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CpG methylation

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https://www.readbyqxmd.com/read/30541061/dna-demethylation-facilitates-the-specific-transcription-of-the-mouse-x-linked-tsga8-gene-in-round-spermatids
#1
Yongjie Lu, Shunyao Liao, Wenling Tu, Bo Yang, Shasha Liu, Xue Pei, Dachang Tao, Yilu Lu, Yongxin Ma, Yuan Yang, Yunqiang Liu
Some X-linked genes necessary for spermiogenesis are specifically activated in the post-meiotic germ cells. However, the regulatory mechanism about this activation is not clearly understood. Here, we examined the potential mechanism controlling the transcriptional activation of the mouse testis specific gene A8 (Tsga8) gene in round spermatids. We observed that the Tsga8 expression was negatively correlated with the methylation level of the CpG sites in its core promoter. During spermatogenesis, the Tsga8 promoter was methylated in spermatogonia, and then demethylated in spermatocytes...
December 12, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/30540994/cpg-island-methylator-phenotype-may-predict-poor-overall-survival-of-patients-with-stage-iv-colorectal-cancer
#2
Kuo-Hsing Chen, Liang-In Lin, Li-Hui Tseng, Yu-Lin Lin, Jau-Yu Liau, Jia-Huei Tsai, Jin-Tung Liang, Been-Ren Lin, Ann-Lii Cheng, Kun-Huei Yeh
OBJECTIVE: We aimed to study the prognostic role of CpG island methylator phenotype (CIMP) in patients with different stages of colorectal cancer (CRC). MATERIAL AND METHODS: We analyzed CIMP in stage I-IV CRC specimens from patients who were diagnosed between 2005 and 2013. CIMP status was determined using a 5-gene MethyLight-based assay. The clinicopathologic characteristics were reviewed and the overall survival (OS) was compared between patients with CIMP-high CRC and those with CIMP-low/negative CRC...
December 12, 2018: Oncology
https://www.readbyqxmd.com/read/30540848/exploring-the-influence-from-whole-blood-dna-extraction-methods-on-infinium-450k-dna-methylation
#3
Hanne Sagsveen Hjorthaug, Kristina Gervin, Petter Mowinckel, Monica Cheng Munthe-Kaas
Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potentially confounding DNA methylation studies. DNA was isolated from healthy blood donors (n = 10) using three different extraction methods (i.e. two automatic extractions methods based on magnetic beads or isopropanol precipitation, and manual organic extraction)...
2018: PloS One
https://www.readbyqxmd.com/read/30537986/a-novel-fli1-exonic-circular-rna-promotes-metastasis-in-breast-cancer-by-coordinately-regulating-tet1-and-dnmt1
#4
Naifei Chen, Gang Zhao, Xu Yan, Zheng Lv, Hongmei Yin, Shilin Zhang, Wei Song, Xueli Li, Lingyu Li, Zhonghua Du, Lin Jia, Lei Zhou, Wei Li, Andrew R Hoffman, Ji-Fan Hu, Jiuwei Cui
BACKGROUND: Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is known about the mechanisms underlying the activation of this proto-oncogene in tumors. RESULTS: Immunohistochemical staining showed that FLI1 is aberrantly overexpressed in advanced stage and metastatic breast cancers. Using a CRISPR Cas9-guided immunoprecipitation assay, we identify a circular RNA in the FLI1 promoter chromatin complex, consisting of FLI1 exons 4-2-3, referred to as FECR1...
December 11, 2018: Genome Biology
https://www.readbyqxmd.com/read/30537372/bioinformatic-analysis-of-the-prognostic-value-of-the-lncrnas-encoding-snornas-in-hepatocellular-carcinoma
#5
Qingyao Zhu, Hongjie Yang, Peng Cheng, Qian Han
Some lncRNAs can encode small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which exert diverse regulatory effects on cellular processes. In this study, using RNA-seq and survival data in the Cancer Genome Atlas (TCGA)-Liver Hepatocellular Carcinoma (LIHC), we examined the expression profile of some SNHG genes and explored their prognostic value in hepatocellular carcinoma (HCC). Level-3 RNA-sequencing data, the clinicopathological and survival data of patients with primary HCC were downloaded from the UCSC Xena browser (https://xenabrowser...
December 8, 2018: BioFactors
https://www.readbyqxmd.com/read/30537139/tamoxifen-therapy-benefit-predictive-signature-combining-with-prognostic-signature-in-surgical-only-er-positive-breast-cancer
#6
Feng Lv, Wei-Hua Jin, Xian-Lin Zhang, Zhong-Rui Wang, Ai-Jun Sun
Tamoxifen treatment is important assistant for estrogen-receptor-positive breast cancer (BRCA) after resection. This study aimed to identify signatures for predicting the prognosis of patients with BRCA after tamoxifen treatment. Data of gene-specific DNA methylation (DM), as well as the corresponding clinical data for the patients with BRCA, were obtained from The Cancer Genome Atlas and followed by systematic bioinformatics analyses. After mapping these DM CPG sites onto genes, we finally obtained 352 relapse-free survival (RFS) associated DM genes, with which 61,776 gene pairs were combined, including 1,614 gene pairs related to RFS...
December 7, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/30536762/the-array-of-clinical-phenotypes-of-males-with-mutations-in-methyl-cpg-binding-protein-2
#7
Jeffrey L Neul, Timothy A Benke, Eric D Marsh, Steven A Skinner, Jonathan Merritt, David N Lieberman, Shannon Standridge, Timothy Feyma, Peter Heydemann, Sarika Peters, Robin Ryther, Mary Jones, Bernhard Suter, Walter E Kaufmann, Daniel G Glaze, Alan K Percy
Mutations in the X-linked gene MECP2 are associated with a severe neurodevelopmental disorder, Rett syndrome (RTT), primarily in girls. It had been suspected that mutations in Methyl-CpG-binding protein 2 (MECP2) led to embryonic lethality in males, however such males have been reported. To enhance understanding of the phenotypic spectrum present in these individuals, we identified 30 males with MECP2 mutations in the RTT Natural History Study databases. A wide phenotypic spectrum was observed, ranging from severe neonatal encephalopathy to cognitive impairment...
December 7, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/30535864/receptor-tyrosine-kinase-ephb3-a-prognostic-indicator-in-colorectal-carcinoma
#8
Zhuoqi Xuan, Jianming Huang, Lin Gao, Yong Wang, Jiandong Wang, Yueming Sun
Although EphB3 expression is down-regulated in colorectal cancer (CRC) cells compared with normal intestinal epithelial cells, the relationship between EphB3 expression and clinicopathological parameters in CRC is unclear. We examined EphB3 expression in 128 CRC tissue specimens and in 19 adenoma specimens using immunohistochemistry. The relationships between EphB3 expression and clinicopathological parameters, KRAS mutations, BRAF V600E mutation, MSI and survival were evaluated using Spearman's rank correlation and Kaplan-Meier survival analyses, respectively...
December 7, 2018: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/30533020/validation-of-epigenetic-mechanisms-regulating-gene-expression-in-canine-b-cell-lymphoma-an-in-vitro-and-in-vivo-approach
#9
Silvia Da Ros, Luca Aresu, Serena Ferraresso, Eleonora Zorzan, Eugenio Gaudio, Francesco Bertoni, Mauro Dacasto, Mery Giantin
Despite canine B-cell Lymphoma (BCL) representing the most common haematological tumour, epigenetic events driving development and progression are scarcely known. Recently, canine Diffuse Large BCL (DLBCL) DNA methylome by genome-wide CpG microarray has identified genes and pathways associated to pathogenesis. To validate data previously obtained by array analysis, the CLBL-1 cell line was used and the HOXD10, FGFR2, ITIH5 and RASAL3 genes were selected. CLBL-1 cells were treated with two hypomethylating drugs (HDs; IC50, 50% inhibitory concentration), i...
2018: PloS One
https://www.readbyqxmd.com/read/30531021/mgmt-is-down-regulated-independently-of-promoter-dna-methylation-in-rats-with-all-trans-retinoic-acid-induced-spina-bifida-aperta
#10
He-Nan Zhang, Yi Guo, Wei Ma, Jia Xue, Wei-Lin Wang, Zheng-Wei Yuan
O6-methylguanine DNA methyltransferase (MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expression and methylation levels in the early embryo and in different embryonic stages, as well as the relationship between MGMT and neural tube defects. Spina bifida aperta was induced in rats by a single intragastric administration of all-trans retinoic acid on embryonic day (E) 10, whereas normal control rats received the same amount of olive oil on the same embryonic day...
February 2019: Neural Regeneration Research
https://www.readbyqxmd.com/read/30530921/dna-methylation-based-age-prediction-and-telomere-length-in-white-blood-cells-and-cumulus-cells-of-infertile-women-with-normal-or-poor-response-to-ovarian-stimulation
#11
Scott J Morin, Xin Tao, Diego Marin, Yiping Zhan, Jessica Landis, Jenna Bedard, Richard T Scott, Emre Seli
An algorithm assessing the methylation levels of 353 informative CpG sites in the human genome permits accurate prediction of the chronologic age of a subject. Interestingly, when there is discrepancy between the predicted age and chronologic age (age acceleration or "AgeAccel"), patients are at risk for morbidity and mortality. Identification of infertile patients at risk for accelerated reproductive senescence may permit preventative action. This study aimed to assess the accuracy of the "epigenetic clock" concept in reproductive age women undergoing fertility treatment by applying the age prediction algorithm in peripheral (white blood cells [WBCs]) and follicular somatic cells (cumulus cells [CCs]), and to identify whether women with premature reproductive aging (diminished ovarian reserve) were at risk of AgeAccel in their age prediction...
December 8, 2018: Aging
https://www.readbyqxmd.com/read/30529013/identification-of-a-robust-methylation-classifier-for-cutaneous-melanoma-diagnosis
#12
Kathleen Conway, Sharon N Edmiston, Joel S Parker, Pei Fen Kuan, Yi-Hsuan Tsai, Pamela A Groben, Daniel C Zedek, Glynis A Scott, Eloise A Parrish, Honglin Hao, Michelle V Pearlstein, Jill S Frank, Craig C Carson, Matthew D Wilkerson, Xiaobei Zhao, Nathaniel A Slater, Stergios J Moschos, David W Ollila, Nancy E Thomas
Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screen, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists...
December 6, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/30526669/genome-wide-dna-methylation-profiling-shows-a-distinct-epigenetic-signature-associated-with-lung-macrophages-in-cystic-fibrosis
#13
Youdinghuan Chen, David A Armstrong, Lucas A Salas, Haley F Hazlett, Amanda B Nymon, John A Dessaint, Daniel S Aridgides, Diane L Mellinger, Xiaoying Liu, Brock C Christensen, Alix Ashare
BACKGROUND: Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls...
December 10, 2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/30522400/dna-methylation-inhibitor-5-aza-2-deoxycytidine-modulates-endometrial-receptivity-through-upregulating-hoxa10-expression
#14
Li Wang, Ya Jing Tan, Min Wang, Yi Fei Chen, Xin Yan Li
Endometrial receptivity is a critical factor for embryo implantation. A decrease in endometrial homeobox A10 (HOXA10) expression is associated with hypermethylation of its promoter and lower endometrial receptivity in animals and humans. 5-Aza-2'-deoxycytidine (AZA) is a DNA methyltransferase inhibitor. However, whether demethylation of the HOXA10 gene could increase the receptivity of the human endometrium remains unknown. Homeobox A10 promoter methylation was analyzed using bisulfite genomic sequencing polymerase chain reaction...
December 6, 2018: Reproductive Sciences
https://www.readbyqxmd.com/read/30521419/cannabinoid-exposure-and-altered-dna-methylation-in-rat-and-human-sperm
#15
Susan K Murphy, Nilda Itchon-Ramos, Zachary Visco, Zhiqing Huang, Carole Grenier, Rose Schrott, Kelly Acharya, Marie-Helene Boudreau, Thomas M Price, Douglas J Raburn, David L Corcoran, Joseph E Lucas, John T Mitchell, F Joseph McClernon, Marty Cauley, Brandon J Hall, Edward D Levin, Scott H Kollins
Little is known about the reproductive effects of paternal cannabis exposure. We evaluated associations between cannabis or tetrahydrocannabinol (THC) exposure and altered DNA methylation in sperm from humans and rats, respectively. DNA methylation, measured by reduced representation bisulfite sequencing, differed in the sperm of human users from non-users by at least 10% at 3,979 CpG sites. Pathway analyses indicated Hippo Signaling and Pathways in Cancer as enriched with altered genes (Bonferroni p<0.02)...
December 6, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/30516085/genome-epigenome-interactions-associated-with-myalgic-encephalomyelitis-chronic-fatigue-syndrome
#16
Santiago Herrera, Wilfred C de Vega, David Ashbrook, Suzanne D Vernon, Patrick O McGowan
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, potential interactions between DNA methylation and genetic background in relation to ME/CFS have not been examined. In this study we explored this association by characterizing the epigenetic (~480 thousand CpG loci) and genetic (~4...
December 5, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/30514328/promoter-hypomethylation-mediated-upregulation-of-microrna-10b-3p-targets-foxo3-to-promote-the-progression-of-esophageal-squamous-cell-carcinoma-escc
#17
Yi-Fang Lu, Jia-Rui Yu, Zhao Yang, Guan-Xia Zhu, Peng Gao, Huan Wang, Si-Yuan Chen, Jie Zhang, Mei-Yue Liu, Yi Niu, Xiao-Mei Wei, Wei Wang, Feng-Jin Ye, Li-Xin Zhang, Yue Zhao, Guo-Gui Sun
BACKGROUND: Esophageal cancer is a high incident cancer worldwide with poor survival and limited therapeutic options. Alterations of microRNAs are common in cancers, and many of these micro RNAs are potential therapeutic and diagnostic targets to treat these cancers. miR-10b-3p located in chromosome region 2q31.1, and its expression is frequently increased in esophageal squamous cell carcinoma (ESCC). However, the biological functions, clinical significance and therapeutic implications of miR-10b-3p in ESCC remain unclear...
December 4, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/30513988/supplementation-of-ju%C3%A3-ara-berry-euterpe-edulis-mart-modulates-epigenetic-markers-in-monocytes-from-obese-adults-a-double-blind-randomized-trial
#18
Aline Boveto Santamarina, Giovana Jamar, Laís Vales Mennitti, Helena de Cássia César, Verdiana Vera de Rosso, José Ronnie Vasconcelos, Lila Missae Oyama, Luciana Pellegrini Pisani
Nutrigenomics is an emerging field in obesity since epigenetic markers can be modified by environmental factors including diet. Considering juçara composition-rich in anthocyanins, monounsaturated fatty acids (MUFAs) and fibers-it has the potential for epigenetic modulation. We evaluated the juçara supplementation modulating the serum fatty acids profile and epigenetic markers in monocytes of adult obese humans. It was a randomized double-blind, controlled trial with 27 obese (Body mass index between 30.0 and 39...
December 3, 2018: Nutrients
https://www.readbyqxmd.com/read/30511892/sycp2-expression-is-a-novel-prognostic-biomarker-in-luminal-a-b-breast-cancer
#19
Chihua Wu, Youlin Tuo
AIM: To explore the prognostic value of synaptonemal complex protein-2 (SYCP2) in different subtypes of breast cancer. Patients & materials: In silico bioinformatic analysis was conducted using large databases. RESULTS: SYCP2 was only significantly upregulated in luminal B tumors compared with the adjacent normal tissues. SYCP2 expression was an independent indicator of shorter overall survival in luminal A patients (hazard ratio: 2.269; 95% CI: 1.059-4.862; p = 0...
December 4, 2018: Future Oncology
https://www.readbyqxmd.com/read/30510602/hypermethylation-of-apc2-is-a-predictive-epigenetic-biomarker-for-chinese-colorectal-cancer
#20
Yuan He, Li-Yue Sun, Jing Wang, Rui Gong, Qiong Shao, Zi-Chen Zhang, Zu-Lu Ye, Hai-Yun Wang, Rui-Hua Xu, Jian-Yong Shao
Objective: To investigate methylation of the adenomatosis polyposis coli homologue (APC2) promoter and its correlation with prognostic implications in Chinese colorectal cancer (CRC). Methods: The mRNA expression of APC2 in colorectal tissues was evaluated using the database of The Cancer Genome Atlas (TCGA). Methylation analysis of APC2 in tumor ( n = 66) and corresponding adjacent formalin-fixed and paraffin-embedded (FFPE) tissues ( n = 44) was performed by Sequenom EpiTYPER® and verified by cloning-based bisulfite sequencing analysis...
2018: Disease Markers
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