'; ?> 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, 29 Apr 2025 01:15:01 EDT Tue, 29 Apr 2025 01:15:01 EDT jirtle@radonc.duke.edu james001@jirtle.com Exploring omics solutions to reduce micro/nanoplastic toxicity in plants: A comprehensive overview. Arif SM, Khan I, Saeed M, Chaudhari SK, Ghorbanpour M, Hasan M, Mustafa G
Sci Total Environ (Apr 2025)

The proliferation of plastic waste, particularly in the form of microplastics (MPs) and nanoplastics (NPs), has emerged as a significant environmental challenge with profound implications for agricultural ecosystems. These pervasive pollutants accumulate in soil, altering its physicochemical properties and disrupting microbial communities. MPs/NPs can infiltrate plant systems, leading to oxidative stress and cytotoxic effects, which in turn compromise essential physiological functions such as water uptake, nutrient absorption, and photosynthesis. This situation threatens crop yield and health, while also posing risks to human health and food security through potential accumulation in the food chain. Despite increasing awareness of this issue, substantial gaps still remain in our understanding of the physiological and molecular mechanisms that govern plant responses to MP/NP stress. This review employs integrative omics techniques including genomics, transcriptomics, proteomics, metabolomics, and epigenomics to elucidate these responses. High-throughput methodologies have revealed significant genetic and metabolic alterations that enable plants to mitigate the toxicity associated with MPs/NPs. The findings indicate a reconfiguration of metabolic pathways aimed at maintaining cellular homeostasis, activation of antioxidant mechanisms, and modulation of gene expression related to stress responses. Additionally, epigenetic modifications suggest that plants adapt to prolonged plastics exposure, highlighting unexplored avenues for targeted research. By integrating various omics approaches, a comprehensive understanding of molecular interactions and their effects on plant systems can be achieved. This review underscores potential targets for biotechnological and agronomic interventions aimed at enhancing plant resilience by identifying key stress-responsive genes, proteins, and metabolites. Ultimately, this work addresses critical knowledge gaps and highlights the importance of multi-omics strategies in developing sustainable solutions to mitigate the adverse effects of MP/NP pollution in agriculture, thereby ensuring the integrity of food systems and ecosystems.]]> Wed, 31 Dec 1969 19:00:00 EST Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology. Jia BB, Sun BK, Lee EY, Ren B
J Invest Dermatol (May 2025)

Molecular pathology, such as high-throughput genomic and proteomic profiling, identifies precise disease targets from biopsies but require tissue dissociation, losing valuable histologic and spatial context. Emerging spatial multi-omic technologies now enable multiplexed visualization of genomic, proteomic, and epigenomic targets within a single tissue slice, eliminating the need for labeling multiple adjacent slices. Although early work focused on RNA (spatial transcriptomics), spatial technologies can now concurrently capture DNA, genome accessibility, histone modifications, and proteins with spatially-resolved single-cell resolution. This review outlines the principles, advantages, limitations, and potential for spatial technologies to advance dermatologic research. By jointly profiling multiple molecular channels, spatial multiomics enables novel studies of copy number variations, clonal heterogeneity, and enhancer dysregulation, replete with spatial context, illuminating the skin's complex heterogeneity.]]> Wed, 31 Dec 1969 19:00:00 EST Development and validation of a machine learning prognostic model based on an epigenomic signature in patients with pancreatic ductal adenocarcinoma. Zaccaria GM, Altini N, Mongelli V, Marino F, Bevilacqua V
Int J Med Inform (Jul 2025)

In Pancreatic Ductal Adenocarcinoma (PDAC), current prognostic scores are unable to fully capture the biological heterogeneity of the disease. While some approaches investigating the role of multi-omics in PDAC are emerging, the analysis of methylation data is under exploited.]]> Wed, 31 Dec 1969 19:00:00 EST Applying blood-derived epigenetic algorithms to saliva: cross-tissue similarity of DNA-methylation indices of aging, physiology, and cognition. Zarandooz S, Raffington L
Clin Epigenetics (Apr 2025)

Epigenetic algorithms of aging, health, and cognition, based on DNA-methylation (DNAm) patterns, are prominent tools for measuring biological age and have been linked to age-related diseases, cognitive decline, and mortality. While most of these methylation profile scores (MPSs) are developed in blood tissue, there is growing interest in using less invasive tissues like saliva. The aim of the current study is to probe the cross-tissue intraclass correlation coefficients (ICCs) of MPSs developed in blood applied to saliva DNAm from the same people. While our primary focus is on MPSs that were previously found to be robustly correlated with social determinants of health, including second- and third-generation clocks and MPSs of physiology and cognition, we also report ICC values for first-generation clocks to enable comparison across metrics. We pooled three publicly available datasets that had both saliva and blood DNAm from the same individuals (total n = 107, aged 5-74 years), corrected MPSs for cell composition within each tissue, and computed the cross-tissue ICCs.]]> Wed, 31 Dec 1969 19:00:00 EST Pathogenomic fingerprinting to identify associations between tumor morphology and epigenetic states. Monabbati S, Corredor G, Pathak T, Peacock C, Yang K, Koyfman S, Scacheri P, Lewis J, Madabhushi A, Viswanath SE, Gryder B
Eur J Cancer (May 2025)

Measuring the chromatin state of a tumor provides a powerful map of its epigenetic commitments; however, as these are generally bulk measurements, it has not yet been possible to connect changes in chromatin accessibility to the pathological signatures of complex tumors. In parallel, recent advances in computational pathology have enabled the identification of spatial features and immune cells within oral cavity tumors and their microenvironment.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis. Landragin C, Saichi M, Laisné M, Durand A, Prompsy P, Leclere R, Mesple J, Borgman K, Trouchet A, Faraldo MM, Chiche A, Vincent-Salomon A, Salmon H, Vallot C
Mol Cancer (Apr 2025)

In breast cancer related to the BRCA1 mutation, luminal progenitor cells are believed to be the cells of origin, yet how these cells transform into invasive cancer cells remain poorly understood. Here, we combine single-cell epigenomic and transcriptomic data to reconstitute sequences of events in luminal cells that lead to tumorigenesis. Upon deletion of Trp53 and Brca1, we find that luminal progenitors display an extensive epigenomic disorder associated with a loss of cell identity. These cells then progress to tumor formation through a partial epithelial-to-mesenchymal transition, orchestrated by Snail and the timely activation of immunosuppressive and FGF signaling with their microenvironment. In human samples, pre-tumoral changes can be detected in early stage, basal-like tumors, which rarely recur, as well as in normal-like mammary glands of BRCA1 mutation carriers who have had cancer. Our study fills critical gaps in our understanding of BRCA1-driven tumorigenesis, opening perspectives for the early monitoring of individuals with high cancer risk.]]> Wed, 31 Dec 1969 19:00:00 EST Depressive symptoms partially mediate the relationship between psychosocial factors and epigenetic age acceleration in a multi-racial/ethnic sample of older adults. Opsasnick LA, Zhao W, Schmitz LL, Ratliff SM, Faul JD, Zhou X, Needham BL, Smith JA
Brain Behav Immun Health (May 2025)

Psychosocial factors, including cumulative psychosocial stress and loneliness, have been linked to epigenetic aging in older adults. Further, depressive symptoms have established relationships with both psychosocial factors and epigenetic aging. However, it is not known whether depressive symptoms mediate the association between psychosocial factors and epigenetic aging.We conducted linear regression models to examine associations between psychosocial stress, loneliness, and depressive symptoms and five epigenetic age acceleration (AA) measures estimated by DNA methylation in a multi-racial/ethnic sample of 2681 older adults from the Health and Retirement Study (mean age: 70.4 years). For all identified associations, we tested for effect modification by sex and educational attainment and performed mediation analysis to characterize the role of depressive symptoms on these associations.Psychosocial stress, loneliness, and depressive symptoms were each associated with at least one measure of epigenetic AA (FDR q < 0.05). Further, we observed interactions between loneliness, psychosocial stress, and sex on DunedinPACE, as well as loneliness and educational attainment on GrimAA, PhenoAA, and DunedinPACE, with females and individuals without a college degree appearing more sensitive to the psychosocial effects on epigenetic aging. Depressive symptoms mediated between 24 % and 35 % of the relationships between psychosocial stress and HannumAA, GrimAA, and DunedinPACE, as well as 40 % and 37 % of the relationships between loneliness and both GrimAA and DunedinPACE, respectively.]]> Wed, 31 Dec 1969 19:00:00 EST The demographic history of populations and genomic imprinting have shaped the transposon patterns in Arabidopsis lyrata. Padilla-García N, Le Veve A, Čermák V, Ä°ltaş Ã–, Contreras-Garrido A, Legrand S, Aury JM, Horvath R, Lafon Placette C
Mol Biol Evol (Apr 2025)

Purifying selection is expected to prevent the accumulation of transposable elements within their host, especially when located in and around genes and if affected by epigenetic silencing. However, positive selection may favour the spread of TEs causing genomic imprinting under parental conflict, as genomic imprinting allows parent-specific influence over resource accumulation to the progeny. Concomitantly, the number and frequency of TE insertions in natural populations are conditioned by demographic events. In this study, we aimed to test how demography and selective forces interact to affect the accumulation of TEs around genes, depending on their epigenetic silencing and with a particular focus on imprinted genes. To this aim, we compared the frequency and distribution of TEs in A. lyrata from Europe and North America. Generally, we found that TE insertions showed a lower frequency when they were inserted in or near genes, especially TEs targeted by epigenetic silencing, suggesting purifying selection at work. We also found that many TEs were lost or got fixed in North American populations during the colonization and the postglacial range expansion from refugia of the species in North America, as well as during the transition to selfing, suggesting a potential "TE load'. Finally, we found that silenced TEs increased in frequency and even tended to reach fixation when they were linked to imprinted genes. We conclude that in A. lyrata, genomic imprinting has spread in natural populations through demographic events and positive selection acting on silenced TEs, potentially under a parental conflict scenario.]]> Wed, 31 Dec 1969 19:00:00 EST Design and exploration of integrating bioinformatic analysis into comprehensive and exploratory epigenetic experiments. An SN, Yang HC, Jiang S, Li JX, Zhang GF
Yi Chuan (May 2025)

As the most thoroughly studied epigenetic modification, DNA methylation-induced silencing of suppressor genes is closely related with the development of cancers. Bioinformatic analysis is an important research tool in the fields of life sciences, medicine, and so on. To introduce the application of bioinformatic analysis in cancer epigenetic research to students and to change the current situation that students usually passively perform experiments during the experimental teaching of genetics, we established a comprehensive and exploratory epigenetic experiment which was integrated with bioinformatic analysis. The implement of this experiment followed the principles of centering on students and cultivating scientific research capabilities. Students selected the genes that were potentially silenced by high DNA methylation in lung adenocarcinoma through bioinformatic analysis and literature review under the guidance of teachers and formulated experimental scheme by their own. They then conducted real-time PCR and methylation-specific PCR to explore whether DNA methylation caused the expression silencing of genes of interest and to identify the DNA methyltransferase responsible for the methylation of genes of interest. To comprehensively assess the capability of students, we designed diversified evaluation methods which intensify the assessment of experiment process. This experiment has the characteristics of interdisciplinarity, comprehensiveness, and inquiry, which can help to cultivate the scientific thinking and practical ability of students.]]> 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 Cardiometabolic disease management: influences from epigenetics. Atzemian N, Mohammed S, Di Venanzio L, Gorica E, Costantino S, Ruschitzka F, Paneni F
Epigenomics (May 2025)

Epigenomics is a rapidly emerging field that has gathered significant attention as a "non-genetic determinant" implicated in the manifestation of non-communicable diseases. Exploring epigenetic modifications provides novel insights into the management of cardiometabolic disease (CMD). Epigenetics signatures are influenced by environmental stressors such as air pollution, toxins, and urban noises as well as by established cardiovascular risk factors including smoking, sedentary lifestyle, obesity, and diabetes. Understanding how epigenetic alterations lead to CMD as well as inter-individual differences in epigenetic makeup could unveil new molecular targets and new epi-drugs to be employed for precision medicine approaches in the growing population of patients with cardiometabolic disease to reduce cardiovascular risk. Herein, we provide an overview of the latest advancements in epigenetic mechanisms implicated in CMD and possible therapeutic opportunities.]]> Wed, 31 Dec 1969 19:00:00 EST Developmental epigenomic effects of maternal financial problems. Holuka C, Menta G, Caro JC, Vögele C, D'Ambrosio C, Turner JD
Dev Psychopathol (May 2025)

Early-life adversity as neglect or low socioeconomic status is associated with negative physical/mental health outcomes and plays an important role in health trajectories through life. The early-life environment has been shown to be encoded as changes in epigenetic markers that are retained for many years.We investigated the effect of maternal major financial problems (MFP) and material deprivation (MD) on their children's epigenome in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Epigenetic aging, measured with epigenetic clocks, was weakly accelerated with increased MFP. In subsequent EWAS, MFP, and MD showed strong, independent programing effects on children's genomes. MFP in the period from birth to age seven was associated with genome-wide epigenetic modifications on children's genome visible at age 7 and partially remaining at age 15.These results support the hypothesis that physiological processes at least partially explain associations between early-life adversity and health problems later in life. Both maternal stressors (MFP/MD) had similar effects on biological pathways, providing preliminary evidence for the mechanisms underlying the effects of low socioeconomic status in early life and disease outcomes later in life. Understanding these associations is essential to explain disease susceptibility, overall life trajectories and the transition from health to disease.]]> Wed, 31 Dec 1969 19:00:00 EST Mechanisms of Impaired Wound Healing in Type 2 Diabetes: The Role of Epigenetic Factors. Bauer TM, Moon JY, Shadiow J, Buckley SD, Gallagher KA
Arterioscler Thromb Vasc Biol (May 2025)

Despite decades of research, impaired extremity wound healing in type 2 diabetes remains a significant driver of patient morbidity, mortality, and health care costs. Advances in surgical and medical therapies, including the advent of endovascular interventions for peripheral artery disease and topical therapies developed to promote wound healing, have not reduced the frequency of lower leg amputations for nonhealing wounds in type 2 diabetes. This brief report is aimed at reviewing the roles of various cell types in tissue repair and summarizing the known dysfunctions of these cell types in diabetic foot ulcers. Recent advances in our understanding of the epigenetic regulation in immune cells identified to be altered in type 2 diabetes are summarized, and particular attention is paid to the developing research defining the epigenetic regulation of structural cells, including keratinocytes, fibroblasts, and endothelial cells. Gaps in knowledge are highlighted, and potential future directions are suggested based on the current state of the field.]]> Wed, 31 Dec 1969 19:00:00 EST Advances in single-cell DNA sequencing enable insights into human somatic mosaicism. Shao DD, Kriz AJ, Snellings DA, Zhou Z, Zhao Y, Enyenihi L, Walsh C
Nat Rev Genet (Apr 2025)

DNA sequencing from bulk or clonal human tissues has shown that genetic mosaicism is common and contributes to both cancer and non-cancerous disorders. However, single-cell resolution is required to understand the full genetic heterogeneity that exists within a tissue and the mechanisms that lead to somatic mosaicism. Single-cell DNA-sequencing technologies have traditionally trailed behind those of single-cell transcriptomics and epigenomics, largely because most applications require whole-genome amplification before costly whole-genome sequencing. Now, recent technological and computational advances are enabling the use of single-cell DNA sequencing to tackle previously intractable problems, such as delineating the genetic landscape of tissues with complex clonal patterns, of samples where cellular material is scarce and of non-cycling, postmitotic cells. Single-cell genomes are also revealing the mutational patterns that arise from biological processes or disease states, and have made it possible to track cell lineage in human tissues. These advances in our understanding of tissue biology and our ability to identify disease mechanisms will ultimately transform how disease is diagnosed and monitored.]]> Wed, 31 Dec 1969 19:00:00 EST Omics technologies as powerful approaches to unravel colorectal cancer complexity and improve its management. Fatfat Z, Hussein M, Fatfat M, Gali-Muhtasib H
Mol Cells (May 2025)

Colorectal cancer (CRC) continues to rank among the deadliest and most prevalent cancers worldwide, necessitating an innovative and comprehensive approach that addresses this serious health challenge at various stages, from screening and diagnosis to treatment and prognosis. As CRC research progresses, the adoption of an omics-centered approach holds transformative potential to revolutionize the management of this disease. Advances in omics technologies encompassing genomics, transcriptomics, proteomics, metabolomics, and epigenomics allow to unravel the oncogenic alterations at these levels, elucidating the intricacies and the heterogeneous nature of CRC. By providing a comprehensive molecular landscape of CRC, omics technologies enable the discovery of potential biomarkers for early non-invasive detection of CRC, definition of CRC subtypes, prediction of its staging, prognosis, and overall survival of CRC patients. They also allow the identification of potential therapeutic targets, prediction of drug response, tracking treatment efficacy, detection of residual disease and cancer relapse, and deciphering the mechanisms of drug resistance. Moreover, they allow the distinction of non-metastatic CRC patients from metastatic ones as well as the stratification of metastatic risk. Importantly, omics technologies open up new opportunities to establish molecular-based criteria to guide the selection of effective treatment paving the way for the personalization of therapy for CRC patients. This review consolidates current knowledge on the omics-based preclinical discoveries in CRC research emphasizing the significant potential of these technologies to improve CRC screening, diagnosis, and prognosis and promote the implementation of personalized medicine to ultimately reduce CRC prevalence and mortality.]]> Wed, 31 Dec 1969 19:00:00 EST CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome. Bartas M, Petrovič M, Brázda V, Trenz O, Ďurčanský A, Å tastný J
J Biol Chem (Apr 2025)

With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation; with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetic ageing clocks: statistical methods and emerging computational challenges. Teschendorff AE, Horvath S
Nat Rev Genet (May 2025)

Over the past decade, epigenetic clocks have emerged as powerful machine learning tools, not only to estimate chronological and biological age but also to assess the efficacy of anti-ageing, cellular rejuvenation and disease-preventive interventions. However, many computational and statistical challenges remain that limit our understanding, interpretation and application of epigenetic clocks. Here, we review these computational challenges, focusing on interpretation, cell-type heterogeneity and emerging single-cell methods, aiming to provide guidelines for the rigorous construction of interpretable epigenetic clocks at cell-type and single-cell resolution.]]> Wed, 31 Dec 1969 19:00:00 EST Regulatory Relationships between DNA Methylation and Long Non-Coding RNAs in Neuroblastoma. Fang Y, Xu F, Dong R, Chen L, Wang Y
Curr Med Chem (Apr 2025)

Neuroblastoma (NB) is a prevalent pediatric solid malignancy associated with significant morbidity and mortality, largely driven by epigenetic alterations. This review aims to identify novel biomarkers related to long non-coding RNAs (lncRNAs) and DNA methylation in NB to enhance prognostic capabilities.]]> 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 Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age. Perez-Correa JF, Stiehl T, Marioni RE, Corley J, Cox SR, Costa IG, Wagner W
Genome Biol (Apr 2025)

Epigenetic aging signatures provide insights into human aging, but traditional clocks rely on linear regression of DNA methylation levels, assuming linear trajectories. This study explores a non-parametric approach using 2D-kernel density estimation to determine epigenetic age. Our weighted model achieves similar predictive accuracy as conventional clocks and provides a variation score reflecting the inherent variability of age-related epigenetic changes within samples. This score is significantly increased in various diseases and associated with mortality risk in the Lothian Birth Cohort 1921. Thus, weighted 2D-kernel density estimation facilitates accurate epigenetic age predictions and offers an additional variable for biological age estimation.]]> Wed, 31 Dec 1969 19:00:00 EST