7,020 results match your criteria Epigenomics [Journal]


Rutaecarpine inhibited imiquimod-induced psoriasis-like dermatitis via inhibiting the NF-κB and TLR7 pathways in mice.

Biomed Pharmacother 2019 Jan 26;109:1876-1883. Epub 2018 Nov 26.

Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha 410011, China.

Psoriasis is a chronic, immune-mediated inflammatory skin disease. As psoriasis rarely occurs in nonhuman animals, the lack of an ideal animal model reflecting the histopathological and molecular immunological characteristics of psoriasis remains an urgent issue. In the present study, an imiquimod-induced psoriasis-like dermatitis mouse model was constructed under natural immune conditions and verified by evaluations of the Psoriasis Area and Severity Index (PASI) score and Baker score, H&E staining, immunohistochemical examination of the CD3 and Gr1 levels, measurement of plasmacytoid dendritic cell- (pDC) and Th17-associated cytokine levels, and evaluation of p65 phosphorylation and TLR7 expression. Read More

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January 2019
1 Read

Integrated comparison of the miRNAome and mRNAome in muscles of dermatomyositis and polymyositis reveals common and specific miRNA-mRNAs.

Epigenomics 2018 Dec 7. Epub 2018 Dec 7.

Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.

Aim: Dermatomyositis (DM) and polymyositis (PM) are refractory systemic autoimmune diseases with unknown pathogenesis. miRNAs is an important epigenetic mechanism to regulate gene expression.

Methods: We performed whole miRNAs analysis, transcription analysis and the association between miRNAome and mRNAome. Read More

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December 2018

Interplay between exercise and BMI; results from an equal access, racially diverse biopsy study.

Cancer Causes Control 2018 Dec 6. Epub 2018 Dec 6.

Division of Urology, Veterans Affairs Medical Center, Durham, NC, USA.

Purpose: It is unclear if exercise and BMI interact to influence prostate cancer (PC) risk. We hypothesized BMI is linked with increased aggressive PC risk but this link will be attenuated with increased exercise.

Methods: Men undergoing prostate biopsy completed a questionnaire and metabolic equivalent (MET) hours of exercise was calculated. Read More

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December 2018
3 Reads

Invasive breast cancers in adolescent and young adult women show more aggressive immunohistochemical and clinical features than those in women aged 40-44 years.

Breast Cancer 2018 Dec 11. Epub 2018 Dec 11.

Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.

Background: Limited knowledge exists concerning the clinicopathological features of breast cancers (BCs) occurring in adolescent and young adult (AYA) women. We evaluated tumor characteristics in AYA women in comparison with those in middle-aged premenopausal women.

Methods: From consecutive AYA patients (< 35-year-old) with invasive BC in a single institute, 82 patients first treated with surgery were examined. Read More

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December 2018
1 Read

Myocardial infarction cell by cell.

Nat Immunol 2019 Jan;20(1):7-9

Department for Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.

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January 2019

Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques.

Proc Natl Acad Sci U S A 2018 Dec 11. Epub 2018 Dec 11.

Department of Evolutionary Anthropology, Duke University, Durham, NC 27708;

Low social status is an important predictor of disease susceptibility and mortality risk in humans and other social mammals. These effects are thought to stem in part from dysregulation of the glucocorticoid (GC)-mediated stress response. However, the molecular mechanisms that connect low social status and GC dysregulation to downstream health outcomes remain elusive. Read More

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December 2018

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.

Cancer Cell 2018 Dec;34(6):996-1011.e8

Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany; Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany. Electronic address:

Identifying the earliest somatic changes in prostate cancer can give important insights into tumor evolution and aids in stratifying high- from low-risk disease. We integrated whole genome, transcriptome and methylome analysis of early-onset prostate cancers (diagnosis ≤55 years). Characterization across 292 prostate cancer genomes revealed age-related genomic alterations and a clock-like enzymatic-driven mutational process contributing to the earliest mutations in prostate cancer patients. Read More

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December 2018
1 Read

From Basic Knowledge to Effective Therapies.

Cancer Cell 2018 Dec;34(6):871-873

Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany; The German Cancer Research Consortium. Electronic address:

In this issue of Cancer Cell, Ott et al. use integrative analysis of histone ChIP-seq and ATAC-seq to describe enhancer-based regulatory circuits in chronic lymphocytic leukemia. This work identified and validated transcription factor PAX5 as main driver of an oncogenic circuitry, which can be disrupted by BET bromodomain inhibition. Read More

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December 2018
1 Read

Prospective exosome-focused translational research for afatinib study of non-small cell lung cancer patients expressing EGFR (EXTRA study).

Thorac Cancer 2018 Dec 8. Epub 2018 Dec 8.

Division of Medical Oncology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan.

Patients with EGFR-mutated non-small cell lung cancer (NSCLC) exhibit resistance to EGFR-tyrosine kinase inhibitors (TKIs) within 9-14 months of therapy. Recently, EGFR-mutated NSCLC has demonstrated the potential for heterogeneity; therefore, the manner of clonal heterogeneity may impact the duration of progression-free and overall survival and other parameters affecting EGFR-TKI treatment efficacy. However no predictive biomarker of these favorable treatment efficacies has been identified to date. Read More

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December 2018

Transcriptome and protein interaction profiling in cancer cells with mutations in histone H3.3.

Sci Data 2018 Dec 11;5:180283. Epub 2018 Dec 11.

Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Gyeonggi-do, Republic of Korea.

Mutations of histone variant H3.3 are highly recurrent in childhood glioblastoma and in young adults with Giant Cell Tumor of the Bone (GCTB). The heterozygotic representation of the mutations in the tumors, and with potential histone H3 and H3. Read More

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December 2018

Integrative analysis of genome-wide association study and chromosomal enhancer maps identified brain region related pathways associated with ADHD.

Compr Psychiatry 2019 Jan 28;88:65-69. Epub 2018 Nov 28.

School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China. Electronic address:

Attention deficit/hyperactivity disorder (ADHD) is among the most common childhood onset psychiatric behavioral disorders, and the pathogenesis of ADHD is still unclear. Utilizing the latest genome wide association studies (GWAS) data and enhancer map, we explored the brain region related biological pathways associated with ADHD. The GWAS summary data of ADHD was driven from a published study, involving 20,183 ADHD cases and 35,191 healthy controls. Read More

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January 2019
2.252 Impact Factor

Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells.

Epigenomics 2018 Dec 11. Epub 2018 Dec 11.

Institute of Epigenetics & Epigenomics & College of Animal Science & Technology, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu 225009, China.

Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation.

Materials & Methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. mRNA m5C modification and gene expression were assessed using RNA-BisSeq and RNA-Seq. Read More

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December 2018

Identification and regulation pattern analysis of long noncoding RNAs in meibomian gland carcinoma.

Epigenomics 2018 Dec 7. Epub 2018 Dec 7.

Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.

Aim: To identify long noncoding RNAs (lncRNAs) and to elucidate regulation patterns of lncRNAs in meibomian gland carcinoma (MGC).

Materials & Methods: We used RNA-Seq, gene ontology, ClueGO, Ingenuity Pathway Analysis and co-expression network analyses to profile the expression and regulation patterns of lncRNAs and mRNAs in MGC.

Results: We identified 500 lncRNAs and 326 mRNAs as differentially expressed. Read More

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December 2018

Acute Exercise Increases the Expression of KIR2DS4 by Promoter Demethylation in NK Cells.

Int J Sports Med 2018 Dec 3. Epub 2018 Dec 3.

Department of molecular and cellular sport medicine, Institute of cardiovascular research and sports medicine; German Sport University Cologne, Cologne, Germany.

Positive effects of exercise on cancer prevention and progression have been proposed to be mediated by stimulating natural killer (NK) cells. Because NK cell receptors are regulated by epigenetic modifications, we investigated whether acute aerobic exercise and training change promoter DNA methylation and gene expression of the activating KIR2DS4 and the inhibiting KIR3DL1 gene. Sixteen healthy women (50-60 years) performed a graded exercise test (GXT) and were randomized into either a passive control group or an intervention group performing a four-week endurance exercise intervention. Read More

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December 2018
2 Reads

Epigenetic mapping of the metabolome reveals mediators of the epigenotype-phenotype map.

Genome Res 2018 Nov 30. Epub 2018 Nov 30.

Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.

Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Read More

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November 2018

Significance of molecular classification of ependymomas: C11orf95-RELA fusion-negative supratentorial ependymomas are a heterogeneous group of tumors.

Acta Neuropathol Commun 2018 Dec 4;6(1):134. Epub 2018 Dec 4.

Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.

Extensive molecular analyses of ependymal tumors have revealed that supratentorial and posterior fossa ependymomas have distinct molecular profiles and are likely to be different diseases. The presence of C11orf95-RELA fusion genes in a subset of supratentorial ependymomas (ST-EPN) indicated the existence of molecular subgroups. However, the pathogenesis of RELA fusion-negative ependymomas remains elusive. Read More

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December 2018
1 Read

Advances in multiple omics of natural-killer/T cell lymphoma.

J Hematol Oncol 2018 Dec 4;11(1):134. Epub 2018 Dec 4.

State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, 200025, China.

Natural-killer/T cell lymphoma (NKTCL) represents the most common subtype of extranodal lymphoma with aggressive clinical behavior. Prevalent in Asians and South Americans, the pathogenesis of NKTCL remains to be fully elucidated. Using system biology techniques including genomics, transcriptomics, epigenomics, and metabolomics, novel biomarkers and therapeutic targets have been revealed in NKTCL. Read More

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December 2018
3 Reads

Automatic detection of genomic regions with informative epigenetic patterns.

BMC Genomics 2018 Nov 28;19(1):847. Epub 2018 Nov 28.

National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049, Madrid, Spain.

Background: Epigenetic phenomena are crucial for explaining the phenotypic plasticity seen in the cells of different tissues, developmental stages and diseases, all holding the same DNA sequence. As technology is allowing to retrieve epigenetic information in a genome-wide fashion, massive epigenomic datasets are being accumulated in public repositories. New approaches are required to mine those data to extract useful knowledge. Read More

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November 2018
8 Reads

Interaction between genetic ancestry and common breast cancer susceptibility variants in Colombian women.

Int J Cancer 2018 Nov 28. Epub 2018 Nov 28.

Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Latino women show lower incidences of breast cancer (BC) than non-Hispanic whites. Large-scale genetic association studies have identified variants robustly associated with BC risk in European women. We examine here the relevance of these variants to Colombian BC and possible interactions with genetic ancestry. Read More

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November 2018
1 Read

The Aberrant Epigenetic Modifications in the Pathogenesis of Psoriasis.

J Investig Dermatol Symp Proc 2018 Dec;19(2):S81-S82

Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China. Electronic address:

Psoriasis is a chronic and recurrent inflammatory skin disease that is characterized by abnormal keratinocyte proliferation, vascular hyperplasia, and infiltration of inflammatory cells into the dermis and epidermis. It is generally accepted that the central pathogenesis of psoriasis is dysfunction of T lymphocytes, which are affected by the complex interplay between genetic and environmental factors, including trauma, infections, stress, drugs, smoking, and alcohol consumption (Nestle et al., 2009). Read More

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December 2018
1 Read

Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples.

Proteomics Clin Appl 2018 Nov 24:e1700166. Epub 2018 Nov 24.

Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.

Purpose: Profiling histone posttranslational modifications (PTMs) in clinical samples holds great potential for the identification of epigenetic biomarkers and the discovery of novel epigenetic targets. MS-based approaches to analyze histone PTMs in clinical samples usually rely on SDS-PAGE separation following histone enrichment in order to eliminate detergents and further isolate histones. However, this limits the digestions options and hence the modification coverage. Read More

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November 2018
1 Read

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation.

Leukemia 2018 Nov 23. Epub 2018 Nov 23.

Division of Hematology, Oncology and Stem Cell Transplantation, Department of Internal Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.

DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2'-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. Read More

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November 2018
4 Reads

Methylation profiles of IL33 and CCL26 in bronchial epithelial cells are associated with asthma.

Epigenomics 2018 Dec 23;10(12):1555-1568. Epub 2018 Nov 23.

Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada.

Aim: This study aimed to characterize DNA methylation (DNA-me) in promoter region of IL33, IL1RL1 and CCL26 in asthma and their impacts on transcriptional activity in bronchial epithelial cells (BECs).

Patients & Methods: We performed bis-pyrosequencing, quantitative real-time PCR and sequencing in BECs from ten asthmatic and ten control individuals.

Results: We detected lower DNA-me levels of IL33 and CCL26 in asthmatic than control BECs. Read More

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December 2018
2 Reads

Statistical-based database fingerprint: chemical space dependent representation of compound databases.

J Cheminform 2018 Nov 22;10(1):55. Epub 2018 Nov 22.

Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico.

Background: Simplified representation of compound databases has several applications in cheminformatics. Herein, we introduce an alternative and general method to build single fingerprint representations of compound databases. The approach is inspired on the previously published modal fingerprints that are aimed to capture the most significant bits of a fingerprint representation for a compound data set. Read More

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November 2018

An oviduct-on-a-chip provides an enhanced in vitro environment for zygote genome reprogramming.

Nat Commun 2018 11 22;9(1):4934. Epub 2018 Nov 22.

Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands.

Worldwide over 5 million children have been conceived using assisted reproductive technology, and research has concentrated on increasing the likelihood of ongoing pregnancy. However, studies using animal models have indicated undesirable effects of in vitro embryo culture on offspring development and health. In vivo, the oviduct hosts a period in which the early embryo undergoes complete reprogramming of its (epi)genome in preparation for the reacquisition of (epi)genetic marks. Read More

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November 2018
2 Reads

Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder.

Epigenomics 2018 Nov 20. Epub 2018 Nov 20.

Department of Psychiatry & Behavioral Sciences & Department of Obstetrics & Gynecology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA 30322, USA.

Aim: Trauma exposure is a necessary, but not deterministic, contributor to post-traumatic stress disorder (PTSD). Epigenetic factors may distinguish between trauma-exposed individuals with versus without PTSD.

Materials & Methods: We conducted a meta-analysis of PTSD epigenome-wide association studies in trauma-exposed cohorts drawn from civilian contexts. Read More

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November 2018
10 Reads

TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets.

Nat Commun 2018 11 19;9(1):4866. Epub 2018 Nov 19.

Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.

Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes. Read More

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November 2018
7 Reads

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression.

Cell 2018 Nov 15;175(6):1701-1715.e16. Epub 2018 Nov 15.

La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK. Electronic address:

While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Read More

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November 2018
7 Reads

Circular RNA circRHOT1 is upregulated and promotes cell proliferation and invasion in pancreatic cancer.

Epigenomics 2018 Nov 16. Epub 2018 Nov 16.

Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China.

Aim: We aimed to identify the roles of circRHOT1 in pancreatic cancer.

Materials & Methods: The circRHOT1 was acquired from our previous study followed by quantitative real-time PCR and fluorescence in situ hybridization validation in pancreatic cancer. We used siRNA and shRNA to explore the function of circRHOT1 in pancreatic cancer cells. Read More

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November 2018
4 Reads

Antibiotics suppress colon tumorigenesis through inhibition of aberrant DNA methylation in an azoxymethane and dextran sulfate sodium colitis model.

Cancer Sci 2018 Nov 16. Epub 2018 Nov 16.

Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.

Chronic inflammation is involved in the development of colon cancer by inducing mutations and aberrant DNA methylation in colon epithelial cells. Furthermore, there is growing evidence that colonic microbiota modulates the inflammation response in the host and influences colon tumorigenesis. However, the influence of colonic microbiota on aberrant DNA methylation remains unknown. Read More

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November 2018
6 Reads

DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis.

Epigenomics 2018 Nov 14. Epub 2018 Nov 14.

Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia.

Aim: To determine whether epigenetic modifications of DNA regulate gene expression and alternative splicing during terminal granulopoiesis.

Materials & Methods: Using whole genome bisulfite sequencing, reduced representation hydroxymethylation profiling and mRNA sequencing, we compare changes in DNA methylation, DNA hydroxymethylation, gene expression and alternative splicing in mouse promyelocytes and granulocytes.

Results & Conclusion: We show reduced DNA methylation at the promoters and enhancers of key granulopoiesis genes, indicating a regulatory role in the activation of lineage-specific genes during differentiation. Read More

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November 2018
3 Reads

The quantitative profiling of blood mSEPT9 determines the detection performance on colorectal tumors.

Epigenomics 2018 Nov 14. Epub 2018 Nov 14.

Department of Radiotherapy, the Chinese PLA 309th Hospital, Beijing, PR China.

Aim: To investigate the quantitative relationship between the positive detection rate (PDR) in colorectal tumor detection and the mSEPT9 level.

Materials & Methods: The level of blood mSEPT9 in various colorectal diseases was quantified by the Epi proColon 2.0 assay. Read More

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November 2018
1 Read

Comprehensive analysis of miRNA-mRNA-lncRNA networks in severe asthma.

Epigenomics 2018 Nov 14. Epub 2018 Nov 14.

Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, 29 Xinlong Road, Changzhou 213003, PR China.

Aim: This study aimed to explore the molecular mechanism of severe asthma.

Materials & Methods: The shared and divergent differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs) in asthma and severe asthma were identified by RNA-sequencing. Severe asthma-specific and shared DEmiRNA-DEmRNA-DElncRNA interaction networks were performed. Read More

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November 2018
10 Reads

DNA hydroxymethylation changes in response to spinal cord damage in a multiple sclerosis mouse model.

Epigenomics 2018 Nov 14. Epub 2018 Nov 14.

Department of Orthopedics, Clinical Medical College, Yangzhou University, Yangzhou City, PR China.

Aim: Roles of DNA 5-hydroxymethylcytosine (5hmC) in myelin repair were investigated in an experimental autoimmune encephalomyelitis (EAE) mouse model via its regulation on brain-derived neurotrophic factor (BDNF).

Methods: DNA 5hmC level and its limiting enzymes were detected in EAE mice.

Results: Global 5hmC modification, Tet1 and Tet2 significantly decreased in the spinal cord tissues of EAE mice. Read More

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November 2018
3 Reads

Effectiveness of the physical activity intervention program in the PREDIMED-Plus study: a randomized controlled trial.

Int J Behav Nutr Phys Act 2018 11 13;15(1):110. Epub 2018 Nov 13.

CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.

Background: The development and implementation of effective physical activity (PA) intervention programs is challenging, particularly in older adults. After the first year of the intervention program used in the ongoing PREvención con DIeta MEDiterránea (PREDIMED)-Plus trial, we assessed the initial effectiveness of the PA component.

Methods: PREDIMED-Plus is an ongoing randomized clinical trial including 6874 participants randomized to an intensive weight-loss lifestyle intervention based on an energy-restricted Mediterranean diet (MedDiet), physical activity promotion and behavioral support and to a control group using MedDiet recommendations but without calorie restriction or PA advice. Read More

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November 2018
5 Reads

DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications.

Bioinformatics 2018 Sep;34(17):i891-i900

Department of Computer Science, University of Virginia, Charlottesville, VA, USA.

Motivation: Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing differential gene regulation. Recent studies either failed to capture combinatorial effects on differential prediction or primarily only focused on cell type-specific analysis. In this paper we develop a novel attention-based deep learning architecture, DeepDiff, that provides a unified and end-to-end solution to model and to interpret how dependencies among histone modifications control the differential patterns of gene regulation. Read More

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September 2018

Correlation between genomic index lesions and mpMRI and Ga-PSMA-PET/CT imaging features in primary prostate cancer.

Sci Rep 2018 Nov 12;8(1):16708. Epub 2018 Nov 12.

Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany.

Magnetic resonance imaging (MRI) and prostate specific membrane antigen (PSMA)- positron emission tomography (PET)/computed tomography (CT)-imaging of prostate cancer (PCa) are emerging techniques to assess the presence of significant disease and tumor progression. It is not known, however, whether and to what extent lesions detected by these imaging techniques correlate with genomic features of PCa. The aim of this study was therefore to define a genomic index lesion based on chromosomal copy number alterations (CNAs) as marker for tumor aggressiveness in prostate biopsies in direct correlation to multiparametric (mp) MRI and Ga-PSMA-PET/CT imaging features. Read More

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November 2018
1 Read

Prognostic models in primary biliary cholangitis.

J Autoimmun 2018 Dec 9;95:171-178. Epub 2018 Nov 9.

Division of Gastroenterology, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy; Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom. Electronic address:

Risk prediction modelling is important to better understand the determinants of the course and outcome of PBC and to inform the risk across the disease continuum in PBC enabling risk-stratified follow-up care and personalised therapy. Current prognostic models in PBC are based on treatment response to ursodeoxycholic acid because of the well-established relationship between alkaline phosphatase on treatment and long-term outcome. In addition, serum alkaline phosphatase correlates with ductular reaction and biliary metaplasia, which are hallmark of biliary injury. Read More

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December 2018
5 Reads

Fbxo22-mediated KDM4B degradation determines selective estrogen receptor modulator activity in breast cancer.

J Clin Invest 2018 Dec 12;128(12):5603-5619. Epub 2018 Nov 12.

Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.

The agonistic/antagonistic biocharacter of selective estrogen receptor modulators (SERMs) can have therapeutic advantages, particularly in the case of premenopausal breast cancers. Although the contradictory effects of these modulators have been studied in terms of crosstalk between the estrogen receptor α (ER) and coactivator dynamics and growth factor signaling, the molecular basis of these mechanisms is still obscure. We identify a series of regulatory mechanisms controlling cofactor dynamics on ER and SERM function, whose activities require F-box protein 22 (Fbxo22). Read More

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December 2018
8 Reads

DNA methylation profiling as a tool for testicular germ cell tumors subtyping.

Epigenomics 2018 Nov 12. Epub 2018 Nov 12.

Cancer Biology & Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.

Aim: Assess differential patterns of selected five genes' promoter methylation among testicular germ cell tumors (TGCT) subtypes.

Materials & Methods:  CRIPTO, HOXA9, MGMT, RASSF1A and SCGB3A1 promoter methylation levels were evaluated by quantitative methylation-specific PCR in 161 TGCT and 16 controls. Associations between clinicopathological parameters and promoter methylation levels were assessed, and receiver operating characteristics curve analysis was performed. Read More

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November 2018
12 Reads

Identification and integrated analysis of key differentially expressed circular RNAs in ER-positive subtype breast cancer.

Epigenomics 2018 Nov 12. Epub 2018 Nov 12.

Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China.

Aim: To systematically profile and characterize the circular RNA (circRNA) expression pattern in estrogen receptor (ER)-positive breast cancer (BC).

Materials & Methods: CircRNA expression profile was performed in ER-positive BC and adjacent nontumor tissues. The differentially expressed circRNAs (DECs) was analyzed by bioinformatics. Read More

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November 2018
3 Reads

ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.

EMBO Rep 2018 Dec 9;19(12). Epub 2018 Nov 9.

Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan

We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data ( > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data-mining platform-designated ChIP-Atlas (http://chip-atlas.org). ChIP-Atlas is able to show alignment and peak-call results for all public ChIP-seq and DNase-seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. Read More

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December 2018
6 Reads

Comprehensive analysis of HPV infection, EGFR exon 20 mutations and LINE1 hypomethylation as risk factors for malignant transformation of sinonasal-inverted papilloma to squamous cell carcinoma.

Int J Cancer 2018 Nov 9. Epub 2018 Nov 9.

Unit of Pathology, Department of Medicine and Surgery, University of Insubria and ASST Sette-Laghi, Varese, Italy.

Different risk factors are suspected to be involved in malignant transformation of sinonasal papillomas and include HPV infection, tobacco smoking, occupational exposure, EGFR/KRAS mutations and DNA methylation alterations. In our study, 25 inverted sinonasal papillomas (ISPs), 5 oncocytic sinonasal papillomas (OSP) and 35 squamous cell carcinomas (SCCs) from 54 patients were genotyped for 10 genes involved in EGFR signalling. HPV-DNA detection was performed by in-situ hybridisation and LINE-1 methylation was quantitatively determined by bisulphite-pyrosequencing. Read More

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November 2018
5 Reads

Molecular Control of Follicular Helper T cell Development and Differentiation.

Front Immunol 2018 25;9:2470. Epub 2018 Oct 25.

Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China.

Follicular helper T cells (Tfh) are specialized helper T cells that are predominantly located in germinal centers and provide help to B cells. The development and differentiation of Tfh cells has been shown to be regulated by transcription factors, such as B-cell lymphoma 6 protein (Bcl-6), signal transducer and activator of transcription 3 (STAT3) and B lymphocyte-induced maturation protein-1 (Blimp-1). In addition, cytokines, including IL-21, have been found to be important for Tfh cell development. Read More

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October 2018
11 Reads

LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells.

Genome Biol 2018 11 7;19(1):189. Epub 2018 Nov 7.

Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081, Ulm, Germany.

Background: The decline of hematopoietic stem cell (HSC) function upon aging contributes to aging-associated immune remodeling and leukemia pathogenesis. Aged HSCs show changes to their epigenome, such as alterations in DNA methylation and histone methylation and acetylation landscapes. We previously showed a correlation between high Cdc42 activity in aged HSCs and the loss of intranuclear epigenetic polarity, or epipolarity, as indicated by the specific distribution of H4K16ac. Read More

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November 2018
2 Reads

Dietary Intake in Population with Metabolic Syndrome: Is the Prevalence of Inadequate Intake Influenced by Geographical Area? Cross-Sectional Analysis from PREDIMED-Plus Study.

Nutrients 2018 Nov 4;10(11). Epub 2018 Nov 4.

Department of Preventive Medicine and Public Health, Medical School, University of Navarre, 31008 Pamplona, Spain.

Inadequate diet influences chronic diseases such as cardiovascular disease (CVD), the leading cause of death in Spain. CVD figures vary from one geographical region to another; this could be associated with different food choices. Our aim was to analyse the influence of geographical area on nutrient intakes among the Spanish adult population with Metabolic Syndrome (MetS). Read More

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November 2018
8 Reads

Polo-Like Kinase 4 (PLK4) Is Overexpressed in Central Nervous System Neuroblastoma (CNS-NB).

Bioengineering (Basel) 2018 Nov 4;5(4). Epub 2018 Nov 4.

Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.

Neuroblastoma (NB) is the most common extracranial solid tumor in pediatrics, with rare occurrences of primary and metastatic tumors in the central nervous system (CNS). We previously reported the overexpression of the polo-like kinase 4 (PLK4) in embryonal brain tumors. PLK4 has also been found to be overexpressed in a variety of peripheral adult tumors and recently in peripheral NB. Read More

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November 2018
4 Reads

Lipopolysaccharide-induced testicular dysfunction and epididymitis in mice: a critical role of tumor necrosis factor alpha.

Biol Reprod 2018 Nov 6. Epub 2018 Nov 6.

Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.

Systemic inflammation may impair male fertility, and its underlying mechanisms remain poorly understood. The present study investigates the effect of lipopolysaccharide (LPS)-induced systemic inflammation on the testis and epididymis in mice. Intraperitoneal injection of LPS significantly impaired testicular functions, including testosterone production, spermatogenesis, and blood-testis barrier permeability. Read More

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November 2018
7 Reads

Longitudinal personal DNA methylome dynamics in a human with a chronic condition.

Nat Med 2018 Dec 5;24(12):1930-1939. Epub 2018 Nov 5.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Epigenomics regulates gene expression and is as important as genomics in precision personal health, as it is heavily influenced by environment and lifestyle. We profiled whole-genome DNA methylation and the corresponding transcriptome of peripheral blood mononuclear cells collected from a human volunteer over a period of 36 months, generating 28 methylome and 57 transcriptome datasets. We found that DNA methylomic changes are associated with infrequent glucose level alteration, whereas the transcriptome underwent dynamic changes during events such as viral infections. Read More

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December 2018
47 Reads