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https://www.readbyqxmd.com/read/29156793/methylation-of-microrna-129-5p-modulates-nucleus-pulposus-cell-autophagy-by-targeting-beclin-1-in-intervertebral-disc-degeneration
#1
Kangcheng Zhao, Yukun Zhang, Liang Kang, Yu Song, Kun Wang, Shuai Li, Xinghuo Wu, Wenbin Hua, Zengwu Shao, Shuhua Yang, Cao Yang
MicroRNAs play an important role in the etiology and progression of many diseases, including intervertebral disc degeneration (IVDD). The miRNA miR-129-5P regulates autophagy in various cancers, but its role in human nucleus pulposus (NP) cells is unclear. The present study investigated whether miR-129-5p regulates the expression of Beclin-1 which is known to induce autophagy in NP cells by evaluating their levels in normal and degenerative disc tissues and human NP cells transfected with miR-129-5P mimic or inhibitor by quantitative real-time (qRT-)PCR, western blotting, flow cytometry, and immunofluorescence analysis...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29152649/identification-of-key-genes-in-glioma-cpg-island-methylator-phenotype-via-network-analysis-of-gene-expression-data
#2
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
Gene expression data were analysed using bioinformatic tools to demonstrate molecular mechanisms underlying the glioma CpG island methylator phenotype (CIMP). A gene expression data set (accession no. GSE30336) was downloaded from Gene Expression Omnibus, including 36 CIMP+ and 16 CIMP- glioma samples. Differential analysis was performed for CIMP+ vs. CIMP‑ samples using the limma package in R. Functional enrichment analysis was subsequently conducted for differentially expressed genes (DEGs) using Database for Annotation, Visualization and Integration Discovery...
October 19, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29145503/zinc-sulfate-contributes-to-promote-telomere-length-extension-via-increasing-telomerase-gene-expression-telomerase-activity-and-change-in-the-tert-gene-promoter-cpg-island-methylation-status-of-human-adipose-derived-mesenchymal-stem-cells
#3
Raheleh Farahzadi, Ezzatollah Fathi, Seyed Alireza Mesbah-Namin, Nosratollah Zarghami
The use of mesenchymal stem cells (MSCs) for cell therapy and regenerative medicine has received widespread attention over the past few years, but their application can be complicated by factors such as reduction in proliferation potential, the senescent tendency of the MSCs upon expansion and their age-dependent decline in number and function. It was shown that all the mentioned features were accompanied by a reduction in telomerase activity and telomere shortening. Furthermore, the role of epigenetic changes in aging, especially changes in promoter methylation, was reported...
2017: PloS One
https://www.readbyqxmd.com/read/29143365/epigenetic-down-regulation-of-sox2-is-an-independent-poor-prognostic-factor-for-hypopharyngeal-cancers
#4
Mehmet Ozgur Avincsal, Naoe Jimbo, Kohei Fujikura, Hirotaka Shinomiya, Naoki Otsuki, Koichi Morimoto, Tatsuya Furukawa, Naruhiko Morita, Ritsuko Maehara, Tomoo Itoh, Ken-Ichi Nibu, Yoh Zen
AIMS: We recently reported that a small subset (7%) of oesophageal squamous cell carcinomas completely lacking SOX2 expression had unique clinicopathological features and a dismal prognosis. The present study aimed to elucidate whether the findings obtained in oesophageal cancers are applicable to hypopharyngeal or oropharyngeal squamous cell carcinomas (HPSCCs or OPSCCs, respectively). METHODS AND RESULTS: The study cohort consisted of consecutive patients with HPSCC (n=130) and OPSCC (n=65) who underwent surgery without preoperative therapy...
November 15, 2017: Histopathology
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#5
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29141580/usability-of-human-infinium-methylationepic-beadchip-for-mouse-dna-methylation-studies
#6
Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic
BACKGROUND: The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. RESULTS: In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137369/lrh-1-expression-patterns-in-breast-cancer-tissues-are-associated-with-tumour-aggressiveness
#7
Jia-Min B Pang, Ramyar Molania, Ashwini Chand, Kevin Knower, Elena A Takano, David J Byrne, Thomas Mikeska, Ewan K A Millar, Cheok Soon Lee, Sandra A O'Toole, Colin Clyne, Kylie L Gorringe, Alexander Dobrovic, Stephen B Fox
The significance and regulation of liver receptor homologue 1 (LRH-1, NR5A2), a tumour-promoting transcription factor in breast cancer cell lines, is unknown in clinical breast cancers. This study aims to determine LRH-1/NR5A2 expression in breast cancers and relationship with DNA methylation and tumour characteristics. In The Cancer Genome Atlas breast cancer cohort NR5A2 expression was positively associated with intragenic CpG island methylation (1.4-fold expression for fully methylated versus not fully methylated, p=0...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137324/loss-of-brca1-promotor-hypermethylation-in-recurrent-high-grade-ovarian-cancer
#8
Katharina Prieske, Stefan Prieske, Simon A Joosse, Fabian Trillsch, Donata Grimm, Eike Burandt, Sven Mahner, Barbara Schmalfeldt, Karin Milde-Langosch, Leticia Oliveira-Ferrer, Linn Woelber
Background: Approximately 20-25% of ovarian cancers are attributable to germline or somatic BRCA1/2 mutations, resulting in defects in the homologous recombination pathway. Inactivation of these genes can also be mediated by epigenetic changes, e.g., hypermethylation of CpG islands in the promoter regions. In such homologous recombination deficient tumors, platinum based chemotherapy is in general effective, however, loss of hypermethylation might lead to refractory disease. The aim of this study was to evaluate the stability of BRCA1 promoter hypermethylation in recurrent disease after platinum based chemotherapy...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29131441/genetic-and-epigenetic-regulation-of-major-histocompatibility-complex-class-i-gene-expression-in-bovine-trophoblast-cells
#9
Bi Shi, Aaron J Thomas, Abby D Benninghoff, Benjamin R Sessions, Qinggang Meng, Parveen Parasar, Heloisa M Rutigliano, Kenneth L White, Christopher J Davies
PROBLEM: The regulatory mechanisms governing differential expression of classical major histocompatibility complex (MHC) class I (MHC-Ia) and non-classical MHC class I (MHC-Ib) genes are poorly understood. METHOD OF STUDY: Quantitative reverse transcription- polymerase chain reaction (PCR) was used to compare the abundance of MHC-I transcripts and related transcription factors in peripheral blood mononuclear cells (PBMC) and placental trophoblast cells (PTC). Methylation of MHC-I CpG islands was detected by bisulfite treatment and next-generation sequencing...
November 12, 2017: American Journal of Reproductive Immunology: AJRI
https://www.readbyqxmd.com/read/29125844/significant-associations-between-driver-gene-mutations-and-dna-methylation-alterations-across-many-cancer-types
#10
Yun-Ching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski
Recent evidence shows that mutations in several driver genes can cause aberrant methylation patterns, a hallmark of cancer. In light of these findings, we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected. We measured this relationship using principal component analyses and methylation-mutation associations applied at the nucleotide level and with respect to genome-wide trends. We found that a few mutated driver genes were associated with genome-wide patterns of aberrant hypomethylation or CpG island hypermethylation in specific cancer types...
November 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29123240/dna-methylation-regulates-tmem16a-ano1-expression-through-multiple-cpg-islands-in-head-and-neck-squamous-cell-carcinoma
#11
Andrey Finegersh, Scott Kulich, Theresa Guo, Alexander V Favorov, Elana J Fertig, Ludmila V Danilova, Daria A Gaykalova, Joseph A Califano, Umamaheswar Duvvuri
ANO1 is a calcium-activated chloride channel that is frequently overexpressed in head and neck squamous cell carcinoma (HNSCC) and other cancers. While ANO1 expression negatively correlates with survival in several cancers, its epigenetic regulation is poorly understood. We analyzed HNSCC samples from TCGA and a separate dataset of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) samples to identify differentially methylated regions. E6 and E7 transfected normal oral keratinocytes (NOK) were used to induce hypermethylation of the ANO1 promoter...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29121543/up-stream-mechanisms-for-up-regulation-of-mir-125b-from-triclosan-exposure-to-zebrafish-danio-rerio
#12
Jiebo Lin, Caihong Wang, Jinfeng Liu, Randy A Dahlgren, Weiming Ai, Aibing Zeng, Xuedong Wang, Huili Wang
Triclosan (TCS) exposure has widely adverse biological effects such as influencing biological reproduction and endocrine disorders. While some studies have addressed TCS-induced expression changes of miRNAs and their related down-stream target genes, no data are available concerning how TCS impairs miRNA expression leading us to study up-stream regulating mechanisms. Four miRNAs (miR-125b, miR-205, miR-142a and miR-203a) showed differential expression between TCS-exposure treatments and the control group; their functions mainly involved fatty acid synthesis and metabolism...
November 6, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/29120694/analysis-of-pig-vomeronasal-receptor-type-1-v1r-promoter-region-reveals-a-common-promoter-motif-but-poor-cpg-islands
#13
Hunduma Dinka, Minh Thong Le
Promoters are, generally, located immediately upstream of a transcription start site (TSS) and have a variety of regulatory motifs, such as transcription factors (TFs) and CpG islands (CGIs), that participate in the regulation of gene expression. Here analysis of the promoter region for pig vomeronasal receptor type 1 (V1R) was described. In the analysis, TSSs for pig V1R genes was first identified and five motifs (MV1, MV2, MV3, MV4, and MV5) were found that are shared by at least 50% of the pig V1R promoter input sequences from both strands...
November 9, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29120412/bortezomib-induced-mirnas-direct-epigenetic-silencing-of-locus-genes-and-trigger-apoptosis-in-leukemia
#14
Yu-Yi Chu, Chiung-Yuan Ko, Shao-Ming Wang, Pin-I Lin, Han-Ying Wang, Wen-Chi Lin, Dong-Yu Wu, Lu-Hao Wang, Ju-Ming Wang
MicroRNAs (miRNAs) have been suggested to repress transcription via binding the 3'-untranslated regions of mRNAs. However, the involvement and details of miRNA-mediated epigenetic regulation, particularly in targeting genomic DNA and mediating epigenetic regulation, remain largely uninvestigated. In the present study, transcription factor CCAAT/enhancer binding protein delta (CEBPD) was responsive to the anticancer drug bortezomib, a clinical and highly selective drug for leukemia treatment, and contributed to bortezomib-induced cell death...
November 9, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29115522/role-of-epigenetics-in-the-pathogenesis-of-chronic-rhinosinusitis-with-nasal-polyps
#15
Jong-Yeup Kim, Dong-Kyu Kim, Myeong Sang Yu, Min-Ji Cha, Seong-Lan Yu, Jaeku Kang
Chronic rhinosinusitis (CRS) is a highly prevalent disease characterized by mucosal inflammation of the nose and paranasal sinuses. CRS can be divided into two main categories, CRS with nasal polyps (NPs; CRSwNP) and CRS without NPs (CRSsNP). Although the pathophysiology of CRS remains unclear, DNA methylation has been implicated in the etiology of CRSwNP. The aim of the present study was to elucidate whether DNA methylation of specific genes is involved in the development of NPs. In total, 18 individuals were included in the present study, and were divided into three groups: CRSwNP (n=7), CRSsNP (n=7) and healthy controls (n=4)...
November 7, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29115507/cytochrome-p450-1a1-and-1b1-promoter-cpg-island-methylation-regulates-rat-liver-injury-induced-by-isoniazid
#16
Yanhui Li, Yuhong Li, Guoying Zheng, Lingyan Zhu, Jishun Wang, Shasha Mu, Qi Ren, Fumin Feng
DNA methylation is an important component of epigenetics that is involved in the occurrence and development of a variety of diseases. The present study aimed to clarify the relationship between cytochrome P450 (CYP)1A1 and CYP1B1 promoter CpG island methylation and isoniazid‑induced liver injury in rats, and to explore the possible mechanism, rats were given an intragastric dose of isoniazid (55 mg·kg‑1·d‑1). High performance liquid chromatography was used to analyze the DNA methylation level of the whole genome in liver tissue...
October 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29112847/evidence-for-converging-dna-methylation-pathways-in-placenta-and-cancer
#17
Matthew C Lorincz, Dirk Schübeler
CpG island promoters are generally devoid of DNA methylation in somatic cells but are frequently methylated during tumorigenesis. Reporting recently in Nature, Smith et al. (2017) show that the signaling-induced methylome in early extraembryonic tissues resembles that of many cancers, suggesting that placental nuclear programming might be co-opted in tumorigenesis.
November 6, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29106391/aberrant-gata2-epigenetic-dysregulation-induces-a-gata2-gata6-switch-in-human-gastric-cancer
#18
S H Song, M S Jeon, J W Nam, J K Kang, Y J Lee, J Y Kang, H P Kim, S W Han, G H Kang, T Y Kim
Six GATA transcription factors play important roles in eukaryotic development. Among these, GATA2, an essential factor for the hematopoietic cell lineage, exhibits low expression in human gastric tissues, whereas GATA6, which is crucial for gastrointestinal development and differentiation, is frequently amplified and/or overexpressed in human gastric cancer. Interestingly, we found that GATA6 was overexpressed in human gastric cancer cells only when GATA2 expression was completely absent, thereby showing an inverse correlation between GATA2 and GATA6...
November 6, 2017: Oncogene
https://www.readbyqxmd.com/read/29102610/systematic-analysis-of-the-determinants-of-gene-expression-noise-in-embryonic-stem-cells
#19
Andre J Faure, Jörn M Schmiedel, Ben Lehner
Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core promoter architecture of a gene, with CpG island promoters and a TATA box associated with low and high noise, respectively. High noise is also associated with "conflicting" chromatin states-the absence of transcription-associated histone modifications or the presence of repressive ones in active genes...
October 31, 2017: Cell Systems
https://www.readbyqxmd.com/read/29099869/selection-for-avian-leukosis-virus-integration-sites-determines-the-clonal-progression-of-b-cell-lymphomas
#20
Sanandan Malhotra, Shelby Winans, Gary Lam, James Justice, Robin Morgan, Karen Beemon
Avian leukosis virus (ALV) is a simple retrovirus that causes a wide range of tumors in chickens, the most common of which are B-cell lymphomas. The viral genome integrates into the host genome and uses its strong promoter and enhancer sequences to alter the expression of nearby genes, frequently inducing tumors. In this study, we compare the preferences for ALV integration sites in cultured cells and in tumors, by analysis of over 87,000 unique integration sites. In tissue culture we observed integration was relatively random with slight preferences for genes, transcription start sites and CpG islands...
November 2017: PLoS Pathogens
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