geneimprint : Hot off the Press

'; ?> geneimprint : Hot off the Press http://www.geneimprint.com/site/hot-off-the-press Daily listing of the most recent articles in epigenetics and imprinting, collected from the PubMed database. en-us Sat, 14 Feb 2026 04:11:24 EST Sat, 14 Feb 2026 04:11:24 EST jirtle@radonc.duke.edu james001@jirtle.com Distinct transcriptional and epigenomic programs define Hofbauer cells in term placenta. BarÃ¡th BR, Bojcsuk D, Bene K, Caballero-SÃ¡nchez N, Cseh T, de Freitas JC, Tzerpos P, Toth M, Tang Z, Guller S, Krasznai ZT, Neuperger P, Szebeni GJ, Nagy G, Deli T, Nagy L
JCI Insight (Feb 2026)

Hofbauer cells (HBCs) are fetal macrophages located in the placenta that contribute to antimicrobial defense, angiogenesis, tissue remodeling, and metabolic processes within the chorionic villi. Although their roles in placental biology are increasingly recognized, the mechanisms that regulate HBC identity and function are not yet fully defined. This study aimed to define the core transcriptomic and epigenomic features of HBCs in term placentas and to examine their capacity for transcriptional responsiveness and phenotypic variation. Using chromatin accessibility profiling and bulk RNA-seq, we found that HBCs exhibit a unique gene expression and chromatin accessibility profile compared with other fetal and adult macrophages. We identified a coordinated transcriptional network involving nuclear receptors (NRs) NR4A1-3, the glucocorticoid receptor, and RFX family members (RFX1, RFX2, RFX5) that appears to shape HBC identity, particularly through pathways linked to lipid metabolism and angiogenesis. Although exploratory in nature, in vitro stimulation studies showed that HBCs exhibited increased transcriptional activity in response to combined IL-4 and rosiglitazone treatment, including induction of the lipid transporter CD36. Mass cytometry analysis revealed surface markers indicative of both immature and mature macrophage states. These results together indicate that HBCs are a distinct and diverse population of macrophages with a specialized, adaptable regulatory program in the human placenta.]]> Wed, 31 Dec 1969 19:00:00 EST Trimethylated H3K4 and Acetylated H3K14 Expression as Prognostic Markers in Oral Squamous Cell Carcinoma. Borges DC, Costa ARGF, Bernardino Neto M, Matsuo FS, Andrade MF, Servato JPS, Loyola AM, Cardoso SV, da Silva Moraes A, da Luz FAC, de Faria PR
Appl Immunohistochem Mol Morphol (Feb 2026)

This study investigated the immunohistochemical expression of histone post-translational modifications (HPTMs) H3K4me2, H3K4me3, and H3K14ac in OSCC and their relationship with metastasis and prognosis. Paraffin-embedded tissue samples of 90 OSCC patients were retrospectively retrieved and immunostained. The sample was divided into primary nonmetastatic (PNM) and primary metastatic (PM) tumors. Nuclear HPTM expression was digitally measured using the integrated optical density index (IOD), and expression levels were divided into low and high based on the median IOD values. Results: All tumor samples were positive. The median H3K14ac IOD was significantly higher in the PM than in the PNM group. High H3K4me2 expression was frequently observed in small and initial tumors, while high H3K4me3 was observed in recurrent OSCC. The ROC curves indicate that H3K14ac might be explored as a screening test for metastasis, showing a sensitivity of 0.81. High H3K4me3-expressing patients had lower survival probabilities and a 3-fold increased risk of death. Conclusions: Our findings suggest that methylation and acetylation of lysine residues 4 and 14 of histone H3 are potential biomarkers of OSCC prognosis and metastasis.]]> Wed, 31 Dec 1969 19:00:00 EST A cell type enrichment analysis tool for brain DNA methylation data (CEAM). MÃ¼ller J, Laroche VT, Imm J, Weymouth L, Harvey J, Reijnders RA, Smith AR, van den Hove D, Lunnon K, Cavill R, Pishva E
Epigenetics (Dec 2026)

DNA methylation (DNAm) signatures are highly cell type-specific, yet most epigenome-wide association studies (EWAS) are performed on bulk tissue, potentially obscuring critical cell type-specific patterns. Existing computational tools for detecting cell type-specific DNAm changes are often limited by the accuracy of cell type deconvolution algorithms. Here, we introduce CEAM (Cell-type Enrichment Analysis for Methylation), a robust and interpretable framework for cell type enrichment analysis in DNA methylation data. CEAM applies over-representation analysis with cell type-specific CpG panels from Illumina EPIC arrays derived from nuclei-sorted cortical post-mortem brains from neurologically healthy aged individuals. The constructed CpG panels were systematically evaluated using both simulated datasets and published EWAS results from Alzheimer's disease, Lewy body disease, and multiple sclerosis. CEAM demonstrated resilience to shifts in cell type composition, a common confounder in EWAS, and remained robust across a wide range of differentially methylated positions, when upstream modeling of cell type composition was modeled with sufficient accuracy. Application to existing EWAS findings generated in neurodegenerative diseases revealed enrichment patterns concordant with established disease biology, confirming CEAM's biological relevance. The workflow is publicly available as an interactive Shiny app (https://um-dementia-systems-biology.shinyapps.io/CEAM/) enabling rapid, interpretable analysis of cell type-specific DNAm changes from bulk EWAS.]]> Wed, 31 Dec 1969 19:00:00 EST Multi-omics biomarkers in psychiatric disorders diagnosis and stratification. Khatami SH, Anoosheh S, Khodaparast M, Maghsoudloonejad A, Dadgostar E, Asadi A, Kaveh M, Haghighi MM
Clin Chim Acta (Feb 2026)

The precise diagnosis and stratification of psychiatric disorders remain formidable challenges in modern medicine, hindered by the absence of objective biomarkers and reliance on subjective clinical criteria. Recent advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and epigenomics, have revolutionized our understanding of complex neuropsychiatric conditions such as schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorder. This review critically evaluates the current landscape of multi-omics research in psychiatry, highlighting methodological innovations, integrative strategies, and translational potential for biomarker discovery and clinical implementation. By synthesizing data across diverse molecular layers, multi-omics approaches enable a systems-level view of psychiatric disorders as multifactorial entities shaped by molecular, cellular, environmental, and neurocircuitry interactions. Despite promising advances in diagnostic accuracy and personalized treatment, significant barriers persist, including data heterogeneity, analytical complexity, and the translational gap between molecular signatures and clinical phenotypes. This review systematically explores the contributions of individual omics domains, emerging frameworks for multimodal data integration, the role of systems biology and network-based models, and the impact of large-scale consortia in driving clinical translation.]]> Wed, 31 Dec 1969 19:00:00 EST : a computational suite for DNA methylation sequencing data analysis. Loyfer N, Rosenski J, Kaplan T
Life Sci Alliance (Apr 2026)

Next-generation methylation-aware sequencing of DNA sheds light on the fundamental role of methylation in cellular function in health and disease, increasing the number of covered CpG sites from hundreds of thousands in previous array-based approaches to tens of millions across the whole genome. While array-based approaches are limited to single-CpG resolution, next-generation sequencing allows for a more detailed, single-molecule fragment-level analysis; however, existing tools to fully use this capability are not yet well developed. Here, we present , an extensive computational suite tailored for methylation sequencing data. allows fast access and ultracompact anonymized representation of high-throughput methylome data, obtained through various library preparation and sequencing methods, with a custom epiread file format achieving a compression factor of over 100x from the input BAM file. In addition, contains state-of-the-art algorithms for genomic segmentation, biomarker identification, genetic and epigenetic data integration, and more. offers fragment-level analysis and informative visualizations, across multiple genomic regions and samples.]]> Wed, 31 Dec 1969 19:00:00 EST CRISPR 2.0: Expanding the genome engineering Toolbox for epigenetics, RNA editing, and molecular diagnostics. Pradhan K, Anoop S
Gene (Feb 2026)

Non-canonical CRISPR systems adaptation has led to genome editing through nucleases, and the development of transcriptional and epigenetic regulation, transcriptome editing, and molecular diagnostics has resulted in a diversified set of tools-CRISPR 2.0. In this review, the author summarizes the mechanisms and recent engineering advances of (i) dCas9-based epigenetic effectors, (ii) RNA-targeting Cas13 systems and engineered RNA editors, (iii) DNA base editors and prime editors, and (iv) CRISPR-powered diagnostic platforms and their translational readiness. There is a critical comparison of the various approaches (e.g., RNAi/ASO versus Cas13-based methods; base editing versus prime editing) along with practical translational considerations such as delivery technologies, safety (off-target/edit windows, mosaicism), and regulatory pathways which are evaluated. Three concise case studies refer to map laboratory evidence to clinical or near-clinical outcomes and the ethical and governance discussion is widened to include global access, intellectual property and equity in deployment. Finally, the authors classify technologies according to their level of readiness - diagnostics and some ex-vivo therapeutic approaches are already in or very close to clinical use, chosen in-vivo editing methods are undergoing early trials, and AI-assisted nuclease design is still mostly theoretical but is getting better fast. This comprehensive viewpoint is intended to help researchers and physicians understand which CRISPR tools are most likely to be translated soon and where more validation is required.]]> Wed, 31 Dec 1969 19:00:00 EST Synergistic integration of clinical and multi-omics data for early MCI diagnosis using an attention-based graph fusion network. Yu S, Zhao J, Ouyang J, Wang X, Kou P, Zhu K, Liu P
J Neurosci Methods (Apr 2026)

Mild cognitive impairment (MCI), a precursor to Alzheimer's disease (AD), requires precise early diagnosis. Single-omics approaches often miss disease complexity, motivating integrative and interpretable solutions.]]> Wed, 31 Dec 1969 19:00:00 EST High-Grade Serous Ovarian Carcinoma in the Genomics Era: Current Applications, Challenges and Future Directions. Lewis ME, Caricato C, Roberts HL, Ganesan S, Seksaf NA, Maniati E, Sideris M
Int J Mol Sci (Feb 2026)

High-grade serous ovarian carcinoma (HGSOC) is characterised by profound genomic instability and limited durable responses to standard therapy, leading to poor prognosis. The use of next-generation sequencing technologies has improved understanding of its molecular landscape, revealing consistent Tumour Protein p53 () mutations, homologous recombination defects, pathway alterations, and epigenetic dysregulation. Such genomic profiling now underpins the classification criteria between the ovarian cancer subtypes described by the Cancer Genome Atlas. Widespread chromosomal instability and pathogenic variants in multiple genes distinguish HGSOC from other subtypes of ovarian cancer and, further, from low-grade serous ovarian cancer. Importantly, the new-found understanding of the genomic landscape of HGSOC guides the use of platinum-based chemotherapies and Poly(ADP-ribose) Polymerase (PARP) inhibitors, with homologous recombination deficiency emerging as a cancer vulnerability that enhances treatment response. A combined multi-omics approach integrates transcriptomics, proteomics, metabolomics, and epigenomics to further the understanding of the characteristics, therapeutic targets and treatment resistance within HGSOC. Despite these advances, major challenges persist, including intratumoural heterogeneity and the poor diversity of genomic datasets. Artificial Intelligence (AI) technology, Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing, neoantigen-guided immunotherapy and ovarian cancer vaccination indicate a promising future for genomics-guided interventions and support the integration of genomics within multi-omic approaches to improve HGSOC outcomes.]]> Wed, 31 Dec 1969 19:00:00 EST âfolate axis as a modulator of the epigenetic landscape in autoimmune diseases (Review). Navarro-RodrÃguez PM, Bajeca-Serrano RF, Turrubiates-HernÃ¡ndez FJ, Ceja-GÃ¡lvez HR, HernÃ¡ndez-Bello J, HernÃ¡ndez-RamÃrez CO, RamÃrez-de Los Santos S, MuÃ±oz-Valle JF
Int J Mol Med (Mar 2026)

The oneâcarbon metabolism pathway, regulated by the methylenetetrahydrofolate reductase (MTHFR) enzyme, represents a key nexus where genetic predisposition and nutrient status converge to shape the epigenetic landscape of autoimmune diseases. The objective of the present review is to synthesize evidence of how the âfolate axis drives epigenomic patterns in these conditions. One of the main diseases involved is rheumatoid arthritis, where drugânaÃ¯ve patients show Tâcell and synovial hypomethylation with cytokineâdriven DNMT suppression, a process aggravated by reduced folate availability and polymorphisms that constrain Sâadenosylmethionine supply. Similarly, in systemic lupus erythematosus, CD4 T cells exhibit global hypomethylation with an interferonâskewed signature (such as ), associated with impaired activity and a folateâdependent SAM:SAH imbalance that further diminishes DNMT function. Finally, in celiac disease, intestinal differential methylation, including LINEâ1 hypomethylation, is observed, driven by glutenâinduced villous atrophy and folate malabsorption. Overall, impaired oneâcarbon metabolism and âdependent methylation capacity may be key determinants of epigenomic dysfunction underlying autoimmune disease and its clinical severity.17.]]> Wed, 31 Dec 1969 19:00:00 EST Melatonin-enabled omics: understanding plant responses to single and combined abiotic stresses for climate-smart agriculture. Raza A, Li Y, Charagh S, Guo C, Zhao M, Hu Z
GM Crops Food (Dec 2026)

Climate change-driven single and combined abiotic stresses pose escalating threats to sustainable, climate-smart agriculture and global food security. Melatonin (MLT, a powerful plant biostimulant) has established noteworthy potential in improving stress tolerance by regulating diverse physiological, biochemical, and molecular responses. Therefore, this review delivers a comprehensive synopsis of MLT-enabled omics responses across genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, and microbiomics levels that collectively regulate plant adaptation to multiple abiotic stresses. We also highlight the crosstalk between these omics layers and the power of integrated multi-omics (panomics) approaches to harness the complex regulatory networks underlying MLT-enabled stress tolerance. Lastly, we argue for translating these omics insights into actionable strategies through advanced genetic engineering and synthetic biology platforms to develop MLT-enabled, stress-smart crop plants.]]> Wed, 31 Dec 1969 19:00:00 EST Computational methods for spatial multi-omics integration. Geng A, Cui C, Luo Z, Xu J, Meng Y, Cui F, Wei L, Zou Q, Zhang Z
Biotechnol Adv (2026)

The rapid development of spatial multi-omics technologies has enabled the simultaneous acquisition of transcriptomic, proteomic, and epigenomic information from the same tissue section. However, substantial differences in distributional properties, data dimensionality, and noise levels across modalities, together with the inherent sparsity and incompleteness of spatial information, pose major challenges for data integration and modeling. In recent years, deep learning-based spatial multi-omics integration algorithms have emerged rapidly, offering new approaches for constructing unified latent representations and achieving cross-modal fusion. In this review, we systematically summarize existing spatial multi-omics integration methods for the first time, categorizing and comparing them from two perspectives. We not only systematically surveyed the datasets employed by these methods, but also highlighted the key downstream analytical tasks they support, and further summarized the major challenges currently faced in spatial multi-omics integration research. Furthermore, we compare the strengths and limitations of different approaches to assist researchers in selecting appropriate methods more efficiently, thereby advancing the application of spatial multi-omics in uncovering multilayer regulatory mechanisms of tissue microenvironments and disease processes.]]> Wed, 31 Dec 1969 19:00:00 EST A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling. Van den Berge K, Bakalar D, Chou HJ, Kunda D, Risso D, Street K, Purdom E, Dudoit S, Ngai J, Heavner W
Stem Cell Reports (Feb 2026)

The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration in response to injury. In this study, we used single-cell sequencing to identify transcriptional and epigenetic processes involved in determining olfactory epithelial stem cell fate during injury-induced regeneration. By combining gene expression and accessible chromatin profiles of individual lineage-traced olfactory stem cells, we identified transcriptional heterogeneity among activated stem cells at a stage when cell fates are being specified. We further identified a subset of resting cells that appears poised for activation, characterized by accessible chromatin around silent genes prior to their expression in response to injury. These results provide evidence for a latent activated stem cell state in which a subset of quiescent olfactory epithelial stem cells are epigenetically primed to support injury-induced regeneration.]]> Wed, 31 Dec 1969 19:00:00 EST Erythropoietin Expression and Regulation: Piecing Together Known Mechanisms and Emerging Insights. Idriss S, Hoogewijs D, Girodon F, Gardie B
Am J Hematol (Mar 2026)

Erythropoietin (EPO) is a circulating glycoprotein hormone essential for red blood cell production. The history of EPO stretches from early observations of hypoxia in the mid-19th century to its gene cloning and the clinical use of recombinant forms. Structurally, EPO's extensive glycosylation shapes stability, receptor binding, and therapeutic potential, inspiring engineered analogs with distinct pharmacokinetics. Developmentally, EPO expression shifts from embryonic neural crest and fetal hepatocytes to renal interstitial fibroblasts after birth. EPO gene regulation integrates hypoxia-inducible factors, transcriptional repressors, enhancers, with HIF-2Î± as the principal activator, and post-translational mechanisms. Recent findings reveal genetic variants within the EPO gene in patients with erythrocytosis. Isoelectric focusing profiles of EPO in these patients was similar to the hepatic-derived EPO profiles in premature newborns, highlighting a dynamic and context-dependent regulation. These findings suggest that reactivation of EPO expression in the liver could be therapeutically valuable, given that hepatic-derived EPO exhibits enhanced activity. Clinically, erythropoiesis-stimulating agents transformed anemia management but raised safety concerns, leading to refined guidelines. The recent introduction of hypoxia-inducible factor prolyl hydroxylase inhibitors represents a new strategy that restores endogenous EPO production and coordinates iron metabolism through transient HIF stabilization. Outstanding challenges include the absence of faithful human EPO-producing cell models and incomplete understanding of the full molecular mechanisms controlling EPO expression and production. Combining insights from developmental biology, genetics, and epigenomics may open new avenues for therapies targeting disorders of erythropoiesis and oxygen homeostasis.]]> Wed, 31 Dec 1969 19:00:00 EST CentriVision: An integrated platform for multiscale centromere analysis in plants. Lan MF, Wang XY, Zhang XC
Plant Commun (Feb 2026)

Centromeres are essential for accurate chromosome segregation and genome stability; with the advent of telomere-to-telomere genome assemblies, they have become central targets of genome-wide studies. Here, we present CentriVision, a modular bioinformatics platform that integrates candidate centromere identification, structural similarity assessment, DNA repeat unit decomposition, and a framework for exploring potential relationships between single-nucleotide conservation and functional features. CentriVision provides a comprehensive suite of analytical tools, including edit-distance dot plots, intra-segment heatmaps, kilobase-scale mini-dot plots, repeat monomer scanning with conserved-site visualization, and satellite DNA expansion-divergence estimation, all of which can be seamlessly integrated with CENH3 chromatin immunoprecipitation sequencing (ChIP-seq) data. When applied to representative plant species, CentriVision achieved high predictive accuracy and revealed diverse organizational patterns. Arabidopsis thaliana centromeres are primarily composed of 178-188-bp repeats interspersed with rarer â¼502-bp variants that exhibit pronounced sequence conservation but only background CENH3-ChIP signal, suggesting that these elements represent pre-centromeric sequences overlooked in earlier studies. Oryza sativa contains two dominant classes of centromeric repeats rather than the single class previously reported. In contrast, Zea mays exhibits strongly biased expansion toward the evolution of a single dominant repeat unit, reflecting a distinct evolutionary strategy of centromere reconstruction, whereas Papaver setigerum displays a notable three-layered nested repeat structure. Integration of repeat sequence divergence with CENH3 binding further revealed lineage-specific evolutionary trajectories of centromere specification. Collectively, these findings advance our understanding of centromere structure and function. CentriVision offers a reproducible, scalable, and user-friendly framework that quantitatively links repeat evolution, structural variation, and functional epigenomics, providing new insights into the architecture and diversification of plant centromeres.]]> Wed, 31 Dec 1969 19:00:00 EST Emerging Cardiovascular Risk Factors in Chronic Kidney Disease in the "Omics" Era: Gut and Beyond. Sumida K, Kovesdy CP
Mayo Clin Proc (Feb 2026)

Chronic kidney disease (CKD) is a significant public health problem worldwide because of its increasing prevalence and strong association with poor outcomes. In particular, patients with CKD have a disproportionately high risk of premature cardiovascular morbidity and mortality, which increases exponentially as CKD progresses to end-stage kidney disease. Whereas traditional cardiovascular risk factors are highly prevalent in patients with CKD, several nontraditional risk factors, such as inflammation, also come into play in cardiovascular diseases, especially in advanced CKD stages. Furthermore, recent advances in high-throughput "omics" technologies and sophisticated bioinformatics and modeling approaches have identified an increasing number of novel cardiovascular risk factors in CKD across various omics levels, including the microbiomics, proteomics, metabolomics, transcriptomics, epigenomics, and genomics. These molecular markers identified from high-dimensional omics data have not only advanced our understanding of cardiovascular disease mechanisms in CKD but also facilitated the development of target-driven therapeutic strategies to reduce excess cardiovascular morbidity and mortality in this population. However, significant challenges to their research and clinical applications remain, including the high cost of multiomics profiling and the complexity of assessing comparative cardiovascular risk between multidimensional omics data across different stages of CKD. In this article, based on a comprehensive literature search on PubMed and Google Scholar, we review emerging cardiovascular risk factors in the era of integrated multidimensional omics approaches, with an emphasis on recent findings from microbiomics, and discuss their prognostic implications, current challenges, and future directions in the context of translational epidemiology toward improving cardiovascular outcomes in patients with CKD.]]> Wed, 31 Dec 1969 19:00:00 EST Genome-wide profiling of salivary promoter-region DNA methylationÂ in periodontitis: the TromsÃ¸ study. Petrenya N, JÃ¶nsson B, Hadler-Olsen E, Larsson L, Flatberg A, BeisvÃ¥g V, Holde GE, Zykova SN, Asa'ad F
BMC Med Genomics (Feb 2026)

]]> Wed, 31 Dec 1969 19:00:00 EST Unraveling the Tapestry: Lessons from multiomics and spatial biology in hepatocellular cancer. Massoudi D, Srivastava A, Dhanasekaran R
Hepatology (Feb 2026)

Hepatocellular carcinoma (HCC) is a biologically and clinically heterogeneous cancer in which the spatial organization of the tumor microenvironment dictates progression, immune escape, and therapeutic response. Traditional genomic and transcriptomic profiling have revealed key molecular pathways, yet they do not capture the spatial relationships that govern tumor-immune-stromal interactions. Spatial omics technologies now bridge this gap, allowing molecular profiling within intact tissue architecture and revealing how cellular neighborhoods, immune barriers, and stromal niches shape tumor behavior. In this review, we summarize recent advances in technologies like spatial transcriptomics, proteomics, genomics, epigenomics, and metabolomics as applied to HCC. We discuss how these technologies have illuminated the spatial dynamics of the invasive margin, macrophage and fibroblast niches, and immune evasion, identifying both prognostic and predictive biomarkers. We further highlight how spatially resolved analyses have uncovered previously unrecognized axes of communication between cancer cells and key stromal and parenchymal populations that were not apparent from bulk or single-cell molecular analyses alone. These spatially mapped ligand-receptor networks reveal coordinated signaling circuits that define targetable mechanisms of resistance and progression within the microenvironment. Finally, we explore the translational implications where spatial signatures may guide risk stratification, treatment selection, and clinical trial design. By integrating spatial architecture with molecular function, spatial omics is transforming our understanding of liver cancer biology and paving the way for spatially informed precision oncology.]]> Wed, 31 Dec 1969 19:00:00 EST A New Complexity Layer: DNA Methylation and the Predictive Impact of Epigenetic Tests. Ladisa G, Montenegro F, Picerno A, Nigro A, Cicirelli A, Stasi A, Fiorentino M, Pontrelli P, Gesualdo L, Sallustio F
Int J Mol Sci (Feb 2026)

The increasing complexity of disease mechanisms challenges accurate diagnosis, prevention, and early risk stratification. Beyond genetic predisposition, epigenetic regulation-particularly DNA methylation-represents a dynamic molecular interface linking environmental exposures, metabolic imbalance, inflammation, and disease development. DNA methylation is the most extensively studied epigenetic mechanism and plays a central role in controlling gene expression across physiological and pathological conditions. In this review, we provide an integrated overview of DNA methylation biology and its involvement in inflammatory, metabolic, and oncological diseases, with a specific focus on pathways related to chronic inflammation and oxidative stress. We summarize evidence demonstrating how aberrant methylation patterns contribute to disease initiation and progression, highlighting recurrent epigenetic signatures affecting key regulatory genes. In parallel, we discuss current and emerging technologies for DNA methylation analysis, ranging from targeted methylation-specific assays to next-generation sequencing-based approaches, including nanopore adaptive sampling. Finally, we explore the translational potential of DNA methylation-based tests as predictive and preventive tools, emphasizing their ability to identify disease-associated molecular alterations before clinical onset. Overall, this evidence supports the integration of epigenetic profiling into future precision medicine strategies aimed at early risk assessment, prognosis refinement, and personalized prevention.]]> Wed, 31 Dec 1969 19:00:00 EST A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. KrÃ¤tschmer I, Robinson MR
Genetics (Feb 2026)

An individual's phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents' DNA. Here, we derive how the genetic variance within a population is changed under the influence of indirect maternal, paternal and parent-of-origin effects under random mating. We also consider indirect effects of a sibling, in particular how the genetic variance is altered when looking at the phenotypic difference between two siblings. The calculations are then extended to include assortative mating (AM), which alters the variance by inducing increased homozygosity and correlations within and across loci. AM likely leads to covariance of parental genetic effects, a measure of the similarity of parents in the indirect effects they have on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait AM. Our theory shows how the resemblance among relatives increases under both AM, indirect and parent-of-origin effects. When our model is used to predict correlations among relatives in human height, we find that explaining the patterns observed in real data requires both indirect genetic effects and assortative mating. The degree to which direct, indirect and epigenetic effects shape the phenotypic variance of complex traits remains an open question that requires large-scale family data to be resolved.]]> Wed, 31 Dec 1969 19:00:00 EST Divergent epigenetic profile underlie pubertal disorders in MKRN3-associated central precocious puberty and Prader-Willi syndrome: insights from a frameshift variant. Jin YY, Wang X, Yang L, Mu J, Luo FH
World J Pediatr (Feb 2026)

MKRN3 gene loss-of-function mutations cause central precocious puberty (CPP), whereas its deletion in Prader-Willi syndrome (PWS) paradoxically leads to hypogonadism. The mechanistic basis for these opposing reproductive phenotypes remains largely unclear.]]> Wed, 31 Dec 1969 19:00:00 EST