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Methylation enrichment

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https://www.readbyqxmd.com/read/28101802/cold-pcr-technologies-in-the-area-of-personalized-medicine-methodology-and-applications
#1
REVIEW
Florence Mauger, Alexandre How-Kit, Jörg Tost
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation...
January 18, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#2
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28099880/modifications-of-inhibitory-transmission-onto-pyramidal-neurons-by-postnatal-exposure-to-mk-801-effects-of-enriched-environment
#3
Amir Shojaei, Afsaneh Kamali Anaraki, Javad Mirnajafi-Zadeh, Nafiseh Atapour
Early enriched environment (EE) prevents several deficits associated with postnatal MK-801 [N-Methyl-D-Aspartate (NMDA) receptor antagonist] treatment such as cognitive and locomotor deficits. We sought physiological correlates to such changes by looking at inhibitory synaptic inputs onto pyramidal cells in a prefrontal cortex slice preparation. Pharmacologically isolated γ-amino-butyric acid A (GABAA) receptor-mediated currents were measured using whole-cell patch clamp recordings. Wistar rats were raised in standard or EE from birth up to the time of experiments and were injected with saline or MK-801 (1mg/kg) on postnatal days (P) 6-10...
January 15, 2017: International Journal of Developmental Neuroscience
https://www.readbyqxmd.com/read/28096468/o-glcnac-expression-levels-epigenetically-regulate-colon-cancer-tumorigenesis-by-affecting-the-cancer-stem-cell-compartment-via-modulating-expression-of-transcriptional-factor-mybl1
#4
Huabei Guo, Bing Zhang, Alison V Nairn, Tamas Nagy, Kelley W Moremen, Phillip Buckhaults, Michael Pierce
To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with OGT knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of CCSC population was observed in the tumor cells after OGT knockdown, while tumor cells treated with O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment...
January 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28091790/chemically-modified-surface-functional-groups-of-alcaligenes-sp-s-xj-1-to-enhance-its-demulsifying-capability
#5
Yuyan Zhang, Jia Liu, Xiangfeng Huang, Lijun Lu, Kaiming Peng
Cell-surface functional groups (amino, carboxyl, hydroxyl, as well as phosphate) were chemically modified in various ways to enhance the demulsification capability of the demulsifying bacteria Alcaligenes sp. S-XJ-1. Results demonstrated that the demulsifying activity was significantly inhibited by amino enrichment with cetyl trimethyl ammonium bromide, amino methylation, hydroxyl acetylation, and phosphate esterification, but was gradually promoted by carboxyl blocking with increasing the extents of esterification...
January 14, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28090296/endotoxin-and-mechanical-stress-induced-epigenetic-changes-in-the-regulation-of-the-nicotinamide-phosphoribosyltransferase-promoter
#6
Venkateswaran Ramamoorthi Elangovan, Sara M Camp, Gabriel T Kelly, Ankit A Desai, Djanybek Adyshev, Xiaoguang Sun, Stephen M Black, Ting Wang, Joe G N Garcia
Mechanical ventilation, a lifesaving intervention for patients with acute respiratory distress syndrome (ARDS), also unfortunately contributes to excessive mechanical stress and impaired lung physiological and structural integrity. We have elsewhere established the pivotal role of increased nicotinamide phosphoribosyltransferase (NAMPT) transcription and secretion as well as its direct binding to the toll-like receptor 4 (TLR4) in the progression of this devastating syndrome; however, regulation of this critical gene in ventilator-induced lung injury (VILI) is not well characterized...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28089213/a-genome-wide-profiling-of-brain-dna-hydroxymethylation-in-alzheimer-s-disease
#7
Jinying Zhao, Yun Zhu, Jingyun Yang, Lin Li, Hao Wu, Philip L De Jager, Peng Jin, David A Bennett
INTRODUCTION: DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS: Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology...
January 6, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28077784/identification-and-characterization-of-hpv-independent-cervical-cancers
#8
Carolyn E Banister, Changlong Liu, Lucia Pirisi, Kim E Creek, Phillip J Buckhaults
BACKGROUND: Human papillomavirus (HPV) initiates cervical cancer, and continuous expression of HPV oncogenes E6 and E7 is thought to be necessary to maintain malignant growth. Current therapies target proliferating cells, rather than specific pathways, and most experimental therapies specifically target E6/E7. We investigated the presence and expression of HPV in cervical cancer, to correlate HPV oncogene expression with clinical and molecular features of these tumors that may be relevant to new targeted therapies...
January 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#9
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28074068/a-cpg-island-methylator-phenotype-in-acute-myeloid-leukemia-independent-of-idh-mutations-and-associated-with-a-favorable-outcome
#10
A D Kelly, H Kroeger, J Yamazaki, R Taby, F Neumann, S Yu, J T Lee, B Patel, Y Li, R He, S Liang, Y Lu, M Cesaroni, S A Pierce, S M Kornblau, C E Bueso-Ramos, F Ravandi, H M Kantarjian, J Jelinek, J-Pj Issa
Genetic changes are infrequent in acute myeloid leukemia (AML) compared to other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation (DREAM) data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CIMP (A-CIMP(+))...
January 11, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#11
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28069683/targeted-deep-sequencing-reveals-full-methylation-profiles-of-multiple-hpv-types-and-potential-biomarkers-for-cervical-cancer-progression
#12
Pengyuan Liu, Marissa Iden, Samantha Fye, Yi-Wen Huang, Elizabeth Hopp, Chen Chu, Yan Lu, Janet S Rader
BACKGROUND: Invasive cervical cancer (ICC) and its premalignant phase (cervical intraepithelial neoplasia; CIN1-3) are distinguished by gynecological and pathological examination, yet no current methodologies can predict precancerous lesions that are destined to progress to ICC. Thus, development of reliable assays to assess patient prognosis is much needed. METHODS: HPV DNA methylation is significantly altered in cervical disease. Using an HPV-enrichment approach and next-generation DNA sequencing, methylation status was characterized in a case-case comparison of CIN (n = 2 CIN1; n = 2 CIN2; n = 20 CIN3) and ICC (n = 37) samples...
January 9, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28069425/an-epigenome-wide-association-study-of-total-serum-immunoglobulin-e-in-hispanic-children
#13
Wei Chen, Ting Wang, Maria Pino-Yanes, Erick Forno, Liming Liang, Qi Yan, Donglei Hu, Daniel E Weeks, Andrea Baccarelli, Edna Acosta-Perez, Celeste Eng, Yueh-Ying Han, Nadia Boutaoui, Catherine Laprise, Gwyneth A Davies, Julian M Hopkin, Miriam F Moffatt, William O C M Cookson, Glorisa Canino, Esteban G Burchard, Juan C Celedón
BACKGROUND: Total immunoglobulin E (IgE) is a therapeutic target in allergic diseases. DNA methylation in white blood cells (WBCs) was associated with total IgE in an epigenome-wide association study (EWAS) of Caucasians. Whether DNA methylation of eosinophils explains those findings is insufficiently understood. METHODS: We tested for association between genome-wide DNA methylation in WBCs and total IgE in two studies of Hispanic children: the Puerto Rico Genetics of Asthma and Lifestyle Study (PR-GOAL, n = 306) and the Genes-environments and Admixture in Latino Americans (GALA II, n = 573)...
January 6, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28068903/comparative-transcriptome-analysis-reveals-candidate-genes-for-the-biosynthesis-of-natural-insecticide-in-tanacetum-cinerariifolium
#14
Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee, Laiq Ur Rahman
BACKGROUND: Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties. Despite such advantages of commercial value coming with the eco-friendly tag, most enzymes/genes involved in the pyrethrin biosynthesis pathway remain unidentified and uncharacterized. Since the flowers of Tanacetum cinerariifolium are rich in major pyrethrins, next generation transcriptome sequencing was undertaken to compare the flowers and the leaves of the plant de novo to identify differentially expressed transcripts and ascertain which among them might be involved in and responsible for the differential accumulation of pyrethrins in T...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068325/trim28-interacts-with-ezh2-and-swi-snf-to-activate-genes-that-promote-mammosphere-formation
#15
J Li, Y Xi, W Li, R L McCarthy, S A Stratton, W Zou, W Li, S Y Dent, A K Jain, M C Barton
Histone methyl transferase EZH2 (Enhancer of Zeste Homolog 2) is generally associated with H3K27 methylation and gene silencing, as a member of the polycomb repressor 2 (PRC2) complex. Immunoprecipitation and mass spectrometry of the EZH2-protein interactome in estrogen receptor positive, breast cancer-derived MCF7 cells revealed EZH2 interactions with subunits of chromatin remodeler SWI/SNF complex and TRIM28, which formed a complex with EZH2 distinct from PRC2. Unexpectedly, transcriptome profiling showed that EZH2 primarily activates, rather than represses, transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28062796/integrated-cellular-and-plasma-proteomics-of-contrasting-b-cell-cancers-reveals-common-unique-and-systemic-signatures
#16
Harvey E Johnston, Matthew J Carter, Kerry L Cox, Melanie Dunscombe, Antigoni Manousopoulou, Paul A Townsend, Spiro D Garbis, Mark S Cragg
Approximately 800,000 leukaemia and lymphoma cases are diagnosed worldwide each year. Burkitt's lymphoma (BL) and chronic lymphocytic leukaemia (CLL), are examples of contrasting B-cell cancers; BL is a highly aggressive lymphoid tumour, frequently affecting children, whilst CLL typically presents as an indolent, slow-progressing leukaemia affecting the elderly. The B-cell-specific over-expression of the myc and tcl1 oncogenes in mice induce spontaneous malignancies modelling BL and CLL, respectively. Quantitative mass spectrometry proteomics and isobaric labelling were employed to examine the biology underpinning contrasting Eμ-myc and Eμ-TCL1 B-cell tumours...
January 4, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28060835/histone-h3k9-demethylase-jmjd2b-activates-adipogenesis-by-regulating-h3k9-methylation-on-ppar%C3%AE-and-c-ebp%C3%AE-during-adipogenesis
#17
Min-Kyung Jang, Ji-Hyun Kim, Myeong Ho Jung
Previous studies have shown that tri- or di-methylation of histone H3 at lysine 9 (H3K9me3/me2) on the promoter of the peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα) contribute to the repression of PPARγ and C/EBPα and inhibition of adipogenesis in 3T3-L1 preadipocytes. The balance of histone methylation is regulated by histone methyltransferases and demethylases. However, it is poorly understood which demethylases are responsible for removing H3K9me3/me2 on the promoter of PPARγ and C/EBPα...
2017: PloS One
https://www.readbyqxmd.com/read/28059585/initiation-of-aberrant-dna-methylation-patterns-and-heterogeneity-in-precancerous-lesions-of-human-hepatocellular-cancer
#18
Ryan A Hlady, Dan Zhou, William Puszyk, Lewis R Roberts, Chen Liu, Keith D Robertson
While intratumor heterogeneity contributes to disease progression, metastasis, and resistance to chemotherapy, it also provides a route to understanding the evolution and drivers of disease. Defects in epigenetic landscapes are intimately linked to pathogenesis of a variety of human diseases, with epigenetic deregulation promoting tumorigenesis. Understanding epigenetic heterogeneity is crucial in hepatocellular carcinoma (HCC), where epigenetic alterations are frequent, early, and pathogenic events. We determined genome-wide DNA methylation and copy number variation leveraging the Infinium 450 K in a series of regenerative nodules from within single patient livers...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28056824/the-emerging-landscape-of-dynamic-dna-methylation-in-early-childhood
#19
Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma A Jankipersadsing, Pieter van der Vlies, Cleo C van Diemen, Bianca van Rijkom, Jocelyne Just, Inger Kull, Juha Kere, Josep Maria Antó, Jean Bousquet, Alexandra Zhernakova, Cisca Wijmenga, Isabella Annesi-Maesano, Jordi Sunyer, Erik Melén, Yang Li, Dirkje S Postma, Gerard H Koppelman
BACKGROUND: DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. RESULTS: By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053625/lipid-raft-integrity-is-required-for-survival-of-triple-negative-breast-cancer-cells
#20
Anil Badana, Madhuri Chintala, Gayathri Varikuti, Nagaseshu Pudi, Seema Kumari, Vijaya Rachel Kappala, Rama Rao Malla
PURPOSE: Lipid rafts are cholesterol enriched microdomains that colocalize signaling pathways involved in cell proliferation, metastasis, and angiogenesis. We examined the effect of methyl-β-cyclodextrin (MβCD)-mediated cholesterol extraction on the proliferation, adhesion, invasion, and angiogenesis of triple negative breast cancer (TNBC) cells. METHODS: We measured cholesterol and estimated cell toxicity. Detergent resistant membrane (DRM) and non-DRM fractions were separated using the OptiPrep gradient method...
December 2016: Journal of Breast Cancer
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