'; ?> 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 Tue, 24 Feb 2026 04:47:48 EST Tue, 24 Feb 2026 04:47:48 EST jirtle@radonc.duke.edu james001@jirtle.com Hyperglycaemia-induced metabolic stress and epigenetic imprinting in the inflammatory pathogenesis of diabetic neuropathy. Razi FB, Ashraf H, Singhal S, Qamar Z, Moin S
Diabetes Res Clin Pract (Feb 2026)

Diabetic neuropathy (DN), a major microvascular complication of diabetes mellitus, results from a complex interplay among oxidative stress, inflammation, and persistent epigenetic modifications. Hyperglycemia-induced mitochondrial dysfunction increases reactive oxygen species (ROS), which activate redox-sensitive inflammatory cascades, including NF-κB, JAK/STAT, and the NLRP3 inflammasome. These pathways amplify cytokine release and neuronal sensitisation, while reciprocal feedback between ROS and inflammation mediated by Nrf2 suppression further perpetuates nerve damage. Damage-associated molecular patterns (DAMPs), including HMGB1, S100A8/A9, mitochondrial DNA, and extracellular ATP, act as key amplifiers of neuroinflammation. By engaging receptors such as RAGE, Toll-like receptors (TLRs), and NOD-like receptors (NLRs), particularly NLRP3, these DAMPs trigger glial activation and nociceptive signalling, contributing to axonal degeneration and pain hypersensitivity in DN. Epigenetic dysregulation, including DNA methylation drift, histone modification imbalance, and aberrant non-coding RNA expression, constitutes a critical mechanism underlying metabolic memory, wherein prior hyperglycemic exposure leaves lasting molecular imprints. Persistent histone acetylation (H3K9ac), altered methylation (H3K4me1/Set7, H3K9me3/SUV39H1), and stable 5-methylcytosine patterns sustain inflammatory and oxidative pathways, even after glucose normalisation. Therapeutically, DNMT and HDAC inhibitors, miRNA modulators, and agents targeting RAGE/TLR4/NLRP3 pathways show promise in reversing these molecular imprints. Antioxidants and anti-inflammatory compounds with epigenetic effects further represent potential disease-modifying strategies. Future research must focus on longitudinal human studies, nerve-specific epigenomics, and multi-omics integration to enable personalised, mechanism-based therapy for DN. Understanding the interdependence of ROS, DAMPs, and epigenetic memory is key to breaking the cycle of chronic neuroinflammation and neuronal injury.]]> Wed, 31 Dec 1969 19:00:00 EST Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents. Nishitani S, Fujisawa TX, Takiguchi S, Yao A, Murata K, Hiraoka D, Mizuno Y, Ochiai K, Kawata NYS, Makita K, Saito DN, Mizushima S, Suzuki S, Kurata S, Ishiuchi N, Taniyama D, Nakao N, Namera A, Okazawa H, Nagao M, Tomoda A
Mol Psychiatry (Mar 2026)

Child maltreatment (CM) is associated with adverse physical, psychological, and neurodevelopmental outcomes later in life. Epigenetic modifications, particularly DNA methylation, have been proposed as potential mechanisms underlying these long-term effects. To identify robust CM-associated methylation signatures, we conducted epigenome-wide analyses across three independent cohorts: judicial autopsy cases (CM:11, Controls:7), toddlers shortly after social intervention (CM:36, Controls:49), and adolescents who underwent brain MRI (CM:61, Controls:62). Each cohort was analyzed separately, followed by a meta-analysis to identify common methylation sites associated with CM exposure. The meta-analysis identified four significant CpG sites located within the ATE1, SERPINB9P1, CHST11, and FOXP1 genes. Among these, methylation of FOXP1 was consistently associated with structural brain alterations, including increased gray matter volume (GMV) in the orbitofrontal cortex (OFrC) and middle/posterior cingulate gyrus (MPCG), and decreased GMV in the occipital fusiform gyrus (OFuG). These brain regions are implicated in emotional regulation, memory retrieval, and social cognition, suggesting a potential neurobiological mechanism linking CM to later psychopathology. Furthermore, methylation risk scores (MRS) derived from these four CpGs successfully discriminated individuals who experienced early-life adversity in an independent validation dataset, achieving an area under the receiver operating characteristic curve (AUC) of 0.672, highlighting their potential utility as biomarkers. Gene ontology and pathway analyses revealed enrichment of cholinergic and glutamatergic synaptic transmission pathways, supporting their involvement in traumatic memory formation. Our findings provide novel insights into the epigenetic mechanisms underlying CM and identify potential biomarkers for early detection, prevention, and therapeutic intervention, ultimately contributing to breaking the intergenerational cycle of maltreatment.]]> Wed, 31 Dec 1969 19:00:00 EST A cell type enrichment analysis tool for brain DNA methylation data (CEAM). Müller 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 Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis. Artes MH, Iacobucci S, Barallobre MJ, Carballeira P, Garcia-Cajide M, Pérez-Venteo A, Padilla N, Viegas BS, Díaz-Vásquez A, Nacht AS, Vicent GP, Arbonés ML, de la Cruz X, Nieto M, Agell N, Mauvezin C, Martínez-Balbás MA
EMBO Rep (Feb 2026)

Progenitor proliferation during neurodevelopment requires tight coordination of epigenetic regulation and metabolism. However, the crosstalk between these processes remains poorly understood. To investigate this, we examine in neural stem cells the role of PHF8, a histone demethylase whose mutations are linked to Siderius-Hamel syndrome, a rare neurodevelopmental disorder. Through an integrated multi-omics approach - combining transcriptomics, epigenomics, and metabolomics - we identify PHF8 as a key driver of the serine biosynthesis pathway, safeguarding the intracellular serine pool essential for neural progenitor proliferation. PHF8 fine-tunes chromatin accessibility at promoters of metabolic genes, ensuring their activation during development. Loss of PHF8 disrupts amino acid metabolism, blocks autophagy, and hinders vesicle formation. Ultimately PHF8 depletion leads to replication defects, DNA damage, and proliferation arrest. In vivo, PHF8 deficiency in mouse embryos halts neurogenesis, progenitor expansion, and neuron generation in the developing brain. These findings identify PHF8 as a key molecular link between chromatin regulation, metabolic control, and neural development, offering new insights into the epigenetic basis of neurodevelopmental and metabolic disorders.]]> Wed, 31 Dec 1969 19:00:00 EST DNA methylation-mediated alterations in Copper(I/II) redox equilibrium underlie lead-induced neurotoxicity. Hu J, Wang WX
Environ Pollut (Apr 2026)

Lead (Pb), a ubiquitous environmental toxin, poses significant risks to central nervous system health, primarily by disrupting essential metal homeostasis in the brain. While epigenetic regulation and proteomic expression are significantly affected by Pb, its specific molecular impact on copper (Cu) redox states remains poorly understood. This study systematically investigated the molecular mechanisms underlying Pb-induced neurotoxicity in SH-SY5Y cells through integrated epigenomics and proteomics analysis. DNA methylation analysis revealed 141,357 differentially methylated regions (DMRs), primarily in CpG sites, with 62.6 % hypermethylated and 37.4 % hypomethylated. These DMRs were enriched in genes associated with critical processes such as metal ion binding, cell cycle regulation, and nervous system development. Promoter-specific methylation changes were notably pronounced, impacting pathways linked to neurodegenerative diseases, including Alzheimer's disease. Proteomic analysis identified 740 differentially expressed proteins (DEPs), with 366 upregulated and 374 downregulated in Pb-treated cells. Functional annotation revealed significant enrichment of DEPs in mitochondria, where Pb exposure disrupted processes related to oxidative phosphorylation, ion transport, and transmembrane processes. These proteomic changes aligned with the observed epigenetic modifications, reinforcing the role of Pb in impairing neuronal function via its effects on cellular energy metabolism and metal ion dynamics. Notably, Pb exposure disrupted Cu redox transitions between Cu(I) and Cu(II) as well as glutathione (GSH) activity, underscoring its impact on cellular metal homeostasis regulation and oxidative imbalance. In summary, this study provides a comprehensive view of how Pb exposure alters epigenetic and proteomic landscapes, disrupting key biological processes and pathways essential for neuronal health.]]> Wed, 31 Dec 1969 19:00:00 EST Oxidized LDL Induces Pro-Inflammatory Transcriptomic and Epigenomic Responses in Human CD4 T Cells. Brown TA, Chalisey A, Jiang J, O'Callaghan CA
FASEB J (Feb 2026)

Elevated circulating low-density lipoprotein cholesterol (LDL-C) is a key risk factor for coronary artery disease (CAD). The pathogenesis of CAD is multifactorial, driven by heritable and lifestyle-related risk factors. Although CD4 T cells are one of the main cell types in atherosclerotic lesions, their interaction with atherogenic oxidized LDL (ox-LDL) remains poorly understood. Therefore, we sought to characterize the transcriptomic and epigenomic consequences of ox-LDL on activated human CD4 T cells. We find that ox-LDL causes a shift towards a pro-inflammatory, cytokine-producing CD4 T cell transcriptomic state. Concurrently, ox-LDL induces genome-wide changes in chromatin accessibility, notably in promoter regions. By integrating our multiomic data, we identify the NRF1 and SP1 transcription factors as likely mediators of ox-LDL-induced changes in gene expression. In contrast, the influence of AP-1 related factors over CD4 T cell gene expression decreases following ox-LDL stimulation. We leveraged our multiomic data to investigate the disease relevance of ox-LDL exposure, by investigating genomic locations where CAD-associated single nucleotide polymorphisms were found within dynamic ox-LDL-regulated accessible chromatin regions. Together, we demonstrate a disease-relevant role for ox-LDL in atherogenic conditioning of CD4 T cells. Understanding such cell-type specific interactions with CAD risk factors may facilitate the development of targeted therapies for CAD.]]> 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 Noninvasive diagnosis of colorectal adenoma: The emerging potential of blood-based biomarkers. Qi CY, Wang R, Wang JW, Ye GL, Yang P, Zhou YP
World J Gastroenterol (Feb 2026)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related death globally. Most CRCs arise from colorectal adenomas (CRAs), particularly advanced adenomas, which are recognized as critical precancerous lesions. Early detection and intervention at the adenoma stage are essential for alleviating the global disease burden of CRC. However, conventional screening methods such as colonoscopy are invasive and have poor compliance, underscoring the urgent need for efficient, noninvasive diagnostic alternatives. Blood-based biomarkers have gained substantial attention because of their accessibility, reproducibility, and potential for early detection. Advances in multiomics technologies including proteomics, metabolomics, transcriptomics, and epigenomics have led to the identification of numerous plasma- and serum-derived biomarkers. These include noncoding RNAs (, microRNAs, circular RNAs, PIWI-interacting RNAs), DNA methylation signatures, disease-specific proteins, and metabolic profiles. Moreover, emerging platforms such as liquid biopsy, extracellular vesicle profiling, and machine learning further expand the landscape of early CRA detection. The integration of multiomics data holds promise for substantially increasing the sensitivity and specificity of early adenoma detection, offering a transformative framework for precise CRC screening and risk stratification.]]> 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 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 Epigenetic Clocks of Biological Aging and Risk of Incident Mild Cognitive Impairment and Dementia: The Women's Health Initiative Memory Study. Nguyen S, Lu AT, Horvath S, Espeland MA, Rapp SR, Maihofer AX, Nievergelt CM, LaCroix AZ, McEvoy LK, Resnick SM, Beckman K, Shadyab AH
Aging Cell (Mar 2026)

Aging is the strongest risk factor for dementia; however, few studies have examined the association of biological aging with incident dementia. We analyzed 6069 cognitively unimpaired women (mean age = 70.0 ± 3.8 years) in the Women's Health Initiative Memory Study to examine the association of accelerated biological aging, measured with second and third-generation epigenetic clocks (AgeAccelPheno and AgeAccelGrim2, and DunedinPACE, respectively) with incident mild cognitive impairment (MCI) and probable dementia. Multivariable Cox proportional hazards models adjusted for age, education, race, ethnicity, smoking, hormone therapy regimen, physical activity, body mass index, and estimated white blood cell counts. For comparison, we also examined first-generation epigenetic clocks (AgeAccelHorvath; AgeAccelHannum). We evaluated effect modification by age, race/ethnicity, hormone therapy regimen, menopause type (natural vs. surgical), and APOE ε4 carriage. There were 1307 incident MCI or probable dementia events over a median follow-up of 9.3 (25th percentile = 6.1, 75th percentile = 16.1) years. The adjusted HRs (95% CI; p-value) for incident MCI/probable dementia per one-standard deviation increment were 1.07 (1.01-1.15; p = 0.03) for DunedinPACE, 1.11 (1.02-1.20; p = 0.01) for AgeAccelGrim2, and 1.01 (0.95-1.07; p = 0.74) for AgeAccelPheno. Only AgeAccelGrim2 remained significant under the Bonferroni-corrected threshold for significance (p < 0.02). Other epigenetic clocks were not associated with incident MCI/probable dementia. There was no effect modification in most subgroup analyses (p-interaction ≥ 0.05). In this cohort study of older women, accelerated biological aging measured by AgeAccelGrim2 was associated with higher risk of incident MCI/probable dementia. These findings provide evidence linking epigenetic biomarkers of biological aging with MCI and dementia development, independent of chronological age.]]> Wed, 31 Dec 1969 19:00:00 EST Maternal O-GlcNAc Transferase Is Required for the Asymmetry of Epigenetic Modifications in Mouse Zygotes. Wang H, Liu D, Honda S, Ikeda S
FASEB J (Feb 2026)

After fertilization in mammals, there is an epigenetic asymmetry reflected by differences in DNA demethylation and histone modifications between female and male pronuclei (FPN and MPN, respectively). Based on its expression level and amount, we investigated the role of maternal O-GlcNAc transferase (OGT), a key enzyme mediating O-GlcNAcylation, in regulating this asymmetry. By using a specific small-molecule inhibitor and small interfering RNA (siRNA)-mediated knockdown of OGT during oocyte maturation in mice, we evaluated the downstream effects on epigenetic modifications and early developmental capability. OGT inhibition significantly reduced fertilization rates and led to developmental arrest at the zygote or 2-cell stage, whereas the siRNA-mediated decrease of Ogt mRNA had less or no significant effect on preimplantation development. Immunostaining analyses revealed that OGT inhibition reduced 5-hydroxymethylcytosine levels in MPN, attributed to a reduction in Tet methylcytosine dioxygenase 3. In contrast, FPN showed delayed epigenetic changes, with the loss of 5-methylcytosine protection mediated by H3K9me2. Moreover, OGT inhibition increased histone methylation levels in MPN and disrupted epigenetic and size asymmetry between FPN and MPN. These alterations suggest that maternal OGT regulates multiple layers of epigenetic reprogramming in early zygotes. Taken together, these findings suggest that maternal OGT is essential for maintaining epigenetic asymmetry between parental pronuclei, primarily by modulating DNA demethylation and histone methylation in MPN.]]> Wed, 31 Dec 1969 19:00:00 EST ‑folate axis as a modulator of the epigenetic landscape in autoimmune diseases (Review). Navarro-Rodríguez PM, Bajeca-Serrano RF, Turrubiates-Hernández FJ, Ceja-Gálvez HR, Hernández-Bello J, Hernández-Ramírez CO, Ramírez-de Los Santos S, Muñoz-Valle JF
Int J Mol Med (Mar 2026)

The one‑carbon 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 ‑folate axis drives epigenomic patterns in these conditions. One of the main diseases involved is rheumatoid arthritis, where drug‑naïve patients show T‑cell and synovial hypomethylation with cytokine‑driven DNMT suppression, a process aggravated by reduced folate availability and polymorphisms that constrain S‑adenosylmethionine supply. Similarly, in systemic lupus erythematosus, CD4 T cells exhibit global hypomethylation with an interferon‑skewed signature (such as ), associated with impaired activity and a folate‑dependent SAM:SAH imbalance that further diminishes DNMT function. Finally, in celiac disease, intestinal differential methylation, including LINE‑1 hypomethylation, is observed, driven by gluten‑induced villous atrophy and folate malabsorption. Overall, impaired one‑carbon metabolism and ‑dependent 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 How Imprinted Genes Shape Nurturing Behaviours and Neural Circuits. Jones RA, Higgs MJ, Isles AR
Brain Behav Evol (Feb 2026)

Genomic imprinting is an epigenetic phenomenon that, in animals, is found only in placental mammals and, to a lesser extent, marsupials. Broadly, differential epigenetic marking of the genomes during gametogenesis leads to parent-of-origin specific silencing of imprinted genes, with some solely expressed from the maternally inherited allele, and others solely expressed from the paternally inherited allele. From an evolutionary perspective, genomic imprinting is fascinating, as it appears to negate the benefits of diploidy and yet correct expression of imprinted genes essential for normal development and function. Genomic imprinting influences a number of key mammalian physiologies, including brain and behaviour. Imprinted gene expression is particularly enriched in the hypothalamus and the wider defined parental care circuitry. We provide an overview of this here and detail the role imprinted genes play shaping nurturing and parental behaviours.]]> 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 Advances in spatial omics for the analysis of prostate cancer. Xu J, Wang D, Di X, Liu Y
Anal Bioanal Chem (Feb 2026)

Prostate cancer is one of the most common malignancies in men and is marked by extensive clinical and molecular heterogeneity. Although genomic and transcriptomic studies have revealed recurrent alterations and lineage plasticity, these approaches lack spatial resolution and therefore cannot capture the microenvironmental context that underpins tumor progression and therapeutic resistance. Spatial omics technologies have emerged as transformative tools by integrating high-dimensional molecular profiling with preserved tissue architecture. Advances in spatial transcriptomics, proteomics, epigenomics, and metabolomics now permit the mapping of gene expression, protein signaling, chromatin accessibility, modifications, and folding, along with metabolic gradients at cellular to subcellular resolution. Spatial analysis of prostate cancer has revealed key features of disease progression, including stromal remodeling, immune evasion, lipid metabolic rewiring, and therapy-resistant niches. This review highlights recent spatial omics technologies, their emerging integrative and clinical applications in prostate cancer, and the future challenges in standardization, data integration, and clinical translation.]]> 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-2α 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 Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies. Wu J, Chu SA, Cho J, Movahed-Ezazi M, Galbraith K, Fang CS, Yang Y, Schroff C, Sikkink K, Perez-Arreola M, Van Meter L, Gemus S, Belton JM, Song X, Gurumurthy A, Xiao H, Nardi V, Louissant A, Pillai RK, Song JY, Shasha D, Tsirigos A, Perry A, Brown N, Gindin T, Shao L, Cieslik MP, Kim M, Schmitt AD, Snuderl M, Ryan RJH
Cell Genom (Feb 2026)

Standard techniques for detecting genomic rearrangements in formalin-fixed paraffin-embedded (FFPE) biopsies have important limitations. We performed FFPE-compatible Hi-C on 44 clinical biopsies comprising large B cell lymphomas (n = 18), plasma cell neoplasms (n = 14), and other diverse lymphoid cancers, identifying consistent topological differences between malignant B cell and plasma cell states. Hi-C detected expected oncogene rearrangements at high concordance with fluorescence in situ hybridization (FISH) and supported enhancer hijacking in recurrent rearrangements of BCL2, CCND1, and MYC plus unanticipated variants involving homologous loci. Hi-C identified unanticipated non-coding rearrangements involving PD-1 ligand genes and other loci of potential therapeutic relevance, distinguished between functionally divergent classes of BCL6 rearrangements, and provided topological information supporting interpretation of variant MYC rearrangements. Hi-C revealed disease-selective MYC locus topological features that correlated with disease-selective MYC locus enhancers and rearrangement breakpoint distributions. FFPE-compatible Hi-C detects oncogene rearrangements and their topological consequences at genome-wide scale, finding clinically relevant drivers missed by standard approaches.]]> Wed, 31 Dec 1969 19:00:00 EST Artificial intelligence, machine learning and omic data integration in osteoarthritis. Sharma D
Osteoarthritis Cartilage (Mar 2026)

Artificial intelligence (AI), particularly its subfield of machine learning (ML), offer promising tools for integrating and interpreting high-dimensional omic data to advance our understanding of osteoarthritis (OA), a complex, multifactorial disease. The objective of this review is to summarize recent progress in applying ML approaches to single and integrative multi-omic data in OA and to highlight emerging trends, challenges, and opportunities.]]> Wed, 31 Dec 1969 19:00:00 EST Machine Learning for Predicting Stroke Risk Stratification Using Multiomics Data: Systematic Review. Yoo HY, Shin H, Kim EJ, Son YJ
J Med Internet Res (Feb 2026)

Stroke is a complex, multidimensional disorder influenced by interacting inflammatory, immune, coagulation, endothelial, and metabolic pathways. Single-omics approaches seldom capture this complexity, whereas multiomics techniques provide complementary insights but generate high-dimensional and correlated feature spaces. Machine learning (ML) offers strategies to manage these challenges; however, the predictive accuracy and reproducibility of multiomics-based ML models for stroke remain poorly characterized.]]> Wed, 31 Dec 1969 19:00:00 EST