DNA methylation as an oncogenic driver in breast cancer: Therapeutic targeting via epigenetic reprogramming of DNA methyltransferases.

Non-coding RNAs (ncRNAs), comprising microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are increasingly recognized as central regulators of epigenetic programming in T lymphocytes with critical implications for immune tolerance and autoimmunity. We conducted a systematic review to investigate the influence of non-coding RNAs on DNA methylation, histone modifications, and chromatin accessibility in T cells across diverse autoimmune diseases. The majority of studies identified consistent patterns of dysregulation, including increased expression of miR21, miR148a, and miR155, and decreased expression of miR146a, GAS5, and IL21AS1. These alterations were associated with hypomethylation of proinflammatory gene loci, reduction of repressive histone marks, and increased chromatin accessibility at promoters of genes driving pathogenic T cell responses. Mechanistic data from both human and animal models demonstrated that microRNAs frequently regulate the abundance or activity of DNA methyltransferases and upstream signaling molecules, whereas long non-coding RNAs influence the recruitment or activity of chromatin modifying complexes, serve as scaffolds for transcriptional regulators, or function as competitive endogenous RNAs. Experimental manipulation of these non-coding RNAs attenuated disease-associated epigenetic and functional changes in T cells, supporting a causal role in autoimmune pathogenesis. Collectively, the non-coding RNAs as potential biomarkers of disease activity and as therapeutic targets capable of restoring physiological epigenetic regulation in a cell type specific manner. Future research should prioritize longitudinal and single cell multiomics approaches to delineate the dynamic interactions between non-coding RNAs and the chromatin landscape in order to accelerate the translation of these findings into targeted RNA based interventions for autoimmune diseases. Systematic review registration https://inplasy.com/ , Identifier INPLASY202580041.

Hematopoiesis changes over the lifetime to adapt to the physiology of development, maturation, and aging. Temporal changes in hematopoiesis parallel age-dependent incidences of certain blood diseases. Several heterochronic regulators of hematopoiesis have been identified, but how the master transcription factor (TF) circuitry of definitive hematopoietic stem cells (HSCs) adapts to changes in physiology over the lifespan is unknown. Here, we show that programmed upregulation of expression of the ETS family TF Erg during prenatal to adult maturation is evolutionarily conserved and required for implementation of adult patterns of HSC self-renewal and myeloid, erythroid, and lymphoid differentiation. Erg deficiency maintains fetal transcriptional and epigenetic programs in adulthood, and persistent juvenile phenotypes in Erg haploinsufficient mice are at least in part dependent on deregulation of the fetal-biased factor Hmga2. Overall, we identify a mechanism whereby master HSC TF networks are rewired to specify stage-specific hematopoiesis, a finding directly relevant to age-biased blood diseases.

Chromatin remodeler SATB2 thorough Bmi1/PRC1 activity controls transformation and reprogramming of ph+ B-cell progenitors

Single-cell multi-omics uncovers differentiation-dependent transcriptional programs shaping epigenetic subgroups in AML

Regulation of atrial and ventricular cardiomyocyte identity.

Cold-season programming reinforces the brown fat-cardiometabolic health link.

Chronic restraint stress associations with sperm global DNA hypermethylation: Impacts on male reproductive function in rats.

Understanding and targeting erythroid cell metabolism.

Disclosure: S.E. Khoury: None. E. Morales-Grahl: None. L. Thompson: None. A.C. Gore: None. N.Y. Eldiraoui: None.This study aims to evaluate how early life exposure of rats to endocrine-disrupting chemicals (EDCs) affects development and sexual differentiation of the brain through molecular and epigenetic programming. Our lab and others have shown that EDC exposure affects the hypothalamus in a sex, time, and exposure dependent manner. These effects lead to changes in gene expression related to gonadal steroid hormone signaling in the brain, shifts in pubertal timing, and altered DNA methylation patterns in hypothalamic regions. Current work is addressing effects of EDC exposure on mating behaviors in rats and whether epigenetic modification in brain regions involved in these behaviors underlie any observed physiological changes. In our lab we use NeuroMix, an EDC mixture containing 9 common industrial chemicals at environmentally relevant doses. We expose rats orally to NeuroMix in early postnatal life through feeding of rat dams, during hormone sensitive periods of brain development in the offspring. Brain tissues are collected at postnatal day 1, adolescence, and during early adulthood and bed nucleus of the stria terminalis and preoptic area of the hypothalamus are dissected for Tag-Seq to look at mRNA expression and whole genome bisulfite sequence (WGBS) to assess changes to gene expression and DNA methylation associated with sex differences at these time points. In adulthood, a subset of early adult males are observed in a natural mating environment and number of and latency to mounts, intromission, and ejaculation are counted. A subset of early adult females are tested and recorded in a paced mating paradigm to uncover differences in female typical sexual behaviors due to NeuroMix treatment. The results of these experiments will provide novel insights into the effects of NeuroMix treatment on sexually dimorphic behaviors and brain epigenetics. Supported by NIH R35 ES035024Presentation: Saturday, July 12, 2025

Abstract Disclosure: P. van Houten: None. M. Jaeger: None. P. Changoer: None. L. van Emst: None. W. Mulder: None. I.C. van Engen-van Grunsven: None. M. Bremmers: None. H.J. Bonenkamp: None. J.H. de Wilt: None. W. Hobo: None. M.G. Netea: None. R.T. Netea-Maier: None. Objectives: The prognosis of patients with metastasized and radioactive refractory non-medullary thyroid cancer (NMTC) is poor and treatment options are limited. In NMTC tumors, myeloid cells, such as tumor-associated macrophages, are abundant and have an immunosuppressive and pro-tumoral phenotype. Trained immunity describes a specific epigenetic and metabolic program in innate immune cells that leads to an increased proinflammatory phenotype. The aim of the present study is to assess whether this mechanism can be used to reprogram the myeloid cells, from different bodily compartments, from patients with NMTC and thus whether this could be explored as a new treatment strategy of NMTC patients. Methods: Peripheral blood and bone marrow were obtained from 50 NMTC patients with different NMTC histological forms (36 differentiated and 14 anaplastic NMTC) and 13 healthy volunteers. White blood cell counts and subtypes were measured in whole blood and compared between healthy controls and patients. Peripheral monocytes and CD34-positive bone marrow progenitors from bone marrow were isolated and in these cells trained immunity was induced ex vivo using different stimuli. Subsequently those cells differentiated into macrophages which were restimulated by TLR-agonists to measure cytokine production. Additionally, macrophage phenotype was assessed using flow cytometry. Results: White blood cell counts and percentages of different subtypes were comparable between healthy controls and patients with differentiated NMTC. However, compared to healthy controls and patients with differentiated NMTC, patients with anaplastic NMTC showed significantly higher white blood cell counts, with higher percentages of neutrophils and lower percentages of lymphocytes. In circulating monocytes, trained immunity could be induced with the stimuli β-glucan, BCG and interleukin-4 (IL-4), characterized by an increased production of proinflammatory cytokines IL-6 and TNF after restimulation with either LPS or Pam3Cys. Fold changes in increase in cytokine production after restimulation were comparable between healthy controls, patients with differentiated NMTC and patients with anaplastic NMTC. Flow cytometry showed that β-glucan-, IL-1β- and IL-4-trained stem cells developed into macrophages with lower CD206 and CD163 and higher CD86 expression, markers associated with a less immunosuppressive and more anti-tumoral phenotype. Conclusion: Using our ex vivo model, we show that reprogramming of myeloid progenitor cells from patients with NMTC in our trained immunity setting is possible. This results in macrophages with an increased proinflammatory cytokine production and differentiation towards an anti-tumoral phenotype. This suggests that trained immunity might be explored as a potential novel treatment strategy for patients with aggressive forms of NMTC. Presentation: Sunday, July 13, 2025

Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double-strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Lastly, we successfully combined genetic and epigenetic engineering using orthogonal CRISPR Cas12a-dCas9 systems for targeted chimeric antigen receptor (CAR) knock-in and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR-T cell-mediated in vivo tumor control and survival.

Induced pluripotent stem cells (iPSCs) offer a groundbreaking technology, which has transformed translational research and clinical applications in a wide range of fields, such as regenerative medicine, tissue engineering, cell therapy, disease modeling, developmental biology, etc. iPSCs are derived from terminally differentiated somatic cells by reprogramming the genetic and epigenetic program back to the pluripotent stem cell characteristics. iPSCs are very identical to embryonic stem cells in regards to differentiation into many cell types; however, iPSCs are exempt from the legal or ethical issues. These advantages enable iPSCs to advance the cell therapy and transplantation strategies. Nonetheless, low reprogramming efficiency and the risk for tumorigenicity are still limitations in the application of iPSCs in practice because the usage of the same pluripotency factors in all somatic cell types remains incapable of an efficient reprogramming. Here, we accomplished a holistic meta-analysis of the transcriptome datasets in a bidirectional perspective to achieve significant pluripotency-related genes that can commonly be applicable in all origin cells. The current study suggested prospective reprogramming factors, such as POLR3G, TERF1, and PHC1. Meanwhile, integrated drug repurposing also revealed certain small chemical molecules, which can promote transgene-free reprogramming and safer iPSC generation protocols.

Endocrine science remains under-represented in European Union (EU) research programmes despite the fundamental role of hormone health in human wellbeing. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritisation. At the national funding level, endocrine societies report limited or little attention of national research funding towards endocrinology. The EndoCompass project-a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges. Research priorities were established through comprehensive analysis of the EU CORDIS database focusing the Horizon 2020 framework period (2014-2020). Expert analysis examined endocrine regulation and health from gametogenesis through embryonic development, early life, puberty, adulthood, and aging, integrating evidence across developmental stages. Research priorities encompass understanding epigenetic programming from embryonic life; elucidating developmental origins of adult disease; investigating brain-gut communication across ages; and addressing endocrine aspects of healthy aging. Special emphasis is placed on critical developmental windows, transgenerational effects, and the need for integrated research approaches spanning paediatric and adult endocrinology. This component of the EndoCompass project provides an evidence-based roadmap for understanding hormone regulation across life stages. The analysis demonstrates the need for coordinated research spanning conception to aging to address Europe's demographic challenges. The findings support strategic investment in lifespan approaches to endocrine health.

Metamorphosis is one of the most fascinating developmental processes in the natural world. The underlying molecular events resulting in the transformation of a caterpillar into a butterfly, including the epigenetic and transcriptomic programs, remain elusive. By integrating DNA and RNA long-read sequencing of the entire body of five consecutive stages from larval to late-pupal development in a laboratory butterfly, we characterise the fundamental metabolic and developmental transitions taking place. We identify a progression from lipid metabolism in larvae towards an up-regulation of muscle formation and mitochondrial energy generation in pupae. Intra-genic CpG methylation correlates with, but does not appear to dictate, gene expression. The level of 5-hydroxymethlcytosine modification detected was very low. The use of long-read mRNA sequencing provided access to complete transcript isoform sequences, and differential isoform usage was notably detected in genes for energy metabolism, and for muscle and neural development during the metamorphic process.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-18794-1.

Multiple sclerosis (MS) onset risk factors include Epstein-Barr virus (EBV) indices (including host response), lower serum 25-vitamin D (25(OH)D) levels, low sun exposure, and HLA-DRB1*1501. The underlying molecular mechanisms are unclear. Here, we examined mediation through differential DNA methylation (DNAm) to better understand possible epigenetic programming. Two case-control studies (Ausimmune Study, Australia = 206 cases + 348 controls; and Epidemiologic Investigations of MS [EIMS], Sweden = 140 cases + 139 controls). DNAm was measured using Illumina arrays. Dimension-reduction methods generated MS-associated DNAm modules. Pathway enrichment analyses were used to describe DNAm modules' system-level biological characteristics. Individual and joint associations with MS risk were assessed using logistic regression. DNAm module mediation of risk factor-outcome associations were assessed using mediation analysis. A range of temporality analyses were used. EBV indices (infectious mononucleosis history and anti-EBNA IgG titer), lower 25(OH)D, low sun exposure, and HLA-DRB1*1501 risk variant were individually and jointly associated with MS risk. In each study, 2 DNAm modules were found which mediated multiple exposure-MS associations. Proportions mediated ranged from 21 to 47% in Ausimmune and 25 to 53% in EIMS. Results were robust to sensitivity analyses. Top-ranked genomewide association study (GWAS) MS risk-associated genes were over-represented in both Ausimmune DNAm modules, A1 3.5-fold (p = 0.004) and A2 3-fold (p = 0.015). Reactome pathways enriched for DNAm had cross-study overlap - 45% of pathways enriched in Ausimmune DNAm modules were also enriched in EIMS (4.82-fold, p < 0.001). EBV, lower vitamin D, low sun exposure, and HLA-DRB1*1501 risk variant act in concert and through common epigenetic pathways to impact MS onset risk. ANN NEUROL 2025.

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high-fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor α (Esr1) was significantly increased by HFD, concomitant with a downregulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation, and improved insulin sensitivity upon HFD challenge; mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation, and improved insulin sensitivity in HFD-challenged mice. Our study demonstrated that DNA methylation at Esr1 promoter played an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

Osteosarcoma is a genomically complex tumor characterized by widespread structural rearrangements. This complexity has limited development of therapeutic strategies informed by molecular mechanisms of oncogenesis. We hypothesized that epigenetic mechanisms could drive distinct subtypes of osteosarcoma. Through analysis of chromatin accessibility, we identified an "early osteoblast-derived" (EOD) cell state characterized by upregulation of transcription factors associated with early bone development, and a "late osteoblast-derived" state (LOD), characterized by upregulation of genes involved in late bone development. We then defined core regulatory circuitries governing the underlying gene expression programs in these two cell states. Multiomic single-cell analysis indicates that these cell states co-exist in a single tumor. Finally, using a panel of patient-derived xenograft models, we identified differential drug responses dependent on these cellular states. These findings create opportunities for developing new combination therapy strategies for osteosarcoma treatment and underscore the value of defining epigenetic subtypes in highly genomically complex cancers.

Environmental factors accelerate epigenetic aging of sperm via mechanistic target of rapamycin/blood-testis barrier mechanism.

DNA methylation (DNAm) is a key epigenetic modification that dynamically regulates eukaryotic development over time. DNAm has been found to influence a variety of biological processes in both normative and pathological states, such as depression. Since DNAm can serve as an interface between environmental influence and gene expression, it is a mechanism studied in the context of many pathologies, including psychiatric. Depression is a complex and heterogeneous disorder strongly influenced by puberty, as evidenced by increased rates in both sexes after sexual maturation. However, this effect is more pronounced in females, contributing to its twofold increased lifetime prevalence compared to males. Additionally, depression is consistently associated with altered DNAm at specific genomic sites. In this review, we discuss how DNAm programming can affect functional pathways during puberty and in turn, influence disease outcomes. Here, we highlight the bidirectional relationship of steroid hormone surges during this sensitive period and DNAm, adding a layer of complexity and insight into the pathophysiology of depression. Specifically, we explore the extent of DNAm change throughout puberty, how it contributes to individual and sex-specific differences in puberty, and how it may influence the risk for depression.