'; ?> 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 Wed, 02 Apr 2025 22:33:38 EDT Wed, 02 Apr 2025 22:33:38 EDT jirtle@radonc.duke.edu james001@jirtle.com Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies. Holleley CE, Hahn EE
Mol Ecol Resour (Apr 2025)

Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism-wide gene expression at the time of death. While DNA methylation and RNA-Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid-preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue-specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase-seq and FAIRE-seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species.]]> Wed, 31 Dec 1969 19:00:00 EST Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling. Zeng C, Wei M, Li H, Yu L, Wang C, Mu Z, Huang Z, Ke Y, Li LY, Xiao Y, Wu M, Chen MK
Epigenomics (Apr 2025)

Epigenetic alterations are critical regulators in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the dynamic epigenomic landscapes are not well defined. Our previous study found that H3K27ac and H3K9me3 play important roles in regulating lipid metabolic pathways in the early stages of MASLD. However, the epigenomic status in the inflammation stages still needs to be determined.]]> Wed, 31 Dec 1969 19:00:00 EST On integrative analysis of multi-level gene expression data in Kidney cancer subgrouping. Jeyananthan P, W P N M, S M R
Urologia (May 2025)

Kidney cancer is one of the most dangerous cancer mainly targeting men. In 2020, around 430, 000 people were diagnosed with this disease worldwide. It can be divided into three prime subgroups such as kidney renal cell carcinoma (KIRC), kidney renal papilliary cell carcinoma (KIRP) and kidney chromophobe (KICH). Correct identification of these subgroups on time is crucial for the initiation and determination of proper treatment. On-time identification of this disease and its subgroup can help both the clinicians and patients to improve the situation. Hence, this study checks the possibility of using multi-omics data in the kidney cancer subgrouping, whether integrating multiple omics data will increase the subgrouping accuracy or not. Four different molecular data such as genomics, proteomics, epigenomics and miRNA from The Cancer Genome Atlas (TCGA) are used in this study. As the data is in a very high dimension world, this study starts with selecting the relevant features of the study using Pearson's correlation coefficient. Those selected features are used with three different classification algorithms such as k-nearest neighbor (KNN), supporting vector machines (SVMs) and random forest. Performances are compared to see whether the integration of multi-omics data can improve the accuracy of kidney cancer subgrouping. This study shows that integration of multi-omics data can improve the performance of the kidney cancer subgrouping. The highest performance (accuracy value of 0.98±0.03) is gained by top 400 features selected from integrated multi-omics data, with support vector machines.]]> Wed, 31 Dec 1969 19:00:00 EST Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms. Fonseca PAS, Suarez-Vega A, Esteban-Blanco C, Marina H, Pelayo R, Gutiérrez-Gil B, Arranz JJ
BMC Genomics (Mar 2025)

Feed efficiency (FE) is an essential trait in livestock species because of the constant demand to increase the productivity and sustainability of livestock production systems. A better understanding of the biological mechanisms associated with FEs might help improve the estimation and selection of superior animals. In this work, differentially methylated regions (DMRs) were identified via genome-wide bisulfite sequencing (GWBS) by comparing the DNA methylation profiles of milk somatic cells from dairy ewes that were divergent in terms of residual feed intake. The DMRs were identified by comparing divergent groups for residual feed intake (RFI), the feed conversion ratio (FCR), and the consensus between both metrics (Cons). Additionally, the predictive performance of these DMRs and genetic variants mapped within these regions was evaluated via three machine learning (ML) models (xgboost, random forest (RF), and multilayer feedforward artificial neural network (deeplearning)). The average performance of each model was based on the root mean squared error (RMSE) and squared Spearman correlation (rho2). Finally, the best model for each scenario was selected on the basis of the highest ratio between rho2 and RMSE.]]> Wed, 31 Dec 1969 19:00:00 EST Long non coding RNA function in epigenetic memory with a particular emphasis on genomic imprinting and X chromosome inactivation. Le LTT
Gene (Apr 2025)

Cells preserve and convey certain gene expression patterns to their progeny through the mechanism called epigenetic memory. Epigenetic memory, encoded by epigenetic markers and components, determines germline inheritance, genomic imprinting, and X chromosome inactivation. First discovered long non coding RNAs were implicated in genomic imprinting and X-inactivation and these two phenomena clearly demonstrate the role of lncRNAs in epigenetic memory regulation. Undoubtedly, lncRNAs are well-suited for regulating genes in close proximity at imprinted loci. Due to prolonged association with the transcription site, lncRNAs are able to guide chromatin modifiers to certain locations, thereby enabling accurate temporal and spatial regulation. Nevertheless, the current state of knowledge regarding lncRNA biology and imprinting processes is still in its nascent phase. Herein, we provide a synopsis of recent scientific advancements to enhance our comprehension of lncRNAs and their functions in epigenetic memory, with a particular emphasis on genomic imprinting and X chromosome inactivation, thus gaining a deeper understanding of the role of lncRNAs in epigenetic regulatory networks.]]> Wed, 31 Dec 1969 19:00:00 EST GWAS for Defining the Pathogenesis of Hypertension: Have They Delivered? Alexander MR, Edwards TL, Harrison DG
Hypertension (Apr 2025)

Genome-wide association studies have identified >3500 associated single nucleotide polymorphisms and over 1000 independent loci associated with hypertension. These individually have small effect sizes, and few associated loci have been experimentally tested for causal roles in hypertension using animal models or in humans. Thus, methods to prioritize and maximize the relevance of identified single nucleotide polymorphisms and associated loci are critical to determine their importance in hypertension. We propose several approaches to aid in these efforts, including: (1) integration of genome-wide association study data with multiomic data sets, including proteomics, transcriptomics, and epigenomics, (2) utilizing linked clinical and genetic data sets to determine genetic contributions to hypertension subphenotypes with distinct drivers, and (3) performing whole exome/genome sequencing on cohorts of individuals with severe hypertension to enrich for rare variants with larger effect sizes. Rather than creating longer lists of hypertension-associated single nucleotide polymorphisms, these approaches are needed to identify key mediators of hypertension pathophysiology.]]> Wed, 31 Dec 1969 19:00:00 EST PCMR: a comprehensive precancerous molecular resource. Xiong Y, Li J, Jin W, Sheng X, Peng H, Wang Z, Jia C, Zhuo L, Zhang Y, Huang J, Zhai M, Lyu B, Sun J, Zhou M
Sci Data (Apr 2025)

Early detection and intervention of precancerous lesions are crucial in reducing cancer morbidity and mortality. Comprehensive analysis of genomic, transcriptomic, proteomic and epigenomic alterations can provide insights into the early stages of carcinogenesis. However, the lacke of an integrated, well-curated data resource of molecular signatures limits our understanding of precancerous processes. Here, we introduce a comprehensive PreCancerous Molecular Resource (PCMR), which compiles 25,828 molecular profiles of precancerous samples paired with normal or malignant counterparts. These profiles cover precancerous lesions of 35 cancer types across 20 organs and tissues, derived from tissue samples, liquid biopsies, cell lines and organoids, with data from transcriptomics, proteomics and epigenomics. PCMR includes 62,566 precancer-gene associations derived from differential analysis and text-mining using the ChatGPT large language model. We examined PCMR dataset reliability and significance by the authoritative precancerous molecular signature, along with its biological and clinical relevance. Overall, PCMR will serve as a valuable resource for advancing precancer research and ultimately improving patient outcomes.]]> Wed, 31 Dec 1969 19:00:00 EST Genome-wide methylation association study in monozygotic twins discordant for curve severity of adolescent idiopathic scoliosis. Wu Z, Dai Z, Feng Z, Qiu Y, Zhu Z, Xu L
Spine J (Apr 2025)

Emerging evidence suggests that abnormal DNA methylation patterns may play a role in the progression of adolescent idiopathic scoliosis (AIS). However, the mechanisms underlying the influence of DNA methylation on curve severity remain largely unknown.]]> Wed, 31 Dec 1969 19:00:00 EST A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules. Zhao M, Xue G, He B, Deng J, Wang T, Zhong Y, Li S, Wang Y, He Y, Chen T, Zhang J, Yan Z, Hu X, Guo L, Qu W, Song Y, Yang M, Zhao G, Yu B, Ma M, Liu L, Sun X, Zhao D, Xie D, Chen C, She Y
Sci Data (Apr 2025)

Diagnosing lung cancer at a curable stage offers the opportunity for a favorable prognosis. The emerging epigenomics analysis on plasma cell-free DNA (cfDNA), including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications, has acted as a promising approach facilitating the identification of lung cancer. And, integrating 5mC biomarker with chest computed tomography (CT) image features could optimize the diagnosis of lung cancer, exceeding the performance of models built on single feature. However, the clinical applicability of integrated markers might be limited by the potential risk of overfitting due to small sample size. Hence, we prospectively collected peripheral blood sample and the paired chest CT images of 2032 patients with indeterminate pulmonary nodules across 5 centers, and constructed a large-scale, multi-institutional, multiomics database that encompass CT imaging data and plasma cfDNA fragmentomic in 5mC-, 5hmC-enriched regions. To our best knowledge, this dataset is the first radio-epigenomic dataset with the largest sample size, and provides multi-dimensional insights for early diagnosis of lung cancer, facilitating the individuated management for lung cancer.]]> Wed, 31 Dec 1969 19:00:00 EST Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease. O'Sullivan J, Patel S, Leventhal GE, Fitzgerald RS, Laserna-Mendieta EJ, Huseyin CE, Konstantinidou N, Rutherford E, Lavelle A, Dabbagh K, DeSantis TZ, Shanahan F, Temko A, Iwai S, Claesson MJ
Gut Microbes (Dec 2025)

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.]]> Wed, 31 Dec 1969 19:00:00 EST Integration of ATAC-seq and RNA-seq reveals the dynamics of chromatin accessibility and gene expression in zoysiagrass response to drought. Shen L, Qi Z, Ai Y, Zhang J, Chao Y, Han L, Xu L
Plant Cell Rep (Apr 2025)

The 'X4' accession of zoysiagrass demonstrated superior drought tolerance compared to other accessions. Integration analysis of transcriptomics and epigenomics revealed a positive correlation between ATAC-seq peak intensity and gene expression levels. Six motifs involved in regulating drought responses were identified, which are similar to the domains of the ERF and C2H2 transcription factor families. Heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress, allowing robust growth even at high PEG6000 concentrations. Zoysiagrass is renowned for its drought tolerance and serves as an exceptional domestic turfgrass in China. However, the changes in chromatin accessibility during drought in zoysiagrass are not well understood. We conducted a preliminary evaluation of the phenotypic changes in drought tolerance for six zoysiagrass cultivars, taking into account their growth characteristics and physiological traits under drought conditions. Additionally, we utilized an integrated multi-omics strategy, encompassing RNA sequencing (RNA-seq), Assay for Transposase Accessible Chromatin using high-throughput sequencing (ATAC-seq), and reverse transcription quantitative PCR (RT-qPCR) verification experiments, to gain deeper understanding of the chromatin accessibility patterns linked to gene expression in response to drought stress in zoysiagrass. Preliminary analysis of the trends in relative water content and proline content suggested that the variety 'X4' exhibited superior drought tolerance compared to the other five accessions. The KEGG pathway enrichment analysis revealed that zoysiagrass responded to environmental stress by regulating stress response and antioxidant defense pathways. Notably, the expression levels of genes Zja03G031540 and Zja11G000860 were significantly increased in the 'X4' zoysiagrass genotype, which exhibited improved drought tolerance, compared to the 'X1' zoysiagrass genotype with reduced drought tolerance. This study suggested that 63 high-confidence genes are related to drought stress, including Zja03G031540 and Zja11G000860. Additionally, six motifs regulating drought responses were unearthed. Furthermore, the heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress. The study discovered a positive correlation between ATAC-seq peak intensity and gene expression levels. The expression of high-confidence genes was linked to zoysiagrass resistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related gene expression in zoysiagrass, elucidating the grass adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork for zoysiagrass improvement and breeding.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetics in evolution and adaptation to environmental challenges: pathways for disease prevention and treatment. Abdolmaleky HM, Nohesara S, Zhou JR, Thiagalingam S
Epigenomics (Apr 2025)

Adaptation to challenging environmental conditions is crucial for the survival/fitness of all organisms. Alongside genetic mutations that provide adaptive potential during environmental challenges, epigenetic modifications offer dynamic, reversible, and rapid mechanisms for regulating gene expression in response to environmental changes in both evolution and daily life, without altering DNA sequences or relying on accidental favorable mutations. The widespread conservation of diverse epigenetic mechanisms - like DNA methylation, histone modifications, and RNA interference across diverse species, including plants - underscores their significance in evolutionary biology. Remarkably, environmentally induced epigenetic alterations are passed to daughter cells and inherited transgenerationally through germline cells, shaping offspring phenotypes while preserving adaptive epigenetic memory. Throughout anthropoid evolution, epigenetic modifications have played crucial roles in: i) suppressing transposable elements and viral genomes intruding into the host genome; ii) inactivating one of the X chromosomes in female cells to balance gene dosage; iii) genetic imprinting to ensure expression from one parental allele; iv) regulating functional alleles to compensate for dysfunctional ones; and v) modulating the epigenome and transcriptome in response to influence from the gut microbiome among other functions. Understanding the interplay between environmental factors and epigenetic processes may provide valuable insights into developmental plasticity, evolutionary dynamics, and disease susceptibility.]]> Wed, 31 Dec 1969 19:00:00 EST Personalized Nutrition for the Enhancement of Elite Athletic Performance. Sutehall S, Pitsiladis Y
Scand J Med Sci Sports (Apr 2025)

Enhancing athletic performance through the manipulation of nutritional intake has ancient roots, with early guidance from "philosophical giants" like Hippocrates, who describes the balance between diet and exercise. Modern sports nutrition emerged in the 20th century, with research identifying carbohydrate (CHO) intake as beneficial for endurance. Studies like Gordon's in the 1920s linked blood glucose levels to marathon performance, while Cade's research in the 1960s on fluid and electrolyte intake led to the founding of Gatorade and the shift toward drinking during exercise to allegedly prevent dehydration and improve sporting performance. Today, sports nutrition is in a "holding pattern" after significant developments in the 1980s, 1990s, and the 2000s. A new era will involve personalized nutrition, but this development will require a game-changing injection of momentum, recognizing that athletes' responses to nutrition interventions vary widely. New technologies will also need to be developed and perfected, including wearables for real-time biometric monitoring (e.g., heart rate variability, glucose, and sweat composition and rate), which offer potential for tailored nutrition (i.e., diet and hydration) strategies. Applications of genetic and multi-omics technologies (like genomics, transcriptomics, metabolomics, proteomics, and epigenomics) are needed to unlock the potential of personalized sports nutrition by analyzing individual responses to factors such as sleep, nutrition, and exercise. The future lies in fast integration of all available data using next-generation bioinformatics and AI to generate personalized recommendations, with an emphasis on empirical evidence rather than solely commercial interests. As technology matures, sports (and exercise) nutrition will continue refining its practices but will need a paradigm shift to deliver precise interventions that may offer athletes the crucial edge needed to maximize performance while promoting short-term and long-term health.]]> Wed, 31 Dec 1969 19:00:00 EST Ripple Effects of Early Life Stress on Vascular Health. Kellum CE, Kelly GC, Pollock JS
Hypertension (Apr 2025)

The term early life stress encompasses traumatic events occurring before the age of 18 years, such as physical abuse, verbal abuse, household dysfunctions, sexual abuse, childhood neglect, child maltreatment, and adverse childhood experiences. Adverse psychological experiences in early life are linked to enduring effects on mental and physical health in adulthood. In this review, we first describe the effects and potential mechanisms of early life stress on the components of the vasculature. Next, we dive into the impact of early life stress on the vasculature across the lifespan through alterations of the epigenetic landscape. Finally, we consolidate the critical gaps in knowledge for focusing future research including the potential for resilience in combatting the impact of early life stress on vascular health.]]> Wed, 31 Dec 1969 19:00:00 EST Parent-of-Origin Effects in Childhood Asthma at Seven Years of Age. Lee Y, Gjerdevik M, Jugessur A, Gjessing HK, Corfield E, Havdahl A, Harris JR, Magnus MC, HÃ¥berg SE, Magnus P
Genet Epidemiol (Apr 2025)

Childhood asthma is more common among children whose mothers have asthma than among those whose fathers have asthma. The reasons for this are unknown, and we hypothesize that genomic imprinting may partly explain this observation. Our aim is to assess parent-of-origin (PoO) effects on childhood asthma by analyzing SNP array genotype data from a large population-based cohort. To estimate PoO effects in parent-reported childhood asthma at 7 years of age, we fit a log-linear model implemented in the HAPLIN R package to SNP array genotype data from 915 mother-father-child case triads, 603 mother-child case dyads, and 113 father-child case dyads participating in the Norwegian Mother, Father, and Child Cohort Study (MoBa). We found that alleles at two SNPs-rs3003214 and rs3003211-near the adenylosuccinate synthase 2 gene (ADSS2 on chromosome 1q44) showed significant PoO effects at a false positive rate ≤ 0.05. The ratio of the effect of the maternally and paternally inherited G-allele at rs3003214 was 1.68 (95% CI: 1.41-2.03, p value = 1.13E-08). Our results suggest PoO effects at the ADSS2 gene, particularly the maternally inherited G-allele at rs3003214, may contribute to the maternal effect in childhood asthma.]]> Wed, 31 Dec 1969 19:00:00 EST Rare Causes and Differential Diagnosis in Patients With Silver-Russell Syndrome. Braga BL, da Cunha Scalco R, Homma TK, Freire BL, Cellin LP, Canton APM, Lerario AM, de Assis Funari MF, de Souza V, Bertola DR, Malaquias AC, Mendonca BB, de Lima Jorge AA
Clin Genet (Apr 2025)

Silver-Russell syndrome (SRS) is an imprinting disorder mainly characterized by pre- and postnatal growth restriction. Most SRS cases are due to 11p15.5 loss of methylation (11p15.5 LOM) or maternal uniparental disomy of chromosome 7 [UPD(7)mat], but several patients remain molecularly undiagnosed. This study describes the molecular investigation of children with a clinical diagnosis or suspicion of SRS at a tertiary center specialized in growth disorders. Thirty-nine patients were evaluated with multiplex ligation-dependent probe amplification, chromosomal microarray and/or massively parallel sequencing. The most common result was 11p15.5 LOM (n = 17; 43.5%), followed by UPD(7)mat (n = 2; 5.1%). Additionally, we found maternal duplications of the imprinting centers in 11p15.5 (n = 2; 5.1%), and genetic defects in SRS-causing genes (IGF2 and HMGA2) (n = 3; 7.7%; two mutations and one deletion). Alternative molecular diagnoses included UPD(14)mat (n = 1; 2,6%), UPD(20)mat (n = 1;2,6%), copy number variants (n = 2; 5.1%), and mutations in genes associated with other growth disorders (n = 4; 10.3%), leading to diagnoses of Temple syndrome, Mulchandani-Bhoj-Conlin syndrome, IGF-1 resistance (IGF1R), Bloom syndrome (BLM), Gabriele-De Vries syndrome (YY1), Intellectual developmental disorder autosomal dominant 50 with behavioral abnormalities (NAA15), and Intellectual developmental disorder 64 (ZNF292). These findings underscore the importance of establishing the molecular diagnosis of SRS and its differential diagnoses to guide appropriate management and genetic counseling.]]> Wed, 31 Dec 1969 19:00:00 EST Stage-specific DNA methylation dynamics in mammalian heart development. Zhang F, Evans T
Epigenomics (Apr 2025)

Cardiac development is a precisely regulated process governed by both genetic and epigenetic mechanisms. Among these, DNA methylation is one mode of epigenetic regulation that plays a crucial role in controlling gene expression at various stages of heart development and maturation. Understanding stage-specific DNA methylation dynamics is critical for unraveling the molecular processes underlying heart development from specification of early progenitors, formation of a primitive and growing heart tube from heart fields, heart morphogenesis, organ function, and response to developmental and physiological signals. This review highlights research that has explored profiles of DNA methylation that are highly dynamic during cardiac development and maturation, exploring stage-specific roles and the key molecular players involved. By exploring recent insights into the changing methylation landscape, we aim to highlight the complex interplay between DNA methylation and stage-specific cardiac gene expression, differentiation, and maturation.]]> Wed, 31 Dec 1969 19:00:00 EST Embryo-restricted responses to maternal IL-17A promote neurodevelopmental disorders in mouse offspring. Andruszewski D, Uhlfelder DC, Desiato G, Regen T, Schelmbauer C, Blanfeld M, Scherer L, Radyushkin K, Pozzi D, Waisman A, Mufazalov IA
Mol Psychiatry (Apr 2025)

Prenatal imprinting to interleukin 17A (IL-17A) triggers behavioral disorders in offspring. However, reported models of maternal immune activation utilizing immunostimulants, lack specificity to elucidate the anatomical compartments of IL-17A's action and the distinct behavioral disturbances it causes. By combining transgenic IL-17A overexpression with maternal deficiency in its receptor, we established a novel model of prenatal imprinting to maternal IL-17A (acronym: PRIMA-17 model). This model allowed us to study prenatal imprinting established exclusively through embryo-restricted IL-17A responses. We demonstrated a transfer of transgenic IL-17A across the placental barrier, which triggered the development of selected behavioral deficits in mouse offspring. More specifically, embryonic responses to IL-17A resulted in communicative impairment in early-life measured by reduced numbers of nest retrieval calls. In adulthood, IL-17A-imprinted offspring displayed an increase in anxiety-like behavior. We advocate our PRIMA-17 model as a useful tool to study neurological deficits in mice.]]> Wed, 31 Dec 1969 19:00:00 EST Modified carbon dot-mediated transient transformation for genomic and epigenomic studies in wheat. She L, Cheng X, Jiang P, Shen S, Dai F, Run Y, Zhu M, Tavakoli M, Yang X, Wang XE, Xiao J, Chen C, Kang Z, Huang J, Zhang W
Plant Biotechnol J (Apr 2025)

Genotype restriction poses a significant bottleneck to stable transformation in the vast majority of plant species, thereby severely impeding advancement in plant bioengineering, particularly for crops. Nanoparticles (NPs) can serve as effective carriers for the transient delivery of nucleic acids, facilitating gene overexpression or silencing in plants in a genotype-independent manner. However, the applications of NP-mediated transient systems in comprehensive genomic studies remained underexplored in plants, especially in crops that face challenges in genetic transformation. Consequently, there is an urgent need for efficient NP-mediated delivery systems capable of generating whole plants or seedlings with uniformly transformed nucleic acids. We have developed a straightforward and efficient modified carbon dot (MCD)-mediated transient transformation system for delivering DNA plasmids into the seeds of wheat, which is also applicable to other plant species. This system facilitates the generation of whole seedlings that contain the transferred DNA plasmids. Furthermore, our study demonstrates that this system serves as an excellent platform for conducting functional genomic studies in wheat, including the validation of gene functions, protein interactions and regulation, omics studies, and genome editing. This advancement significantly enhances functional genomic research for any plants or crops that face challenges in stable transformation. Thus, our study provides for the first time evidence of new applications for MCDs in functional genomics and epigenomic studies, and bioengineering potentially leading to the improvement of desirable agronomic traits in crops.]]> Wed, 31 Dec 1969 19:00:00 EST Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors. Wu P, Liu Z, Zheng L, Du Y, Zhou Z, Wang W, Lu C
Commun Biol (Mar 2025)

Epigenomic mechanisms are critically involved in mediation of genetic and environmental factors that underlie cancer development. Histone modifications represent highly informative epigenomic marks that reveal activation and repression of gene activities and dysregulation of transcriptional control due to tumorigenesis. Here, we present a comprehensive epigenomic and transcriptomic mapping of 18 stage I and II tumor and 20 non-neoplastic tissues from non-small cell lung adenocarcinoma patients. Our profiling covers 5 histone marks including activating (H3K4me3, H3K4me1, and H3K27ac) and repressive (H3K27me3 and H3K9me3) marks and the transcriptome using only 20 mg of tissue per sample, enabled by low-input omic technologies. Using advanced integrative bioinformatic analysis, we uncover cancer-driving signaling cascade networks, changes in 3D genome modularity, differential expression and functionalities of transcription factors and noncoding RNAs. Many of these identified genes and regulatory molecules show no significant change in their expression or a single epigenomic modality, emphasizing the power of integrative multimodal and multiomic analysis using patient samples.]]> Wed, 31 Dec 1969 19:00:00 EST