Search Results (318)

Juvenile myelomonocytic leukemia (JMML) is a rare, aggressive myeloproliferative neoplasm of early childhood characterized by constitutive activation of the RAS-MAPK signaling pathway. RASopathies are a heterogeneous group of complex genetic disorders arising from germline mutations that dysregulate RAS-MAPK signaling. Noonan syndrome, CBL syndrome, and neurofibromatosis type 1 (NF1) are the three major RASopathies predisposing to JMML. More than 90% of JMML cases harbor germline or somatic mutations in one of five canonical driver genes—PTPN11, NRAS, KRAS, NF1, or CBL—establishing JMML as the prototypical malignant manifestation of RASopathy biology. The fifth edition of the World Health Organization Classification of Tumours reclassified JMML as a myeloproliferative neoplasm while the International Consensus Classification adopted JMML under pediatric and/or germline mutation-associated disorders, introducing a JMML-like category for cases lacking five canonical mutations but harboring emerging drivers such as SH2B3::LNK alterations and ALK::ROS1 fusions. The distinction between germline and somatic mutations profoundly influences prognosis: e.g., germline PTPN11-associated myeloproliferations and many germline CBL cases undergo spontaneous resolution, whereas somatic PTPN11- and NF1-mutated JMML is more aggressive and requires prompt allogeneic hematopoietic stem cell transplantation. DNA methylation profiling has emerged as the most robust prognostic framework, with consensus defining high-, intermediate-, and low-methylation subgroups that independently predict outcome. Both genotype and DNA methylation subclassification have been integrated into clinical decision-making, incorporating pretransplant azacitidine, watch-and-wait approaches for favorable-risk patients, and emerging targeted therapies including MEK inhibitors. This review synthesizes recent advances in understanding JMML as a bona fide RASopathy; provides a diagnostic algorithm, molecular landscapes, and prognostic models; and highlights opportunities for molecularly targeted therapeutic intervention. Full article

Congenital heart disease (CHD) is the most common anatomical malformation occurring in live-born infants and an increasing cause of morbidity and mortality all over the world. Population-based observations have described associations between maternal cardiometabolic disorders and the risk of CHD in offspring. The present article is a narrative review. The aim of this study was to review the epidemiological evidence and clinical observations relating maternal obesity and diabetes mellitus to the risk of CHD in offspring, with particular attention paid to first trimester disturbances of fetal cardiac development and the influence of genetic, epigenetic and environmental factors. Studies have shown that maternal diabetes is a risk factor associated with nearly all subtypes of CHDs in offspring, while obesity and overweight are associated with increased risk for complex defects and outflow tract obstruction and decreased risk for ventricular septal defects. Diabetes and obesity share several phenotypes, which could be transmissible from mother to fetus via the placenta. This means that an increase in maternal glucose could be responsible for the prevalence of CHD in newborns of obese women. On the other hand, maternal diabetes may induce epigenetic modifications in the developing fetus. DNA methylation changes can impact gene expression patterns relevant to heart development. The abovementioned studies are heterogenous, express different opinions and are often difficult to compare. Therefore, the results from these meta-analyses must be interpreted with caution. Optimal diabetes control is responsible for the prevention of oxidative stress in diabetic pregnancies, and a deeper understanding of maternal risk factors holds the potential to improve both prenatal detection of CHDs by identifying at-risk pregnancies and primary prevention of diseases by improving preconception management. Full article

Endometrial cancer (EC) is increasingly recognized as a heterogeneous disease, yet current treatment strategies often fail to explain why tumors with similar molecular profiles respond differently or develop resistance. This gap points to regulatory mechanisms beyond static genomic alterations. Epigenetic dysregulation through DNA methylation, histone modification, and non-coding RNA (ncRNAs) networks acts as a dynamic and reversible system that governs how tumors adapt under therapeutic pressure. In EC, alterations affecting key regulators such as MLH1, PTEN, and hormone receptors directly influence sensitivity to immunotherapy, targeted therapy, and endocrine treatment, defining treatment-responsive and treatment-resistant states. These observations shift the role of epigenetics from a descriptive feature of tumor biology to a determinant of therapeutic behaviour. Epigenetic states influence immune recognition, pathway activation, and cell cycle control, thereby shaping response to chemotherapy and immune checkpoint blockade. Biomarkers derived from these alterations, including methylation signatures and circulating RNAs, offer opportunities for patient stratification and longitudinal monitoring of treatment response. Therapeutically, targeting epigenetic regulators provides a strategy to reverse resistance and restore treatment sensitivity. DNA methyltransferase and histone deacetylase inhibitors, particularly in combination with established therapies, have shown potential to enhance treatment efficacy. Emerging approaches, including locus-specific epigenetic editing and liquid biopsy–guided monitoring, further support adaptive treatment strategies. Integrating epigenetic reprogramming into clinical decision-making offers a practical path toward improving treatment response and overcoming resistance in EC. Here, we propose an Epigenetic State–Response Framework (ESRF) in which dynamic epigenetic states define treatment-sensitive and resistant phenotypes, map to specific therapeutic vulnerabilities, and can be actively reprogrammed to restore treatment response. Full article

Understanding the phenotypic consequences of epigenetic variation and its role in adaptation remains a central challenge in evolutionary biology. Marine and freshwater sticklebacks provide a powerful system to study the interplay between genetic and epigenetic components of phenotypic plasticity that enables colonization of contrasting salinity habitats. Here, we used whole-genome bisulfite sequencing (WGBS) to characterize DNA methylation entropy—a measure of epigenetic stochasticity—in gill tissue from marine and freshwater ecotypes. We found that freshwater sticklebacks exhibit elevated methylation entropy in divergence islands (DIs), genomic regions known as hotspots of genetic divergence between marine and freshwater populations. Within DIs, we identified a subset of genes exhibiting concurrent increases in methylation entropy and transcriptional variance, including osmoregulatory candidates involved in growth modulation, cytoskeletal reorganization, metabolism, and extracellular matrix remodeling. Their linked variability suggests that they may act as “adaptation capacitors” facilitating phenotypic plasticity during salinity transitions. Exploratory enrichment analysis further revealed overrepresented epigenetic regulators within DIs, such as DNA demethylase TET1 and chromatin remodelers ARID5B and BPTF, indicating a potential regulatory basis by which these factors may convert genetic variation into epigenetic diversity. Collectively, our findings demonstrate that DIs are focal points of both genetic divergence and epigenetic heterogeneity, consistent with a model in which DIs may act as multi-layered genomic regions associated with adaptive responses to salinity change. Full article

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder caused by the interaction between genetic and environmental influences, potentially mediated by epigenetic mechanisms such as DNA methylation. Genome-wide DNA methylation profiling was performed using the Infinium MethylationEPIC v2.0 array on peripheral blood mononuclear cells (PBMCs) from 100 children with ASD and 50 typically developing controls. Differential methylation analyses were conducted by adjusting for age, sex, and estimated blood-cell-type composition as covariates. Functional enrichment, SFARI gene-overlap analysis, and cross-cohort validation were performed. We identified 3507 differentially methylated positions (DMPs) in the ASD cohort. Functional enrichment revealed pathways involved in neuronal signaling, synaptic activity, and immune regulation, suggesting coordinated neurodevelopmental and immune processes in ASD. Stratification by clinical severity demonstrated common and unique biological characteristics between the moderate and severe ASD groups. Furthermore, DMP-associated genes significantly overlapped with high-confidence ASD risk genes from the SFARI database and established transcriptomic signatures of neurodevelopmental disorders. Comparisons with independent post mortem brain tissue and peripheral blood datasets revealed partial overlap and directional concordance. However, the strength of concordance varied across datasets and was limited in the most directly comparable peripheral blood cohort. Our findings suggested that DNA methylation profiling of PBMCs provided peripheral epigenetic signatures and candidate loci for further validation in larger independent cohorts. Full article

Glioblastoma (GBM) remains one of the most challenging forms of cancer to treat, despite that extensive molecular profiling is now available. Indeed, intratumoral cellular heterogeneity, receptor redundancy, and adaptive resistance through compensatory signaling limit the impact of targeted therapies. Moreover, immunotherapies also underperform: checkpoint blockade and vaccine strategies did not obtain consistent benefits in a low mutational burden, poorly immunogenic tumor microenvironment (TME) dominated by immunosuppressive myeloid cells. In this article, we provide evidence that tumor-associated macrophages (TAMs), a form of CNS resident microglia and infiltrating macrophage, derived from bone marrow, adopt a spatially and transcriptionally distinct, non-binary continuum, shaped by tumor-derived signals and niche constraints, allowing glioma cells to resist to immune and pharmaceutical therapeutics. Metabolic rewiring, including hypoxia-linked glycolytic pressure, lactate signaling, and lipid-associated programs, determine immunosuppressive outputs and restrict plasticity, while epigenetic imprinting (DNA methylation, histone modifications, and chromatin regulators) stabilizes these programs and limits access to inflammatory loci. We discuss how stem cell secretome, and extracellular vesicles (EVs) and their cargo may act as tunable autocrine/paracrine inputs that may bias microglial regulatory control. Finally, we highlight major translational confounders, including EV operational definitions, blood–brain barrier (BBB) permeability and regional exposure, inconsistent dosing units, mixed myeloid compartments, and manufacturing dependent variability. Therefore, an exposure-aware framework that integrates product identity, delivery evidence, state-sensitive potency assays, and functional endpoints would be highly desirable. Full article

Background/Objectives: High-altitude exposure represents a complex psychophysiological stressor involving hypoxia, physical effort, sleep disruption and psychological strain. The endocannabinoid system (ECS) plays a key role in stress regulation, yet its epigenetic modulation under extreme environmental conditions remains poorly characterized. This pilot and exploratory study investigated DNA methylation and descriptive microRNA (miRNA) expression patterns of CNR1 and FAAH genes, and their associations with mood and anxiety outcomes, in trekkers exposed to Himalayan high altitude. Methods: Twenty-one healthy lowlanders completed a longitudinal expedition from 2860 m to 5050 m. Psychometric measures (SVARAD, BDI, SAS, SHAPS) and saliva samples were collected at baseline (T0) and at high altitude (T1). DNA methylation of CNR1 and FAAH regulatory regions was quantified by pyrosequencing. Exosomal miRNAs targeting these genes were profiled using qRT-PCR, on pooled samples; results are presented descriptively. Results: DNA methylation analysis revealed heterogeneous, sex-specific epigenetic patterns following high-altitude exposure. A significant increase in CNR1 promoter methylation at CpG4 was observed in males at T1, whereas methylation remained largely stable in females. Descriptive miRNA expression data showed bidirectional differences between groups, consistent with context-dependent stress regulation. Convergent directional patterns between miR-23b-3p expression and CNR1 methylation in males were observed. However, given the descriptive nature of the miRNA data, this observation is purely exploratory and requires replication before any mechanistic conclusions can be drawn. Psychometrically, participants showed a mild mood decline without overt clinical symptoms. Sex-specific differences in the relationship between CNR1 methylation and psychometric outcomes were observed and warrant further investigation in adequately powered cohorts. Conclusions: These preliminary findings suggest that CNR1 epigenetic regulation warrants further investigation as a potential indicator of stress adaptation and psychological responses and underscore the need to consider sex differences when evaluating resilience and vulnerability to extreme environments. Full article

Background: Gliomas are the most common malignant brain tumors in adults, characterized by a poor prognosis. Although the current World Health Organization (WHO) classification provides clear guidelines for classifying oligodendroglioma, astrocytoma, and glioblastoma patients, significant heterogeneity persists within each class, limiting the effectiveness of current treatment strategies. With the increasing availability of large-scale multi-omics datasets resulting from advancements in sequencing technologies and online repositories that provide them, such as The Cancer Genome Atlas (TCGA), it is now possible to investigate these tumors at multiple molecular levels. Methods: In this work, we apply integrative multi-omics analysis to explore the interplay between genomic (mutations), epigenomic (DNA methylation), and transcriptomic (mRNA and miRNA) layers. Our approach relies on Multi-Omics Factor Analysis (MOFA), a Bayesian latent factor analysis model designed to capture sources of variation across different omics types. Results: Our results highlight distinct molecular profiles across the three glioma types and identify potential relationships between methylation and genetic expression. In particular, we uncover novel candidate biomarkers associated with survival as well as a transcriptional profile associated with neural system development. Conclusions: These findings may contribute to more personalized therapeutic strategies, potentially improving treatment effectiveness and survival outcomes in this disease. Full article

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, with prognosis critically dependent on the stage at diagnosis. Traditional tissue biopsy presents well-known limitations, including tumor heterogeneity and invasiveness. Liquid biopsy, encompassing the analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, and other cell-free biomarkers, has emerged as a transformative approach for non-invasive tumor profiling. This comprehensive narrative review outlines the recent evidence published on the current state and future perspectives of liquid biopsy in CRC, with a focused emphasis on the role of artificial intelligence (AI), machine learning (ML), and deep learning (DL) in data analysis and clinical translation. Methods: A narrative review of the literature was conducted by searching PubMed/MEDLINE, EMBASE, and ClinicalTrials.gov for articles published between January 2020 and January 2026, using a predefined Boolean search string combining terms related to liquid biopsy biomarkers, colorectal cancer, and artificial intelligence methodologies. Filters were applied to include only English-language human studies. Additional relevant sources were consulted to ensure comprehensive coverage of the available literature. Liquid biopsy platforms, particularly ctDNA sequencing and methylation profiling, demonstrate increasing clinical utility across the CRC care continuum from population screening to post-surgical minimal residual disease (MRD) detection and real-time therapy monitoring. AI-driven analytical frameworks, including Random Forest, Convolutional Neural Networks, LSTM models, and more recently Large Language Models (LLMs), substantially augment the sensitivity and specificity of liquid biopsy interpretation, enabling multimodal data integration. The convergence of liquid biopsy technology and AI-driven analytics represents a paradigm shift toward precision oncology in CRC. Remaining challenges include analytical standardization, model explainability, regulatory harmonization, and equitable access. Future integration of federated learning frameworks and LLM-based clinical decision support tools will be essential for responsible clinical translation. Full article

Acute myeloid leukemia (AML) is a heterogeneous malignancy, with clonal complexity and somatic mutations critically influencing prognosis and treatment. While global genomic profiling efforts have revolutionized AML classification and risk stratification, the molecular landscape in Pakistani patients remains underexplored. Our aim is to perform targeted next-generation sequencing (NGS) for somatic mutational profiling of newly diagnosed AML patients in Pakistan. This prospective study was conducted at the Armed Forces Institute of Pathology, Pakistan, from January 2021 to January 2026. Among 104 patients, 204 somatic variants were identified (mean: 1.96 variants/patient), predominantly single-nucleotide variants (49.5%). Missense mutations (38.2%) were most common, with enriched transitions (Ti/Tv: 1.27:1). Frequently mutated genes included TP53 (22.1%), KIT (9.8%), CEBPA (8.8%), and NRAS (5.9%). Cell-signaling genes (30.4%) and tumor suppressor genes (27.0%) were the most affected functional groups. Co-mutation analysis showed clustering led by DNMT3A–IDH1 co-occurrence (ρ ≈ 0.43). DNA-methylation alterations frequently co-occurred with tumor suppressors (OR ≈ 4.6, p = 0.007), transcription factors (OR ≈ 3.9, p = 0.023), and NPM1 (ρ = 0.32). This study provides the first comprehensive genomic map of Pakistani AML patients, revealing unique mutational signatures. The findings lay the groundwork for population-specific precision oncology in low- and middle-income countries. Full article

Liquid biopsy has emerged as a transformative tool in oncology, enabling minimally invasive and dynamic characterization of tumor biology. In prostate cancer, marked by high heterogeneity and frequent bone metastases, tissue biopsy is often challenging, highlighting the clinical value of circulating biomarkers. Circulating tumor DNA (ctDNA) is the most clinically advanced analyte, supporting detection of actionable alterations such as BRCA1/2 and ATM mutations, guiding targeted therapies, and enabling real-time monitoring of treatment response and resistance. Circulating tumor cells (CTCs) and extracellular vesicles (EVs) provide complementary insights into tumor biology and disease progression. However, challenges remain, including limited sensitivity in low tumor burden and biological confounders such as clonal hematopoiesis (CH), which can lead to false-positive findings. Emerging approaches, including fragmentomics and methylation profiling, offer improved tumor specificity and may help overcome these limitations. Together, these advances support the integration of liquid biopsy into clinical practice for personalized management and longitudinal monitoring in prostate cancer. Full article

Background: The early detection of prostate and testicular tumors remains challenging as standard diagnostic tools often lack sensitivity and produce ambiguous results. Seminal fluid is a biologically rich medium that closely reflects the state of male reproductive tissues and has therefore emerged as a promising source of non-invasive molecular biomarkers. Objective: This study aimed to critically evaluate the evidence regarding cell-free DNA, RNA, proteins and metabolites in seminal fluid, and to assess their potential for improving the early detection of male reproductive cancers. Methods: A systematic review was performed according to PRISMA guidelines. Comprehensive searches of the PubMed and Scopus databases were conducted to identify original clinical studies analyzing molecular biomarkers in seminal fluid from patients with prostate or testicular tumors. For each study, data were extracted on biomarker types, cohort characteristics, analytical methods and diagnostic performance. Results: Forty-two eligible studies were included, covering multiple biomarker classes. Most were observational, single-center investigations classified as level 3b evidence. Across the different types of biomarkers, seminal fluid was associated with tumor-associated molecular changes. Alterations in the concentration, fragmentation and methylation patterns of cell-free DNA (e.g., GSTP1, RARβ2, LGALS3 and OCT3/4) distinguished malignant from benign conditions with sensitivities of up to 80–100%. RNA-based markers, including microRNAs, small non-coding RNAs, and tRNA fragments, showed improved performance in several studies, with multimarker models achieving areas under the curve (AUCs) of 0.85–0.93. Proteomic analyses identified high-specificity candidates such as TGM4, AMACR, PROS1 and DKK3. Metabolomic profiling further strengthened the diagnostic potential; reduced seminal citrate outperformed prostate-specific antigen (AUC 0.748 vs. 0.548), and reproducible shifts in amino acid and lipid profiles were observed in testicular tumors. However, substantial heterogeneity in study design, patient selection, and analytical platforms was observed. Risk of bias varied, and large prospective validation cohorts were lacking. Conclusions: Current evidence suggests that seminal fluid contains molecular signals associated with tumors that could be used for diagnosis. However, the available data are predominantly exploratory and methodologically heterogeneous. Before seminal fluid-based biomarkers can be considered for routine clinical implementation, robust prospective studies with standardized protocols are required. Full article

Chordoma is a rare malignant neoplasm of the axial skeleton, arising from notochordal remnants. No approved systemic therapies exist, and the 10-year overall survival is below 60%. Accurate molecular and pathological classification is a prerequisite for improved prognostication and the identification of actionable therapeutic targets; however, molecular classification of chordoma remains significantly less advanced than that of other neoplasms. This narrative review synthesizes proposed classification frameworks for chordoma across histological, radiological, surgical, genomic, epigenomic, transcriptomic, and proteomic domains. PubMed and CENTRAL were searched on 1 February 2026 using five queries: ‘chordoma classification’, ‘chordoma DNA sequencing’, ‘chordoma RNA sequencing’, ‘chordoma methylation’, and ‘chordoma copy number’. Original research articles describing more than one patient and reporting a classification or subtyping framework were included; review articles, case reports, and non-English publications were excluded. Sample size and the use of a validation dataset were identified for each study. Results were synthesized qualitatively. A total of 108 studies encompassing 6349 individuals were included. Across six domains, four cross-cutting themes with prognostic and potential theranostic value emerged: copy number alterations, particularly CDKN2A/B loss; SWI/SNF complex dysfunction; stroma–tumor ratio; and immune microenvironment heterogeneity. Full article

Early diagnosis of ovarian cancer remains one of the most important unmet needs in gynecologic oncology because survival is strongly stage-dependent and most patients still present with disseminated disease. Conventional non-invasive tools, particularly CA-125, transvaginal ultrasound, and composite triage algorithms, remain clinically useful but are limited by suboptimal sensitivity for stage I disease and by reduced specificity in premenopausal women and in benign inflammatory or endometriosis-associated conditions. Circulating tumor DNA (ctDNA) has therefore emerged as a candidate biomarker capable of extending liquid biopsy beyond conventional serology. In ovarian cancer, however, ctDNA implementation is constrained by low tumor shedding in early-stage disease, marked biologic heterogeneity across histotypes, clonal hematopoiesis-related background noise, and major pre-analytical and analytical sources of variability. This narrative review, informed by structured searches of PubMed, Scopus, and Web of Science, examines the evolving evidence for ctDNA mutations, methylation-based assays, multi-omic platforms, and machine-learning models across three distinct clinical contexts: population screening, preoperative triage of adnexal masses, and post-treatment assessment of molecular residual disease. We also discuss positive predictive value, false-positive harms, health-economic implications, standardization initiatives, and ongoing prospective studies. Overall, current evidence suggests that the most plausible near-term role for liquid biopsy in ovarian cancer is not as a universal stand-alone screening test, but as an integrated component of risk stratification and disease-monitoring frameworks that combine molecular signals with clinicopathologic and imaging data. Full article

Nucleoside analogs (NAs) play a central role in cancer therapy, either through direct cytotoxicity or epigenome reprogramming. They are clinically effective but have shortcomings in their long-term effectiveness because of variable patient responses and the emergence of resistance. There is growing evidence that DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs (ncRNAs) are key factors that determine sensitivity and resistance to NAs. This review summarizes existing evidence on the epigenetic control of cytotoxic and epigenetic nucleoside analogs, discusses predictive biomarkers of human Equilibrative Nucleoside Transporter 1 (hENT1) and deoxycytidine kinase (dCK) promoter methylation, histone modifications, and ncRNA signatures, and assesses the emerging strategies of multi-omic integration. Improvements in detection methods, such as high-resolution sequencing, single-cell profiling, and liquid biopsy, are addressed, along with the issues of reproducibility, tumor heterogeneity, and clinical translation. Epigenetic biomarkers are promising for patient stratification in clinical trials, although a lack of uniformity in technical and methodological approaches currently constrains their full potential. The future focus will be on standardized panels of biomarkers, real-time monitoring, rational combination strategies, and biomarker-directed clinical trial designs. Overall, epigenetic biomarkers are capable of changing nucleoside analog therapy into a more precise, durable, and personalized treatment approach. Full article