Journal of Molecular Pathology doi: 10.3390/jmp7020019

Authors: Marta Arrabito Giulio Pulvirenti Maria Santagati Stefania Stefani Giovanna Russo Luca Lo Nigro

The human microbiota, comprising bacteria, fungi, and viruses, primarily resides in the gut, skin, and oral and nasal cavities. The gut microbiota represents the largest and most functionally relevant microbial community, playing a crucial role in digestion, metabolism and immunity. Microbiota composition and diversity have been associated with several diseases such as cancer, affecting drug efficacy, toxicity and clinical outcome. Interactions between the gut microbiota and the host immune system may contribute to the aetiology and progression of childhood acute lymphoblastic leukaemia (ALL). In this review, we summarized the general features of the gut microbiota in cancer patients and its specific role in aetiology, treatment and prognosis of paediatric ALL. Profiling the gut microbiota may help to shed the light on the mechanism of onset and to support the development of personalized treatment strategies and follow-up in children with ALL, contributing to precision medicine.

Journal of Molecular Pathology doi: 10.3390/jmp7020018

Authors: Viriya Keo Sakshi Khurana Vindhya Udhane Alexandra Larson Jennifer N. Adams Daniel Sanchez Tarin Peltier Anthony Acevedo Kathleen Mitchell Kala F. Schilter Qian Nie Honey V. Reddi

Background: Evaluation of gene-level copy number variants (CNVs) for diagnosis and therapeutic decision making has become standard of care with next-generation sequencing (NGS), immunohistochemistry (IHC), and/or fluorescence in situ hybridization (FISH) being used to detect gene amplifications/deletions in tumor tissue. In contrast to most solid tumors, CNS cancers are challenging to evaluate by resection and/or biopsy due to the associated risks with invasive brain surgery that can also result in death or associated morbidity and therefore alternate methods are required.Methods: This study presents the analytical validation of using quantitative PCR (qPCR) to detect gene CNVs directly from cerebrospinal fluid (CSF)-derived DNA and from the AscentTM low-pass whole genome sequencing (LP-WGS) libraries, demonstrating concordance with the gold standard of NGS/IHC/FISH used in tumor tissue. Results: The analytical sensitivity of qPCR to detect gene amplification calls for ERBB2 (erb-b2 receptor tyrosine kinase 2) was demonstrated to be 100% and that of EGFR (epidermal growth factor receptor) was 83%, with specificities of 96% and 100%, respectively. The analytical sensitivity of qPCR to detect gene deletions for CDKN2A/2B (cyclin-dependent kinase inhibitor 2A/2B) was 60% and that for MTAP (methylthioadenosine phosphorylase) was 100% with a specificity of 100% for all three genes. AscentTM was demonstrated to have a higher sensitivity (100%) when compared to qPCR for the same genes evaluated and demonstrated 100% positive agreement and 100% negative agreement with known CNV status. Conclusions: The results demonstrate that given the paucity of cells in CSF limiting the use of IHC and FISH, qPCR and AscentTM provide highly sensitive, novel, minimally invasive methods for the evaluation of gene copy number (CN) status to inform the diagnosis and management of CNS cancers.

Journal of Molecular Pathology doi: 10.3390/jmp7020017

Authors: Massimo Barberis Yinxiu Zhan

Endometrial cancer (EC) is the sixth most common cancer in women. Its overall incidence has increased by 132% over the past 30 years, reflecting an increase in the prevalence of risk factors. The mortality rate decreased by 15% in the last 30 years, despite the high number of endometrial cancer-related deaths occurring world-wide. An inverse relationship has been observed between the incidence of EC, mortality and socio-economic status: more patients living in low-income countries die from EC because they do not have access to timely and effective treatment. About 80% of EC cases are diagnosed in an early stage and have a good prognosis. However, about 20% of cases present in advanced stages and are characterized by a poor prognosis. The molecular classification proposed by The Cancer Genome Atlas (TGCA) and its surrogate for clinical use allowed the adoption of personalized treatments. The assessment of the status of the MMR has revolutionized the treatment of advanced ECs, leading to significant results both in terms of PFS and OS. In this review we will focus on MMR deficiency (dMMR)/microsatellite instability-hypermutated (MSI-H) tumors, which globally account for 20–30% of ECs. The dMMR group encompasses multiple etiologies, including sporadic defects in MMR genes, germline mutations, and hypermethylation of the MLH1 promoter. Currently, the combination of immunotherapy (I-O) with standard chemotherapy has become the new standard first-line treatment for dMMR advanced or recurrent ECs. Although the main clinical trials involving patients with MMRd/MSI-H ECs treated with I-O and chemotherapy have demonstrated efficacy and long-term control of the disease, a significant number of patients do not respond to treatment (intrinsic or primary resistance) and others develop progression during treatment (acquired or secondary resistance). In this narrative approach the biological and molecular bases of these tumors have been integrated with recent advances involving diagnostic techniques, therapeutic opportunities and the genomic and phenotypical alterations underpinning the mechanisms of resistance. Special attention was given to the need for robust, clinically affordable biomarkers to promptly identify responders and non-responders to the current treatment regimens.

Journal of Molecular Pathology doi: 10.3390/jmp7020016

Authors: Mrunmayi Prashant Marathe Snehavardhan Pandey Anusha Kulkarni Thenral S. Geetha Ashish Bavdekar

Ciliopathies, initially known as fibrocystic liver diseases, encompass a group of inherited disorders characterized by cystic dilatation of intrahepatic bile ducts and portal fibrosis, frequently associated with renal anomalies. These disorders are now recognized as resulting from defects in primary cilia. The hepatic manifestations, such as congenital hepatic fibrosis (CHF), Caroli syndrome, and polycystic liver disease, arise from ductal plate malformation. Recent studies have implicated variants in the TULP3 (Tubby related protein variant 3) gene in a novel monogenic ciliopathy affecting the liver, kidneys, and heart. We report an 8-year-old boy who presented with variceal bleeding and evolved to a progressive phenotype of CHF. Whole exome sequencing revealed a homozygous novel TULP3 mutation. The patient was managed by endotherapy and propranolol prophylaxis. Due to repeated episodes of variceal bleeding and progressive worsening of hepatic synthetic functions, he underwent a living donor liver transplantation at the age of 12 years.

Journal of Molecular Pathology doi: 10.3390/jmp7020015

Authors: Niels K. Nguedia Emmanuel C. Amadi Irrinus F. Kintung Olubanke O. Ogunlana Shalom N. Chinedu

Prostate cancer is a major cause of cancer-related deaths among men in Sub-Saharan Africa, where late-stage diagnoses are common due to limited access to affordable and sensitive diagnostic tools. Early detection is essential to improve survival and reduce the disease burden. This review explores the integration of epigenetic biomarkers and CRISPR-Cas12a technology as a transformative approach for early, non-invasive prostate cancer detection in resource-limited settings. Among the many complexities of cancer development, molecular dysregulation plays a critical role. Epigenetic modifications including DNA methylation, histone changes, and non-coding RNA expression have emerged as stable and specific biomarkers with significant potential for the early detection and characterisation of prostate carcinogenesis. However, their low concentration in body fluids poses a significant challenge for detection. CRISPR-Cas12a, renowned for its high specificity and sensitivity, offers a promising solution. When integrated with isothermal amplification and liquid biopsy techniques, it enables rapid, point-of-care diagnostics. This review proposes a CRISPR-Cas12a-based diagnostic pipeline for the detection of specific epigenetic markers in liquid biopsies that could be associated with prostate cancer. The adoption of this technology in Sub-Saharan Africa has the potential to significantly improve early diagnosis, reduce mortality, and promote health equity.

Journal of Molecular Pathology doi: 10.3390/jmp7010014

Authors: Zeki Ali Mohamed

Background/Objectives: Chronic lymphocytic leukemia (CLL) is characterized by genetic and epigenetic alterations. This study aimed to assess the methylation status of E-Cadherin and MMP-9 gene promoters and to explore their relationships with disease pathogenesis and hematological parameters in CLL patients. Methods: A case–control study was conducted with 70 newly diagnosed CLL patients and 70 age- and sex-matched healthy controls. Promoter methylation of E-Cadherin and MMP-9 genes was evaluated using methylation-specific PCR (MSP) and methylation-sensitive restriction enzyme PCR (MSRE-PCR), respectively. Results: The median patient age was 62 years, and 68.5% were males. Binet stage A was the most common stage (57.3%). E-Cadherin promoter methylation was detected in 75.7% of CLL patients and 77.1% of controls (p = 0.91), showing no significant association with disease occurrence; however, it showed a significant correlation with higher lymphocyte counts (p = 0.01). In contrast, MMP-9 promoter methylation was significantly less frequent in CLL cases (70.0%) than in controls (100%, p = 0.001). Unmethylated MMP-9 correlated significantly with female gender (p = 0.02), lower hemoglobin (p = 0.031), reduced platelet counts (p = 0.001), and higher lymphocyte counts (p = 0.035). Conclusions: MMP-9 promoter hypomethylation may play a pathogenic role in CLL and is associated with female gender and cytopenia, whereas E-Cadherin methylation appears to be non-specific. MMP-9 methylation status could therefore serve as a potential biomarker for CLL biology and prognosis.

Journal of Molecular Pathology doi: 10.3390/jmp7010013

Authors: Georgios S. Markopoulos Emilios E. Pakos Vasilios Gavrielatos Dimitrios Kosmas Ioannis Gkiatas George A. Alexiou Anna Batistatou Evangeli Lampri George Vartholomatos

Materials and Methods [...]

Journal of Molecular Pathology doi: 10.3390/jmp7010012

Authors: Ksenia A. Gaptulbarova Sergey V. Vtorushin Marina K. Ibragimova Irina A. Tsydenova Natalia A. Tarabanovskaya Vitaly P. Shubin Aleksey S. Tsukanov Evgeny O. Rodionov Sergey I. Achkasov Nikolai V. Litviakov

Objective: This study examined the frequency of entosis in solid tumors of various origins (colorectal cancer, breast cancer, and lung cancer) and its association with clinical and pathological characteristics. It also examined survival and copy number alterations (CNAs) in genes associated with stem cells. The aim was to assess the potential prognostic value of entotic events in tumors. Methods: A total of 238 patients were included: 96 with colorectal cancer (CRC), 45 with lung cancer (LC), and 97 with breast cancer (BC). Entotic cell-in-cell (CIC) structures were evaluated on hematoxylin–eosin–stained slides using Mackay’s criteria. A CIC frequency >0.1 per 20 high-power fields was considered positive. Clinicopathological parameters, overall survival (CRC), metastasis-free survival (LC and BC), and CNA profiles of stemness-related genes were analyzed. Amplifications of MAP1LC3A and other chromosomal loci were assessed. Results: CRC demonstrated the highest entosis rate, more than two-fold higher compared with BC and LC (p < 0.05). Entosis correlated with high tumor grade (G3) in CRC (p = 0.03). In LC, CIC-positive tumors were more frequent in patients with lymph-node metastases (p = 0.02), whereas in BC, the opposite trend was observed (p = 0.02). It was noted that in patients with stage III–IV LC, the frequency of entosis was significantly higher than in patients with stage I–II cancer (p = 0.03). CIC-positive status was associated with poorer overall survival in CRC (p = 0.03) and reduced metastasis-free survival in LC (p = 0.011). In breast cancer, no statistically significant survival differences were observed. Tumors harboring two or more stemness-gene amplifications showed significantly higher entosis frequency regardless of tumor site. A strong association was identified between entosis and MAP1LC3A amplification. Conclusions: Enosis is not a random morphological phenomenon but a process associated with unfavorable tumor characteristics, high malignancy, reduced survival, and amplification of stem cell-related genes. The results of this study confirm the working hypothesis that entosis may contribute to the emergence of aneuploid clones of tumor cells, including those containing amplifications of stem cell-associated genes. This positions entosis as a potential factor in tumor genetic heterogeneity, which is particularly important in the context of therapeutic selection pressure. The observed association between high entosis frequency and the presence of ≥2 stem cell gene amplifications, as well as its association with poor prognosis in colorectal and lung cancer, highlights its potential value as a prognostic indicator. Furthermore, MAP1LC3A amplification data may serve as a molecular marker of entotic activity and a potential therapeutic target.

Journal of Molecular Pathology doi: 10.3390/jmp7010011

Authors: Hadeel Mazin Akram Saif Sehaam Saliem

Periodontitis is a dysbiosis-driven inflammatory disease in which a pathogenic subgingival biofilm disrupts the host–microbe equilibrium and promotes progressive loss of tooth-supporting tissues. While periodontal destruction has traditionally been explained mainly through the host immune response, increasing experimental and clinical evidence suggests that epithelial–mesenchymal transition (EMT)-like changes in the gingival epithelium may contribute to barrier failure and tissue remodeling during disease progression. EMT is characterized by reduced epithelial adhesion and polarity, alongside a shift toward a mesenchymal-like phenotype with enhanced motility and impaired epithelial barrier function. This narrative review focuses on how periodontal pathogens, particularly red complex organisms and keystone species, may trigger gingival EMT through virulence factors such as gingipains, fimbriae, lipopolysaccharide, and outer membrane vesicles. These microbial signals can hijack host pathways including TGF-β/Smad, Wnt/β-catenin, and Notch to drive EMT-associated transcriptional changes and downstream functional consequences. Collectively, pathogen-induced gingival EMT may facilitate deeper microbial invasion, perpetuate chronic inflammation, impair wound healing, and contribute to fibrotic remodeling, ultimately linking microbial dysbiosis to connective tissue destruction. Understanding these mechanisms may support the development of EMT-related biomarkers and targeted interventions aimed at preserving epithelial barrier stability in periodontitis.

Journal of Molecular Pathology doi: 10.3390/jmp7010010

Authors: Izabela Janus-Ziółkowska Joanna Bubak Ewa Sawińska Marcin Nowak Agnieszka Noszczyk-Nowak

Background: Amyloidosis involving the heart is one of the types of the disease recognized in humans and has been previously described in dogs. To date, no data regarding the presence of amyloid in cardiac tissues of a large group of feline patients have been published. Our research aimed to analyze the presence and localization of amyloid in the atrial and ventricular cardiac tissue in retrospectively enrolled cats diagnosed with various types of primary cardiomyopathies, hyperthyroidism-induced cardiomyopathy, myocarditis, and generalized disorders. Methods: This study was conducted on atrial specimens obtained from 119 animals and on ventricular specimens obtained from 69 animals from that group. The atrial and ventricular specimens obtained from the enrolled animals were stained with Congo Red and evaluated in a light microscope and polarized light for the presence of amyloid deposits. Results: Five cases from the enrolled group turned out positive for amyloid deposits: three cats diagnosed with feline hyperthyroidism, one cat diagnosed with kidney glomerulonephritis, and one cat diagnosed with restrictive cardiomyopathy. In all positive cats, the amyloid deposits were present within the small intramural coronary arteries of the left ventricular free wall and interventricular septum and/or left and right atrium. No myocardial amyloid deposits were identified in the study group. Conclusions: In conclusion, cardiac coronary arterial amyloidosis, although infrequent, can be observed in cats.

Journal of Molecular Pathology doi: 10.3390/jmp7010009

Authors: Giulia Martinelli Rossella Bruno Marco Maria Germani Anello Marcello Poma Paola Vignali Chiara Cremolini Clara Ugolini

Background/Objectives: In metastatic colorectal cancer (mCRC) the evaluation of mismatch repair (MMR) and microsatellite instability (MSI) status is essential to identify patients eligible for treatment with immune-checkpoint inhibitors (ICI). This study aims to evaluate the potential utility of Comprehensive Genomic Profiling (CGP) in assessing MSI status, in addition to other immunotherapy-predictive biomarkers such as high tumor molecular burden (TMB) and the POLE and POLD1 mutations. Methods: A total of 138 mCRC tumor samples underwent a first-level molecular test (MMR status by immunohistochemistry, MSI by a melting-based PCR approach and RAS/BRAF mutational status by a small next-generation sequencing (NGS) panel) and second-level CGP analysis by the FoundationOne CDx assay. The prevalence of dMMR and MSI tumors was reported. Moreover, the concordance between the MMR and MSI status was determined, and discordant cases were discussed. Results: Twelve cases (8.7%) were MMR-deficient (dMMR); 10 showed high MSI and TMB (>10 mut/Mb). MSI status assessed by CGP and PCR was concordant in all cases except one MSH6-deficient tumor. Two dMMR cases were stable with low TMB. Moreover, in two MLH1/PMS2-deficient cases CGP revealed pathogenic alterations in the MSH2 and MSH6 genes; in both cases, the MLH1 promoter was hypermethylated. A high TMB was the only positive biomarker in 11 cases with a proficient MMR system and no MSI. Conclusions: MSI assessment by CGP analysis showed high concordance (98%) with MMR and was helpful in evaluating ICI eligibility in three out of twelve dMMR cases. Overall, compared to standard methods, analyzing a broader range of microsatellite loci and the simultaneous assessment of multiple predictive biomarkers by CGP may increase diagnostic accuracy and improve therapeutic assessment.

Journal of Molecular Pathology doi: 10.3390/jmp7010008

Authors: Marie-Helene Godin Pagé Debbie Montjean Cyntia Duval Fabien Joao Annabelle Calvé Rosalie Cabry Marie-Claire Bélanger Moncef Benkhalifa Pierre Miron

Background/Objectives: Phospholipase C zeta (PLCZ1; PLCζ) is a sperm-specific enzyme responsible for the Ca2+ oscillations required for oocyte activation, and altered PLCζ expression has been associated with fertilization failure in assisted reproductive technologies, particularly intracytoplasmic sperm injection (ICSI). This study aimed to develop and analytically validate a flow cytometry–based protocol for PLCζ quantification in human spermatozoa. Methods: The assay was established using normozoospermic samples and included validated positive and negative technical controls. Antibody specificity was confirmed by Western blot analysis. A defined gating strategy was used to assess linearity between fluorescence intensity and PLCζ expression. Analytical performance was evaluated for precision, reproducibility, stability, and sensitivity, including applicability to low sperm concentrations. Results: A linear relationship between fluorescence intensity and PLCζ expression was demonstrated. The assay showed high precision, reproducibility, and stability, with consistent results in samples stored up to 24 h at room temperature or up to one week post-fixation at 4 °C. Sensitivity testing confirmed suitability for low sperm concentrations. Conclusions: This work provides a standardized and analytically validated framework for PLCζ quantification using flow cytometry. Although the assay measures protein expression rather than functional competence or subcellular localization, it establishes a solid analytical basis for future studies to define clinically relevant PLCζ thresholds and assess its value as a biomarker of fertilization capacity.

Journal of Molecular Pathology doi: 10.3390/jmp7010007

Authors: Riddhi Tiwari Archana Tiwari Lalit P. Singh

Diabetic retinopathy (DR) is a progressive retinal disorder and a leading cause of vision impairment worldwide affecting the livelihood of millions. Its pathogenesis is driven by chronic hyperglycemia-induced neuronal and microvascular injury, leading to capillary occlusion, increased vascular permeability, and the eventual formation of fragile neo vessels. These changes mark the progression from non-proliferative diabetic retinopathy (NPDR) to proliferative diabetic retinopathy (PDR). Diabetic macular edema (DME), characterized by blood–retinal barrier disruption and macular fluid accumulation, further contributes to vision loss. This review provides an integrative perspective on the cellular and molecular mechanisms of DR, highlighting both vascular and neuroglial contributions to retinal pathology. Current therapeutic approaches, including anti-VEGF agents and corticosteroids, offer symptomatic relief but are limited by the need for repeated administration and variability in patient response. Emerging evidence implicates the role of thioredoxin-interacting protein (TXNIP) as one of mediators of the disease progression. Strongly upregulated under hyperglycaemic stress, TXNIP induces oxidative damage, inflammation, and neuronal apoptosis, exacerbating neurovascular dysfunction. We explore potential therapeutic strategies such as gene therapy, TXNIP-targeted molecular interventions, and stem cell-based approaches aimed at achieving long-term modulation of disease mechanisms. This article thus attempts to address a comprehensive understanding of DR pathophysiology and innovative new strategies to improve long-term visual outcomes.

Journal of Molecular Pathology doi: 10.3390/jmp7010006

Authors: Christian Khoswanto Ira Kusuma Dewi

Objectives: This study evaluated the impact of combining icariin with a bovine xenograft on the enhancement of early socket healing in Wistar rats. Methods: Male Wistar rats underwent incisive extraction and were randomized into three groups (n = 8/group): (1) control, (2) xenograft, and (3) icariin–xenograft. On days 7 and 14, the animals were decapitated and their mandibles were examined. Histological analysis was conducted to assess the collagen matrix and the expression of BMP-2 and HIF-1α. Results: The icariin–xenograft group exhibited superior outcomes compared to the xenograft-alone and control groups. Histological analysis showed an earlier arrangement of connective tissue and an improved collagen matrix outcome in the icariin-treated sockets. Immunohistochemistry revealed elevated BMP-2 and HIF-1α expression in the icariin–xenograft group, indicating enhanced osteogenic and angiogenic signaling. Conclusions: Icariin-enhanced xenografts speed up the repair of early extraction sockets by enhancing the development of the collagen matrix and increasing the activity of pathways that promote osteogenesis and angiogenesis in low-oxygen conditions. This bioactive grafting technology appears to be a cost-effective method for preserving sockets and performing regenerative therapy in dentistry.

Journal of Molecular Pathology doi: 10.3390/jmp7010005

Authors: Angelina Mollova-Kyosebekirova Ekaterina Uchikova Anna Mihaylova Mariya Koleva-Ivanova Mariana Parahuleva Nikoleta Parahuleva

Background: Differentiating atypical endometrial hyperplasia, also known as endometrial intraepithelial neoplasia (EAH/EIN) from endometrial hyperplasia without atypia is crucial due to the higher risk of progression to endometrioid adenocarcinoma, associated with atypical lesions. Immunohistochemical markers such as PAX2 and PTEN have emerged as potential adjuncts to improve diagnostic accuracy in morphologically challenging cases. Objective: To evaluate the diagnostic value of PAX2 and PTEN expression in distinguishing atypical from endometrial hyperplasia without atypia in the Bulgarian population. Materials and Methods: A total of 96 endometrial hyperplasia cases (48 typical, 48 atypical) were included. Histopathological evaluation was performed on hematoxylin and eosin–stained sections, with two experienced pathologists confirming diagnoses according to the WHO criteria. Immunohistochemical analysis of PTEN and PAX2 was conducted on formalin-fixed, paraffin-embedded tissue sections. Results: PTEN expression loss was observed in 6% (3/48) of hyperplasia without atypia cases, compared with 81.3% (38/48) of EAH/EIN cases. For PAX2, strong nuclear staining was retained in 60% (29/48) of endometrial hyperplasia without atypia cases, with no complete loss of expression. In contrast, 64.6% (31/48) of EAH/EIN cases showed complete loss of PAX2 expression, while only 35.4% (17/48) preserved nuclear immunoreactivity. Together, these results highlight clear and consistent differences in PTEN and PAX2 expression between hyperplasia without atypia and EAH/EIN and may aid pathologists in distinguishing these two entities in routine diagnostic practice. Conclusions: Expression loss of PAX2 and PTEN is significantly associated with EAH/EIN. Immunohistochemical evaluation of these markers provides valuable adjunctive information for the diagnosis of morphologically ambiguous cases and may enhance diagnostic reproducibility and accuracy. Incorporating PAX2 and PTEN into routine assessment may guide appropriate clinical management and risk stratification of patients with endometrial hyperplasia.

Journal of Molecular Pathology doi: 10.3390/jmp7010004

Authors: Doris Plećaš Ozren Polašek

The human microbiome is often presented as “the next genetics,” with the expectation that microbial profiles will explain complex diseases and yield new therapies. Yet for most conditions, it remains unclear whether microbiome changes act as causal drivers or primarily mirror underlying host biology and pathology. In this narrative review, we argue that microbiome causality is frequently overstated relative to the roles of host genetics and the environment, and we explore the implications for molecular pathology. We outline a simple framework in which the microbiome can act as (i) a primary driver, (ii) a conditional mediator or effect modifier or (iii) an association biomarker that mainly reflects upstream processes. We then use marital and household studies as natural experiments to test whether chronic diseases track more strongly with a shared microbiome or with a shared lifestyle and host susceptibility. Across metabolic, inflammatory, neurodegenerative and ageing-related outcomes, spouses show only low to modest disease concordance, which is difficult to reconcile with a universally strong, transmissible microbiome causality. Adult microbiomes instead appear mostly host-constrained and context-dependent, acting more as destabilisers of homeostasis and amplifiers of allostatic load than as independent disease-causing factors. For molecular pathology, this suggests that microbiome features are often most informative as biomarkers integrated alongside host genomics, immune context and histopathology, rather than as standalone targets. Study designs and diagnostic workflows should therefore jointly model the host genome, environment, behaviour and microbiome within broader systems medicine frameworks.

Journal of Molecular Pathology doi: 10.3390/jmp7010003

Authors: Derek Gu Vincent Yuan

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.

Journal of Molecular Pathology doi: 10.3390/jmp7010002

Authors: Samya A. Omoush Jihad A. M. Alzyoud Nidhal Kamel Taha El-Omari Ahmad J. A. Alzyoud

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.

Journal of Molecular Pathology doi: 10.3390/jmp7010001

Authors: Vishesh Rajbhandari Frienson Pradhan Kriti Rajbhandari Rasika Ghulu Ashna Dhakal Amol Dahal

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040033

Authors: Hersh Abdul Ham-Karim

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040032

Authors: Aafreen Ansari Kishu Ranjan Ashish Kumar Chandramani Pathak

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040031

Authors: Sergii Vernygorodskyi Anton B. Tonchev Nikolai T. Evtimov Kameliya Zhechkova Bratoeva

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040030

Authors: 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 Attapol Titapun

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040029

Authors: Md S. Zaman Robert C. Sizemore Draven Rodriguez Emilio Lopez S. M. Golam Alam Suleyman Tufa Juan C. Lopez-Alvarenga Nuraly S. Akimbekov Mohammed S. Razzaque

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040028

Authors: Jeffrey Jean William D. Wallace Guang-Qian Xiao

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040027

Authors: Nausheen Henna Bellary Kuruba Manjunatha Goud Rajani Dube Sarah Riaz Akhtar Sohail Chughtai Abdul Hannan Nagi

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040026

Authors: 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 Oana Elena Ciurcanu

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.

Journal of Molecular Pathology doi: 10.3390/jmp6040025

Authors: Qinyun Li Nik Nasihah Nik Ramli

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030024

Authors: Sergii Vernygorodskyi Anton B. Tonchev Kameliya Zhechkova Bratoeva

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030023

Authors: Alyssa Steller Ashley Childress Alayna Koch Emma Vallee Scott Raskin

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030022

Authors: 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 Caterina De Luca

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030021

Authors: Francis Hong Xin Yap Jen-Hwei Sng Jeremy Wee Kiat Ng Hanis Abdul Kadir Pei Yi Chan Timothy Kwang Yong Tay

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030020

Authors: Getnet Molla Molalegne Bitew

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030019

Authors: 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 Lukas Bubendorf

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030018

Authors: Hideaki Yamamoto Muhammad Usman Aristides Koutrouvelis Satoshi Yamamoto

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030017

Authors: Emma Vallee Alyssa Steller Ashley Childress Alayna Koch Scott Raskin

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030016

Authors: Carlos Garcia-Padilla David García-Serrano Diego Franco

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030015

Authors: Bayram Bayramov Nigar Karimova Nigar Mehdiyeva Hagigat Valiyeva Rena Karimova Royal Shirinov Hazi Aslanov Zumrud Safarzade Orkhan Isayev Nuru Bayramov

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.

Journal of Molecular Pathology doi: 10.3390/jmp6030014

Authors: Adam Bednarczyk Grzegorz Kowalski Agata Gawrychowska Joanna Bronikowska Zenon P. Czuba Jacek Gawrychowski

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020013

Authors: Ashley Childress Alayna Koch Emma Vallee Alyssa Steller Scott Raskin

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020012

Authors: Uchechukwu G. Joseph Mega O. Oyovwi Ejayeta Jeroh Daniel T. Esuku Benneth Ben-Azu

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020011

Authors: Alayna Koch Ashley Childress Emma Vallee Alyssa Steller Scott Raskin

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020010

Authors: 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 Federico Rea

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020009

Authors: Ruby Singhrao Michael J. Clark Shikha Chugh Lisha Capucion Shuba Krishna Ranga Yerram Lili Niu Adama Parham Amy Harrell John Duncan Kristina Clark Manana Javey

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020008

Authors: Siew-Wai Pang Subasri Armon Jack-Bee Chook Kaik-Boo Peh Suat-Cheng Peh Sin-Yeang Teow

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.

Journal of Molecular Pathology doi: 10.3390/jmp6020007

Authors: Serena Salzano Giuseppe Broggi Andrea Russo Teresio Avitabile Antonio Longo Rosario Caltabiano Manuel Mazzucchelli

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.

Journal of Molecular Pathology doi: 10.3390/jmp6010006

Authors: Anurag Dutta A. Ramamoorthy M. Gayathri Lakshmi Pijush Kanti Kumar

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 7.8361%. 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.

Journal of Molecular Pathology doi: 10.3390/jmp6010005

Authors: Magdalena Jurkiewicz Raymond Yeh Catherine A. Shu Susan J. Hsiao Mahesh M. Mansukhani Anjali Saqi Helen Fernandes

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.

Journal of Molecular Pathology doi: 10.3390/jmp6010004

Authors: Hsiao-Chi Wang Tsung-Chieh Shih

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.

Journal of Molecular Pathology doi: 10.3390/jmp6010003

Authors: Jan Jeroch Melanie Winter Anna Bieber Agnes Boger Christina Schmitt Silvana Ebner Morva Tahmasbi Rad Henning Reis Peter. J. Wild

The occurrence of cervical cancer is often linked to a previous infection with a human papillomavirus (HPV). In order to detect HPV infections in cervical smears, a broad range of tests can be used. This study compares the two hybridisation-based DNA-microarray systems “HPV 3.5 LCD-Array” (Chipron GmbH) and “PapilloCheck®” (Greiner Bio-One GmbH), based on their ability to detect and differentiate HPV infections in 42 different cervical smears. PapilloCheck® can detect and individually identify 24 HPV types, whereas the 3.5 LCD-Array can differentiate among 32 HPV genotypes. However, both systems include all 13 high-risk (HR)-classified types. With Chipron having already stopped the production of the 3.5 LCD-Array test, quite a few laboratories are confronted with the need to establish a new HPV testing method. The two methods were found to have a high agreement regarding the clinical significance of the detected HR HPV types. Discrepant cases were additionally validated with the help of a third test (VisionArray® HPV, ZytoVision GmbH). The results of the VisionArray® test corresponded rather well with the results of the 3.5 LCD-Array.

Journal of Molecular Pathology doi: 10.3390/jmp6010002

Authors: Rina Kansal

Background: T cell clonality is commonly assessed in the diagnostic work-up of mature T cell lymphoid neoplasms. Although fragment-length polymerase chain reaction (FL-PCR) assays are most widely used, next-generation sequencing (NGS) of the TRG and TRB genes is increasingly being used to assess T cell clonality. Objective: The present work is a scoping review of studies that assessed T cell clonality by NGS for diagnostic purposes, including only studies that provided integrated clinicopathologic diagnoses in comparing FL-PCR and NGS assays to evaluate if it is preferable to use NGS-based assays for T cell clonality evaluation in diagnostic pathology. Methods: Papers published from 1992 to 3 August 2024 were searched in PubMed. Twenty-nine cohort studies and five instructive case reports, published from 2013–2024 from the USA, UK, Europe, and Australia that provided integrated clinicopathologic diagnoses and used NGS to evaluate T cell clonality in clinical specimens from patients with mature T cell neoplasms and related non-neoplastic and neoplastic diseases were included, with additional relevant studies. Results: Ten (34.4%) of the 29 cohorts included clinical samples from patients having various cutaneous and non-cutaneous T cell malignancies, related neoplasms, and reactive conditions; 2 (6.8%) studies focused on T cell prolymphocytic leukemia, 16 (55%) on cutaneous T cell lymphoma, and one on pediatric pityriasis lichenoides. Eleven (38%) of the 29 cohort studies compared NGS with FL-PCR assays in 908 clinical samples. Eight (72.7%) of the 11 studies compared TRG FL-PCR with TRG NGS (n = 5), TRB NGS (n = 2), and TRG NGS and TRB NGS (n = 1); the remaining three compared EuroClonality/BIOMED-2 FL-PCR (TRG and TRB) with TRG NGS (n = 1), TRB NGS (n = 1), and the EuroClonality-NGS DNA capture assay (n = 1). TRB NGS was used in 16 (55%) of 29, TRG NGS in 6 (20.6%) of 29, and both TRG and TRB NGS in 7 (24%) of 29. Two (6.8%) of the 29 studies compared TRB NGS with flow cytometric immunophenotyping assays for Vβ and T cell receptor β constant region 1. One additional study compared long-read sequencing with NGS for TRG and TRB rearrangements. Conclusions: NGS is highly specific and sensitive for assessing T cell clonality. NGS precisely tracks unique rearranged sequences, which FL-PCR cannot. NGS findings for clonality must be interpreted in the context of all clinicopathologic and immunophenotypic findings, like FL-PCR. With such interpretations, NGS is much preferable to FL-PCR for evaluating T cell clonality for diagnostic purposes. It is necessary to reduce costs, increase accessibility, and educate providers about NGS for clonality evaluation. TRB NGS has been primarily assessed in the peripheral blood and skin, whereas TRG NGS has also been evaluated in formalin-fixed and non-cutaneous fresh lymphoid tissues. TRG NGS performed better than TRB NGS in comparative studies.

Journal of Molecular Pathology doi: 10.3390/jmp6010001

Authors: Jerzy K. Kulski Abigail L. Pfaff Sulev Koks

Background/Objectives: The highly polymorphic Major Histocompatibility Complex (MHC) genomic region, located on the short arm of chromosome 6, is implicated genetically in Parkinson’s disease (PD), a progressive neurodegenerative disorder with motor and non-motor symptoms. Previously, we reported significant associations between SINE-VNTR-Alu (SVA) expression quantitative trait loci (eQTLs) and Human Leucocyte Antigen (HLA) class I genotypes in PD. In this study, we aimed to evaluate SVA associations and their regulatory effects on transposable element (TE) transcription in the MHC class I region. Methods: Transcriptome data from the peripheral blood cells of 1530 individuals in the Parkinson’s Progression Markers Initiative (PPMI) cohort were reanalyzed for TE and gene expression using publicly available bioinformatics tools, including Salmon and Matrix-eQTL. Results: Four structurally polymorphic SVAs regulated the transcription of 18 distinct clusters of 235 TE loci, comprising LINEs (33%), SINEs (19%), LTRs (35%), and ancient transposon DNA elements (12%) located near HLA genes. The transcribed TEs were predominantly short, with an average length of 445 nucleotides. The regulatory effects of these SVAs varied significantly in terms of TE types, numbers, and transcriptional activation or repression. The SVA-regulated TE RNAs in blood cells appear to function as enhancer-like elements, differentially influencing the expression of HLA class I genes, non-HLA genes, and noncoding RNAs. Conclusions: These findings highlight the roles of SVAs and their associated TEs in the complex regulatory networks governing coding and noncoding gene expression in the MHC class I region, with potential implications for immune function and disease susceptibility.

Journal of Molecular Pathology doi: 10.3390/jmp5040037

Authors: Daleum Nam Hyejung Kim Sun Jung Han Ilhong Son Dong Hwan Ho

Calcium ions (Ca2+) are vital intracellular messengers that regulate a multitude of neuronal functions, including synaptic transmission, plasticity, exocytosis, and cell survival. Neuronal cell death can occur through a variety of mechanisms, including excitotoxicity, apoptosis, and autophagy. In the context of excitotoxicity, the excessive release of glutamate in the synapses can trigger the activation of postsynaptic receptors. Upon activation, Ca2+ influx into the cell from the extracellular space via their associated ion channels, most notably L-type Ca2+ channels. Previous studies have indicated that α-synuclein (α-syn), a typical cytosolic protein, plays a significant role in the pathogenesis of Parkinson’s disease (PD). It is also worth noting that the aggregated form of α-syn has the capacity to affect Ca2+ homeostasis by altering the function of Ca2+ regulation. The upregulation of leucine-rich repeat kinase 2 (LRRK2) is closely associated with PD pathogenesis. LRRK2 mutants exhibit a dysregulation of calcium signaling, resulting in dopaminergic neuronal degeneration. It could therefore be proposed that α-syn and LRRK2 play important roles in the mechanisms underlying Ca2+ dyshomeostasis and excitotoxicity in PD.

Journal of Molecular Pathology doi: 10.3390/jmp5040036

Authors: Mauro Scimia Francesco Pepe Gianluca Russo Umberto Malapelle Simone Scimia Annalaura Alfieri Valentina Olivieri Rachel Chuang Hiromi Tanaka Michael Sha David Chen Claudia Scimone Lucia Palumbo Shuo Shen Yulia Gavrilov Stav Edelstein Maria Antonia Bianco Giancarlo Troncone

Introduction: Colorectal cancer screening programs are effective in reducing incidence and mortality. In Europe, every FIT+ patient is referred to colonoscopy. The available data show that ~75.0% of these patients are negative. It is desirable to select patients at a greater risk of having a positive colonoscopy. Materials and Methods: 711 subjects, aged 50–74, attending the screening program of ASL-NA-3-SUD (Naples, Italy), were enrolled in a cross-sectional study to evaluate the performance of the QuantiDNA™ test and the non-inferiority of an alternative approach (AAP). This evaluation is based on FIT+ and QuantiDNA™+ patients referred to colonoscopy, compared to Standard of Care (SOC) colonoscopy following a FIT+ test alone. A non-inferiority margin (NIM) for colorectal neoplasia (CN) and advanced adenomas (AA) was set at −10% and at −3.8% for CRC. Results: The odds ratio was 1.76 (p-value = 0.009). The detection rate of AAP was 15.9% for colorectal neoplasia, 13.0% for advanced adenoma, and 3.0% for CRC. The risk difference between AAP and SOC was −5.07% (95% C.I. −9.23, −0.90) for colorectal neoplasia, −4.02% (95% C.I. −7.89, −0.16) for advanced adenomas, and −1.04% (95% C.I. −3.16, 1.07) for CRC. This data suggests that AAP is non-inferior to SOC for detecting CN, AA, and CRC. The expected decrease in colonoscopies is 33.4%. Conclusions: The QuantiDNA™ test is straightforward, non-invasive, and well-tolerated. Data from this study indicate that it is effective in the reduction of the need for colonoscopy examinations (−33.4%) and is non-inferior to SOC in the detection of significant colorectal lesions.

Journal of Molecular Pathology doi: 10.3390/jmp5040035

Authors: Ahmed Bendari Sunder Sham Hamed Hammoud Oana Vele Brett Baskovich David Huang Alaa Bendari Rachel Saks Reham Al-Refai Tasneem Bendari Layth Kataw Fnu Kiran Fnu Anjali Sanjay Kirshan Kumar Manju Harshan

Glioblastoma is a highly aggressive malignancy affecting the brain and central nervous system. It is the most common malignant primary brain tumor, yet its prognosis remains poor. Median survival typically ranges from around 13 months with standard treatment to up to 19.9 months in some recent clinical trials. Despite advances in treatment, the aggressive nature of glioblastoma continues to present significant challenges for improving patient outcomes. This study aimed to analyze various biological, radiological, and molecular factors associated with glioblastoma recurrence and to estimate survival outcomes. A total of 104 glioblastoma patients diagnosed between January 2017 and September 2022 were included. Patient demographics, treatment received, and molecular characteristics were obtained from the Electronic Patient Record (EPR). Tumor molecular characteristics were analyzed using the OnkoSight Advanced CNS NGS panel. Statistical analyses were performed to develop a prognostic model for glioblastoma recurrence and estimate survival rates. Among the patients, 65.4% had no recurrence, with a mean age of 63 years. No gender or BMI differences were observed, but ages <60 years were associated with recurrence. Radiological findings showed no significant differences in tumor size, necrosis, site, or focality. In multivariate analysis, the female gender, obesity, old age (>60 years), or bifocal tumors were associated with decreased glioblastoma recurrence. However, factors like tumor site, size, necrosis, MGMT promoter methylation, and EGFR alteration showed no significant association with recurrence. Median survival was 12 months, with older age significantly associated with shorter survival. Tumor sizes >4 cm showed shorter survival trends but not statistically significantly. Patients who lived longer experienced more tumor recurrence incidents. Standard or non-standard treatments were associated with longer median survival compared to no treatment. Our findings provide insights into factors influencing glioblastoma recurrence and survival. Age, gender, and tumor characteristics play pivotal roles in recurrence. Understanding these factors could aid in optimizing treatment strategies and improving patient outcomes. However, further multicentric investigations are needed to validate these findings. This study emphasizes the importance of considering biological and radiological factors in clinical decision-making for glioblastoma cases.

Journal of Molecular Pathology doi: 10.3390/jmp5040034

Authors: Thais Maloberti Sara Coluccelli Viviana Sanza Elisa Gruppioni Annalisa Altimari Stefano Zagnoni Lidia Merlo Antonietta D’Errico Michelangelo Fiorentino Daniela Turchetti Sara Miccoli Giovanni Tallini Antonio De Leo Dario de Biase

Background/Objectives: Colorectal cancer (CRC) is the third leading cause of cancer death globally, with rising incidence. The immunohistochemistry (IHC) for mismatch repair (MMR) proteins is the first technique used in routine practice to evaluate an MMR status. Microsatellite instability (MSI) may be tested in case of doubt during IHC staining. This study introduces a novel high-resolution melt (HRM) protocol for MSI detection and compares it with traditional fragment length analysis (FLA) via capillary electrophoresis. Methods: A total of 100 formalin-fixed and paraffin-embedded CRC specimens were analyzed using two distinct protocols: one based on FLA (TrueMark MSI Assay kit) and another one based on HRM (AmoyDx® Microsatellite Instability Detection Kit). Results: Overall, 68 (68.0%) of the cases were MSS, and 32 (32.0%) were MSI-H. HRM analysis was first successfully carried out in all the cases. A perfect concordance in MSI evaluation between HRM and FLA was observed. HRM showed slightly shorter hands-on time and turnaround time. Conclusions: We provided evidence of the validity of this new HRM approach in determining the MSI status of colorectal carcinomas.

Journal of Molecular Pathology doi: 10.3390/jmp5040033

Authors: Elisabetta Ferrara Francesco Mastrocola

Periodontal disease remains a significant global health concern, characterized by complex host–pathogen interactions leading to tissue destruction. This review explored the role of pattern recognition receptors (PRRs) in the pathogenesis of periodontal disease, synthesizing current knowledge on their molecular mechanisms and potential as therapeutic targets. We examined the diverse family of PRRs, focusing on toll-like receptors (TLRs) and NOD-like receptors (NLRs), elucidating their activation by periodontal pathogens and subsequent downstream signaling cascades. This review highlights the intricate interplay between PRR-mediated pathways, including NF-κB and MAPK signaling, and their impact on inflammatory responses and bone metabolism in periodontal tissues. We discussed the emerging concept of PRR crosstalk and its implications for periodontal homeostasis and disease progression. Furthermore, this review addressed the potential of PRR-targeted therapies, exploring both challenges and opportunities in translating molecular insights into clinical applications. By providing an overview of PRRs in periodontal health and disease, this review aims to stimulate future research directions and inform the development of novel diagnostic and therapeutic strategies in periodontology.

Journal of Molecular Pathology doi: 10.3390/jmp5040032

Authors: Behtash G. Nezami Bin Tean Teh Xiaoqi Lin Ximing J. Yang

Birt–Hogg–Dubé syndrome (BHDS) is an autosomal dominant disease characterized by skin, lung, and renal manifestations. This syndrome is caused by a germline mutation in the FLCN gene, which leads to disruption in multiple downstream pathways. Renal cell carcinomas are one of the serious clinical manifestations of the disease, which usually presents as bilateral and multiple tumors. Morphologically, most of these tumors are classified as hybrid oncocytic tumors. Recent advances in molecular techniques have shed light on the pathogenesis of these renal tumors. In this review, we evaluate and summarize the current knowledge of BHDS, pathologic changes, and its molecular basis with the focus on the renal hybrid oncocytic tumor (HOT), their pathogenesis, and molecular underpinning.

Journal of Molecular Pathology doi: 10.3390/jmp5040031

Authors: Irene Ray Carla S. Möller-Levet Agnieszka Michael Lisiane B. Meira Patricia E. Ellis

The rising global incidence of uterine cancer has been linked to the escalating prevalence of obesity. Obesity results in insulin resistance which alters the IGF system, thereby driving cancer progression via increased cell proliferation and the inhibition of apoptosis, although the precise mechanisms remain unclear. In a previous study, we compared the levels of IGF1 and IGF2 between fifty endometrial cancer patients (study group) and fifty age-matched non-cancer patients with benign gynaecological conditions (control group), identifying a correlation with menopause. Building on these data, we now report that IGF levels in pre-menopausal women were significantly lower in the study group compared to the control group, a pattern not observed in post-menopausal women. We undertook the receiver operating characteristic (ROC) curve analysis for calculating the potential of IGF1 and IGF2 to effectively distinguish pre-menopausal women with endometrial cancer from those without it. For pre-menopausal women, the area under ROC curve values were 0.966 for IGF1 and 0.955 for IGF2, both with significant p-values, indicating that IGF1 and IGF2 levels have the potential to be diagnostic biomarkers for distinguishing pre-menopausal women with endometrial cancer from those without it. In summary, our findings emphasise the importance of considering menopausal status in the context of IGF level assessments and suggest that IGF1 and IGF2 could play a crucial role in the early diagnosis of endometrial cancer in pre-menopausal women.

Journal of Molecular Pathology doi: 10.3390/jmp5040030

Authors: Anastasia V. Poznyak Tatyana Vladimirovna Kirichenko Dmitry Felixovich Beloyartsev Alexey V. Churov Tatiana Ivanovna Kovyanova Irina Alexandrovna Starodubtseva Vasily N. Sukhorukov Stanislav A. Antonov Alexander N. Orekhov

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by symmetrical joint inflammation, cartilage degradation, and bone erosion. This review explores the multifaceted aspects of RA pathogenesis, focusing on the dynamic interplay between innate and adaptive immune responses, genetic predisposition, and environmental triggers. The development of RA involves genetic susceptibility and trigger events such as infections, trauma, smoking, obesity, and microbiome alterations, fostering autoimmune reactions and tissue/organ destruction. The innate immune response, including toll-like receptor activation and synovial fibroblasts’ roles, contributes to the acceleration of inflammatory processes in joint tissues. Monocytes and macrophages organize and sustain chronic joint inflammation, leading to tissue damage and bone resorption, while highlighting the significance of CD14 and CD16 subsets in RA pathogenesis. In the adaptive immune response, aberrant activation and proliferation of CD4+ T cells and the role of regulatory T cells in maintaining immune tolerance are discussed. Target cytokines like TNF-α, IL-6, IL-1, IL-17, and BAFF, as well as chemokines such as CCL2, CXCL10, CCL5, and CXCL12, have emerged as critical components in managing chronic inflammation and joint damage in RA. This comprehensive overview provides insights into the pathophysiology of RA and potential therapeutic avenues, emphasizing the importance of understanding these complex immunological and genetic mechanisms for developing more effective treatment strategies.

Journal of Molecular Pathology doi: 10.3390/jmp5040029

Authors: Ilya Klabukov Anna Smirnova Anna Yakimova Alexander E. Kabakov Dmitri Atiakshin Daria Petrenko Victoria A. Shestakova Yana Sulina Elena Yatsenko Vasiliy N. Stepanenko Michael Ignatyuk Ekaterina Evstratova Michael Krasheninnikov Dmitry Sosin Denis Baranovskii Sergey Ivanov Peter Shegay Andrey D. Kaprin

The extracellular matrix is an organized three-dimensional network of protein-based molecules and other macromolecules that provide structural and biochemical support to tissues. Depending on its biochemical and structural properties, the extracellular matrix influences cell adhesion and signal transduction and, in general, can influence cell differentiation and proliferation through specific mechanisms of chemical and mechanical sensing. The development of body tissues during ontogenesis is accompanied by changes not only in cells but also in the composition and properties of the extracellular matrix. Similarly, tumor development in carcinogenesis is accompanied by a continuous change in the properties of the extracellular matrix of tumor cells, called ‘oncomatrix’, as the tumor matures, from the development of the primary focus to the stage of metastasis. In this paper, the characteristics of the composition and properties of the extracellular matrix of tumor tissues are considered, as well as changes to the composition and properties of the matrix during the evolution of the tumor and metastasis. The extracellular matrix patterns of tumor tissues can be used as biomarkers of oncological diseases as well as potential targets for promising anti-tumor therapies.

Journal of Molecular Pathology doi: 10.3390/jmp5040028

Authors: Katharina D. Faißt Cora C. Husemann Karsten Kleo Monika Twardziok Michael Hummel

Aggressive B-cell lymphoma encompasses Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL), and, as per the 2016 WHO classification, high-grade B-cell lymphoma (HGBL) not otherwise specified (NOS) and HGBL double/triple hit (DH/TH). However, the diagnostic distinction of HGBL from BL and DLBCL is difficult by means of histology/immunostaining in a substantial number of patients. This study aimed to improve subtyping by the identification of molecular features of aggressive B-cell lymphomas, with a specific focus on HGBL. To this end, we performed a comprehensive gene expression and mutational pattern analysis as well as the detection of B-cell clonality of 34 cases diagnosed with BL (n = 4), DLBCL (n = 16), HGBL DH (n = 8), and HGBL NOS (n = 6). Three distinct molecular subgroups were identified based on gene expression, primarily influenced by MYC expression/translocation and cell proliferation. In HGBL, compared to BL, there was an upregulation of PRKAR2B and TERT. HGBL DH exhibited elevated expression of GAMT and SMIM14, while HGBL NOS showed increased expression of MIR155HG and LZTS1. Our gene mutation analysis revealed MYC, ARID1A, BCL2, KMT2D, and PIM1 as the most affected genes in B-cell lymphoma, with BCL2 and CREBBP predominant in HGBL DH, and MYC and PIM1 in HGBL NOS. Clonality analysis of immunoglobulin heavy and light chain rearrangements did not show distinguishable V- or J-usage between the diagnostic subgroups.

Journal of Molecular Pathology doi: 10.3390/jmp5030027

Authors: Francis Hong Xin Yap Yancey Wilson Joanne Peverall Benhur Amanuel Ben Allanson Sukeerat Ruba

Primary endometrial serous carcinoma, known for its aggressive nature and poor prognosis, shares similarities with breast and gastric cancers in terms of potential HER2 overexpression as a therapeutic target. Assessing HER expression is complicated by tumor heterogeneity and discrepancies between primary and metastatic sites. In this study, we retrospectively analyzed HER amplification and expression in 16 pairs of primary endometrial serous carcinoma resections and corresponding metastases. HER2 status was determined using immunohistochemistry (IHC), with criteria based on the percentage and intensity of tumor cell staining. Confirmatory techniques, such as dual in situ hybridization (DISH) and fluorescence in situ hybridization (FISH), were also employed. This study reports on the concordance rates and the presence and pattern of HER2 heterogeneity. Our results showed an 87.5% concordance rate in HER2 amplification status between primary and metastatic sites, with 33% of cases scored as 2+ being amplified. Heterogeneity was observed in 100% of amplified cases and 95% of non-amplified cases on in situ testing, with variations in heterogeneity patterns between techniques. In conclusion, our findings emphasize the importance of testing both primary and metastatic sites or recurrences, with a concordance rate of 87.5%. In addition, a review of the literature and combining the results showed a concordance rate of up to 68%. The presence and pattern of heterogeneity, particularly in cases of mosaic or clustered heterogeneity in the primary tumor, may serve as reliable indicators of concordance, predicting a non-amplified HER2 status in corresponding metastases.

Journal of Molecular Pathology doi: 10.3390/jmp5030026

Authors: Alexey Loktionov Ksenia Kobzeva Anna Dorofeeva Maryana Babkina Elizaveta Kolodezhnaya Olga Bushueva

Cardiovascular diseases (CVDs) significantly exacerbate the severity and mortality of COVID-19. We aimed to investigate whether GWAS-significant SNPs correlate with CVDs in severe COVID-19 patients. DNA samples from 199 patients with severe COVID-19 hospitalized in intensive care units were genotyped using probe-based PCR for 10 GWAS SNPs previously implicated in severe COVID-19 outcomes. SNPs rs17713054 SLC6A20-LZTFL1 (risk allele A, OR = 2.14, 95% CI 1.06–4.36, p = 0.03), rs12610495 DPP9 (risk allele G, OR = 1.69, 95% CI 1.02–2.81, p = 0.04), and rs7949972 ELF5 (risk allele T, OR = 2.57, 95% CI 1.43–4.61, p = 0.0009) were associated with increased risk of coronary artery disease (CAD). SNPs rs7949972 ELF5 (OR = 2.67, 95% CI 1.38–5.19, p = 0.003) and rs61882275 ELF5 (risk allele A, OR = 1.98, 95% CI 1.14–3.45, p = 0.01) were linked to a higher risk of cerebral stroke (CS). No associations were observed with AH. Bioinformatics analysis revealed the involvement of GWAS-significant loci in atherosclerosis, inflammation, oxidative stress, angiogenesis, and apoptosis, which provides evidence of their role in the molecular mechanisms of CVDs. This study provides novel insights into the associations between GWAS-identified SNPs and the risk of CAD and CS.

Journal of Molecular Pathology doi: 10.3390/jmp5030025

Authors: Suzanne M. De La Monte Yiwen Yang Ming Tong

Background: Alcohol-related brain degeneration (ARBD) is associated with cognitive–motor impairments that can progress to disability and dementia. White matter (WM) is prominently targeted in ARBD due to chronic neurotoxic and degenerative effects on oligodendrocytes and myelin. Early detection and monitoring of WM pathology in ARBD could lead to therapeutic interventions. Objective: This study examines the potential utility of a non-invasive strategy for detecting WM ARBD using exosomes isolated from serum. Comparative analyses were made with paired tissue (Tx) and membrane vesicles (MVs) from the temporal lobe (TL). Methods: Long Evans rats were fed for 8 weeks with isocaloric liquid diets containing 37% or 0% caloric ethanol (n = 8/group). TL-Tx, TL-MVs, and serum exosomes (S-EVs) were used to examine ethanol’s effects on oligodendrocyte glycoprotein, astrocyte, and oxidative stress markers. Results: Ethanol significantly decreased the TL-Tx expression of platelet-derived growth factor receptor alpha (PDGFRA), 2′,3′-cyclic nucleotide 3′ phosphodiesterase (CNPase), proteolipid protein (PLP), myelin oligodendrocyte glycoprotein (MOG), glial fibrillary acidic protein (GFAP), and 8-OHdG, whereas in the TL-MVs, ethanol increased CNPase, PDGFRA, and 8-OHdG, but decreased MOG and GFAP concordantly with TL-Tx. Ethanol modulated the S-EV expression by reducing PLP, nestin, GFAP, and 4-hydroxynonenal (HNE). Conclusion: Chronic ethanol exposures differentially alter the expression of oligodendrocyte/myelin, astrocyte, and oxidative stress markers in the brain, brain MVs, and S-EVs. However, directionally concordant effects across all three compartments were limited. Future studies should advance these efforts by characterizing the relationship between ABRD and molecular pathological changes in brain WM-specific exosomes in serum.

Journal of Molecular Pathology doi: 10.3390/jmp5030024

Authors: Caroline Christine Pincela da Costa Leandro do Prado Assunção Kamilla de Faria Santos Laura da Silva Rodrigo da Silva Santos Angela Adamski da Silva Reis

Diabetic Nephropathy (DN) stands as a primary cause of end-stage renal disease and its etiology remains unclear. Thus, this study aims to construct a genetic panel with potential biomarkers linked to the inflammatory pathway of DN associated with the pathology’s susceptibility. Through a systematic review and meta-analysis, we selected observational studies in English, Portuguese, and Spanish, selected from the PubMed, SCOPUS, Virtual Health Library, Web of Science, and EMBASE databases. Additionally, a protein–protein interaction network was constructed to list hub genes, with differential expression analysis by microarray of kidneys with DN from the GSE30529 database to further refine results. Seventy-two articles were included, and 54 polymorphisms in 37 genes were associated with the inflammatory pathway of DN. Meta-analysis indicated a higher risk of complication associated with SNPs 59029 G/A, −511 C/T, VNTR 86 bp, −308 G/A, and −1031 T/C. Bioinformatics analyses identified differentially expressed hub genes, underscoring the scarcity of studies on CCL2 and VEGF-A genes in relation to DN. This study highlighted the intrinsic relationship between inflammatory activity in the etiology and progression of DN, enabling the effective application of precision medicine in diabetic patients for potential prognosis of the complications and contributing to cost reduction in the public health system.

Journal of Molecular Pathology doi: 10.3390/jmp5030023

Authors: Siarhei A. Dabravolski Nikolay A. Orekhov Alexey V. Churov Irina A. Starodubtseva Dmitry F. Beloyartsev Tatiana I. Kovyanova Vasily N. Sukhorukov Alexander N. Orekhov

Cathelicidins (human LL-37 and rat CRAMP) are multifunctional peptides involved in various cardiovascular conditions. This review integrates the recent findings about the functional involvement of LL-37/CRAMP across atherosclerosis, acute coronary syndrome, myocardial infarction, heart failure, diabetic cardiomyopathy, and platelet aggregation/thrombosis. In atherosclerosis, LL-37 interacts with scavenger receptors to modulate lipid metabolism and binds with mitochondrial DNA and lipoproteins. In acute coronary syndrome, LL-37 influences T cell responses and mitigates calcification within atherosclerotic plaques. During myocardial infarction and ischaemia/reperfusion injury, LL-37/CRAMP exhibits dual roles: protecting against myocardial damage through the AKT and ERK1/2 signalling pathways, while exacerbating inflammation via TLR4 and NLRP3 inflammasome activation. In heart failure, LL-37/CRAMP attenuates hypertrophy and fibrosis via NF-κB inhibition and the activation of the IGFR1/PI3K/AKT and TLR9/AMPK pathways. Moreover, in diabetic cardiomyopathy, these peptides alleviate oxidative stress and fibrosis by inhibiting TGFβ/Smad and AMPK/mTOR signalling and provide anti-inflammatory effects by reducing NF-κB nuclear translocation and NLRP3 inflammasome formation. LL-37/CRAMP also modulates platelet aggregation and thrombosis through the FPR2 and GPVI receptors, impacting apoptosis, autophagy, and other critical cellular processes. This comprehensive overview underscores LL-37/CRAMP as a promising therapeutic target in cardiovascular diseases, necessitating further elucidation of its intricate signalling networks and biological effects for clinical translation.

Journal of Molecular Pathology doi: 10.3390/jmp5030022

Authors: Rixt S. Bruinsma Marta F. Fiocco Wendy W. J. de Leng Lennart A. Kester Karin P. S. Langenberg Godelieve A. M. Tytgat Max M. van Noesel Marc H. W. A. Wijnen Alida F. W. van der Steeg Ronald R. de Krijger

ALK is related to poor survival in neuroblastoma patients. We investigated the prognostic relevance of ALK mRNA expression and the relationship with ALK immunohistochemical expression, histological subtype and ALK aberrations. Whole transcriptome sequencing data were available from 54 patients. Overall survival (OS) and event-free survival (EFS) were estimated with Kaplan–Meier’s methodology. ALK protein expression was analyzed by immunohistochemistry. ALK aberrations were detected using whole exome sequencing, single nucleotide polymorphism array, next generation sequencing and/or fluorescence in situ hybridization. OS was 74.8% and EFS was 60%. ALK mRNA expression was not associated with OS (HR 1.127, 95% CI (0.812–1.854), p = 0.331) and adjusted EFS (HR 1.134, 95% CI (0.783–1.644), p = 0.505), but was associated with histological subtype (OR 1.914, 95% CI (1.083–3.382), p = 0.025) and ALK protein expression (negative versus weak: OR 2.829, 95% CI (1.290–6.204), p = 0.009) (negative versus moderate/strong: OR 2.934, 95% CI (0.889–9.679), p = 0.077). ALK mutated tumors had significantly higher ALK mRNA expression than non-mutated tumors (p < 0.001). MYCN-amplified neuroblastomas have higher MYCN mRNA expression (p ≤ 0.001), but not ALK mRNA expression (p = 0.553). ALK mRNA expression is higher in ALK mutated neuroblastomas and is associated with poorer differentiation degree and higher protein expression. ALK mRNA expression is not significantly associated with OS and EFS.

Journal of Molecular Pathology doi: 10.3390/jmp5030021

Authors: Chidimma Agatha Akpa Cora Husemann Chris Allen Ann-Christin von Brünneck Jana Ihlow Michael Hummel

Mucosa-associated lymphoid tissue (MALT) lymphomas are slow-growing B-cell lymphomas mainly diagnosed in the stomach and termed gastric MALT lymphoma (G-MALT). Despite histological evaluation, immunostaining, and additional B-cell clonality analysis by fragment analysis, a clear-cut diagnosis is not feasible in all cases, especially for clinical follow-up of patients after treatment. We examined clonally rearranged immunoglobulin heavy- and light-chain gene sequences of 36 genomic DNA samples from six different patients obtained at different time points over the course of several years using the OncomineTM B-cell receptor pan-clonality next-generation sequencing (NGS) assay. Each case consisted of samples diagnosed with G-MALT and samples without evidence of lymphoma, based on histological examinations. We show a robust correlation (100%) of the results between the applied NGS method and histology-diagnosed G-MALT-positive patients. We also detected malignant clonotypes in samples where histology assessment failed to provide clear evidence of G-MALT (15 out of 19 samples). Furthermore, this method revealed malignant clonotypes much earlier in the disease course, with NGS of the immunoglobulin light chain being crucial in complementing immunoglobulin heavy-chain analysis. Hence, the value of NGS in routine lymphoma diagnostics is greatly significant and can be explored in order to provide better diagnoses and proffer the early detection of lymphoma relapse.

Journal of Molecular Pathology doi: 10.3390/jmp5030020

Authors: Quiana C. Wilkerson-Vidal Moses A. David James Gerard Wolfsberger Madushika M. Wimalarathne Evann Fowler John R. Diaz Alexis Fink Elijah S. Sterkel Ian Ross Bernhard Vogler Sharifa T. Love-Rutledge

Characterizing changes in beta cell function during prolonged hyperinsulinemia and dietary stress is important to study to prevent diseases like metabolic dysfunction-associated steatotic liver disease and insulin resistance. This research investigates how a moderate sucrose (MS) diet affects insulin resistance and β-cell mass in two rat strains: LEW.1WR1 and Wistar Furth (WF). LEW.1WR1 rats seem to be sensitive to beta cell disruptions as weanlings. Twenty-one male LEW.1WR1 rats and sixteen male WF rats were studied over 18 weeks. The rats were divided into groups and given either the control or MS diet. Their body weight was monitored twice a week. Insulin tolerance tests (ITTs) and fasting blood glucose measurements were taken at intervals. Urine samples were analyzed to assess metabolic shifts, and pancreas tissue was examined to evaluate changes in β-cell mass. The LEW.1WR1 rats became overweight and showed higher insulin resistance than the WF rats. Both strains of rats on the MS diet displayed changes in urine metabolite profiles in terms of levels of lactic acid and alanine. This study highlights the impact or lack thereof of a moderate sucrose diet on body mass, insulin resistance, and β-cell mass, with notable effects observed specifically in LEW.1WR1 rats. These findings contribute to our understanding of how dietary sugar intake can affect metabolism when observed in models sensitive to metabolic defects.

Journal of Molecular Pathology doi: 10.3390/jmp5030019

Authors: Gerardo Cazzato Nadia Casatta Carmelo Lupo Giuseppe Ingravallo Domenico Ribatti

DICER1 syndrome, a rare autosomal dominant genetic disorder, stems from mutations in the DICER1 gene, disrupting RNA interference and leading to various tumors. These tumors, affecting organs like the lung, kidney, ovaries, and brain, pose diagnostic challenges due to diverse presentations. Understanding DICER1-associated tumors, including pleuropulmonary blastoma, ovarian Sertoli–Leydig cell tumors, and others, is vital for early detection and management. Surgical resection, chemotherapy, and targeted therapies are primary treatment modalities, with genetic counseling playing a crucial role. Multidisciplinary care is essential for optimal management, offering hope for improved outcomes in affected individuals.

Journal of Molecular Pathology doi: 10.3390/jmp5030018

Authors: Brandon S. Sheffield Kassandra R. Bisson Andrea Beharry Michael D. Carter Shaan Dudani Jonathan M. Loree Stephanie Snow Jennifer R. Won Stephen Yip John G. Garratt

We thank Drs [...]

Journal of Molecular Pathology doi: 10.3390/jmp5030017

Authors: Emina Torlakovic Nicola Normanno

We have read, with great interest, a recently published article by Bisson KR et al [...]

Journal of Molecular Pathology doi: 10.3390/jmp5020016

Authors: Bernardo Bonilauri

Iatrogenic amyloidosis results from medical therapeutic interventions, leading to the misfolding and aggregation of proteins into amyloid fibrils or to their direct deposition in different tissues. This review aims to provide a comprehensive overview of the iatrogenic amyloidosis pathology, underlying the possible molecular mechanisms, associated pathological manifestations, and clinical implications within modern medicine. By conducting a systematic analysis of the current literature, this paper highlights the diverse instances of iatrogenic amyloidosis triggered by medical procedures such as dialysis, organ and tissue transplantation, and therapeutic drugs. Exploring the intricate molecular pathways and contributing factors involved in protein misfolding and amyloidogenesis, and uncovering the pathological consequences observed in various tissues and organs, allows us to establish appropriate nomenclature and to gain a more profound understanding of the condition, working towards improved medical interventions and treatments.

Journal of Molecular Pathology doi: 10.3390/jmp5020015

Authors: Elena Vigliar Claudio Bellevicine Gennaro Acanfora Allan Argueta Morales Anna Maria Carillo Domenico Cozzolino Mariantonia Nacchio Caterina De Luca Pasquale Pisapia Maria D. Lozano Sinchita Roy-Chowdhuri Giancarlo Troncone

Over the past decade, molecular cytopathology has emerged as a relevant area of modern pathology. Notably, in patients with advanced-stage cancer, cytological samples could be the only material available for diagnosis and molecular biomarker testing to identify patients suitable for targeted therapies. As a result, the contemporary cytopathologist’s role extends beyond morphological assessments to include critical skills such as evaluating the adequacy of the cytological samples and managing these specimens for molecular testing. This case collection can be a valuable source of insight, especially for young pathologists, who should learn to combine the opportunities offered by molecular biology with the basis of morphological evaluation.

Journal of Molecular Pathology doi: 10.3390/jmp5020014

Authors: Mukesh Kumar Yadav Zeeshan Ahmad Khan Jing-Hua Wang AbuZar Ansari

The hepatobiliary system is vital for the biotransformation and disposition of endogenous molecules. Any impairment in the normal functioning of the hepatobiliary system leads to a spectrum of hepatobiliary diseases (HBDs), such as liver cirrhosis, fatty liver, biliary dyskinesia, gallbladder cancer, etc. Especially in pregnancy, HBD may result in increased maternal and fetal morbidity and mortality. Maternal HBD is a burden to the fetus’s growth, complicates fetal development, and risks the mother’s life. In fetal programming, the maternal mechanism is significantly disturbed by multiple factors (especially diet) that influence the development of the fetus and increase the frequency of metabolic diseases later in life. Additionally, maternal under-nutrition or over-nutrition (especially in high-fat, high-carbohydrate, or protein-rich diets) lead to dysregulation in gut hormones (CCK, GLP-1, etc.), microbiota metabolite production (SCFA, LPS, TMA, etc.), neurotransmitters (POMC, NPY, etc.), and hepatobiliary signaling (insulin resistance, TNF-a, SREBPs, etc.), which significantly impact fetal programming. Recently, biotherapeutics have provided a new horizon for treating HBD during fetal programming to save the lives of the mother and fetus. This review focuses on how maternal impaired hepatobiliary metabolic signaling leads to disease transmission to the fetus mediated through the gut–brain axis.

Journal of Molecular Pathology doi: 10.3390/jmp5020013

Authors: Nikki Higa Lisa Welter Liya Xu Anand Kolatkar Kelli S. Bramlett Ole V. Gjoerup Ryon Graf Richard S.P. Huang Rebecca J. Leary Young Lee Jeremy G. Perkins Adam I. Riker Angad P. Singh Lorraine Tafra Carol K. Tweed Craig D. Shriver James Hicks Peter Kuhn

The chief goal of the Blood Profiling Atlas in Cancer (BloodPAC) consortium is to promote collaborative efforts that support the development and implementation of liquid biopsy tests. Here, we report the results of a pilot study conducted by three BloodPAC members that aimed to demonstrate a multisite liquid biopsy testing framework using longitudinal blood specimens from 38 patients with metastatic breast cancer. Three laboratories receiving identical samples from two clinical sites each applied a different targeted sequencing platform to analyze mutations in cell-free DNA (cfDNA). The resulting mutational profiles reflected common breast cancer alterations, including clinically actionable mutations for 40% of hormone- receptor-positive patients. In 12 genes with shared target regions across sequencing panels, perfect inter-assay concordance was also observed for mutations detected above the lowest common assay limit of detection. Whole-genome copy number profiling of cfDNA and circulating tumor cells (CTCs) further revealed marked heterogeneity in copy number alterations and cfDNA tumor fractions across patients. Additionally, comparison of tumor fraction and CTC abundance demonstrated the complementary nature of cfDNA and CTC analyses. Overall, the framework described in this study may serve as a resource for future trials aiming to identify multimodal liquid biopsy biomarkers to guide clinical care.

Journal of Molecular Pathology doi: 10.3390/jmp5020012

Authors: Riccardo Adorisio Giancarlo Troncone Massimo Barberis Francesco Pepe

Endometrial cancer (EC) represents one of the most newly diagnosed cancers across gynecological malignancies. In particular, a plethora of risk factors (both biological and lifestyle-related) drastically impact the incidence rate of novel diagnosis accounting for 8300 cases/year. In the recent era of precision medicine EC molecular classification, integrating ESGO/ESTRO/ESP guidelines, four distinct diagnostic groups have been established including POLE-mutant (POLE-pos); High-instability MSI (H-MSI)–MMR-deficient (MMR-d); p53-abnormal (p53abn); and non-specific molecular profile (NSMP), also known as p53-wild-type EC patients on the basis of clinically relevant emerging biomarkers. In addition, molecular testing also plays a pivotal role in defining the best therapeutical option. In this scenario, the European Society for Medical Oncology (ESMO) recommended d-MMR/MSI-H status evaluation in the diagnostic workflow of Lynch syndrome or selecting EC patients that could benefit from immune checkpoint inhibitors (ICIs). Although immunohistochemistry (IHC) is considered the gold standard approach for d-MMR profiling, a series of molecular PCR-based techniques have rapidly developed to integrate H-MSI status in routine practice. Here, we technically overviewed the most relevant commercially available diagnostic assays for the determination of the H-MSI/dMMR status in EC patients.

Journal of Molecular Pathology doi: 10.3390/jmp5020011

Authors: Ananda Baral

The liver is a multi-potent organ with important metabolic, immunological and endocrine functions. Hepatic physiology is maintained at a balanced state via the delicate actions of different liver-resident cells. Among several factors that modulate hepatic physiology, the harmony between the activity of pro- and anti-inflammatory cytokines is a crucial determinant. However, initiation of inflammatory activity can be detrimental if it goes unresolved, leading to severe consequences such as hepatitis, hepatic fibrosis, cirrhosis or even hepatocellular carcinoma (HCC). Different physiological processes can modulate the hepatic microenvironment; one such factor is a cytosolic protein complex called the inflammasome. Inflammasome activation is a consequence of the cellular encounter with pathogens or products of cellular damage. Once activated, inflammasomes promote the maturation of interleukin-1 family cytokines such as IL-1β and IL-18 via activation of caspase-1. These cytokines have a very potent role in modulating hepatic physiology. Various lines of reports suggest that inflammasome activation and IL-1 cytokines play critical roles in liver diseases, including hepatitis, hepatic fibrosis and HCC. Conversely, inhibition of inflammasome activation and/or IL-1 signaling prevents such effects. This review summarizes the mechanisms leading to inflammasome activation and the role it plays in hepatic physiology.

Journal of Molecular Pathology doi: 10.3390/jmp5020010

Authors: Peerzada Umar Farooq Baba Ashfaq ul Hassan Junaid Khurshid Adil Hafeez Wani

Basal cell carcinoma (BCC) is a slow-growing, locally aggressive, rarely metastasizing, low-grade cutaneous neoplasm that arises from the epidermal basal layer and invades the adjoining tissues. It is the most common skin cancer. It is fairly common in fair Caucasians and quite uncommon in dark-skinned populations. It contributes to 65–75% of cutaneous malignancies in whites and 20–30% in Asian Indians. The most important causal factors appear to be radiation exposure and genetic predisposition. It may present as a nonhealing lesion that occasionally bleeds or as a pruritic lesion with no symptoms. Tumours rarely spread to regional lymph nodes. The clinical appearances and morphology of BCC are diverse. Clinical types include nodular, cystic, superficial, pigmented, morphoeaform, (sclerosing), keratotic and fibroepithelioma of Pinkus. Most of the lesions appear on the head and neck, usually above the line joining the tragus and the angle of the mouth. A biopsy should be performed on all lesions suspected of BCC. The primary aim of treatment is the complete excision of the tumour tissue. Other treatment modalities include cryotherapy, immunomodulatory drugs, laser treatment or locally applicable chemotherapeutic agents. Prevention consists of lifestyle changes such as avoiding sunburn, tanning beds and prolonged direct sun exposure, shade seeking, sunscreen application on the skin, and physical barrier methods such as protective clothing, hats and sunglasses. Regular sunscreen use in childhood and adolescence seems more beneficial than in adulthood.

Journal of Molecular Pathology doi: 10.3390/jmp5010009

Authors: Chilakamarti V. Ramana

Respiratory viruses are the causative agents responsible for seasonal epidemics and occasional pandemic outbreaks and are a leading cause of death worldwide. Type I interferon (IFNα/β) signaling in the lung epithelial cells plays a major role in the innate immunity to respiratory viruses. Gene signatures are a set of differentially expressed genes in a particular disease or condition and are used to diagnose, monitor, and predict disease progression. These signatures can be used to identify regulatory modules and gene regulatory networks (GRNs) in mammalian signal transduction pathways. Considerable progress has been made in the identification of type I interferon-regulated gene signatures in the host response to respiratory viruses, including antiviral, immunomodulatory, apoptosis, and transcription factor signatures. Respiratory virus infections and host defenses require a dramatic change in the metabolic flux of macromolecules involved in nucleotide, lipid, and protein metabolism. The profiling of IFN-stimulated metabolic genes induced in the host response to several respiratory viruses led to the identification of a common gene signature in human lung epithelial cells and in the lungs of mouse models of respiratory virus infection. The regulation of the metabolic gene signature was correlated with the induction of IFN-beta (IFN-β) and IFN-inducible transcription factors at the RNA level in lung epithelial cells. Furthermore, the gene signature was also detected in response to bacterial lipopolysaccharide-induced acute lung injury. A protein interaction network analysis revealed that metabolic enzymes interact with IFN-regulated transcription factors and members of the unfolded protein response (UPR) to form a module and potentially regulate type I interferon signaling, constituting a feedback loop. In addition, components of the metabolic gene expression signature were differentially regulated in the lung tissues of COVID-19 patients compared with healthy controls. These results suggest that the metabolic gene signature is a potential therapeutic target for the treatment of respiratory virus infections and inflammatory diseases.

Journal of Molecular Pathology doi: 10.3390/jmp5010008

Authors: Anna Mennella Giuseppe Ocone Katia Stefanantoni Loredana Frasca

Systemic sclerosis (SSc) is a rare autoimmune disease whose molecular mechanisms are not yet fully understood. There is no definitive cure, and the main causes of death are pulmonary fibrosis and pulmonary arterial hypertension. Here, we focus on the interferon regulators factor 8 (IRF8), a factor involved in the type I interferon (IFN-I) signature, which is present in about half of SSc patients. Variants of this factor may play a role in autoimmunity, but little is known regarding the role of IRF8 in SSc pathogenesis. We carried out a literature search to address the association between the IRF8 factor and SSc susceptibility and clinical manifestations. The current studies appear to confirm a possible association between the alteration of the gene for IRF8 and SSc susceptibility. A link between IRF8 mutations and expression of a pro-fibrotic phenotype at the cellular level also emerges. Additional investigations are needed to confirm the role of IRF8 in SSc. However, IRF8 is worth consideration as a possible new disease marker of fibrosis in SSc patients.

Journal of Molecular Pathology doi: 10.3390/jmp5010007

Authors: Homer S. Black

Type 2 diabetes mellitus (T2DM) accounts for one-sixth of deaths globally, whereas cancer is the second leading cause of death in the U.S. T2DM is a known risk factor for many cancers. Reactive oxygen species (ROS)-altered metabolic and signaling pathways link T2DM to cancer. These reprogrammed metabolic and signaling pathways contribute to diabetic complications, impact the redox balance (oxidative stress), and have differential roles in the early and late stages of cancer. A respiratory chain that is highly reduced (as under hyperglycemic conditions) or if reduced cofactors accumulate, ROS are greatly elevated. ROS may cause mutations in mitochondrial DNA (mtDNA) that result in further ROS elevations. The amplification of ROS results in the activation of PKC, an overarching signaling pathway that activates MAPK with a subsequent regulation in several factors that result in pathophysiological manifestations of T2DM and cancer. An upregulation in PKC leads to a deregulation in NF-kß, which regulates the PKB/P13/Akt pathway and orchestrates the cell survival, growth, proliferation, and glucose metabolism manifested in cancer. It also affects Insulin Receptor Substrate (IRS-1), decreasing insulin-stimulated glucose transport and glucose uptake, disrupting subsequent cell signaling pathways contributing to the development of T2DM. Dyslipidemia is a hallmark of T2DM and cancer. ROS-induced lipid peroxidation leads to systemic inflammation, producing inflammatory prostaglandins, cytokines, and chemokines that result in tumor proliferation, rapid tumor growth, and modulation of immunity. The dual role of ROS in the early and late stages of cancer makes antioxidant therapy precarious and may be responsible for controversial results. A system that delivers an antioxidant directly to mitochondria may be useful in inhibiting the formation of ROS early during the pre-diabetic stage, whereas antioxidant therapy must be halted in later stages to retard metastasis.

Journal of Molecular Pathology doi: 10.3390/jmp5010006

Authors: Roy Khalife Tara M. Love Lara Sucheston-Campbell Michael J. Clark Helle Sorensen Shuba Krishna Anthony Magliocco

Variant annotation is an important step in deciphering the functional impact of genomic variants and their association with diseases. In this study, we analyzed 80 pan-cancer cases that underwent comprehensive genomic testing and compared the auto-classified variant tiers among four globally-available software solutions for variant interpretation from Roche, SOPHiA GENETICS, QIAGEN, and Genoox. The results revealed striking differences in tier classifications, which are believed to be a result of several factors, including subjectivity in the AMP/ASCO/CAP guidelines, threshold settings for variant allele frequencies and population allele frequencies, as well as variation in disease ontologies. Although the software tools described here provide a time-saving and repeatable process for interpretation of genomic data, it is crucial to understand the nuances and various settings for these solutions, as they can strongly influence variant tier classifications and downstream management.

Journal of Molecular Pathology doi: 10.3390/jmp5010005

Authors: Jessica Alejandra Zapata-García Luis Felipe Jave-Suárez Adriana Aguilar-Lemarroy

The RYK gene encodes a receptor-like tyrosine kinase crucial for several biological processes, including development, tissue homeostasis, and cancer. This study utilized data from the Cancer Genome Atlas Project (TCGA) to evaluate RYK expression at both mRNA and protein levels in various cancers, determine its prognostic significance, and explore its involvement in cancer-related signaling pathways. Elevated levels of RYK mRNA were identified in cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), brain lower grade glioma (LGG), head and neck squamous cell carcinoma (HNSC), liver hepatocellular carcinoma (LICH), esophageal carcinoma (ESCA), and colon adenocarcinoma (COAD), while RYK protein levels were observed to be increased in colon adenocarcinoma (COAD), GBM, LICH, cervical and endocervical adenocarcinoma (CESC), and breast invasive carcinoma (BRCA). Additionally, RYK overexpression correlated with poorer prognosis in several cancers, including PAAD, LICH, BRCA, ESCA, COAD, and CESC. Furthermore, RYK showed a positive correlation with the upregulation of multiple receptors and coreceptors in the WNT signaling pathway in various types of cancer. In terms of cancer-related signaling pathways, RYK was found to potentially interact with DNA damage, TSC/mTOR, PI3K/AKT, EMT, RTK, RAS/MAPK, ER hormone, AR hormone, and the cell cycle. This study provides new and previously unreported insights into the role of RYK in cancer biology.

Journal of Molecular Pathology doi: 10.3390/jmp5010004

Authors: Landon Pastushok Shrutii Sarda Karen Mochoruk Wayne Hill Loni T. Pickle Michelle Toro Carolina Gonzalez Stephanie Ostresh Timothy J. Looney Chenchen Yang Julie Stakiw Mark J. Bosch Hadi Goubran C. Ronald Geyer Geoffrey M. Lowman John F. DeCoteau

B-cell neoplasms possess clonal B-cell receptor rearrangements (BCR clonotype lineages) that can be identified by sequencing the B-cell repertoire for use in diagnostics, risk stratification, and high-sensitivity monitoring. BCR somatic hypermutation (SHM) can result in clonality detection failure from point mutations in PCR primer binding regions, often necessitating splitting samples into multiple reactions which increases test costs, turnaround times, and sample requirements. We evaluated the Oncomine BCR Pan-Clonality Assay, a novel single-tube PCR reaction that simultaneously amplifies all BCR loci for next-generation DNA sequencing, using neoplastic B-cell lines and clinical research samples from multiple myeloma (MM) patients, a plasma cell neoplasm associated with high SHM levels. The assay showed a linear detection range down to 1 ng of clonal DNA input, sensitivity to 10−6 in a polyclonal background, and high reproducibility. Clonotype lineages were identified in 42/45 (93%) MM samples. Ion Reporter software packaged with the assay permitted straightforward identification of MM subgroups. As expected, SHM was identified in 94% of MM cases, but several unexpected subgroups were identified including biased IGHV3-11 or IGHV4-34 usage in 20% of MM samples, and two cases with very low levels of SHM. Evidence of intraclonal diversity/ongoing SHM was identified in 18% of samples, suggesting a possible germinal center origin for some MM cases. The single-tube Oncomine BCR Pan-Clonality assay efficiently detects BCR clonotype lineages at rates comparable to existing multiple reaction assays and permits their characterization for cell of origin studies and lymphoma classification.

Journal of Molecular Pathology doi: 10.3390/jmp5010003

Authors: Manuel Campos-Medina Aiden Blumer Patrick Kraus-Füreder Michael Mayrhofer-Reinhartshuber Philipp Kainz Johannes A. Schmid

Microscopy of stained blood smears is still a ubiquitous technique in pathology. It is often used in addition to automated electronic counters or flow cytometers to evaluate leukocytes and their morphologies in a rather simple manner and has low requirements for resources and equipment. However, despite the constant advances in microscopy, computer science, and pathology, it still usually follows the traditional approach of manual assessment by humans. We aimed to extend this technique using AI-based automated cell recognition methods while maintaining its technical simplicity. Using the web platform IKOSA, we developed an AI-based workflow to segment and identify all blood cells in DAPI-Giemsa co-stained blood smears. Thereby, we could automatically detect and classify neutrophils (young and segmented), lymphocytes, eosinophils, and monocytes, in addition to erythrocytes and platelets, in contrast to previously published algorithms, which usually focus on only one type of blood cell. Furthermore, our method delivers quantitative measurements, unattainable by the classical method or formerly published AI techniques, and it provides more sophisticated analyses based on entropy or gray-level co-occurrence matrices (GLCMs), which have the potential to monitor changes in internal cellular structures associated with disease states or responses to treatment. We conclude that AI-based automated blood cell evaluation has the potential to facilitate and improve routine diagnostics by adding quantitative shape and structure parameters to simple leukocyte counts of classical analysis.

Journal of Molecular Pathology doi: 10.3390/jmp5010002

Authors: Ekaterina N. Kosobokova Nadezhda A. Kalinina Ksenia M. Konoplina Anastasiia A. Malchenkova Alexandra E. Evdokimova Marina V. Piniugina Irina I. Khan Ilya A. Kislyak Anna A. Basharina Anna N. Grishanina Anna A. Rudakova Pavel O. Varaksa Maria A. Baryshnikova Vadim S. Pokrovsky Tatiana A. Bogush Vyacheslav S. Kosorukov

The melanoma origin of cell lines obtained from the axillary lymph node (mel Kas, mel Pet, and mel Lap from patients with a verified diagnosis) was confirmed by the detection of the Melan A melanocyte marker expression. A hyperdiploid (2n+) for the mel Kas line; near-diploid (2n), and in some cells near-tertaploid (4n), and even hypo-octaploid (8n) set (172–179 chromosomes) in the mel Pet cell line; and a hypotetraploid (4n−) for the mel Lap line were detected by karyotypic analysis. All three cell lines are tumorigenic; however, mel Pet demonstrates tumor growth in Balb/c nude mice only in the presence of matrigel. All three lines showed a high expression of TUBB3 and PD-L1 markers, while ERa was low (minimum for mel Pet). Significant differences in the expression level were shown for the Cyt molecular marker. In the transplantation of cells to Balb/c nude mice, a stable expression level is observed only for TUBB3. For the rest of the markers, a decrease in their expression level of varying degrees was noted when the cells were growing in solid tumors in vivo. Mutations were detected in oncogenes (BRAF, EZH2, KIT, KRAS, NRAS, ROS1) and tumor suppressor genes (CDKN2A, FAT4, KMT2C, LRP1B, PTEN, PTPRB, TP53). The detailed characterization of the cell lines makes them valuable for various scientific and regulatory experiments, particularly those involving preclinical data on antiproliferative drugs for malignant melanoma or investigations into melanoma cell properties and progression.

Journal of Molecular Pathology doi: 10.3390/jmp5010001

Authors: Kassandra R. Bisson Jennifer R. Won Andrea Beharry Michael D. Carter Shaan Dudani John G. Garratt Jonathan M. Loree Stephanie Snow Stephen Yip Brandon S. Sheffield

Biomarkers are fundamental to modern oncology practice, forming a close link to pathology practice. Pathology results must be accurate, timely, comprehensive, and comprehendible. External proficiency testing is a key tool in maintaining biomarker quality. Here, we demonstrate the feasibility and utility of a novel end-to-end proficiency testing exercise exploring accuracy, turnaround time, and communication. Challenge specimens were made using resected colon cancer tissue, each paired with a fictional clinical vignette, and distributed to participants who were asked to provide all molecular testing required and return a final report for each case upon completion. Reports were redistributed to an assessor team including medical oncologists, each of whom was asked to recommend a systemic therapy based on each lab’s biomarker report. Participants were graded based on their ability to guide oncologists to the correct treatment. Eight laboratories participated. Three laboratories were found to have suboptimal results, two leading oncologists to incorrect therapeutic prescriptions, and one withdrawn. Turnaround time ranged from 6 to 86 days (median 24). Substantial qualitative reporting differences were identified. This study demonstrates the feasibility of end-to-end proficiency testing. The approach provides considerable value beyond analytic accuracy, including specimen management, turnaround time, and communication of results. Results suggest that reporting differences may lead to treatment disparities. This style of quality assurance will help reinforce good practices critical to the delivery of precision cancer care.

Journal of Molecular Pathology doi: 10.3390/jmp4040027

Authors: Evgenia N. Fedorova Anna V. Egorova Dmitry N. Voronkov Natalia M. Mudzhiri Tatiana I. Baranich Valeria V. Glinkina Alexey I. Krapivkin Ilgar S. Mamedov Vladimir S. Sukhorukov

The following review considers current concepts concerning the characteristics of DRP1-related mitochondrial division in brain cells during hypoxic-ischemic pathology. The functional role of DRP1 in neurons and astroglia in cerebral ischemia conditions was analyzed. We discuss the potential for regulating DRP1 activity through the selective inhibitor of mitochondrial fission, mdivi-1. The article also presents data on DRP1 involvement in astro- and microglia-mediated intercellular mitochondrial transport. Understanding of the molecular mechanisms responsible for mitochondrial fission during hypoxic-ischemic exposure will allow us to consider DRP1 as an effective therapeutic target for treating conditions with a hypoxic component.

Journal of Molecular Pathology doi: 10.3390/jmp4040026

Authors: Nella Prevete Daniela Sorriento

A tight association between inflammation and cardiac damage has been extensively recognized. In this review, we will focus on macrophages as key players in the physiology and pathology of the heart and on their role in the functional crosstalk between inflammation and heart disease. In the steady state, macrophages contribute to the homeostasis of cardiac tissue. Indeed, cardiac resident macrophages promote coronary development and tissue homeostasis, favor electric conduction in cardiomyocytes, and contribute to mitochondrial quality control. However, macrophages also take part in adverse cardiac events contributing to the development or the progression of several pathologic conditions. Infiltrating cells derived from circulating monocytes contribute to tissue injury through the release of inflammatory cytokines and catecholamines. In particular, the present review will discuss the role of macrophages in heart failure, atherosclerosis, and anthracycline-dependent cardiotoxicity. Prolonged inflammatory response and increased apoptotic cell death sustained by chronic activation of the transcription factor NFκB are the basis of heart failure pathogenesis. Here, we will discuss the involvement of NFκB signaling in macrophage-dependent cardiac damage and its use as a therapeutic target in the treatment of cardiovascular pathologies.

Journal of Molecular Pathology doi: 10.3390/jmp4040025

Authors: Sam D. Parsons Kate Murphy Alison Finall

Aims: This study aims to investigate the potential influence of melanin content on the performance of the Idylla™ BRAF Mutation Test. Specifically, we assess whether melanin levels in samples impact the test’s reliability, thereby validating its clinical utility in accelerating melanoma diagnosis and potentially improving patient prognosis. Methods: We conducted a retrospective analysis of 98 confirmed melanoma samples collected between February 2020 and November 2020. Formalin-fixed paraffin-embedded (FFPE) slides were evaluated by two independent observers using light microscopy to categorise samples into three groups based on melanin content (no, low, or high) following a standardised system. The samples underwent the Idylla™ BRAF Mutation Test and were compared with results obtained from next-generation sequencing (NGS). Results: Quantification cycle (Cq) values were utilised to assess for interference from melanin levels on the Idylla™ BRAF Mutation Test results. Statistical analyses revealed no significant differences in Cq values based on melanin content categories. Furthermore, analysis of polymerase chain reaction PCR curves did not indicate any notable influence of melanin. Discordant results with NGS are discussed. Conclusions: The study demonstrates that melanin content in samples does not significantly affect the performance of the Idylla™ BRAF Mutation Test. These results provide robust evidence supporting the confident application of the test in clinical settings, even for samples with high melanin content. The ability to obtain rapid on-site results holds promising potential in guiding timely and appropriate treatment decisions, thereby contributing to improved patient prognosis. What is already known on this topic—Prior research conducted by Petty et al. (2020) including 23 melanoma samples suggested that melanin does not significantly interfere with the Idylla™ BRAF Mutation Test by stating they were concordant with reference laboratory testing. What this study adds—This current study builds upon prior research with a larger sample size of 98. In addition to examining concordance between the Idylla™ BRAF Mutation Test and next generation sequencing, this study examines PCR curves and effect on Cq values, providing more robust evidence that melanin content in FFPE samples does not have a significant impact on the accuracy of the Idylla™ BRAF Mutation Test. How this study might affect research, practice or policy—The additional evidence base provided by this study is valuable for researchers, clinicians, and policymakers, as it supports the integration of the Idylla™ BRAF Mutation Test as a rapid and accurate method for detecting these mutations in melanoma patients.

Journal of Molecular Pathology doi: 10.3390/jmp4040024

Authors: Konstantinos Drougkas Roubini Smerla Charalampos Skarlis Clio P. Mavragani

STING-associated vasculopathy with onset in infancy (SAVI) is a rare type Ι interferonopathy caused by gain of function mutations in an encoding stimulator of interferon genes (STING) protein 1. SAVI is characterized by neonatal or infantile-onset systemic inflammation, mainly affecting peripheral cutaneous blood vessels, skin, and lungs. The main disease manifestations include recurrent febrile episodes, cough, dyspnea, and failure to thrive, in association with progressive interstitial lung disease, polyarthritis, and cold-induced red violet plaques or papules on fingers, knees, toes, heels, nasal tip, and ears that can lead to distal ulcerations, skin necrosis, tissue loss, and autoamputation. For the management of SAVI, JAK inhibitors can be a valuable therapeutic intervention that hampers disease progression, while conventional immunosuppressive treatments have shown minimal efficacy. This review aims to describe the underlying pathophysiologic mechanisms of SAVI, highlighting the main clinical manifestations and discussing the current treatment approaches.

Journal of Molecular Pathology doi: 10.3390/jmp4040023

Authors: Hiroshi Kobayashi Chiharu Yoshimoto Sho Matsubara Hiroshi Shigetomi Shogo Imanaka

Background: Ovarian cancer is often characterized by aggressive growth and chemoresistance, leading to a poor prognosis. The energy and nutrient acquisition through metabolic reprogramming has been reported to facilitate cancer cell proliferation, invasion, and metastasis. Therefore, a therapeutic strategy to consider is to rewire energy metabolism. Mitochondrial dynamics have a profound impact on the metabolic profiles. In this review, we summarize the current understanding of the molecular mechanisms governing mitochondrial dynamics and their impact on cell proliferation and invasion and discuss future perspectives for therapeutic strategies and research directions. Methods: A search was conducted for literature published up to 30 June 2023 using the online databases PubMed and Google Scholar in this narrative literature review. Results: Mitochondria are essential for regulating metabolic reprogramming to meet the increasing energy demand for rapid cancer cell proliferation and invasion. A metabolic switch from OXPHOS to glycolysis may promote invasion, and OXPHOS-driven metabolism may be associated with proliferation, chemoresistance, and stemness. Many ovarian cancer cells are known to favor glycolysis over OXPHOS, but the opposite takes place in the subpopulation of cancer cells. The preference for glycolysis versus OXPHOS in ovarian cancer cells may be determined by histopathologic types, the unique genetic profile of energy metabolism, and intrinsic (e.g., oncogenic signaling) and extrinsic (e.g., nutritional status and hypoxia) factors. Conclusions: Preclinical studies suggest that mitochondrial dynamics regulators have therapeutic potential in ovarian cancer, but some factors limit their beneficial effects.

Journal of Molecular Pathology doi: 10.3390/jmp4040022

Authors: Caterina De Luca Francesco Pepe Gianluca Russo Mariantonia Nacchio Pasquale Pisapia Maria Russo Floriana Conticelli Lucia Palumbo Claudia Scimone Domenico Cozzolino Gianluca Gragnano Antonino Iaccarino Giancarlo Troncone Umberto Malapelle

Aims: To date, precision medicine has played a pivotal role in the clinical administration of solid-tumor patients. In this scenario, a rapidly increasing number of predictive biomarkers have been approved in diagnostic practice or are currently being investigated in clinical trials. A pitfall in molecular testing is the diagnostic routine sample available to analyze predictive biomarkers; a scant tissue sample often represents the only diagnostical source of nucleic acids with which to conduct molecular analysis. At the sight of these critical issues, next-generation sequencing (NGS) platforms emerged as referral testing strategies for the molecular analysis of predictive biomarkers in routine practice, but the need for highly skilled personnel and extensive working time drastically impacts the widespread diffusion of this technology in diagnostic settings. Here, we technically validate a fully integrated NGS platform on diagnostic routine tissue samples previously tested with an NGS-based diagnostic workflow by a referral institution. Methods: A retrospective series of n = 64 samples (n = 32 DNA, n = 32 RNA samples), previously tested using a customized NGS assay (SiRe™ and SiRe fusion), was retrieved from the internal archive of the University of Naples Federico II. Each sample was tested by adopting an Oncomine Precision Assay (OPA), which is able to detect 2769 molecular actionable alterations [hotspot mutations, copy number variations (CNV) and gene fusions] on fully integrated NGS platforms (Genexus, Thermo Fisher Scientific (Waltham, MA, USA). The concordance rate between these technical approaches was determined. Results: The Genexus system successfully carried out molecular analysis in all instances. A concordance rate of 96.9% (31 out of 32) was observed between the OPA and SiRe™ panels both for DNA- and RNA-based analysis. A negative predictive value of 100% and a positive predictive value of 96.9% (62 out of 64) were assessed. Conclusions: A fully automatized Genexus system combined with OPA (Thermo Fisher Scientific) may be considered a technically valuable, time-saving sequencing platform to test predictive biomarkers in diagnostic routine practice.

Journal of Molecular Pathology doi: 10.3390/jmp4040021

Authors: Denis Horgan Marc Van den Bulcke Umberto Malapelle Nicola Normanno Ettore D. Capoluongo Arsela Prelaj Carmelo Rizzari Aliki Stathopoulou Jaya Singh Marta Kozaric France Dube Manuel Ottaviano Stefania Boccia Gabriella Pravettoni Ivana Cattaneo Núria Malats Reinhard Buettner Karim Lekadir Francesco de Lorenzo Catherine Alix-Panabieres Sara Badreh Paul Hofman Ruggero De Maria Eric Solary

Effective cancer diagnosis, treatment and control depend on interactions among numerous distinct factors, from technology to data to skills to sociology. But a crucial influence is the extent to which the health system takes account of the distinct perspectives of the many different groups of interdependent stakeholders concerned with cancer, including patients, practitioners and planners. This paper provides some elucidation as to how far and how efficiently these interactions currently take place in Europe. It also makes some tentative suggestions as to how conscious systematic interventions could improve cancer outcomes. It is based on a series of expert panels and surveys conducted by the European Alliance for Personalised Medicine (EAPM) that provided information at the national level on three selected parameters: implementation of next-generation sequencing (NGS) and liquid biopsy (LB), attitudes of patients to prevention and practices of sharing genomic data among healthcare professionals (HCPs). The varying data infrastructure highlights the urgent need for substantial improvements to accommodate the increasing importance of genomics data in cancer diagnosis and care. Additionally, we identify disparities in age-specific approaches to cancer prevention, emphasising the necessity for tailored strategies to address unique age group perspectives. Moreover, distinct regional prioritizations in cancer treatment underscore the importance of considering regional variations when shaping future cancer care strategies. This study advocates for collaborative data sharing supported by technological innovation to overcome these challenges, ultimately fostering a holistic and equitable provision of cancer care in Europe.

Journal of Molecular Pathology doi: 10.3390/jmp4040020

Authors: Georgios S. Markopoulos Emilios E. Pakos Vasilios Gavrielatos Dimitrios Kosmas Ioannis Gkiatas George A. Alexiou Anna Batistatou Evangeli Lampri George Vartholomatos

The accurate assessment of malignancy and the precise characterization of cancer type are pivotal in guiding clinical decisions and ensuring optimal patient outcomes. The challenging task of identifying the primary site of carcinoma, especially during a surgical procedure, is not always possible and necessitates the exploration of novel, innovative diagnostic techniques. In this report, we detail a unique case of carcinoma of unknown primary origin encountered during an orthopedic surgical procedure. We introduce a novel intraoperative flow cytometry (iFC) methodology, distinctly different from traditional flow cytometry, which is tailored for real-time assessment during surgeries. This iFC technique, applied in a bone metastasis case of unknown primary origin, enabled DNA content analysis and the quantification of cytokeratin for rapid malignancy characterization, presenting an avenue for immediate surgical guidance and decision making. The case was distinctively characterized using iFC, shedding light on the potential of this emerging technique. iFC has been gaining traction because of its ability to facilitate cancer cell assessment and margin evaluation. It has been successfully applied across a wide spectrum of neoplastic conditions. Our innovative, two-step approach using iFC encompasses (1) DNA content analysis, which serves as a reliable indicator for the detection of cancer cells, and (2) the quantification of cytokeratin, a pivotal marker, which aids in the characterization and classification of a malignancy. In this case, the malignancy was classified as a carcinoma. The findings obtained from iFC were subsequently validated through pathology assessment, confirming the accuracy and reliability of our approach. This noteworthy case strengthens the potential of iFC as a novel tool in malignancy assessment, which is not just limited to cell cycle analysis but instead extends beyond this application. The promising results obtained from this case study serve as a testament to the need for more extensive research in clinical studies.

Journal of Molecular Pathology doi: 10.3390/jmp4040019

Authors: Ismael Duarte Machado de Almeida Pedro Luiz de Paiva Kamilla de Faria Santos Angela Adamski da Silva Reis Rodrigo da Silva Santos

Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS) are incurable degenerative scleroses with unclear etiology. Neuroinflammation is an important factor in the neurodegeneration characteristic of these diseases. Additionally, Interleukin 10 (IL10) can inhibit the synthesis of inflammatory cytokines and plays a protective role against neurodegeneration associated with neuroinflammation. Thus, we developed a systematic review and meta-analysis in order to clarify the relationship between polymorphisms in the IL10 gene and MS and/or ALS. We searched for observational studies in four international databases without time restrictions. Seventeen studies were added to the systematic review and six polymorphisms were observed: IL10-592 (rs1800872; C>A), IL10-819 (rs1800871; C>T), IL10-1082 (rs1800896; A>G), IL10-2763 (rs6693899; A>C), IL10-2849 (rs6703630; A>G) and IL10-3575 (rs1800890; A>T). In the meta-analysis, we used odds ratio (OR) and 95% confidence interval (CI) to evaluate the association of IL10-1082, IL10-819 and IL10-592 polymorphisms and MS. We found a positive association of MS with the IL10-1082 SNP in genotypic comparison (AG+GG vs. AA) (OR = 1.23; 95% CI = 1.01–1.51; p = 0.04). Our search did not find any article relating polymorphisms in the IL10 gene with ALS. Therefore, our analysis indicates a possible association of IL10 gene SNPs in the development and progression of MS.

Journal of Molecular Pathology doi: 10.3390/jmp4040018

Authors: Mohammed A. Azab

Glioblastoma (GBM) is considered the most aggressive primary brain tumor. Recurrence after treatment is a significant problem with a failed response to optimal therapies. The recurrence of GBM is linked to different cellular and molecular pathways. Not only genetics are involved in gliomagenesis, but also epigenetics. Histone modulation through acetylation, phosphorylation, ubiquitination, and methylation can regulate gene expression and may play a role in the pathogenesis of GBM. Preclinical and clinical studies currently target epigenetic enzymes in gliomas, including a new generation of histone deacetylase (HDAC) inhibitors. Herein, I tried to highlight current research in glioma epigenetics, focusing on the culprit of histone modifications and the use of HDAC target therapies as a possible treatment line for glioblastoma.

Journal of Molecular Pathology doi: 10.3390/jmp4030017

Authors: Oladimeji Adebayo Misheck J. Nkhata Kehinde K. Kanmodi Taiwo Alatishe Eyinade Egbedina Temitope Ojo Samson Ojedokun John Oladapo Abiodun Moshood Adeoye Lawrence A. Nnyanzi

Background: Burnout is increasingly being recognized as a contributory factor to the erosion of a positive psychological state. Studies have examined the relationship between burnout and various inflammatory markers such as IL-1, IL-6, and TNF-alpha. Burnout is also associated with increased systemic inflammation along a continuum of symptom severity. This protocol is for a scoping review looking at the link between burnout, inflammatory markers, and cardiovascular risks or diseases. Methods: This study will be based on the preferred reporting items for systematic reviews and meta-analyses guidelines/checklists and the report of the review will be based on the same guideline. The study seeks to address the following principal questions. (i) What are the relevant inflammatory biomarkers that mediate cardiovascular risk factors in burnout? (ii) How do inflammatory biomarkers mediate cardiovascular risk factors in burnout? The outputs obtained from the literature search will be deduplicated using the Rayyan software. Results: We would create table summaries of findings to inform a narrative synthesis of the evidence from the papers included. Conclusion: The review article would help to concisely synthesize the available evidence on the relationship between burnout, inflammatory markers, and cardiovascular diseases.