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https://www.readbyqxmd.com/read/27913949/epigenetic-cpg-methylation-of-the-promoter-and-reactivation-of-the-expression-of-gstp1-by-astaxanthin-in-human-prostate-lncap-cells
#1
Yuqing Yang, Francisco Fuentes, Limin Shu, Chao Wang, Doug Pung, Wenji Li, Chengyue Zhang, Yue Guo, Ah-Ng Kong
Astaxanthin (AST), a red dietary carotenoid, has synergistic antioxidant effects with polyunsaturated fatty acids at low concentrations via Nuclear factor (erythroid-derived 2)-like 2 (NFE2L2 or Nrf2)/antioxidant response element (ARE) signaling. In addition, chromatin remodeling and DNA methylation-based gene silencing represent a common mechanism in prostate carcinogenesis and tumor progression from normal cells to pre-initiated cells and ultimately to invasive carcinoma. Therefore, the control of epigenetic modification and the transcriptional/translational control of the activation of Nrf2 and Nrf2-target genes, including glutathione S-transferases (GSTs), appear to be an important mechanism that protects cells against injuries from oxidative stress and cancer development...
December 2, 2016: AAPS Journal
https://www.readbyqxmd.com/read/27906971/nullomers-and-high-order-nullomers-in-genomic-sequences
#2
Davide Vergni, Daniele Santoni
A nullomer is an oligomer that does not occur as a subsequence in a given DNA sequence, i.e. it is an absent word of that sequence. The importance of nullomers in several applications, from drug discovery to forensic practice, is now debated in the literature. Here, we investigated the nature of nullomers, whether their absence in genomes has just a statistical explanation or it is a peculiar feature of genomic sequences. We introduced an extension of the notion of nullomer, namely high order nullomers, which are nullomers whose mutated sequences are still nullomers...
2016: PloS One
https://www.readbyqxmd.com/read/27901054/functional-defects-in-cd4-cd25-high-foxp3-regulatory-cells-in-ankylosing-spondylitis
#3
Huifang Guo, Ming Zheng, Kui Zhang, Fengfan Yang, Xin Zhang, Qing Han, Zhi-Nan Chen, Ping Zhu
Forkhead box P3 (FoxP3)-positive regulatory T cells (Tregs) play a pivotal role in the preservation of self-tolerance, and Treg dysfunction has been implicated in many autoimmune diseases. Whether and how Tregs participate in the pathogenesis of ankylosing spondylitis (AS) has not been fully elucidated. Here, we investigated Treg function and found that Tregs in peripheral blood (PB) from patients with active AS had lower FoxP3 mean fluorescence intensity (MFI) than those from healthy controls and could not fully suppress naïve T cell (Tn) proliferation...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899621/cooperative-genomic-alteration-network-reveals-molecular-classification-across-12-major-cancer-types
#4
Hongyi Zhang, Yulan Deng, Yong Zhang, Yanyan Ping, Hongying Zhao, Lin Pang, Xinxin Zhang, Li Wang, Chaohan Xu, Yun Xiao, Xia Li
The accumulation of somatic genomic alterations that enables cells to gradually acquire growth advantage contributes to tumor development. This has the important implication of the widespread existence of cooperative genomic alterations in the accumulation process. Here, we proposed a computational method HCOC that simultaneously consider genetic context and downstream functional effects on cancer hallmarks to uncover somatic cooperative events in human cancers. Applying our method to 12 TCGA cancer types, we totally identified 1199 cooperative events with high heterogeneity across human cancers, and then constructed a pan-cancer cooperative alteration network...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895318/whole-genome-dna-methylation-beyond-genes-silencing
#5
Roberto Tirado-Magallanes, Khadija Rebbani, Ricky Lim, Sriharsa Pradhan, Touati Benoukraf
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the major biological consequences of DNA methylation recently discovered...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27895046/gene-silencing-of-nox4-by-cpg-island-methylation-during-hepatocarcinogenesis-in-rats
#6
Guadalupe S López-Álvarez, Tomasz K Wojdacz, Claudia M García-Cuellar, Hugo C Monroy-Ramírez, Miguel A Rodríguez Segura, Ruth A Pacheco Rivera, Carlos A Valencia-Antúnez, Nancy C Cervantes-Anaya, Ernesto Soto-Reyes, Verónica R Vázquez-Garzón, Yesennia Sánchez-Pérez, Saúl Villa Treviño
The association between the downregulation of genes and DNA methylation in their CpG islands has been extensively studied as a mechanism that favors carcinogenesis. The objective of this study was to analyze the methylation of a set of genes selected based on their microarray expression profiles during the process of hepatocarcinogenesis. Rats were sacrificed at: 24 Hours, 7, 11, 16 and 30 days and 5, 9, 12 and 18 months post-treatment. We evaluated the methylation status in the CpG islands of four deregulated genes (Casp3, Cldn1, Pex11a and Nox4) using methylation-sensitive high-resolution melting technology for the samples obtained from different stages of hepatocarcinogenesis...
November 28, 2016: Biology Open
https://www.readbyqxmd.com/read/27890923/the-epigenetic-landscape-of-renal-cancer
#7
REVIEW
Mark R Morris, Farida Latif
The majority of kidney cancers are associated with mutations in the von Hippel-Lindau gene and a small proportion are associated with infrequent mutations in other well characterized tumour-suppressor genes. In the past 15 years, efforts to uncover other key genes involved in renal cancer have identified many genes that are dysregulated or silenced via epigenetic mechanisms, mainly through methylation of promoter CpG islands or dysregulation of specific microRNAs. In addition, the advent of next-generation sequencing has led to the identification of several novel genes that are mutated in renal cancer, such as PBRM1, BAP1 and SETD2, which are all involved in histone modification and nucleosome and chromatin remodelling...
November 28, 2016: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/27889662/pediatric-pineal-germinomas-epigenetic-and-genomic-approach
#8
Monserrat Pérez-Ramírez, Alejo Justino Hernández-Jiménez, Armando Guerrero-Guerrero, Alicia Georgina Siordia-Reyes, Marta Elena Hernández-Caballero, Antonio García-Méndez, Fernando Chico-Ponce de León, Fabio Abdel Salamanca-Gómez, Normand García-Hernández
OBJECTIVE: We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. METHODS: CGH microarray, methylation and gene expression were performed through the Agilent platform. The results were analyzed with MatLab software, MapViewer, DAVID, GeneCards and Hippie. RESULTS: Amplifications were found in 1q24.2, 1q31.3, 2p11.2, 3p22.2, 7p13, 7p15.2, 8p22, 12p13.2, 14q24.3 y 22q12; and deletions were found in 1q21...
November 19, 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/27885175/cpg-island-methylator-phenotype-high-colorectal-cancers-and-their-prognostic-implications-and-relationships-with-the-serrated-neoplasia-pathway
#9
REVIEW
Ye-Young Rhee, Kyung-Ju Kim, Gyeong Hoon Kang
The concept of a CpG island methylator phenotype (CIMP) was first introduced by Toyota and Issa to describe a subset of colorectal cancers (CRCs) with concurrent hypermethylation of multiple CpG island loci. The concept of CIMP as a molecular carcinogenesis mechanism was consolidated by the identification of the serrated neoplasia pathway, in which CIMP participates in the initiation and progression of serrated adenomas. Distinct clinicopathological and molecular features of CIMP-high (CIMP-H) CRCs have been characterized, including proximal colon location, older age of onset, female preponderance, and frequent associations of high-level microsatellite instability and BRAF mutations...
November 28, 2016: Gut and Liver
https://www.readbyqxmd.com/read/27881847/epigenetic-regulation-of-l-type-voltage-gated-ca-2-channels-in-mesenteric-arteries-of-aging-hypertensive-rats
#10
Jingwen Liao, Yanyan Zhang, Fang Ye, Lin Zhang, Yu Chen, Fanxing Zeng, Lijun Shi
Accumulating evidence has shown that epigenetic regulation is involved in hypertension and aging. L-type voltage-gated Ca(2+) channels (LTCCs), the dominant channels in vascular myocytes, greatly contribute to arteriole contraction and blood pressure (BP) control. We investigated the dynamic changes and epigenetic regulation of LTCC in the mesenteric arteries of aging hypertensive rats. LTCC function was evaluated by using microvascular rings and whole-cell patch-clamp in the mesenteric arteries of male Wistar-Kyoto rats and spontaneously hypertensive rats at established hypertension (3 month old) and an aging stage (16 month old), respectively...
November 24, 2016: Hypertension Research: Official Journal of the Japanese Society of Hypertension
https://www.readbyqxmd.com/read/27881822/lowered-h3k27me3-and-dna-hypomethylation-define-poorly-prognostic-pediatric-posterior-fossa-ependymomas
#11
Jill Bayliss, Piali Mukherjee, Chao Lu, Siddhant U Jain, Chan Chung, Daniel Martinez, Benjamin Sabari, Ashley S Margol, Pooja Panwalkar, Abhijit Parolia, Melike Pekmezci, Richard C McEachin, Marcin Cieslik, Benita Tamrazi, Benjamin A Garcia, Gaspare La Rocca, Mariarita Santi, Peter W Lewis, Cynthia Hawkins, Ari Melnick, C David Allis, Craig B Thompson, Arul M Chinnaiyan, Alexander R Judkins, Sriram Venneti
Childhood posterior fossa (PF) ependymomas cause substantial morbidity and mortality. These tumors lack recurrent genetic mutations, but a subset of these ependymomas exhibits CpG island (CpGi) hypermethylation [PF group A (PFA)], implicating epigenetic alterations in their pathogenesis. Further, histological grade does not reliably predict prognosis, highlighting the importance of developing more robust prognostic markers. We discovered global H3K27me3 reduction in a subset of these tumors (PF-ve ependymomas) analogous to H3K27M mutant gliomas...
November 23, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27880934/tumors-with-unmethylated-mlh1-and-the-cpg-island-methylator-phenotype-are-associated-with-a-poor-prognosis-in-stage-ii-colorectal-cancer-patients
#12
Tao Fu, Yanliang Liu, Kai Li, Weiwei Wan, Emmanouil P Pappou, Christine A Iacobuzio-Donahue, Zachary Kerner, Stephen B Baylin, Christopher L Wolfgang, Nita Ahuja
We previously developed a novel tumor subtype classification model for duodenal adenocarcinomas based on a combination of the CpG island methylator phenotype (CIMP) and MLH1 methylation status. Here, we tested the prognostic value of this model in stage II colorectal cancer (CRC) patients. Tumors were assigned to CIMP+/MLH1-unmethylated (MLH1-U), CIMP+/MLH1-methylated (MLH1-M), CIMP-/MLH1-U, or CIMP-/MLH1-M groups. Age, tumor location, lymphovascular invasion, and mucin production differed among the four patient subgroups, and CIMP+/MLH1-U tumors were more likely to have lymphovascular invasion and mucin production...
November 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27879658/the-emergence-of-pan-cancer-cimp-and-its-elusive-interpretation
#13
REVIEW
Brendan F Miller, Francisco Sánchez-Vega, Laura Elnitski
Epigenetic dysregulation is recognized as a hallmark of cancer. In the last 16 years, a CpG island methylator phenotype (CIMP) has been documented in tumors originating from different tissues. However, a looming question in the field is whether or not CIMP is a pan-cancer phenomenon or a tissue-specific event. Here, we give a synopsis of the history of CIMP and describe the pattern of DNA methylation that defines the CIMP phenotype in different cancer types. We highlight new conceptual approaches of classifying tumors based on CIMP in a cancer type-agnostic way that reveal the presence of distinct CIMP tumors in a multitude of The Cancer Genome Atlas (TCGA) datasets, suggesting that this phenotype may transcend tissue-type specificity...
November 22, 2016: Biomolecules
https://www.readbyqxmd.com/read/27871161/helicobacter-pylori-eradication-modulates-aberrant-cpg-island-hypermethylation-in-gastric-carcinogenesis
#14
Jeongmin Choi, Sang Gyun Kim, Byeong Gwan Kim, Seong Joon Koh, Ji Won Kim, Kook Lae Lee
Background/Aims: Helicobacter pylori infection induces aberrant DNA methylation in gastric mucosa. We evaluated the long-term effect of H. pylori eradication on promotor CpG island hypermethylation in gastric carcinogenesis. Methods: H. pylori-positive patients with gastric adenoma or early gastric cancer who underwent endoscopic resection were enrolled. According to H. pylori eradication after endoscopic resection, the participants were randomly assigned to H. pylori eradication or non-eradication group...
November 25, 2016: Korean Journal of Gastroenterology, Taehan Sohwagi Hakhoe Chi
https://www.readbyqxmd.com/read/27868302/reduced-dna-methylation-of-sphingosine-1-phosphate-receptor-5-in-alveolar-macrophages-in-copd-a-potential-link-to-failed-efferocytosis
#15
Jameel Barnawi, Hubertus Jersmann, Rainer Haberberger, Sandra Hodge, Robyn Meech
BACKGROUND AND OBJECTIVE: We previously showed that alveolar macrophages from COPD patients are defective in their ability to phagocytose apoptotic cells ('efferocytosis') and that this defect is potentially linked to the sphingosine-1 phosphate (S1P) system, in particular the sphingosine-1 phosphate receptor 5 (S1PR5). In alveolar macrophages from COPD patients, S1PR5 mRNA expression levels increased and were correlated with both lung function and efferocytosis. However, it us unknown whether these changes are under epigenetic control via DNA methylation or whether DNA methylation directly modulates macrophage function...
November 20, 2016: Respirology: Official Journal of the Asian Pacific Society of Respirology
https://www.readbyqxmd.com/read/27865843/methylation-effect-on-ipt5b-gene-expression-determines-cytokinin-biosynthesis-in-apple-rootstock
#16
Yi Feng, Xinzhong Zhang, Ting Wu, Xuefeng Xu, Zhenhai Han, Yi Wang
The molecular mechanism of dwarfing in the apple rootstock is poorly understood, and has been attributed to low root cytokinin biosynthesis levels. Here we identified differences in root trans-zeatin content and expression of cytokinin metabolic pathway genes between dwarfing and vigorous rootstocks. Specifically, a stable low expression of IPT5b was identified in the dwarfing rootstocks. Bisulfite sequencing showed that two CpG islands (CpG2 and CpG4) in the IPT5b promoter region showed higher methylation levels in the M9 rootstock (dwarfing) compared to the Mr (vigorous) rootstock...
November 16, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27864689/epstein-barr-virus-infection-and-gene-promoter-hypermethylation-in-rheumatoid-arthritis-patients-with-methotrexate-associated-b-cell-lymphoproliferative-disorders
#17
Kozue Ejima-Yamada, Yumi Oshiro, Seiichi Okamura, Tomoaki Fujisaki, Yasuhito Mihashi, Kazuo Tamura, Tomoko Fukushige, Masaru Kojima, Kazutoshi Shibuya, Morishige Takeshita
We analyzed CpG-island hypermethylation status in 12 genes of paraffin-embedded tissues from 38 rheumatoid arthritis (RA) patients with methotrexate (MTX)-associated large B cell lymphoproliferative disorder (BLPD), 11 RA patients with non-MTX-associated BLPD (non-MTX-BLPD), 22 controls with diffuse large B cell lymphoma (DLBCL), and 10 controls with Epstein-Barr virus (EBV)(+) DLBCL. Among them, tumor cells from EBV(+) MTX-BLPD patients and control EBV(+) DLBCL patients had significantly lower median incidence of CpG island methylator phenotype (CIMP) than those from non-MTX-BLPD and control DLBCL groups (2...
November 18, 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27857867/dna-methylation-signature-of-post-injury-neointimal-cells-during-vascular-remodeling-in-the-rat-balloon-injury-model
#18
Jendai Richards, Henry Ato Ogoe, Wenzhi Li, Oguljahan Babayewa, Wei Xu, Tameka Bythwood, Minerva Garcia-Barrios, Li Ma, Qing Song
Vascular smooth muscle cell (VSMC) accumulation in the neointimal is a common feature in vascular diseases such as atherosclerosis, transplant arteriosclerosis and restenosis. In this study, we isolated the neointimal cells and uninjured residential vascular smooth muscle cells by laser micro dissection and carried out single-cell whole-genome methylation sequencing. We also sequenced the bisulfite converted genome of circulating bone-marrow-derived cells such as peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC)...
July 2016: Molecular Biology (Los Angeles, Calif.)
https://www.readbyqxmd.com/read/27846243/bacterially-associated-transcriptional-remodelling-in-a-distinct-genomic-subtype-of-colorectal-cancer-provides-a-plausible-molecular-basis-for-disease-development
#19
Katie S Lennard, Ryan W Goosen, Jonathan M Blackburn
The relevance of specific microbial colonisation to colorectal cancer (CRC) disease pathogenesis is increasingly recognised, but our understanding of possible underlying molecular mechanisms that may link colonisation to disease in vivo remains limited. Here, we investigate the relationships between the most commonly studied CRC-associated bacteria (Enterotoxigenic Bacteroides fragilis, pks+ Escherichia coli, Fusobacterium spp., afaC+ E. coli, Enterococcus faecalis & Enteropathogenic E. coli) and altered transcriptomic and methylation profiles of CRC patients, in order to gain insight into the potential contribution of these bacteria in the aetiopathogenesis of CRC...
2016: PloS One
https://www.readbyqxmd.com/read/27845898/transcription-factor-lsf-dnmt1-complex-dissociation-by-fqi1-leads-to-aberrant-dna-methylation-and-gene-expression
#20
Hang Gyeong Chin, V K Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, Scott E Schaus, Ulla Hansen, Sriharsa Pradhan
The transcription factor LSF is highly expressed in hepatocellular carcinoma (HCC) and promotes oncogenesis. Factor quinolinone inhibitor 1 (FQI1), inhibits LSF DNA-binding activity and exerts anti-proliferative activity. Here, we show that LSF binds directly to the maintenance DNA (cytosine-5) methyltransferase 1 (DNMT1) and its accessory protein UHRF1 both in vivo and in vitro. Binding of LSF to DNMT1 stimulated DNMT1 activity and FQI1 negated the methyltransferase activation. Addition of FQI1 to the cell culture disrupted LSF bound DNMT1 and UHRF1 complexes, resulting in global aberrant CpG methylation...
November 10, 2016: Oncotarget
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