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https://www.readbyqxmd.com/read/29905852/omics-studies-for-comprehensive-understanding-of-immunoglobulin-a-nephropathy-state-of-the-art-and-future-directions
#1
Francesco Paolo Schena, Grazia Serino, Fabio Sallustio, Mario Falchi, Sharon N Cox
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics...
June 13, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29901700/epigenomics-and-metabolomics-reveal-the-mechanism-of-the-apoa2-saturated-fat-intake-interaction-affecting-obesity
#2
Chao-Qiang Lai, Caren E Smith, Laurence D Parnell, Yu-Chi Lee, Dolores Corella, Paul Hopkins, Bertha A Hidalgo, Stella Aslibekyan, Michael A Province, Devin Absher, Donna K Arnett, Katherine L Tucker, Jose M Ordovas
Background: The putative functional variant -265T>C (rs5082) within the APOA2 promoter has shown consistent interactions with saturated fatty acid (SFA) intake to influence the risk of obesity. Objective: The aim of this study was to implement an integrative approach to characterize the molecular basis of this interaction. Design: We conducted an epigenome-wide scan on 80 participants carrying either the rs5082 CC or TT genotypes and consuming either a low-SFA (<22 g/d) or high-SFA diet (≥22 g/d), matched for age, sex, BMI, and diabetes status in the Boston Puerto Rican Health Study (BPRHS)...
June 12, 2018: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/29898407/integrated-molecular-characterization-of-testicular-germ-cell-tumors
#3
Hui Shen, Juliann Shih, Daniel P Hollern, Linghua Wang, Reanne Bowlby, Satish K Tickoo, Vésteinn Thorsson, Andrew J Mungall, Yulia Newton, Apurva M Hegde, Joshua Armenia, Francisco Sánchez-Vega, John Pluta, Louise C Pyle, Rohit Mehra, Victor E Reuter, Guilherme Godoy, Jeffrey Jones, Carl S Shelley, Darren R Feldman, Daniel O Vidal, Davor Lessel, Tomislav Kulis, Flavio M Cárcano, Kristen M Leraas, Tara M Lichtenberg, Denise Brooks, Andrew D Cherniack, Juok Cho, David I Heiman, Katayoon Kasaian, Minwei Liu, Michael S Noble, Liu Xi, Hailei Zhang, Wanding Zhou, Jean C ZenKlusen, Carolyn M Hutter, Ina Felau, Jiashan Zhang, Nikolaus Schultz, Gad Getz, Matthew Meyerson, Joshua M Stuart, Rehan Akbani, David A Wheeler, Peter W Laird, Katherine L Nathanson, Victoria K Cortessis, Katherine A Hoadley
We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance-KIT, KRAS, and NRAS-exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma...
June 12, 2018: Cell Reports
https://www.readbyqxmd.com/read/29896466/dna-methylation-in-pediatric-obstructive-sleep-apnea-an-overview-of-preliminary-findings
#4
REVIEW
Evanthia Perikleous, Paschalis Steiropoulos, Argyris Tzouvelekis, Evangelia Nena, Maria Koffa, Emmanouil Paraskakis
Obstructive sleep apnea (OSA) is characterized by phenotypic variations, which can be partly attributed to specific gene polymorphisms. Recent studies have focused on the role of epigenetic mechanisms in order to permit a more precise perception about clinical phenotyping and targeted therapies. The aim of this review was to synthesize the current state of knowledge on the relation between DNA methylation patterns and the development of pediatric OSA, in light of the apparent limited literature in the field...
2018: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/29895819/genome-wide-association-study-in-japanese-females-identifies-fifteen-novel-skin-related-trait-associations
#5
Chihiro Endo, Todd A Johnson, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Yuichiro Tsunemi, Naoyuki Kamatani, Makoto Kawashima
Skin trait variation impacts quality-of-life, especially for females from the viewpoint of beauty. To investigate genetic variation related to these traits, we conducted a GWAS of various skin phenotypes in 11,311 Japanese women and identified associations for age-spots, freckles, double eyelids, straight/curly hair, eyebrow thickness, hairiness, and sweating. In silico annotation with RoadMap Epigenomics epigenetic state maps and colocalization analysis of GWAS and GTEx Project eQTL signals provided information about tissue specificity, candidate causal variants, and functional target genes...
June 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29893869/epigenome-wide-association-in-adipose-tissue-from-the-metsim-cohort
#6
Luz D Orozco, Colin Farrell, Christopher Hale, Liudmilla Rubbi, Arturo Rinaldi, Mete Civelek, Calvin Pan, Larry Lam, Dennis Montoya, Chantle Edillor, Marcus Seldin, Michael Boehnke, Karen L Mohlke, Steve Jacobsen, Johanna Kuusisto, Markku Laakso, Aldons J Lusis, Matteo Pellegrini
No abstract text is available yet for this article.
June 9, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29890115/from-chemo-prevention-to-epigenetic-regulation-the-role-of-isothiocyanates-in-skin-cancer-prevention
#7
REVIEW
Melina Mitsiogianni, Tom Amery, Rodrigo Franco, Vasilis Zoumpourlis, Aglaia Pappa, Mihalis I Panayiotidis
Skin cancer incidence is rapidly growing over the last decades and is generally divided into malignant melanoma and non-melanoma (NMSC) with the latter being subdivided into squamous (SCC) and basal cell carcinoma (BCC). Among them, melanoma is the most aggressive type with high mortality rates. On the other hand, aberrant gene expression is a critical step towards malignant transformation. To this end, epigenetic modifications like changes in DNA methylation patterns and miRNA expression profile as well as histone modifications are all capable of inducing an altered gene expression profile involved in various cellular cascades including cell cycle, proliferation and apoptosis...
June 8, 2018: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29890083/connecting-homocysteine-and-obesity-through-pyroptosis-gut-microbiome-epigenetics-peroxisome-proliferator-activator-receptor-%C3%AE-ppar%C3%AE-and-zinc-finger-protein-407-zfp407
#8
Anwesha Laha, Avisek Majumder, Mahavir Singh, Suresh C Tyagi
Although homocysteine (Hcy), a part of the epigenome, contributes to cell death by pyroptosis and decreases PPARγ levels, the mechanisms are unclear. Hcy is found in high concentrations in the sera of obese individuals which can elicit an immune response as well by hypermethylating CpG islands of specific gene promoters, a marker of epigenetics. Hcy has also been established to chelate divalent metal ions like Cu+2 and Zn+2, but this role of Hcy has not been established in relationship with obesity. It has been known for a while that PPARγ dysregulation results in various metabolic disorders including glucose and lipid metabolism...
June 11, 2018: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/29889205/carip-seq-and-chip-seq-methods-to-identify-chromatin-associated-rnas-and-protein-dna-interactions-in-embryonic-stem-cells
#9
Benjamin L Kidder
Embryonic stem (ES) cell self-renewal and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, epigenetic regulators, and post-translation modifications of histones that combinatorially influence the gene expression state of nearby genes. RNA has also been shown to interact with various proteins to regulate chromatin dynamics and gene expression. Chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) is a novel method to survey RNAs associated with chromatin proteins, while chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is a powerful genomics technique to map the location of post-translational modification of histones, transcription factors, and epigenetic modifiers on a global-scale in ES cells...
May 25, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29889009/is-the-goal-of-an-epigenomic-study-to-determine-causality
#10
Philip L De Jager
No abstract text is available yet for this article.
June 2018: Multiple Sclerosis: Clinical and Laboratory Research
https://www.readbyqxmd.com/read/29888956/sex-specific-epigenetic-mediators-between-early-life-social-disadvantage-and-adulthood-bmi
#11
Su H Chu, Eric B Loucks, Karl T Kelsey, Stephen E Gilman, Golareh Agha, Charles B Eaton, Stephen L Buka, Yen-Tsung Huang
AIM: The objective of this study was to identify potential epigenetic mediating pathways linking early life social disadvantage (ELSD) to adulthood BMI. METHODS: Sex-specific epigenome-wide two-stage mediation analyses were conducted in blood and adipose tissue, and mediation estimates were obtained using cross-product mediation analysis. Pathway analyses were conducted using GREAT software (Bejerano Lab, CA, USA). RESULTS: Candidate mediation CpG sites were identified in adipose tissue, but not blood, and were sex-specific...
June 11, 2018: Epigenomics
https://www.readbyqxmd.com/read/29888767/chromatin-succinylation-correlates-with-active-gene-expression-and-is-perturbed-by-defective-tca-cycle-metabolism
#12
John Smestad, Luke Erber, Yue Chen, L James Maher
Succinylation is a post-translational protein acylation modification that converts the cationic lysine side chain to an anion with large potential impacts on protein structure and function. Here we characterize the epigenome-wide distribution of succinyllysine marks in chromatin using chromatin immuno-precipitation sequencing (ChIP-seq). We estimate that more than one-third of all nucleosomes contain lysine succinylation marks and demonstrate a potential role of chromatin succinylation in modulating gene expression...
April 27, 2018: iScience
https://www.readbyqxmd.com/read/29888643/rapid-response-and-slow-recovery-of-the-h3k4me3-epigenomic-marker-in-the-liver-after-light-mediated-phase-advances-of-the-circadian-clock
#13
Dmytro Grygoryev, Michael R Rountree, Furaha Rwatambuga, Anna Ohlrich, Ayaka Kukino, Matthew P Butler, Charles N Allen, Mitchell S Turker
Mammalian tissues display circadian rhythms in transcription, translation, and histone modifications. Here we asked how an advance of the light-dark cycle alters daily rhythms in the liver epigenome at the H3K4me3 (trimethylation of lysine 4 on histone 3) modification, which is found at active and poised gene promoters. H3K4me3 levels were first measured at 4 time points (zeitgeber time [ZT] 3, 8, 15, and 20) during a normal 12L:12D light-dark cycle. Peak levels were observed during the early dark phase at ZT15 and dropped to low levels around lights-on (ZT0) between ZT20 and ZT3...
June 1, 2018: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/29881778/epigenome-associated-phenotypic-acclimatization-to-ocean-acidification-in-a-reef-building-coral
#14
Yi Jin Liew, Didier Zoccola, Yong Li, Eric Tambutté, Alexander A Venn, Craig T Michell, Guoxin Cui, Eva S Deutekom, Jaap A Kaandorp, Christian R Voolstra, Sylvain Forêt, Denis Allemand, Sylvie Tambutté, Manuel Aranda
There are increasing concerns that the current rate of climate change might outpace the ability of reef-building corals to adapt to future conditions. Work on model systems has shown that environmentally induced alterations in DNA methylation can lead to phenotypic acclimatization. While DNA methylation has been reported in corals and is thought to associate with phenotypic plasticity, potential mechanisms linked to changes in whole-genome methylation have yet to be elucidated. We show that DNA methylation significantly reduces spurious transcription in the coral Stylophora pistillata ...
June 2018: Science Advances
https://www.readbyqxmd.com/read/29881475/does-the-prenatal-bisphenol-a-exposure-alter-dna-methylation-levels-in-the-mouse-hippocampus-an-analysis-using-a-high-sensitivity-methylome-technique
#15
Toshiki Aiba, Toshiyuki Saito, Akiko Hayashi, Shinji Sato, Harunobu Yunokawa, Toru Maruyama, Wataru Fujibuchi, Seiichiroh Ohsako
Background: There is still considerable debate about the effects of exposure to bisphenol A (BPA) an endocrine disrupter at low doses. Recently, many studies using animal models have shown that prenatal BPA exposure induces behavioral and neuronal disorders due to epigenetic changes in the brain. However, striking evidence of epigenomic changes has to be shown. Methods: To investigate whether low-dose BPA exposure in the fetal stage can alter CpG methylation levels in the central nervous system, the hippocampus of the inbred C57BL/6 J mouse as the target tissue was collected to detect alterations in CpG methylation levels using a highly sensitive method of genome-wide DNA methylation analysis, methylated site display-amplified fragment length polymorphism (MSD-AFLP)...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/29881472/identifying-mislabeled-and-contaminated-dna-methylation-microarray-data-an-extended-quality-control-toolset-with-examples-from-geo
#16
Jonathan A Heiss, Allan C Just
Background: Mislabeled, contaminated or poorly performing samples can threaten power in methylation microarray analyses or even result in spurious associations. We describe a set of quality checks for the popular Illumina 450K and EPIC microarrays to identify problematic samples and demonstrate their application in publicly available datasets. Methods: Quality checks implemented here include 17 control metrics defined by the manufacturer, a sex check to detect mislabeled sex-discordant samples, and both an identity check for fingerprinting sample donors and a measure of sample contamination based on probes querying high-frequency SNPs...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29876817/fungal-epigenomics-detection-and-analysis
#17
Stephen J Mondo, Rita C Kuo, Vasanth R Singan
Across Eukaryota, DNA modifications play an important role in regulation of gene expression. While 5-methylcytosine (5mC) has been explored in depth, other modifications such as 6-methyladenine (6 mA) have historically been overlooked, in part due to technical difficulties in collecting/analyzing these data. However, recent technological advances have enabled exploration of these marks with much greater detail and on a larger scale. In this chapter, we discuss multiple methods for identifying and analyzing both 5mC and 6 mA across fungi...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29876014/multi-omics-profiling-reveals-a-distinctive-epigenome-signature-for-high-risk-acute-promyelocytic-leukemia
#18
Abhishek A Singh, Francesca Petraglia, Angela Nebbioso, Guoqiang Yi, Mariarosaria Conte, Sergio Valente, Amit Mandoli, Lucia Scisciola, Rik Lindeboom, Hinri Kerstens, Eva M Janssen-Megens, Farzin Pourfarzad, Ehsan Habibi, Kim Berentsen, Bowon Kim, Colin Logie, Simon Heath, Albertus T J Wierenga, Laura Clarke, Paul Flicek, Joop H Jansen, Taco Kuijpers, Marie Laure Yaspo, Veronique Della Valle, Olivier Bernard, Ivo Gut, Edo Vellenga, Hendrik G Stunnenberg, Antonello Mai, Lucia Altucci, Joost H A Martens
Epigenomic alterations have been associated with both pathogenesis and progression of cancer. Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs...
May 22, 2018: Oncotarget
https://www.readbyqxmd.com/read/29876013/combined-hat-ezh2-modulation-leads-to-cancer-selective-cell-death
#19
Francesca Petraglia, Abhishek A Singh, Vincenzo Carafa, Angela Nebbioso, Mariarosaria Conte, Lucia Scisciola, Sergio Valente, Alfonso Baldi, Amit Mandoli, Valeria Belsito Petrizzi, Concetta Ingenito, Sandro De Falco, Valeria Cicatiello, Ivana Apicella, Eva M Janssen-Megens, Bowon Kim, Guoqiang Yi, Colin Logie, Simon Heath, Menotti Ruvo, Albertus T J Wierenga, Paul Flicek, Marie Laure Yaspo, Veronique Della Valle, Olivier Bernard, Stefano Tomassi, Ettore Novellino, Alessandra Feoli, Gianluca Sbardella, Ivo Gut, Edo Vellenga, Hendrik G Stunnenberg, Antonello Mai, Joost H A Martens, Lucia Altucci
Epigenetic alterations have been associated with both pathogenesis and progression of cancer. By screening of library compounds, we identified a novel hybrid epi-drug MC2884, a HAT/EZH2 inhibitor, able to induce bona fide cancer-selective cell death in both solid and hematological cancers in vitro , ex vivo and in vivo xenograft models. Anticancer action was due to an epigenome modulation by H3K27me3, H3K27ac, H3K9/14ac decrease, and to caspase-dependent apoptosis induction. MC2884 triggered mitochondrial pathway apoptosis by up-regulation of cleaved-BID, and strong down-regulation of BCL2...
May 22, 2018: Oncotarget
https://www.readbyqxmd.com/read/29875746/comparative-methylome-analysis-reveals-perturbation-of-host-epigenome-in-chestnut-blight-fungus-by-a-hypovirus
#20
Ru Li, Sisi Zhou, Yongbing Li, Xiaorui Shen, Zhiqiang Wang, Baoshan Chen
In eukaryotic genomes, DNA methylation is an important type of epigenetic modification that plays crucial roles in many biological processes. To investigate the impact of a hypovirus infection on the methylome of Cryphonectria parasitica , the chestnut blight fungus, whole-genome bisulfite sequencing (WGBS) was employed to generate single-base resolution methylomes of the fungus with/without hypovirus infection. The results showed that hypovirus infection alters methylation in all three contexts (CG, CHG, and CHH), especially in gene promoters...
2018: Frontiers in Microbiology
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