Epigenetics - Science topic

Maternal pancreatic β-cells undergo adaptive changes to meet the metabolic demands of pregnancy, and disruptions in this adaptation can lead to gestational diabetes mellitus. However, the mechanisms governing this adaptation remain largely unexplored. Using single-cell transcriptome combined with genetic analyses, we identified a precise process of...

Lipid storage and epigenetic dysregulation are key features for clear cell renal carcinoma (ccRCC). However, the interplay between fatty acid metabolism and epigenetics in ccRCC remains to be further demonstrated. Here, the landscape of active enhancers is profiled in paired ccRCC samples and identifies 10171 gain variant enhancer loci (VELs) in th...

Sirtuinas en Gymnotus carapo: implicancias moleculares en la respuesta al estrés oxidativo y la adaptación ambiental en peces de agua dulce Resumen: Las sirtuinas constituyen una familia de enzimas dependientes de NAD⁺ con funciones esenciales en la regulación epigenética, el metabolismo energético y la respuesta celular al estrés. En este estudio...

Background Epithelial ovarian cancer (EOC) is a deadly and heterogenous disease comprising five major histotypes: clear cell carcinoma (CCC), endometrioid carcinoma (EC), low- and high-grade serous carcinoma (LGSC, HGSC), and mucinous carcinoma (MC). Despite this heterogeneity, EOC is often treated as a homogenous disease, and reliable screening te...

Background Differences in body composition during childhood can influence long-term health, with notable links to cardiometabolic disorders in later life. While genetic associations with body composition traits are well-studied, less is known about the role of epigenetic mechanisms, particularly in low- and middle-income countries where the burden...

Dynamic epigenetic pathways play a crucial role in the onset of type 1 diabetes (T1D), an autoimmune disorder targeting beta cells in the pancreas. DNA methylation, histone modifications, and non-coding RNAs significantly impact immune responses, beta cell function, and the progression of Type 1 Diabetes. Early-life exposures have a lasting impact...

Introduction BCG vaccination can have heterologous or non-specific effects (NSE) that confer resistance against pathogens other than its target Mycobacterium tuberculosis, but the underlying mechanisms are not fully understood. Methods We conducted a systematic review synthesising existing literature on immune mechanisms mediating the heterologous...

Sex differences in late-onset Alzheimers disease (AD) progression include accelerated decrements in cognitive status and greater amyloid and tau biomarker burdens in females. To identify sex-specific differentially methylated positions (DMPs) and genes in persons with mild cognitive impairment (MCI) and AD, we analyzed whole genome methylation sequ...

Maintaining genome integrity is crucial for the proper functioning and development of organisms. One intriguing aspect of genome integrity is the formation and function of neocentromeres at non-centromeric sites. CENP-A, a centromere-specific protein, is essential for centromere identification and function. However, in many cancers, CENP-A is often...

Epigenetic alterations are among the prominent drivers of cellular senescence and/or aging, intricately orchestrating gene expression programs during these processes. This study shows that histone lactylation, plays a pivotal role in counteracting senescence and mitigating dysfunctions of skeletal muscle in aged mice. Mechanistically, histone lacty...

In this study, we tested the hypothesis that the immunosenescence profile could account for the disproportional susceptibility of the elderly to severe forms of COVID‐19. The immunological profiles of volunteers residing in endemic and non‐endemic areas for chronic infectious diseases were analyzed at the early stage of SARS‐CoV‐2 infection. A uniq...

DNA methylation is a key epigenetic regulator often disrupted in cancer, yet how promoter methylation dynamics translate into transcriptional changes during cancer progression remains incompletely understood. Here, we employed targeted bisulfite sequencing and RNA-seq on paired tumor and non-tumor tissues from 80 Korean colorectal cancer (CRC) pati...

As the CNS matures, chromatin at growth associated genes gradually becomes less accessible, but the timing of this shift, the mechanisms behind it, and whether it can be reversed in adults have remained unclear. To address this, we mapped chromatin accessibility in corticospinal neurons across postnatal development and found two distinct waves of r...

Cancers can have a lot of different causes that present differently on each patient, even if they are localized in the same part of the body. For example, colon cancer can be caused by a variety of risk factors such as epigenetic changes, exposure to carcinogens, spontaneous mutations, inheritance and genetic variations of different kinds. Breast c...

Cancer is still one of the leading causes of death in the world. The chance of getting the disease is linked to genetic and epigenetic factors. When it comes to treating local cancer, radiotherapy and surgery work the best. Chemotherapy, hormonal, and biological therapies can reach the rest of the organs and tissues through the circulatory system w...

Several dietary patterns are suggested to benefit health, potentially through DNA methylation changes. However, to what extent adherence to so-called healthy diets overlaps, whether these dietary patterns are equally beneficial, and whether they affect health outcomes through the same molecular mechanisms, remains unclear. Therefore, we investigate...

Introduction Non-small cell lung cancer (NSCLC), which accounts for >85% of all lung cancers, is the most common solid malignant tumor, with high morbidity and mortality worldwide. Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) treatment is widely used clinically because the epidermal growth factor receptor (EGFR) is the main...

Although much is known about the pathophysiology of severe COVID-19, there are still areas that remain to be determined. It is well established that the pivotal molecular event is a hyperinflammatory response also referred to as a cytokine storm. The aim of this retrospective cohort study was to determine miRNAs which might be predictive for the ad...

Background Cancer cells undergo widespread changes in epigenetic patterns that mediate cancer compromised gene expression programs during cancer progression. However, the alterations in higher-order genome organization in which these changes occur and their functional implications are less well understood. To explore how chromatin structure and epi...

Schizophrenia (SZ) is a complex neuropsychiatric disorder influenced by genetic, environmental, and epigenetic factors, including miRNA dysregulation. This study explored the diagnostic and therapeutic potential of miRNAs in SZ, focusing on seven key miRNAs: miR-137-3p, miR-34a-5p, miR-432-5p, miR-130b-3p, miR-346, miR-195-5p, and miR-103a-3p. Resu...

Background Diabetes ranks as the ninth leading cause of death globally, and DNA-methylation age acceleration (DNAmAA) is closely linked to lifespan. However, the impact of DNAmAA on long-term outcomes in specific populations with diabetes and pre-diabetes has not yet been comprehensively studied. Methods This retrospective cohort study utilized da...

Background Human Endogenous RetroVirus (HERV) expression in tumours reflects epigenetic dysregulation of cancer and an oncogenic factor through promoter/enhancer action on genes. While more than 50% of colorectal cancers develop liver metastases, HERV has not been studied in this context.

Parameter estimation in inverse problems involving partial differential equations (PDEs) underpins modeling across scientific disciplines, especially when parameters vary in space or time. Physics-informed Machine Learning (PhiML) integrates PDE constraints into deep learning, but prevailing approaches depend on recursive automatic differentiation...

I present a novel, fully symbolic modeling framework for biological age modulation, constructed entirely within my Alpay Algebra system. My goal is to unify formal mathematics and biomedical data into a single closed logic where every claim is proven (Q.E.D.) or explicitly excluded. I begin by referencing clinical trials on interventions such as NM...

Cancer is a complex and multifaceted disease that affects millions of people worldwide. Despite significant advances in our understanding of the biology of cancer, it remains one of the leading causes of death globally. This review aims to provide a comprehensive overview of the current state of knowledge on cancer, including its causes, diagnosis,...

Long-lived memory CD8⁺ T cells are essential for the control of persistent viral infections. The mechanisms that preserve memory cells are poorly understood. Fate mapping of the transcriptional repressor GFI1 identified that GFI1 was differentially regulated in virus-specific CD8⁺ T cells and was selectively expressed in stem cell memory and centra...

Bacteria are Caenorhabditis elegans’ food, and worms are naturally attracted to many bacteria, including pathogenic Pseudomonas , preferring PA14 over laboratory Escherichia coli (OP50). Despite this natural attraction to PA14, prior PA14 exposure causes the worms to instead avoid PA14. This behavioral switch can happen quickly – even within the du...

Background The pathogenesis of CRC requires primary genetic and epigenetic mechanisms including, methylation of CpG islands of the genes. In the current study, micro RNA-139-5p (miR-139-5p) promoter methylated DNA was evaluated in tumor tissue and plasma samples from CRC affected patients. Methods MiR-139-5p promoter methylation was investigated i...

Background Posttraumatic stress disorder (PTSD) has been associated with advanced epigenetic age cross-sectionally, but the association between these variables over time is unclear. This study conducted meta-analyses to test whether new-onset PTSD diagnosis and changes in PTSD symptom severity over time were associated with changes in two metrics o...

This paper presents a comprehensive framework for investigating IQ enhancement via a continuum of interventions ranging from current methods-such as noninvasive behavioral techniques, pharmacological enhancers, and gene modification-to emerging approaches (advanced gene editing, epigenetic interventions) and speculative future technologies (nanotec...

Background Health status is closely linked to both healthcare access and utilization. While previous research has identified associations between health status and DNA methylation-based biomarkers of aging (epigenetic aging), studies exploring these relationships in the context of healthcare access and utilization remain limited. To address this ga...

Oculopharyngodistal myopathy (OPDM) is caused by CGG triplet repeat expansions in six genes. To explore the genetics and epigenetics of OPDM, we conducted CRISPR/Cas9-targeted resequencing of repeat regions in 89 patients. Repeat regions essentially comprised pure CGG expansions, but exhibited size variability, even within patients. Expanded LRP12...

Obtaining chromosomally complete genome assemblies across the tree of life is a major goal of biodiversity genomics. However, some lineages remain recalcitrant to assembly despite recent advances in sequencing technologies and assembly tools. Birds present a substantial genome assembly challenge due to the presence of tiny, hard to assemble microch...

IDH -wildtype glioblastoma (GBM) is an aggressive brain tumor with poor survival and few therapeutic options. Transcriptionally-defined cell states coexist in GBM and occupy defined regions of the tumor. Evidence indicates that GBM cell states are plastic, but it remains unclear if they are determined by the underlying epigenetic state and/or by mi...

Triple‐negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resi...

This paper extends the Pure Time Theory (PTT) into the domains of memory, instinct, and consciousness, proposing a unified model in which cognitive phenomena are structured interactions with a fundamental scalar temporal field, denoted T relax. In this framework, the brain does not generate meaning-it modulates access. DNA does not contain instinct...

The transcription of satellite DNA is highly sensitive to environmental factors and represents a source of genomic instability. Therefore, tight regulation of (peri)centromeric transcription is essential for genome maintenance. Antibiotics are routinely used for in vitro studies and for medical treatment, however, their effect on pericentromeric sa...

Signaling pathways involving NF‐κB transcription factors have essential roles in inflammation, immunity, cell proliferation, differentiation, and survival. Classical IκB proteins, such as IκBα and IκBβ, bind to NF‐κB via ankyrin repeats to sequester NF‐κB in the cytoplasm and thus suppress NF‐κB activity. Unlike these constitutively expressed class...

The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequen...

Hypomethylating agents are frontline therapies for myelodysplastic neoplasms (MDS), yet clinical responses remain unpredictable. We conducted a phase 2 trial comparing injectable and oral azacitidine (AZA) administered over one or three weeks per four-week cycle, with the primary objective of investigating whether response is linked to in vivo drug...

In this study, we established dozens of single provirus-infected cellular clones offering various transcriptional phenotypes of HIV. We proposed that stochastic fluctuations in HIV transcription can appear at, at least, two levels: (1) the chromosomal landscape and (2) the in situ HIV integration site. In the former case, proviruses integrating at...

Intimate Partner Violence (IPV) is a major public health problem to be addressed with innovative and interconnecting strategies for ensuring the psychophysical health of the surviving woman. According to the World Health Organization, 27% of women worldwide have experienced physical and sexual IPV in their lifetime. Most of the studies on gender-ba...

Aging is a process in which organisms or cells undergo a decline in their functions. Epigenetic modification changes have been recognized as a senescence hallmark in both natural aging and stimulation-induced senescence. An acetylation modification is a dynamic process, which plays a crucial role in the senescence process through DNA stability, met...

Mesenchymal stem cells (MSCs) possess important physiological characteristics such as self- proliferation and multipotent differentiation potential, making them highly promising for applications in tissue repair and regeneration. However, the precise mechanisms underlying these properties remain obscure. Epigenetics is a key clue, which works throu...

Maternal environmental exposures, including viral infections, can exert intergenerational effects on the offspring's epigenome. Herein, based on the Swedish COVID-19 during Pregnancy and Early childhood study (COPE), we explored how mild SARS-CoV-2 infection during pregnancy affected the DNA methylome of peripheral blood mononuclear cells in infant...

Although the co‐existence of metabolic and psychiatric disorders in the same individual (comorbidity) is very prevalent, the mechanisms by which these disorders co‐occur are poorly understood, but a history of early‐life adversity is a common developmental risk factor. Exposure to adverse environments during critical periods of development (e.g. fe...

Genetic equidistance phenomenon (GEP): A simpler species is equally distantly related to two or more complex species in a sequence alignment when the genetic distance is measured by the identity matrix or percentage non-identity. Maximum genetic diversity (MGD): The upper limit in genetic distance or diversity, as measured by the identity matrix or...

Background: Large-scale studies show that adults with major depressive disorder (MDD) generally have a higher imaging-predicted age relative to their chronological age (i.e., positive brain age gap) compared to controls, though considerable within-group variation exists. This study examines lifestyle, early-life, and genetic health risk factors con...

Ankyrin repeat (AR) motif is one of the most abundant repeat motifs found in eukaryotic proteins. It functions in mediating protein–protein interactions and regulating numerous biological functions. Interestingly, some AR-containing proteins are involved in epigenetic and transcriptional events. Our review aims to characterize the structure and pos...

Cardiovascular disorders (CVDs) are the leading cause of mortality worldwide, highlighting an urgent need for innovative therapeutic strategies. Recent advancements highlight the potential of naturally derived bioproducts with epigenetic properties to offer protection against CVDs. These compounds act on key epigenetic mechanisms, DNA methylation,...

Background Transposable Elements (TEs) represent a sizeable amount of mammalian genomes, providing regulatory sequences involved in shaping gene expression patterns. NF-Y is a Transcription factor -TF- trimer that binds to the CCAAT box, belonging to a selected group implicated in determining initiation of coding and noncoding RNAs. Results We foc...

Background The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. Results Increases in BrdU incorporation allow us to measure DNA replication dynamics, inc...

Resumo: No final do século XIX, Freud baseou-se na teoria neuronal para apoiar o seu modelo teórico do aparelho mental. Porém, devido às restrições da neurobiologia da época, migrou suas explorações teóricas para o campo metapsicológico. Apesar dessa mudança, os fundamentos neurobiológicos iniciais permaneceram influentes no desenvolvimento da sua...

Research of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and fibromyalgia (FM), two acquired chronic illnesses affecting mainly females, has failed to ascertain their frequent co-appearance and etiology. Despite prior detection of human endogenous retrovirus (HERV) activation in these diseases, the potential biomarker value of HERV e...

Warming ocean temperatures can increase the metabolic rates of fishes, potentially contributing to changes in their growth and survival to recruitment age. During prolonged marine heatwave conditions in the Gulf of Alaska between 2014 and 2019, Pacific Cod (Gadus macrocephalus) metabolic rates may have increased, but little is known about the relat...

Posttraumatic stress disorder (PTSD) is a disabling psychiatric disorder with both genetic and environmental contributions. Epigenetic mechanisms have been found to, at least partially, mediate the effect of environmental factors in PTSD aetiology. PTSD has also been found to be associated with all-cause morbidity and premature mortality, suggestin...

The progression and metastasis of breast cancer patients are regulated by genetics and epigenetics. Circular RNA (circRNA) plays a pivotal role in modulating the advancement of tumors. The study aimed to explore the clinical performance and regulatory role of hsa-circVIM in breast cancer and its modulatory effect on tamoxifen resistance in hormone...

Studies on Hippo pathway regulation of tumorigenesis largely center on YAP and TAZ, the transcriptional co-regulators of TEADs. Here, we present an oncogenic mechanism involving VGLL and TEAD fusions that is Hippo pathway-related but YAP/TAZ-independent. We characterize two recurrent fusions, VGLL2-NCOA2 and TEAD1-NCOA2 , recently identified in hum...

Over the past two decades, Mesoamerican endemic nephropathy (MeN) has become a major public health problem in certain regions of Mexico and Central American countries. The etiology of this disease is multifactorial, and important environmental factors have been described, such as chronic heat stress, recurrent episodes of dehydration, infections, a...

The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the e...

Social determinants of health are social factors that affect health and survival. Two of the most powerful social determinants are socioeconomic status (SES) and race/ethnicity; people with lower SES or marginalized race/ethnicity tend to experience earlier onset of aging-related diseases and have shorter lifespans. DNA methylation (DNAm) measures...

Depression, a prevalent and debilitating mental health disorder, affects approximately 280 million people worldwide, according to the World Health Organization (WHO). It is estimated that 5% of adults, including 4% of men and 6% of women, experience depression, with the prevalence increasing to 5.7% in individuals over 60 years old. Despite the ava...

Background: Chronic systemic inflammation is implicated in Alzheimer's disease (AD) pathogenesis and has measurable effects on blood cells. There is increasing interest in non-invasive diagnostic tools that use blood-based biomarkers for AD, such as DNA methylation. Notably, DNA methylation changes in blood are also linked to systemic inflammation....

Ovarian cancer (OC) is a severe gynecological malignancy with a high mortality rate among women worldwide. It is often diagnosed at advanced stages due to the lack of effective screening methods. This study investigated the expression patterns of microRNAs (miRNAs) hsa-miR-21-5p and hsa-miR-145-5p as potential OC prognostic and diagnostic biomarker...

Background Epigenetic aging estimators commonly track chronological and biological aging, quantifying its accumulation (i.e., epigenetic age acceleration) or speed (i.e., epigenetic aging pace). Their scores reflect a combination of inherent biological programming and the impact of environmental factors, which are suggested to vary at different lif...

Background Chronic systemic inflammation is implicated in Alzheimer's disease (AD) pathogenesis and has measurable effects on blood cells. There is increasing interest in non-invasive diagnostic tools that use blood-based biomarkers for AD, such as DNA methylation. Notably, DNA methylation changes in blood are also linked to systemic inflammation....

Com base em uma revisão narrativa, este artigo explora como experiências traumáticas afetam não apenas os indivíduos diretamente envolvidos, mas também gerações futuras, por meio de mecanismos epigenéticos e fatores ambientais. A epigenética revela alterações na expressão gênica — sem modificações no DNA — que podem resultar em hipersensibilidade a...

Risk stratification in acute myeloid leukemia (AML) is driven by genetics, yet patient age substantially influences therapeutic decisions. To evaluate how age alters the prognostic impact of genetic mutations, we pooled data from 3062 pediatric and adult AML patients from multiple cohorts. Signaling pathway mutations dominated in younger patients,...

Background We examined the association between placental epigenetic gestational age (eGA) acceleration and adolescent systolic blood pressure (SBP) in a cohort born extremely preterm. Methods Study participants were a subset of the Extremely Low Gestational Age Newborn cohort (born <28 weeks’ gestation) who had placental DNA methylation quantified...

High altitude presents a challenging environment for human settlement. DNA methylation is an essential epigenetic mechanism that responds to environmental stimuli, but its roles in high-altitude short-term acclimatization (STA) and long-term adaptation (LTA) are poorly understood. Here, we conducted a methylome-wide association study involving 687...

Motivation Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of att...

Insulin resistance (IR) is a risk factor for cardiovascular diseases and type 2 diabetes. Associations between DNA methylation (DNAm) and IR have been less studied in African ancestry (AA) populations than those of European ancestry (EA). We aimed to identify associations between whole blood DNAm and IR in up to 1,811 AA and 964 EA participants fro...

El síndrome de ovario poliquístico (SOP) es la endocrinopatía más común en mujeres en edad reproductiva con una prevalencia mayor al 20%. El SOP es una enfermedad heterogénea con signos y síntomas dados por el hiperandrogenismo como el hirsutismo y la disfunción ovárica como la anovulación, acompañados de una morfología clásica de ovario poliquísti...

Aging is associated with the accumulation of senescent cells, which are triggered by tissue injury response and often escape clearance by the immune system. The specific traits and diversity of these cells in aged tissues, along with their effects on the tissue microenvironment, remain largely unexplored. Despite the advances in single-cell and spa...

Diabetic nephropathy (DN) is one of the most important microvascular complications of diabetes. The role of epigenetic regulation in DN has attracted much attention recently. This research was performed to explore the role of FTO in the DN progression. The renal tissues of DN patients were collected and the podocytes were stimulated with high gluco...

Background Mantle cell lymphoma (MCL) is an aggressive subtype of B-cell non-Hodgkin’s lymphoma. The applicability of circulating tumor DNA (ctDNA) for predicting treatment response and prognosis in MCL remains underexplored. Methods This study included 34 MCL patients receiving first-line chemoimmunotherapy. We assessed the ability of plasma ctDN...

Fetal programming suggests that maternal nutrition during gestation influences offspring growth, development, and productivity. This study evaluated the effects of prenatal protein-energy supplementation on the lifetime performance of Nellore cattle. Twenty-eight nulliparous heifers were inseminated and assigned to one of two groups: Non-Programmed...

DNA methylation, a pivotal epigenetic mechanism, plays a critical role in various pathological conditions, including cancers. Notably, cancer‐type‐specific DNA methylation can be advantageous for survival only in specific environments while being disadvantageous in others. To investigate the role of cancer‐type‐specific methylation as a vulnerabili...

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technology for studying genetic and epigenetic regulation. However, ChIP-seq data can be heavily affected by variations in chromatin amount and composition, ChIP enrichment, library preparation, and sequencing depth, affecting its overall reproducibility a...

Introduction Aging is the primary risk factor for sporadic Alzheimer's disease. Chronic low-grade inflammation associated with aging drives cognitive impairment through multiple mechanisms involving oxidative stress, insulin resistance, and dysregulation of metabolic, immunologic, and hematologic systems. Methods In a 7-month, randomized, double-b...