7,005 results match your criteria epigenetic profiling

Epigenetic Features of HIV-Induced T-Cell Exhaustion Persist Despite Early Antiretroviral Therapy.

Front Immunol 2021 4;12:647688. Epub 2021 Jun 4.

Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.

T cell dysfunction occurs early following HIV infection, impacting the emergence of non-AIDS morbidities and limiting curative efforts. ART initiated during primary HIV infection (PHI) can reverse this dysfunction, but the extent of recovery is unknown. We studied 66 HIV-infected individuals treated from early PHI with up to three years of ART. Read More

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Epigenetic Impacts of Early Life Stress in Fetal Alcohol Spectrum Disorders Shape the Neurodevelopmental Continuum.

Front Mol Neurosci 2021 3;14:671891. Epub 2021 Jun 3.

Department of Biology, Faculty of Science, The University of Western Ontario, London, ON, Canada.

Neurodevelopment in humans is a long, elaborate, and highly coordinated process involving three trimesters of prenatal development followed by decades of postnatal development and maturation. Throughout this period, the brain is highly sensitive and responsive to the external environment, which may provide a range of inputs leading to positive or negative outcomes. Fetal alcohol spectrum disorders (FASD) result from prenatal alcohol exposure (PAE). Read More

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Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection.

Life Sci Alliance 2021 Aug 18;4(8). Epub 2021 Jun 18.

Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA

Sepsis, sequela of bloodstream infections and dysregulated host responses, is a leading cause of death globally. Neutrophils tightly regulate responses to pathogens to prevent organ damage. Profiling early host epigenetic responses in neutrophils may aid in disease recognition. Read More

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Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signaling identifies therapeutic targets for colorectal cancer.

Sci Adv 2021 May 19;7(21). Epub 2021 May 19.

Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.

Aberrant activation of Wnt/β-catenin pathway is a key driver of colorectal cancer (CRC) growth and of great therapeutic importance. In this study, we performed comprehensive CRISPR screens to interrogate the regulatory network of Wnt/β-catenin signaling in CRC cells. We found marked discrepancies between the artificial TOP reporter activity and β-catenin-mediated endogenous transcription and redundant roles of T cell factor/lymphoid enhancer factor transcription factors in transducing β-catenin signaling. Read More

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Using cell-free DNA for HCC surveillance and prognosis.

JHEP Rep 2021 Aug 10;3(4):100304. Epub 2021 May 10.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States.

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer. Its incidence is rising faster than any other cancer in the United States and it remains one of the leading causes of cancer-related deaths worldwide. While advances in massive parallel sequencing and integration of 'omics information have transformed the field of oncology, tissue access is often limited in HCC and a single biopsy is poorly representative of the known genetic heterogeneity of tumours. Read More

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Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data.

Bioinformatics 2021 Jun 14. Epub 2021 Jun 14.

Department of Biostatistics, University of Florida, Gainesville, FL.

Summary: Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Read More

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Evaluation of the prognostic value of CBXs in gastric cancer patients.

Sci Rep 2021 Jun 11;11(1):12375. Epub 2021 Jun 11.

Department of Epidemiology, College of Public Health, Hainan Medical University, Longhua District, No.3 Xueyuan Road, Haikou, 570216, China.

Chromobox (CBX) proteins were suggested to exert epigenetic regulatory and transcriptionally repressing effects on target genes and might play key roles in the carcinogenesis of a variety of carcinomas. Nevertheless, the functions and prognostic significance of CBXs in gastric cancer (GC) remain unclear. The current study investigated the roles of CBXs in the prognosis of GC using the Oncomine, The Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, The Cancer Genome Atlas (TCGA), and cBioPortal databases. Read More

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Cellular reprogramming of diabetic foot ulcer fibroblasts triggers pro-healing miRNA-mediated epigenetic signature.

Exp Dermatol 2021 Jun 11. Epub 2021 Jun 11.

Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA.

Diabetic foot ulcers (DFUs), a prevalent complication of diabetes, constitute a major medical challenge with a critical need for development of cell-based therapies. We previously generated induced pluripotent stem cells (iPSCs) from dermal fibroblasts derived from the DFU patients, location-matched skin of diabetic patients and normal healthy donors and re-differentiated them into fibroblasts. To assess the epigenetic microRNA (miR) regulated changes triggered by cellular reprogramming, we performed miRs expression profiling. Read More

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A new molecular classification to drive precision treatment strategies in primary Sjögren's syndrome.

Nat Commun 2021 06 10;12(1):3523. Epub 2021 Jun 10.

Institut de Recherches Internationales Servier, Departments of Translational Medicine and Immuno-Inflammatory Diseases Research and Development, Suresnes, France.

There is currently no approved treatment for primary Sjögren's syndrome, a disease that primarily affects adult women. The difficulty in developing effective therapies is -in part- because of the heterogeneity in the clinical manifestation and pathophysiology of the disease. Finding common molecular signatures among patient subgroups could improve our understanding of disease etiology, and facilitate the development of targeted therapeutics. Read More

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Post-Biopsy Cell-Free DNA From Blood: An Open Window on Primary Prostate Cancer Genetics and Biology.

Front Oncol 2021 24;11:654140. Epub 2021 May 24.

Department of Biomedical Sciences, Humanitas University, Milan, Italy.

Circulating cell-free DNA (ccfDNA), released from normal and cancerous cells, is a promising biomarker for cancer detection as in neoplastic patients it is enriched in tumor-derived DNA (ctDNA). ctDNA contains cancer-specific mutations and epigenetic modifications, which can have diagnostic/prognostic value. However, in primary tumors, and in particular in localized prostate cancer (PCa), the fraction of ctDNA is very low and conventional strategies to study ccfDNA are unsuccessful. Read More

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Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19.

Nat Cell Biol 2021 06 9;23(6):620-630. Epub 2021 Jun 9.

Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often causes severe complications and even death. However, asymptomatic infection has also been reported, highlighting the difference in immune responses among individuals. Here we performed single-cell chromatin accessibility and T cell-receptor analyses of peripheral blood mononuclear cells collected from individuals convalescing from COVID-19 and healthy donors. Read More

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Transcriptional, hormonal, and metabolic changes in susceptible grape berries under powdery mildew infection.

J Exp Bot 2021 Jun 9. Epub 2021 Jun 9.

BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, Lisboa, Portugal.

Vitis vinifera berries are extremely sensitive to infection by the biotrophic pathogen Erysiphe necator causing powdery mildew disease and deleterious effects on grape and wine quality. The combined analysis of the transcriptome and metabolome associated with this common fungal infection has not been previously carried out in any fruit. In order to identify the molecular, hormonal and metabolic mechanisms associated with infection, healthy and naturally infected Carignan berries were collected at two developmental stages: late green (EL33) and early véraison (EL35). Read More

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Somatic Mutation Profiling of Papillary Thyroid Carcinomas by Whole-exome Sequencing and Its Relationship with Clinical Characteristics.

Int J Med Sci 2021 26;18(12):2532-2544. Epub 2021 Apr 26.

Department of Neurosurgery, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China.

The incidence of papillary thyroid carcinomas (PTCs) has increased rapidly during the past several decades. Until now, the mechanisms underlying the tumorigenesis of PTCs have remained largely unknown. Next-generation-sequencing (NGS) provides new ways to investigate the molecular pathogenesis of PTCs. Read More

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Single-cell profiling of D-2-hydroxyglutarate using surface-immobilized resazurin analogs.

Biosens Bioelectron 2021 May 29;190:113368. Epub 2021 May 29.

Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA. Electronic address:

D-2-hydroxyglutarate (D2HG) is over-produced as an oncometabolite due to mutations in isocitrate dehydrogenases (IDHs). Accumulation of D2HG can cause the dysfunction of many enzymes and genome-wide epigenetic alterations, which can promote oncogenesis. Quantification of D2HG at single-cell resolution can help understand the phenotypic signatures of IDH-mutant cancers and identify effective therapeutics. Read More

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DevOmics: an integrated multi-omics database of human and mouse early embryo.

Brief Bioinform 2021 Jun 7. Epub 2021 Jun 7.

Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.

Transcriptomic and epigenetic alterations during early embryo development have been proven to play essential roles in regulating the cell fate. Nowadays, advances in single-cell transcriptomics and epigenomics profiling techniques provide large volumes of data for understanding the molecular regulatory mechanisms in early embryos and facilitate the investigation of assisted reproductive technology as well as preimplantation genetic testing. However, the lack of integrated data collection and unified analytic procedures greatly limits their usage in scientific research and clinical application. Read More

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Genome‑wide profiling of DNA methylation and gene expression unravel the epigenetic landscape in diabetes-related hypothyroidism.

Clin Epigenetics 2021 Jun 6;13(1):123. Epub 2021 Jun 6.

Department of Endocrinology, The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No.1 DaHua Road, Dong Dan, Beijing, 100730, People's Republic of China.

Background: Type 2 diabetes mellitus (T2DM) and hypothyroidism are two common endocrine diseases and the phenomenon that the prevalence of diabetes-related hypothyroidism shows a significant upward trend deserves further attention, but the specific pathogenesis is not yet clear. The study aimed to explore the molecular mechanisms on DNA methylation regulating gene expression and participating in diabetes-related hypothyroidism through genome-wide DNA methylation and RNA sequencing.

Results: The prevalence of hypothyroidism in T2DM patients was significantly higher than that in patients without T2DM (P = 0. Read More

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A Variant Noncoding Region Regulates Prrx1 and Predisposes to Atrial Arrhythmias.

Circ Res 2021 Jun 7. Epub 2021 Jun 7.

Medical Biology, Amsterdam UMC, NETHERLANDS.

Atrial Fibrillation (AF) is the most common cardiac arrhythmia diagnosed in clinical practice. Genome-wide association studies have identified AF-associated common variants across 100+ genomic loci, but the mechanism underlying the impact of these variant loci on AF susceptibility in vivo has remained largely undefined. One such variant region, highly associated with AF, is found at 1q24, close to PRRX1, encoding the Paired Related Homeobox 1 transcription factor. Read More

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Molecular characterisation of sporadic endolymphatic sac tumours and comparison to von Hippel-Lindau disease-related tumours.

Neuropathol Appl Neurobiol 2021 Jun 5. Epub 2021 Jun 5.

Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany.

Aims: Although inactivation of the von Hippel-Lindau gene (VHL) on chromosome 3p25 is considered to be the major cause of hereditary endolymphatic sac tumours (ELSTs), the genetic background of sporadic ELST is largely unknown. The aim of this study was to determine the prevalence of VHL mutations in sporadic ELSTs and compare their characteristics to VHL-disease-related tumours.

Methods: Genetic and epigenetic alterations were compared between 11 sporadic and 11 VHL-disease-related ELSTs by targeted sequencing and DNA methylation analysis. Read More

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Inhibition of EZH2 primes the cardiac gene activation via removal of epigenetic repression during human direct cardiac reprogramming.

Stem Cell Res 2021 May 27;53:102365. Epub 2021 Apr 27.

Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA. Electronic address:

Cardiovascular disease, until now, is still the leading cause of death in the United States. Due to the limited regenerative capacity of adult hearts, the damage caused by heart injury cannot be reversed and eventually progress into heart failure. In need of cardiovascular disease treatment, many therapies aimed at either cell transplantation or cell regeneration have been proposed. Read More

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High nuclear expression of HIF1α, synergizing with inactivation of LIMD1 and VHL, portray worst prognosis among the bladder cancer patients: association with arsenic prevalence.

J Cancer Res Clin Oncol 2021 Jun 2. Epub 2021 Jun 2.

Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata, West Bengal, 700026, India.

Purpose: Our study was aimed to understand the importance of LIMD1-VHL-HIF1α pathway in development of bladder carcinoma (BlCa) in association with arsenic prevalence.

Methods: At first, the mRNA expression pattern of the genes of this pathway (LIMD1, VHL and HIF1α) was checked in GEO datasets and in our samples. Next, genetic and epigenetic profiling of LIMD1 and VHL was done in our sample pool, validated in T24 BlCa cell line. Read More

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Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation.

Genome Biol 2021 Jun 1;22(1):167. Epub 2021 Jun 1.

Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore.

Background: CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Read More

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DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer.

Cancers (Basel) 2021 May 25;13(11). Epub 2021 May 25.

Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia.

We investigated aberrant DNA methylation (DNAm) changes and the contribution of ageing-associated methylomic drift and age acceleration to early-onset colorectal cancer (EOCRC) carcinogenesis. Genome-wide DNAm profiling using the Infinium HM450K on 97 EOCRC tumour and 54 normal colonic mucosa samples was compared with: (1) intermediate-onset CRC (IOCRC; diagnosed between 50-70 years; 343 tumour and 35 normal); and (2) late-onset CRC (LOCRC; >70 years; 318 tumour and 40 normal). CpGs associated with age-related methylation drift were identified using a public dataset of 231 normal mucosa samples from people without CRC. Read More

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MicroRNA Profiles of Maternal and Neonatal Endothelial Progenitor Cells in Preeclampsia.

Int J Mol Sci 2021 May 18;22(10). Epub 2021 May 18.

Gynecology Research Unit, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.

Preeclampsia is associated with an increased cardiovascular morbidity of mother and offspring, thus contributing to a substantial burden in women and children's health. It has been proven that endothelial progenitor cell (EPC) numbers and functional characteristics are impaired in cardiovascular disease and preeclampsia, although causative factors for the latter have remained elusive. MicroRNA (miRNA) modifications are a potential mechanism through which exposure to an altered environment translates into the development of chronic disease. Read More

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MicroRNA as a Prognostic and Diagnostic Marker in T-Cell Acute Lymphoblastic Leukemia.

Int J Mol Sci 2021 May 18;22(10). Epub 2021 May 18.

Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland.

T cell acute lymphoblastic leukemia (T-ALL) is a biologically and genetically heterogeneous disease with a poor prognosis overall and several subtypes. The neoplastic transformation takes place through the accumulation of numerous genetic and epigenetic abnormalities. There are only a few prognostic factors in comparison to B cell precursor acute lymphoblastic leukemia, which is characterized by a lower variability and more homogeneous course. Read More

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Profiling Non-Coding RNA Changes Associated with 16 Different Engineered Nanomaterials in a Mouse Airway Exposure Model.

Cells 2021 May 1;10(5). Epub 2021 May 1.

Human Microbiome Research (HUMI), Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland.

Perturbations in cellular molecular events and their associated biological processes provide opportunities for hazard assessment based on toxicogenomic profiling. Long non-coding RNAs (lncRNAs) are transcribed from DNA but are typically not translated into full-length proteins. Via epigenetic regulation, they play important roles in organismal response to environmental stress. Read More

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miRNA Profiling in the Chicken Liver under the Influence of Early Microbiota Stimulation with Probiotic, Prebiotic, and Synbiotic.

Genes (Basel) 2021 May 1;12(5). Epub 2021 May 1.

Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland.

Epigenetic regulation of gene expression is a form of interaction of the external environment on reading and transcription of genetic information encoded in nucleic acids. We provided evidence that early stimulation of the chicken microbiota with in ovo delivered synbiotics influenced gene expression and DNA methylation in the liver. Therefore, we hypothesize that the stimulation of microbiota by administering bioactive substances in ovo also affects the activity of miRNA in liver. Read More

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Silencing LINC01116 suppresses the development of lung adenocarcinoma via the AKT signaling pathway.

Thorac Cancer 2021 Jun 1. Epub 2021 Jun 1.

Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.

Background: A growing body of evidence has proven that long noncoding ribonucleic acids (lncRNAs) are important epigenetic regulators that play crucial parts in the pathogenesis of human cancers. Previous studies have shown that long intergenic nonprotein coding RNA 01116 (LINC01116) is a carcinogen in several carcinomas; however, its function in lung adenocarcinoma (LUAD) has not been clarified. Here, we aimed to investigate the role of LINC01116 in LUAD. Read More

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Polycomb Repressive Complex 2 Regulates Genes Necessary for Intestinal Microfold Cell (M Cell) Development.

Cell Mol Gastroenterol Hepatol 2021 May 28. Epub 2021 May 28.

Faculty of Medicine and Health Technology, Tampere University Hospital, Tampere University, Tampere, Finland. Electronic address:

Background & Aims: Microfold cells (M cells) are immunosurveillance epithelial cells located in the Peyer's patches (PPs) in the intestine and are responsible for monitoring and transcytosis of antigens, microorganisms, and pathogens. Mature M cells use the receptor glycoprotein 2 (Gp2) to aid in transcytosis. Recent studies have shown transcription factors, Spi-B and Sox8. Read More

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Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma.

Epigenetics 2021 May 30:1-24. Epub 2021 May 30.

Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers because of diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in genomic profiling and biology of this disease have not yet been translated to a relevant improvement in terms of disease management and patient's survival. However, new possibilities for treatment may emerge from studies on key epigenetic factors. Read More

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Epigenetic regulation in medulloblastoma pathogenesis revealed by genetically engineered mouse models.

Cancer Sci 2021 May 29. Epub 2021 May 29.

Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.

Medulloblastoma is the most common malignant cerebellar tumor in children. Recent technological advances in multilayered 'omics data analysis have revealed 4 molecular subgroups of medulloblastoma (Wingless/int, Sonic hedgehog, Group3, and Group4). (Epi)genomic and transcriptomic profiling on human primary medulloblastomas has shown distinct oncogenic drivers and cellular origin(s) across the subgroups. Read More

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