Bridging biological cfDNA features and machine learning approaches. Published: February, 2023 Abstract:
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of ce... Read more »
Impact of FecB Mutation on Ovarian DNA Methylome inSmall-Tail Han Sheep. Published: January, 2023 Abstract:
UNLABELLED: Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mec... Read more »
Consistent DNA Hypomethylations in Prostate Cancer. Published: December, 2022 Abstract:
With approximately 1.4 million men annually diagnosed with prostate cancer (PCa) worldwide, PCa remains a dreaded threat to life and source of devastating morbidity. In recent decades, a significant decrease in age-specific PCa mortality has been ... Read more »
mTORC1 is required for epigenetic silencing during β-cell functionalmaturation. Published: August, 2022 Abstract:
OBJECTIVE: The mechanistic target of rapamycin comple×1 (mTORC1) is a key molecule that links nutrients, hormones, and growth factors to cell growth/function. Our previous studies have shown that mTORC1 is required for β-cell functional... Read more »
Detection of ovarian cancer using plasma cell-free DNA methylomes. Published: June, 2022 Abstract:
BACKGROUND: Ovarian cancer (OC) is a highly lethal gynecologic cancer, and it is hard to diagnose at an early stage. Clinically, there are no ovarian cancer-specific markers for early detection. Here, we demonstrate the use of cell-free DNA (cfDNA... Read more »
A genome-wide screen reveals new regulators of the 2-cell-like cell state Published: June, 2022 Abstract:
In mammals, only the zygote and blastomeres of the early embryo are fully totipotent. This totipotency is mirrored in vitro by mouse "2-cell-like cells" (2CLCs), which appear at low frequency in cultures of Embryonic Stem cells (ESCs). Because tot... Read more »
Hexokinase 2 is a transcriptional target and a positive modulator ofAHR signalling. Published: May, 2022 Abstract:
The aryl hydrocarbon receptor (AHR) regulates the expression of numerous genes in response to activation by agonists including xenobiotics. Although it is well appreciated that environmental signals and cell intrinsic features may modulate this tr... Read more »
Dnmt1 has de novo activity targeted to transposable elements Published: June, 2021 Abstract:
DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a ... Read more »
Epigenetic Plasticity Enables CNS-Trafficking of EBV-infectedB Lymphocytes Published: June, 2021 Abstract:
Subpopulations of B-lymphocytes traffic to different sites and organs to provide diverse and tissue-specific functions. Here, we provide evidence that epigenetic differences confer a neuroinvasive phenotype. An EBV+ B cell lymphoma cell line (M14)... Read more »
Network integration and modelling of dynamic drug responses at multi-omicslevels. Published: October, 2020 Abstract:
Uncovering cellular responses from heterogeneous genomic data is crucial for molecular medicine in particular for drug safety. This can be realized by integrating the molecular activities in networks of interacting proteins. As proof-of-concept we... Read more »
Methylation in pericytes after acute injury promotes chronic kidneydisease. Published: August, 2020 Abstract:
The origin and fate of renal myofibroblasts is not clear after acute kidney injury (AKI). Here, we demonstrate that myofibroblasts were activated from quiescent pericytes (qPericytes) and the cell numbers increased after ischemia/reperfusion injur... Read more »
Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Published: June, 2020 Abstract:
Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-s... Read more »
Human mitochondrial DNA is extensively methylated in a non-CpG context Published: August, 2019 Abstract:
Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global a... Read more »
DNA methylation of the Tacr2 gene in a CUMS model of depression. Published: June, 2019 Abstract:
Tacr2, the gene encoding the NK2 receptor, belongs to G protein-coupled receptors. Accumulating evidence has indicated that the tachykinin receptors may contribute to the pathophysiology of depression. During the last decade, some studies have sho... Read more »
Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Published: November, 2018 Abstract:
The use of liquid biopsies for cancer detection and management is rapidly gaining prominence. Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these method... Read more »
Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor. Published: April, 2018 Abstract:
The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylatio... Read more »
Genome-wide analysis of day/night DNA methylation differences in Populus nigra. Published: January, 2018 Abstract:
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understo... Read more »
Data on novel DNA methylation changes induced by valproic acid in human hepatocytes Published: November, 2017 Abstract:
Valproic acid (VPA) is a widely prescribed antiepileptic drug in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis. However the exact mechanism of the steatosis formation is unknown. The data presented in... Read more »
Dynamics of DNA methylomes underlie oyster development Published: June, 2017 Abstract:
DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a moll... Read more »
Overexpression of LINE-1 Retrotransposons in Autism Brain Published: February, 2017 Abstract:
Long interspersed nuclear elements-1 (LINE-1 or L1) are mobile DNA sequences that are capable of duplication and insertion (retrotransposition) within the genome. Recently, retrotransposition of L1 was shown to occur within human brain leading to ... Read more »
Trichloroethylene-Induced DNA Methylation Changes in Male F344 Rat Liver Published: September, 2016 Abstract:
Trichloroethylene (TCE), a common environmental contaminant, causes hepatocellular carcinoma in mice but not in rats. To understand the mechanisms of the species-specific hepatocarcinogenecity of TCE, we examined the methylation status of DNA in t... Read more »
The Dynamics of DNA Methylation in Maize Roots under Pb Stress. Published: December, 2014 Abstract:
Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under le... Read more »
Genome-wide analysis of DNA methylation patterns in horse Published: July, 2014 Abstract:
Background DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data a... Read more »
Differential methylation of the TRPA1 promoter in pain sensitivity. Published: January, 2014 Abstract:
Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further ... Read more »
DNA unmethylome profiling by covalent capture of CpG sites. Published: July, 2013 Abstract:
Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mappi... Read more »
Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy. Published: July, 2013 Abstract:
BACKGROUND: To investigate epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism (CT8M) as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient; this circ... Read more »
Methylome analysis using MeDIP-seq with low DNA concentrations. Published: March, 2012 Abstract:
DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a t... Read more »
Gene expression and epigenetic changes by furan in rat liver. Published: November, 2011 Abstract:
Furan, a widely used industrial compound, has been found in a number of heated food items. Furan is carcinogenic to rats and mice, but the mechanism behind its carcinogenic effect is still not well understood. In this study, we tested the hypothes... Read more »
Whole genome DNA methylation analysis based on high throughput sequencing technology. Published: November, 2010 Abstract:
There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of ... Read more »
