly summarizes the therapeutic and preventive strategies, and public health measures to combat zoonotic threats.
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Open AccessCommunication
STK11 Mutated Lung Adenocarcinoma: A Molecular and Clinicopathologic Study
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Jeffrey Jean, William D. Wallace and Guang-Qian Xiao
J. Mol. Pathol. 2025, 6(4), 28; https://doi.org/10.3390/jmp6040028 - 17 Nov 2025
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Targetable gene alterations have become increasingly important in the treatment of cancers. Thirty STK11-mutated lung cancers from 199 cases with molecular profiling performed during 2016–2024 were studied for clinical, morphologic, immunohistochemical (IHC) and molecular features. Of the 30 STK11-mutated lung cancers,
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Targetable gene alterations have become increasingly important in the treatment of cancers. Thirty STK11-mutated lung cancers from 199 cases with molecular profiling performed during 2016–2024 were studied for clinical, morphologic, immunohistochemical (IHC) and molecular features. Of the 30 STK11-mutated lung cancers, 29 were lung adenocarcinomas (LADCs) and 1 was large cell neuroendocrine carcinoma (LCNEC). STK11 mutation was not found in other subtypes of lung cancers. Of the 29 STK11-mutated LADCs, 6 (21%) were mucinous and 23 (79%) were non-mucinous. Of the 19 non-mucinous LADCs with sufficient material for IHC, 9 (47%) displayed acinar/papillary/lepidic patterns, 8 (42%) were poorly differentiated (solid/trabecular/basaloid/complex glandular), and 2 (11%) had mixed solid and acinar patterns. The most common concurrent altered genes were KRAS (52%), followed by TP53 (38%), KEAP1 (34%), and DNA repair genes (BRCA2/ATM) (21%). A total of 6/15 (40%) LADCs with a KRAS mutation presented with mucinous morphology. Concurrent EGFR, ROS, or ALK alterations with STK11 mutation were rare or non-existent. Of the 3 LADCs with SMARCA4 deficiency, 2 were mucinous and 1 had basaloid/adenoid cystic-like features. All the cases were microsatellite stable (MSS). The majority (55%) had low TMB (<10). Most (86%) had PD-L1 TPS 0 or <5%. Among the 14 non-mucinous LADCs with IHC performed, 5 (36%) were TTF-1-negative and all displayed poorly differentiated morphology. Overall, 8/10 (80%) of poorly differentiated components in non-mucinous LADCs were negative for TTF-1. In contrast, all LADCs with better differentiated patterns (acini/papillary/lepidic) were positive for TTF-1. The majority (14/21, 67%) of patients with available follow-up presented with metastasis.
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Open AccessArticle
Association of SLC7A5/LAT1 Expression with Clinicopathological Parameters and Molecular Subtypes: Could It Be Considered in the Management of Breast Cancer?
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Nausheen Henna, Bellary Kuruba Manjunatha Goud, Rajani Dube, Sarah Riaz, Akhtar Sohail Chughtai and Abdul Hannan Nagi
J. Mol. Pathol. 2025, 6(4), 27; https://doi.org/10.3390/jmp6040027 - 14 Nov 2025
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Introduction: Breast cancer is a heterogeneous malignancy influenced by diverse molecular profiles. The L-type amino acid transporter 1 (LAT1), encoded by the SLC7A5 gene, plays a key role in tumor metabolism, growth, and angiogenesis. Through its role in amino acid transport and activation
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Introduction: Breast cancer is a heterogeneous malignancy influenced by diverse molecular profiles. The L-type amino acid transporter 1 (LAT1), encoded by the SLC7A5 gene, plays a key role in tumor metabolism, growth, and angiogenesis. Through its role in amino acid transport and activation of the mTORC1 signaling pathway, LAT1 has emerged as a potential therapeutic target. Objective: To evaluate SLC7A5/LAT1 expression and its association with clinicopathological parameters and molecular subtypes of invasive carcinoma of no special type (NST) in a Pakistani cohort. Methods: Eighty-three patients who underwent mastectomy or modified radical mastectomy for histologically confirmed primary invasive carcinoma of no special type were included. Immunohistochemistry was used to assess SLC7A5/LAT1 expression. Associations with clinicopathological features and molecular groups were analyzed using the Chi-square test. Results: The mean age of SLC7A5-positive patients were 48.4 ± 10.8 years. Overall, 24.1% of patients demonstrated SLC7A5 positivity. Although SLC7A5 expression was more frequent in cases categorized as having moderate or poor prognosis based on the Nottingham Prognostic Index (NPI), this trend was not statistically significant. Similarly, no significant associations were observed between SLC7A5 expression and other clinicopathological or molecular variables. Conclusions:SLC7A5/LAT1 expression was identified in approximately one-quarter of invasive breast carcinoma cases. Its expression appeared more common in tumors with poorer NPI categories, but without statistically verified associations. These findings suggest that SLC7A5 may act independently of conventional clinicopathological parameters. Larger, longitudinal studies with survival follow-up are required to clarify its prognostic and therapeutic significance.
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Open AccessArticle
Influence of Diabetes on Expression of Ezrin and MMP-2 in Gingival Tissue of Patients with Periodontal Disease
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Ionut Catalin Botezatu, Maria Luiza Baean, Maria-Alexandra Martu, Ana Emanuela Botez, Cristina Daniela Dimitriu, Carmen Solcan, Anca Ileana Sin, Claudiu Topoliceanu, Elena-Carmen Cotrutz and Oana Elena Ciurcanu
J. Mol. Pathol. 2025, 6(4), 26; https://doi.org/10.3390/jmp6040026 - 31 Oct 2025
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Background: The aim of this study was to determine Ezrin and MMP-2 immunohistochemical expressions in the gingival tissue of patients with or without diabetes and to determine the role of the molecular pattern involvement in the evolution of periodontal disease. Material and Methods:
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Background: The aim of this study was to determine Ezrin and MMP-2 immunohistochemical expressions in the gingival tissue of patients with or without diabetes and to determine the role of the molecular pattern involvement in the evolution of periodontal disease. Material and Methods: In this histological study, we investigated 53 subjects with periodontal disease (test group—27 patients with type 2 DM; control—26 patients without diabetes). Samples from both groups were subjected to the immunohistochemistry (IHC) technique to evaluate the immunoreactivity (IR) intensity of Ezrin and MMP-2. Results: Among diabetic patients with periodontitis, 55.4% of patients exhibited intensely positive expression (+++) of Ezrin, and 44.6% of patients showed moderate expression (++) of Ezrin. All patients with diabetes and periodontitis showed intensely positive expression for MMP-2. In contrast, the control group showed negative expressions of Ezrin and MMP-2 (-) in 100% of cases. Significant statistical differences were found between Ezrin and MMP-2 expression in gingival samples of diabetic patients and non-diabetic patients with periodontal disease (p < 0.05). Conclusions: Ezrin and MMP-2 are significantly overexpressed in patients with diabetes and stage 2–3 periodontitis compared with non-diabetic patients with periodontal disease. Ezrin showed an exclusive pattern of moderate to strong positive staining in the diabetes–periodontitis group and complete absence in controls. MMP-2 displayed a broader range of staining intensities, with a predominance of strong positivity in all locations. Ezrin may represent a more consistent discriminative marker, whereas MMP-2 reflects a wider spectrum of tissue activation related to inflammation and tissue remodeling.
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Open AccessReview
Hypoxia-Inducible Factor Prolyl Hydroxylase (HIF-PHD) Inhibitors: A Therapeutic Double-Edged Sword in Immunity and Inflammation
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Qinyun Li and Nik Nasihah Nik Ramli
J. Mol. Pathol. 2025, 6(4), 25; https://doi.org/10.3390/jmp6040025 - 28 Oct 2025
Cited by 1
Abstract
Hypoxia-inducible factor prolyl hydroxylase (HIF-PHD) inhibitors, clinically established for treating renal anemia, are emerging as potent immunomodulators with therapeutic potential far beyond erythropoiesis. This review dissects the mechanistic basis of their action, centered on the stabilization of hypoxia-inducible factor-alpha (HIF-α), a master transcription
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Hypoxia-inducible factor prolyl hydroxylase (HIF-PHD) inhibitors, clinically established for treating renal anemia, are emerging as potent immunomodulators with therapeutic potential far beyond erythropoiesis. This review dissects the mechanistic basis of their action, centered on the stabilization of hypoxia-inducible factor-alpha (HIF-α), a master transcription factor that orchestrates fundamental shifts in immune cell function. We synthesize evidence showing how HIF-α stabilization alters innate immunity, recalibrates T- and B-cell responses, and reshapes inflammatory signaling. This activity translates to significant efficacy in preclinical models of autoimmune disorders, organ fibrosis, and ischemia–reperfusion injury. However, their broader clinical translation is hindered by a critical paradox in oncology. While HIF-α can potentiate anti-tumor immunity, its sustained activation risks promoting malignancy by driving angiogenesis, metabolic reprogramming, and fostering an immunosuppressive tumor microenvironment. Addressing this duality, alongside the potential for long-term immune dysregulation, is paramount. Future development must therefore prioritize precision-targeting strategies to harness the therapeutic benefits of HIF-PHD inhibitors while mitigating their pro-tumorigenic liabilities.
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(This article belongs to the Special Issue Pathology and Molecular Biology of Inflammatory Diseases)
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Open AccessReview
Gastric Epithelial Cell Plasticity and Molecular Mechanisms of Metaplastic Transformations in the Stomach
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Sergii Vernygorodskyi, Anton B. Tonchev and Kameliya Zhechkova Bratoeva
J. Mol. Pathol. 2025, 6(3), 24; https://doi.org/10.3390/jmp6030024 - 16 Sep 2025
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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
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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.
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Open AccessReview
The Current Landscape of Molecular Pathology for the Diagnosis and Treatment of Ependymoma
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Alyssa Steller, Ashley Childress, Alayna Koch, Emma Vallee and Scott Raskin
J. Mol. Pathol. 2025, 6(3), 23; https://doi.org/10.3390/jmp6030023 - 4 Sep 2025
Cited by 1
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
by
Getnet Molla and Molalegne Bitew
J. Mol. Pathol. 2025, 6(3), 20; https://doi.org/10.3390/jmp6030020 - 28 Aug 2025
Cited by 2
Abstract
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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
by
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
Cited by 1
Abstract
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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
by
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
Abstract
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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
by
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)
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