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Epigenetic methylation signature

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https://www.readbyqxmd.com/read/28811844/lsd1-dual-function-in-mediating-epigenetic-corruption-of-the-vitamin-d-signaling-in-prostate-cancer
#1
Sebastiano Battaglia, Ellen Karasik, Bryan Gillard, Jennifer Williams, Trisha Winchester, Michael T Moser, Dominic J Smiraglia, Barbara A Foster
BACKGROUND: Lysine-specific demethylase 1A (LSD1) is a key regulator of the androgen (AR) and estrogen receptors (ER), and LSD1 levels correlate with tumor aggressiveness. Here, we demonstrate that LSD1 regulates vitamin D receptor (VDR) activity and is a mediator of 1,25(OH)2-D3 (vitamin D) action in prostate cancer (PCa). METHODS: Athymic nude mice were xenografted with CWR22 cells and monitored weekly after testosterone pellet removal. Expression of LSD1 and VDR (IHC) were correlated with tumor growth using log-rank test...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28809126/comprehensive-epigenetic-analysis-of-the-signature-genes-in-lung-adenocarcinoma
#2
Yunfeng Zhang, Weidong Zhao, Jia Zhang
AIM: This study aimed to explore the epigenetic modifications of signature genes in lung adenocarcinoma. MATERIALS & METHODS: The data of miRNA expression, mRNA expression and DNA methylation were downloaded from The Cancer Genome Atlas. Differential analysis was performed, followed by correlation analysis of miRNA-mRNA and DNA methylation-mRNA. RESULTS: A total of 14 significant inverse correlations between gene expression and DNA methylation were identified, the expressions of which were selected for further validation via GSE27262, displaying similar pattern with that of the integrated analysis...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28798132/single-cell-methylomes-identify-neuronal-subtypes-and-regulatory-elements-in-mammalian-cortex
#3
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval, Brian Bui, Terrence J Sejnowski, Timothy T Harkins, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker
The mammalian brain contains diverse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characterize them. DNA methylation is a stable epigenetic mark that distinguishes cell types and marks regulatory elements. We generated >6000 methylomes from single neuronal nuclei and used them to identify 16 mouse and 21 human neuronal subpopulations in the frontal cortex. CG and non-CG methylation exhibited cell type-specific distributions, and we identified regulatory elements with differential methylation across neuron types...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28754676/nsd1-inactivation-and-setd2-mutation-drive-a-convergence-toward-loss-of-function-of-h3k36-writers-in-clear-cell-renal-cell-carcinomas
#4
Xiaoping Su, Jianping Zhang, Roger Mouawad, Eva Compérat, Morgan Roupret, Frederick Allanic, Jérôme Parra, Marc-Olivier Bitker, Erika J Thompson, Banumathy Gowrishankar, Jane Houldsworth, John N Weinstein, Jörg Tost, Bradley M Broom, David Khayat, Jean-Philippe Spano, Nizar M Tannir, Gabriel G Malouf
Extensive dysregulation of chromatin-modifying genes in clear-cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the crosstalk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear-cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of vascular endothelial growth factor receptor genes (FLT4, FLT1 and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development...
July 28, 2017: Cancer Research
https://www.readbyqxmd.com/read/28753237/genetic-and-epigenetic-insight-into-morphospecies-in-a-reef-coral
#5
James L Dimond, Sanoosh K Gamblewood, Steven B Roberts
Incongruence between conventional and molecular systematics has left the delineation of many species unresolved. Reef-building corals are no exception, with phenotypic plasticity among the most plausible explanations for alternative morphospecies. As potential molecular signatures of phenotypic plasticity, epigenetic processes may contribute to our understanding of morphospecies. We compared genetic and epigenetic variation in Caribbean branching Porites spp., testing the hypothesis that epigenetics-specifically, differential patterns of DNA methylation-play a role in alternative morphotypes of a group whose taxonomic status has been questioned...
July 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28728135/prostate-cancer-risk-and-dna-methylation-signatures-in-aging-rats-following-developmental-bpa-exposure-a-dose-response-analysis
#6
Gail S Prins, Shu-Hua Ye, Lynn Birch, Xiang Zhang, Ana Cheong, Han Lin, Esther Calderon-Gierszal, Jacob Groen, Wen-Yang Hu, Shuk-Mei Ho, Richard B van Breemen
BACKGROUND: Previous studies have uncovered heightened prostatic susceptibility to hormone-induced neoplasia from early-life exposure to low-dose bisphenol A (BPA). However, significant data gaps remain that are essential to address for biological relevance and necessary risk assessment. OBJECTIVES: A complete BPA dose-response analysis of prostate lesions across multiple prostatic lobes was conducted that included internal BPA dosimetry, progression to adenocarcinoma with aging and mechanistic connections to epigenetically reprogramed genes...
July 11, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28713819/differential-analysis-of-genetic-epigenetic-and-cytogenetic-abnormalities-in-aml
#7
Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Acute myeloid leukemia (AML) is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc) are found to be predominantly mutated...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28708432/epigenetic-changes-of-the-esr1-gene-in-breast-tissue-of-healthy-women-a-missing-link-with-breast-cancer-risk-factors
#8
Abdolreza Daraei, Pantea Izadi, Ghasemali Khorasani, Nahid Nafissi, Mohammad Mehdi Naghizadeh, Nasim Younosi, Alipasha Meysamie, Yaser Mansoori, Milad Bastami, Javad Tavakkoly-Bazzaz
BACKGROUND: Reproductive history and obesity are among the well-recognized risk factors in the development of breast cancer, which are partially mediated by the increased exposure of breast tissues to estrogens. However, only a few studies have investigated the link between these risk factors and the pattern of methylation signatures in the breast tissue of healthy women. The role of estrogen receptor 1 (ESR1) gene hypermethylation is reportedly important in the development of breast cancer...
July 14, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28708104/fruit-and-juice-epigenetic-signatures-are-associated-with-independent-immunoregulatory-pathways
#9
Jessie Nicodemus-Johnson, Robert A Sinnott
Epidemiological evidence strongly suggests that fruit consumption promotes many health benefits. Despite the general consensus that fruit and juice are nutritionally similar, epidemiological results for juice consumption are conflicting. Our objective was to use DNA methylation marks to characterize fruit and juice epigenetic signatures within PBMCs and identify shared and independent signatures associated with these groups. Genome-wide DNA methylation marks (Illumina Human Methylation 450k chip) for 2,148 individuals that participated in the Framingham Offspring exam 8 were analyzed for correlations between fruit or juice consumption using standard linear regression...
July 14, 2017: Nutrients
https://www.readbyqxmd.com/read/28694447/impacts-of-early-life-stress-on-the-methylome-and-transcriptome-of-atlantic-salmon
#10
Hooman K Moghadam, Hanne Johnsen, Nicholas Robinson, Øivind Andersen, Even H Jørgensen, Helge K Johnsen, Vegar J Bæhr, Helge Tveiten
Exposure to environmental stressors during early-life stages can change the rate and timing of various developmental processes. Epigenetic marks affecting transcriptional regulation can be altered by such environmental stimuli. To assess how stress might affect the methylome and transcriptome in salmon, fish were treated using cold-shock and air-exposure from the eye-stage until start-feeding. The fish were either stressed prior to hatching (E), post-hatching (PH), pre- and post-hatching (EPH) or not stressed (CO)...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693373/prenatal-growth-patterns-and-birthweight-are-associated-with-differential-dna-methylation-and-gene-expression-of-cardiometabolic-risk-genes-in-human-placentas-a-discovery-based-approach
#11
Pao-Yang Chen, Alison Chu, Wen-Wei Liao, Liudmilla Rubbi, Carla Janzen, Fei-Man Hsu, Shanthie Thamotharan, Amit Ganguly, Larry Lam, Dennis Montoya, Matteo Pellegrini, Sherin U Devaskar
Inherent genetic programming and environmental factors affect fetal growth in utero. Epidemiologic data in growth-altered fetuses, either intrauterine growth restricted (IUGR) or large for gestational age (LGA), demonstrate that these newborns are at increased risk of cardiometabolic disease in adulthood. There is growing evidence that the in utero environment leads to epigenetic modification, contributing to eventual risk of developing heart disease or diabetes. In this study, we used reduced representation bisulfite sequencing to examine genome-wide DNA methylation variation in placental samples from offspring born IUGR, LGA, and appropriate for gestational age (AGA) and to identify differential methylation of genes important for conferring risk of cardiometabolic disease...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28691915/forensic-individual-age-estimation-with-dna-from-initial-approaches-to-methylation-tests
#12
REVIEW
A Freire-Aradas, C Phillips, M V Lareu
Individual age estimation is a key factor in forensic science analysis that can provide very useful information applicable to criminal, legal, and anthropological investigations. Forensic age inference was initially based on morphological inspection or radiography and only later began to adopt molecular approaches. However, a lack of accuracy or technical problems hampered the introduction of these DNA-based methodologies in casework analysis. A turning point occurred when the epigenetic signature of DNA methylation was observed to gradually change during an individual´s lifespan...
July 2017: Forensic Science Review
https://www.readbyqxmd.com/read/28691768/microbiome-inflammation-epigenetic-alterations-and-mental-diseases
#13
REVIEW
Reza Alam, Hamid M Abdolmaleky, Jin-Rong Zhou
Major mental diseases such as autism, bipolar disorder, schizophrenia, and major depressive disorder are debilitating illnesses with complex etiologies. Recent findings show that the onset and development of these illnesses cannot be well described by the one-gene; one-disease approach. Instead, their clinical presentation is thought to result from the regulative interplay of a large number of genes. Even though the involvement of many genes are likely, up regulating and activation or down regulation and silencing of these genes by the environmental factors play a crucial role in contributing to their pathogenesis...
July 10, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28684632/immunodeficiency-in-pancreatic-adenocarcinoma-with-diabetes-revealed-by-comparative-genomics
#14
Yuanqing Yan, Ruli Gao, Thao L P Trinh, Maria Bartolomeo Grant
Purpose: Pancreatic adenocarcinomas (PAAD) often are not diagnosed until their late stages leaving no effective treatments. Currently immunotherapy provides a promising treatment option against this malignancy. However, a set of immunotherapy agents benefit patients with many types of cancer, but not PAAD. Sharing the origin in the same organ, diabetes and PAAD tend to occur concurrently. We aimed to identify the impact of diabetes on immunotherapy of PAAD by conducting a comparative genomics analysis.    <p>Experimental Design: We analyzed levels 3 PAAD genomics data (RNAseq, miRNAseq, DNA methylation, somatic copy number and somatic mutation) from TCGA and Firehose...
July 6, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28684528/wnt-%C3%A3-catenin-activation-by-epigenetically-aberrant-stroma-drives-myelodysplastic-syndrome
#15
Tushar Bhagat, Si Chen, Matthias Bartenstein, Trevor S Barlowe, Dagny von Ahrens, Gaurav S Choudhary, Patrick Tivnan, Elianna Amin, A Mario Marcondes, Mathijs A Sanders, Remco M Hoogenboezem, Suman Kambhampati, Nandini Ramachandra, Ioannis Mantzaris, Vineeth Sukrithan, Remi Laurence, Robert Lopez, Prafulla Bhagat, Orsi Giricz, Davendra Sohal, Amittha Wickrema, Cecilia Cs Yeung, Kira Gritsman, Peter D Aplan, Konrad Hochedlinger, Yiting Yu, Kith Pradhan, Jinghang Zhang, John Greally, Siddhartha Mukherjee, Andrea Pellagatti, Jacqueline Boultwood, Britta Will, Ulrich Steidl, Marc Hgp Raaijmakers, H J Deeg, Michael G Kharas, Amit Verma
The bone marrow microenvironment influences malignant hematopoiesis but how it promotes leukemogenesis has not been elucidated. Additionally, the role of the bone marrow stroma in regulating clinical responses to DNA methyltransferase inhibitors (DNMTi) is also poorly understood. In this study, we conducted a DNA methylome analysis of bone marrow-derived stromal cells from myelodysplastic syndrome (MDS) patients and observed widespread aberrant cytosine hypermethylation occurring preferentially outside CpG islands...
July 6, 2017: Cancer Research
https://www.readbyqxmd.com/read/28683715/plant-rrbs-a-bisulfite-and-next-generation-sequencing-based-methylome-profiling-method-enriching-for-coverage-of-cytosine-positions
#16
Martin Schmidt, Michiel Van Bel, Magdalena Woloszynska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
BACKGROUND: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome-wide information on cytosine methylation...
July 6, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28682231/g%C3%A3-n%C3%A3-tique-et-%C3%A3-pig%C3%A3-n%C3%A3-tique-des-troubles-des-conduites-alimentaires
#17
Nicolas Ramoz, Julia Clarke, Philip Gorwood
Eating disorders (EDs) are complex and multifactorial psychiatric illnesses that induce significant and sustained pathological disruption of food intake. The Diagnostic and Statistical Manual of Mental Illnesses (DSM-5) describes the clinical criteria of major disorders including anorexia nervosa (AN), bulimia nervosa (BN) and binge eating disorder (BED). The neurobiological basis of food intake is well characterized. Epidemiological studies reported a heritability about 70% in AN and 60% in BN, suggesting that genetic factors are involved in the vulnerability to EDs...
2017: Biologie Aujourd'hui
https://www.readbyqxmd.com/read/28667006/whole-genome-and-epigenomic-landscapes-of-etiologically-distinct-subtypes-of-cholangiocarcinoma
#18
Apinya Jusakul, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng, Su Pin Choo, Swe Swe Myint, Raynoo Thanan, Sanjanaa Nagarajan, Weng Khong Lim, Cedric Chuan Young Ng, Arnoud Boot, Mo Liu, Choon Kiat Ong, Vikneswari Rajasegaran, Stefanus Lie, Alvin Soon Tiong Lim, Tse Hui Lim, Jing Tan, Jia Liang Loh, John R McPherson, Narong Khuntikeo, Vajaraphongsa Bhudhisawasdi, Puangrat Yongvanit, Sopit Wongkham, Yasushi Totoki, Hiromi Nakamura, Yasuhito Arai, Satoshi Yamasaki, Pierce K H Chow, Alexander Yaw Fui Chung, London Lucien Peng Jin Ooi, Kiat Hon Lim, Simona Dima, Dan G Duda, Irinel Popescu, Philippe Broet, Sen-Yung Hsieh, Ming-Chin Yu, Aldo Scarpa, Jiaming Lai, Di-Xian Luo, Andre Lopes Carvalho, André Luiz Vettore, Hyungjin Rhee, Young Nyun Park, Ludmil Alexandrov, Raluca Gordan, Steven G Rozen, Tatsuhiro Shibata, Chawalit Pairojkul, Bin Tean Teh, Patrick Tan
Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters - Fluke-Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements...
June 30, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28654914/an-epigenetic-signature-of-adhesion-molecules-predicts-poor-prognosis-of-ovarian-cancer-patients
#19
Ping-Ying Chang, Yu-Ping Liao, Hui-Chen Wang, Yu-Chih Chen, Rui-Lan Huang, Yu-Chi Wang, Chiou-Chung Yuan, Hung-Cheng Lai
DNA methylation is a promising biomarker for cancer. The epigenetic effects of cell adhesion molecules may affect the therapeutic outcome and the present study examined their effects on survival in ovarian cancer. We integrated methylomics and genomics datasets in The Cancer Genome Atlas (n = 391) and identified 106 highly methylated adhesion-related genes in ovarian cancer tissues. Univariate analysis revealed the methylation status of eight genes related to progression-free survival. In multivariate Cox regression analysis, four highly methylated genes (CD97, CTNNA1, DLC1, HAPLN2) and three genes (LAMA4, LPP, MFAP4) with low methylation were significantly associated with poor progression-free survival...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644958/translating-cancer-epigenomics-into-the-clinic-focus-on-lung-cancer
#20
REVIEW
Josep Mari-Alexandre, Angel Diaz-Lagares, Maria Villalba, Oscar Juan, Ana B Crujeiras, Alfonso Calvo, Juan Sandoval
Epigenetic deregulation is increasingly being recognized as a hallmark of cancer. Recent studies have identified many new epigenetic biomarkers, some of which are being introduced into clinical practice for diagnosis, molecular classification, prognosis or prediction of response to therapies. O-6-methylguanine-DNA methyltransferase gene is the most clinically advanced epigenetic biomarker as it predicts the response to temozolomide and carmustine in gliomas. Therefore, epigenomics may represent a novel and promising tool for precision medicine, and in particular, the detection of epigenomic biomarkers in liquid biopsies will be of great interest for monitoring diseases in patients...
June 2, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
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