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epigenetic regulation

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https://www.readbyqxmd.com/read/29667778/dna-methylation-biomarkers-for-the-occurrence-of-lung-adenocarcinoma-from-tcga-data-mining
#1
Xiao-Feng Zhu, Bi-Sheng Zhu, Fei-Ma Wu, Hai-Bo Hu
The development of lung cancer is a combination of multifactor, multistage, and multiple genetic alterations processes. DNA methylation is an important factor. Currently, the study on the genome-scale epigenetic modification for studying the pathogenesis of lung cancer is still lacking. Here, we aimed to identify the epigenetic modifications of lung cancer, thus to provide scientific basis for the personalized medicine, and research of classification screening for lung adenocarcinoma patients. The DNA methylation data, and the corresponding clinical information of lung adenocarcinoma samples were extracted from the Cancer Genome Atlas (TCGA) database...
April 18, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29667742/genetic-association-and-expression-analyses-of-the-phosphatidylinositol-4-phosphate-5-kinase-pip5k1c-gene-in-alcohol-use-disorder-relevance-for-pain-signaling-and-alcohol-use
#2
Ji Soo Lee, Jill L Sorcher, Allison D Rosen, Ruslan Damadzic, Hui Sun, Melanie Schwandt, Markus Heilig, John Kelly, Kelsey L Mauro, Audrey Luo, Daniel Rosoff, Christine Muench, Jeesun Jung, Zachary A Kaminsky, Falk W Lohoff
BACKGROUND: The gene encoding Phosphatidylinositol-4-Phosphate 5-Kinase (PIP5K1C) has been recently implicated in pain regulation. Interestingly, a recent cross-tissue and cross-phenotypic epigenetic analysis identified the same gene in alcohol use disorder (AUD). Given the high comorbidity between AUD and chronic pain, we hypothesized that genetic variation in PIP5K1C might contribute to susceptibility to AUD. METHODS: We conducted a case-control association study of genetic variants in PIP5K1C...
April 18, 2018: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29667349/asb1-differential-methylation-in-ischaemic-cardiomyopathy-relationship-with-left-ventricular-performance-in-end-stage-heart-failure-patients
#3
Ana Ortega, Estefanía Tarazón, Carolina Gil-Cayuela, Luis Martínez-Dolz, Francisca Lago, José Ramón González-Juanatey, Juan Sandoval, Manuel Portolés, Esther Roselló-Lletí, Miguel Rivera
AIMS: Ischaemic cardiomyopathy (ICM) leads to impaired contraction and ventricular dysfunction, causing high rates of morbidity and mortality. Epigenomics allows the identification of epigenetic signatures in human diseases. We analyse the differential epigenetic patterns of the ASB gene family in ICM patients and relate these alterations to their haemodynamic and functional status. METHODS AND RESULTS: Epigenomic analysis was carried out using 16 left ventricular (LV) tissue samples, eight from ICM patients undergoing heart transplantation and eight from control (CNT) subjects without cardiac disease...
April 17, 2018: ESC Heart Failure
https://www.readbyqxmd.com/read/29667298/distinct-chromatin-structures-at-the-monoamine-oxidase-a-maoa-promoter-correlate-with-allele-specific-expression-in-sh-sy5y-cells
#4
M Manca, V Pessoa, P Myers, A Pickles, J Hill, H Sharp, C Murgatroyd, V J Bubb, J P Quinn
Monoamine oxidase-A (MAOA) metabolises monoamines and is implicated in the pathophysiology of psychiatric disorders. A polymorphic repetitive DNA domain, termed the uVNTR (upstream variable number tandem repeat), located at the promoter of the MAOA gene is a risk factor for many of these disorders. MAOA is on the X chromosome suggesting gender could play a role in regulation. We analysed MAOA regulation in the human female cell line, SH-SY5Y, which is polymorphic for the uVNTR. This heterozygosity allowed us to correlate allele specific gene expression with allele specific transcription factor binding and epigenetic marks for MAOA...
April 18, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29666625/dying-to-be-noticed-epigenetic-regulation-of-immunogenic-cell-death-for-cancer-immunotherapy
#5
REVIEW
Brianne Cruickshank, Michael Giacomantonio, Paola Marcato, Sherri McFarland, Jonathan Pol, Shashi Gujar
Immunogenic cell death (ICD) activates both innate and adaptive arms of the immune system during apoptotic cancer cell death. With respect to cancer immunotherapy, the process of ICD elicits enhanced adjuvanticity and antigenicity from dying cancer cells and consequently, promotes the development of clinically desired antitumor immunity. Cancer ICD requires the presentation of various "hallmarks" of immunomodulation, which include the cell-surface translocation of calreticulin, production of type I interferons, and release of high-mobility group box-1 and ATP, which through their compatible actions induce an immune response against cancer cells...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29666616/stem-cell-transcription-factor-foxo-controls-microbiome-resilience-in-hydra
#6
Benedikt M Mortzfeld, Jan Taubenheim, Sebastian Fraune, Alexander V Klimovich, Thomas C G Bosch
The aging process is considered to be the result of accumulating cellular deterioration in an individual organism over time. It can be affected by the combined influence of genetic, epigenetic, and environmental factors including life-style-associated events. In the non-senescent freshwater polyp Hydra , one of the classical model systems for evolutionary developmental biology and regeneration, transcription factor FoxO modulates both stem cell proliferation and innate immunity. This provides strong support for the role of FoxO as a critical rate-of-aging regulator...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29666467/ascorbic-acid-induces-global-epigenetic-reprogramming-to-promote-meiotic-maturation-and-developmental-competence-of-porcine-oocytes
#7
Xiao-Xia Yu, Yun-Hua Liu, Xiao-Man Liu, Pei-Chao Wang, Shuai Liu, Jia-Kun Miao, Zhi-Qiang Du, Cai-Xia Yang
L-ascorbic acid (Vitamin C) can enhance the meiotic maturation and developmental competence of porcine oocytes, but the underlying molecular mechanism remains obscure. Here we show the role of ascorbic acid in regulating epigenetic status of both nucleic acids and chromatin to promote oocyte maturation and development in pigs. Supplementation of 250 μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P) during in vitro maturation significantly enhanced the nuclear maturation (as indicated by higher rate of first polar body extrusion and increased Bmp15 mRNA level), reduced level of reactive oxygen species, and promoted developmental potency (higher cleavage and blastocyst rates of parthenotes, and decreased Bax and Caspase3 mRNA levels in blastocysts) of pig oocytes...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666409/exposure-to-phthalate-an-endocrine-disrupting-chemical-alters-the-first-trimester-placental-methylome-and-transcriptome-in-women
#8
N M Grindler, L Vanderlinden, R Karthikraj, K Kannan, S Teal, A J Polotsky, T L Powell, I V Yang, T Jansson
Phthalates are known endocrine disruptors and associated with decreased fecundity, pregnancy loss, and adverse obstetrical outcomes, however the underlying mechanisms remain to be established. Environmental factors can influence gene expression and cell function by modifying epigenetic marks, impacting the developing embryo as well as future generations of offspring. The impact of phthalates on placental gene methylation and expression is largely unknown. We studied the effect of maternal phthalate exposure on the human placental DNA methylome and transcriptome...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666375/association-and-cis-mqtl-analysis-of-variants-in-chrna3-a5-chrna7-chrnb2-and-chrnb4-in-relation-to-nicotine-dependence-in-a-chinese-han-population
#9
Qiang Liu, Haijun Han, Maiqiu Wang, Yinghao Yao, Li Wen, Keran Jiang, Yunlong Ma, Rongli Fan, Jiali Chen, Kunkai Su, Zhongli Yang, Wenyan Cui, Wenji Yuan, Xianzhong Jiang, Jingjing Li, Thomas J Payne, Jundong Wang, Ming D Li
Nicotine dependence (ND) is a worldwide health problem. Numerous genetic studies have demonstrated a significant association of variants in nicotinic acetylcholine receptors (nAChRs) with smoking behaviors. However, most of these studies enrolled only subjects of European or African ancestry. In addition, although an increasing body of evidence implies a causal connection of single-nucleotide polymorphisms (SNPs) and epigenetic regulation of gene expression, few studies of this issue have been reported. In this study, we performed both association and interaction analysis for 67 SNPs in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 with ND in a Chinese Han population (N = 5055)...
April 18, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29666336/investigating-multiple-dysregulated-pathways-in-rheumatoid-arthritis-based-on-pathway-interaction-network
#10
Xian-Dong Song, Xian-Xu Song, Gui-Bo Liu, Chun-Hui Ren, Yuan-Bo Sun, Ke-Xin Liu, Bo Liu, Shuang Liang, Zhu Zhu
The traditional methods of identifying biomarkers in rheumatoid arthritis (RA) have focussed on the differentially expressed pathways or individual pathways, which however, neglect the interactions between pathways. To better understand the pathogenesis of RA, we aimed to identify dysregulated pathway sets using a pathway interaction network (PIN), which considered interactions among pathways. Firstly, RA-related gene expression profile data, protein-protein interactions (PPI) data and pathway data were taken up from the corresponding databases...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666300/a-pan-cancer-landscape-of-interactions-between-solid-tumors-and-infiltrating-immune-cell-populations
#11
David Tamborero, Carlota Rubio-Perez, Ferran Muiños, Radhakrishnan Sabarinathan, Josep Maria Piulats, Aura Muntasell, Rodrigo Dienstmann, Nuria Lopez-Bigas, Abel Gonzalez-Perez
PURPOSE: Throughout their development tumors are challenged by the immune system and they acquire features to evade its surveillance. A systematic view of these traits which sheds light on how tumors respond to immunotherapies is still lacking. EXPERIMENTAL DESIGN: Here, we computed the relative abundance of an array of immune cell populations to measure the immune infiltration pattern of 9,174 tumors of 29 solid cancers. We then clustered tumors with similar infiltration pattern to define immune-phenotypes...
April 17, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29666194/a-catalogue-of-putative-cis-regulatory-interactions-between-long-non-coding-rnas-and-proximal-coding-genes-based-on-correlative-analysis-across-diverse-human-tumors
#12
Swaraj Basu, Erik Larsson
Antisense transcripts and other long non-coding RNAs are pervasive in mammalian cells, and some of these molecules have been proposed to regulate proximal protein-coding genes in cis For example, non-coding transcription can contribute to inactivation of tumor suppressor genes in cancer, and antisense transcripts have been implicated in the epigenetic inactivation of imprinted genes. However, our knowledge is still limited and more such regulatory interactions likely await discovery. Here, we make use of available gene expression data from a large compendium of human tumors to generate hypotheses regarding non-coding-to-coding cis -regulatory relationships with emphasis on negative associations, as these are less likely to arise for reasons other than cis -regulation...
April 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29666172/genetic-editing-of-colonic-organoids-provides-a-molecularly-distinct-and-orthotopic-preclinical-model-of-serrated-carcinogenesis
#13
Tamsin R M Lannagan, Young K Lee, Tongtong Wang, Jatin Roper, Mark L Bettington, Lochlan Fennell, Laura Vrbanac, Lisa Jonavicius, Roshini Somashekar, Krystyna Gieniec, Miao Yang, Jia Q Ng, Nobumi Suzuki, Mari Ichinose, Josephine A Wright, Hiroki Kobayashi, Tracey L Putoczki, Yoku Hayakawa, Simon J Leedham, Helen E Abud, Ömer H Yilmaz, Julie Marker, Sonja Klebe, Pratyaksha Wirapati, Siddhartha Mukherjee, Sabine Tejpar, Barbara A Leggett, Vicki L J Whitehall, Daniel L Worthley, Susan L Woods
OBJECTIVE: Serrated colorectal cancer (CRC) accounts for approximately 25% of cases and includes tumours that are among the most treatment resistant and with worst outcomes. This CRC subtype is associated with activating mutations in the mitogen-activated kinase pathway gene, BRAF , and epigenetic modifications termed the CpG Island Methylator Phenotype, leading to epigenetic silencing of key tumour suppressor genes. It is still not clear which (epi-)genetic changes are most important in neoplastic progression and we begin to address this knowledge gap herein...
April 17, 2018: Gut
https://www.readbyqxmd.com/read/29666150/epigenetics-and-epitranscriptomics-in-temporal-patterning-of-cortical-neural-progenitor-competence
#14
REVIEW
Ki-Jun Yoon, Caroline Vissers, Guo-Li Ming, Hongjun Song
During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis...
April 17, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29665942/-research-progress-of-histone-modification-in-b-cell-lymphoma-pathogenesis-review
#15
Jiao Zhang, Yun Pan, Yan Li
It has been increasingly recognized that the pathogenesis of B-cell lymphoma closely relates to the epigenetic disregulations. Epigenetics is a subdiscipline, which means heritable changes in gene expressions without alterations in the DNA sequence, and the DNA methylation, histone modification and miRNA maily were involved. Histone modification is the most important epigenetic modification, the researches showed that the aberrant histone modification is the important pathogenesis in B-cell lymphoma, especially the aberrant histone methylation and acetylation...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#16
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29665673/cooperative-instruction-of-signaling-and-metabolic-pathways-on-the-epigenetic-landscape
#17
Jung-Ae Kim
Cells cope with diverse intrinsic and extrinsic stimuli in order to make adaptations for survival. The epigenetic landscape plays a crucial role in cellular adaptation, as it integrates the information generated from stimuli. Signaling pathways induced by stimuli communicate with chromatin to change the epigenetic landscape through regulation of epigenetic modifiers. Metabolic dynamics altered by these stimuli also affect the activity of epigenetic modifiers. Here, I review the current understanding of epigenetic regulation via signaling and metabolic pathways...
April 11, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29665672/regulatory-network-of-arf-in-cancer-development
#18
Aram Ko, Su Yeon Han, Jaewhan Song
ARF is a tumor suppressor protein that has a pivotal role in the prevention of cancer development through regulating cell proliferation, senescence, and apoptosis. As a factor that induces senescence, the role of ARF as a tumor suppressor is closely linked to the p53-MDM2 axis, which is a key process that restrains tumor formation. Thus, many cancer cells either lack a functional ARF or p53, which enables them to evade cell oncogenic stress-mediated cycle arrest, senescence, or apoptosis. In particular, the ARF gene is a frequent target of genetic and epigenetic alterations including promoter hypermethylation or gene deletion...
April 18, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29665657/recent-advances-in-the-diagnosis-and-management-of-primary-myelofibrosis
#19
Katsuto Takenaka, Kazuya Shimoda, Koichi Akashi
Primary myelofibrosis (PMF) is a myeloproliferative neoplasm (MPN) in which dysregulation of the Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathways is the major pathogenic mechanism. Most patients with PMF carry a driver mutation in the JAK2, MPL (myeloproliferative leukemia), or CALR (calreticulin) genes. Mutations in epigenetic regulators and RNA splicing genes may also occur, and play critical roles in PMF disease progression. Based on revised World Health Organization diagnostic criteria for MPNs, both screening for driver mutations and bone marrow biopsy are required for a specific diagnosis...
April 20, 2018: Korean Journal of Internal Medicine
https://www.readbyqxmd.com/read/29665409/epigenomic-biomarkers-for-prognostication-and-diagnosis-of-gastrointestinal-cancers
#20
REVIEW
Chi Chun Wong, Weilin Li, Bertina Chan, Jun Yu
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development...
April 14, 2018: Seminars in Cancer Biology
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