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Metabolism and epigenetics

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https://www.readbyqxmd.com/read/27913608/the-clinical-utility-of-circulating-neuroendocrine-gene-transcript-analysis-in-well-differentiated-paragangliomas-and-pheochromocytomas
#1
M Pęczkowska, J Cwikla, M Kidd, A Lewczuk, A Kolasinska-Ćwikła, D Niec, I Michałowska, A Prejbisz, A Januszewicz, J Chiarelli, L Bodei, I Modlin
CONTEXT: Paragangliomas and pheochromocytomas (PPGLs) exhibit variable malignancy, which is difficult to determine by histopathology, amine measurements or tissue genetic analyses. OBJECTIVE: To evaluate whether a 51-neuroendocrine gene blood analysis has clinical utility as a diagnostic and prognostic marker. DESIGN: Prospective cohort study. Well-differentiated PPGLs (n = 32), metastatic (n = 4); SDHx mutation (n = 25); 12 biochemically active, Lanreotide treated (n = 4)...
February 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27912843/the-reduced-concentration-of-citrate-in-cancer-cells-an-indicator-of-cancer-aggressiveness-and-a-possible-therapeutic-target
#2
Icard Philippe, Lincet Hubert
Proliferating cells reduce their oxidative metabolism and rely more on glycolysis, even in the presence of O2 (Warburg effect). This shift in metabolism reduces citrate biosynthesis and diminishes intracellular acidity, both of which promote glycolysis sustaining tumor growth. Because citrate is the donor of acetyl-CoA, its reduced production favors a deacetylation state of proteins favoring resistance to apoptosis and epigenetic changes, both processes contributing to tumor aggressiveness. Citrate levels could be monitored as an indicator of cancer aggressiveness (as already shown in human prostate cancer) and/or could serve as a biomarker for response to therapy...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27912059/microbiota-diurnal-rhythmicity-programs-host-transcriptome-oscillations
#3
Christoph A Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911843/impact-of-the-gut-microbiota-on-enhancer-accessibility-in-gut-intraepithelial-lymphocytes
#4
Nicholas P Semenkovich, Joseph D Planer, Philip P Ahern, Nicholas W Griffin, Charles Y Lin, Jeffrey I Gordon
The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ(+) and γδ(+) intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling-weaning transition...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27909741/the-role-of-epigenetic-modifiers-in-extended-cultures-of-functional-hepatocyte-like-cells-derived-from-human-neonatal-mesenchymal-stem-cells
#5
M Cipriano, J C Correia, S P Camões, N G Oliveira, P Cruz, H Cruz, M Castro, J L Ruas, J M Santos, J P Miranda
The development of predictive in vitro stem cell-derived hepatic models for toxicological drug screening is an increasingly important topic. Herein, umbilical cord tissue-derived mesenchymal stem cells (hnMSCs) underwent hepatic differentiation using an optimized three-step core protocol of 24 days that mimicked liver embryogenesis with further exposure to epigenetic markers, namely the histone deacetylase inhibitor trichostatin A (TSA), the cytidine analogue 5-azacytidine (5-AZA) and dimethyl sulfoxide (DMSO)...
December 1, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27906710/who-s-your-daddy-paternal-inheritance-of-metabolic-disease-risk
#6
Elvira Isganaitis, Harumi Suehiro, Connie Cardona
PURPOSE OF REVIEW: Although the importance of optimizing mothers' health prior to conception and during pregnancy is now well accepted, recent data also implicate health and nutritional status of fathers as contributors to chronic disease risk in their progeny. This brief review will highlight recent epidemiological and experimental studies linking paternal overnutrition, undernutrition, and other forms of stress, to metabolic disease in the offspring. RECENT FINDINGS: The past 2 years have brought tremendous insights into the mechanisms by which paternal exposures can contribute to disease susceptibility in the next generation...
November 30, 2016: Current Opinion in Endocrinology, Diabetes, and Obesity
https://www.readbyqxmd.com/read/27906649/a-common-bacterial-metabolite-elicits-prion-based-bypass-of-glucose-repression
#7
David M Garcia, David Dietrich, Jon Clardy, Daniel F Jarosz
Robust preference for fermentative glucose metabolism has motivated domestication of the budding yeast Saccharomyces cerevisiae. This program can be circumvented by a protein-based genetic element, the [GAR(+)] prion, permitting simultaneous metabolism of glucose and other carbon sources. Diverse bacteria can elicit yeast cells to acquire [GAR(+)], although the molecular details of this interaction remain unknown. Here we identify the common bacterial metabolite lactic acid as a strong [GAR(+)] inducer. Transient exposure to lactic acid caused yeast cells to heritably circumvent glucose repression...
November 29, 2016: ELife
https://www.readbyqxmd.com/read/27902459/anti-tumor-activity-of-metformin-from-metabolic-and-epigenetic-perspectives
#8
REVIEW
Xilan Yu, Wuxiang Mao, Yansheng Zhai, Chong Tong, Min Liu, Lixin Ma, Xiaolan Yu, Shanshan Li
Metformin has been used to treat type 2 diabetes for over 50 years. Epidemiological, preclinical and clinical studies suggest that metformin treatment reduces cancer incidence in diabetes patients. Due to its potential as an anti-cancer agent and its low cost, metformin has gained intense research interest. Its traditional anti-cancer mechanisms involve both indirect and direct insulin-dependent pathways. Here, we discussed the anti-tumor mechanism of metformin from the aspects of cell metabolism and epigenetic modifications...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27898587/maternal-epigenetics-and-fetal-and-neonatal-growth
#9
Sofia Kitsiou-Tzeli, Maria Tzetis
PURPOSE OF REVIEW: The article provides an update on new insights of factors altering inherited maternal epigenome that ultimately affect fetal and neonatal growth. RECENT FINDINGS: A number of new publications have identified mechanisms through which maternal nutrition, environmental exposures such as stress and toxic substances altering expression of imprinted genes during pregnancy can influence fetal and neonatal phenotype and susceptibility to disease development later in life...
November 24, 2016: Current Opinion in Endocrinology, Diabetes, and Obesity
https://www.readbyqxmd.com/read/27898055/increased-dna-methylation-variability-in-type-1-diabetes-across-three-immune-effector-cell-types
#10
Dirk S Paul, Andrew E Teschendorff, Mary A N Dang, Robert Lowe, Mohammed I Hawa, Simone Ecker, Huriya Beyan, Stephanie Cunningham, Alexandra R Fouts, Anita Ramelius, Frances Burden, Samantha Farrow, Sophia Rowlston, Karola Rehnstrom, Mattia Frontini, Kate Downes, Stephan Busche, Warren A Cheung, Bing Ge, Marie-Michelle Simon, David Bujold, Tony Kwan, Guillaume Bourque, Avik Datta, Ernesto Lowy, Laura Clarke, Paul Flicek, Emanuele Libertini, Simon Heath, Marta Gut, Ivo G Gut, Willem H Ouwehand, Tomi Pastinen, Nicole Soranzo, Sabine E Hofer, Beate Karges, Thomas Meissner, Bernhard O Boehm, Corrado Cilio, Helena Elding Larsson, Åke Lernmark, Andrea K Steck, Vardhman K Rakyan, Stephan Beck, R David Leslie
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#11
Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Pietro Liò, Ivan Merelli
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27891191/birth-weight-for-gestational-age-is-associated-with-dna-methylation-at-birth-and-in-childhood
#12
Golareh Agha, Hanine Hajj, Sheryl L Rifas-Shiman, Allan C Just, Marie-France Hivert, Heather H Burris, Xihong Lin, Augusto A Litonjua, Emily Oken, Dawn L DeMeo, Matthew W Gillman, Andrea A Baccarelli
BACKGROUND: Both higher and lower fetal growth are associated with cardio-metabolic health later in life, suggesting that prenatal developmental programming determines long-term cardiovascular disease risk. Epigenetic mechanisms, which orchestrate fetal growth and development, may offer insight on the early programming of health and disease. We investigated whether birth weight-for-gestational is associated with DNA methylation at birth and mid-childhood, measured via the Infinium 450K array...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27890772/integrative-analysis-of-dna-methylation-and-gene-expression-in-butyrate-treated-cho-cells
#13
Anna Wippermann, Oliver Rupp, Karina Brinkrolf, Raimund Hoffrogge, Thomas Noll
The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays...
November 24, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27890035/epigenetics-in-type-1-diabetes-tnfa-gene-promoter-methylation-status-in-chilean-patients-with-type-1-diabetes-mellitus
#14
Viviana Arroyo-Jousse, Diego F Garcia-Diaz, Ethel Codner, Francisco Pérez-Bravo
TNF-α is a pro-inflammatory cytokine that is involved in type 1 diabetes (T1D) pathogenesis. The TNFa gene is subject of epigenetic regulation in which folate and homocysteine are important molecules because they participate in the methionine cycle where the most important methyl group donor (S-adenosylmethionine) is formed. We investigated whether TNFa gene promoter methylation status in T1D patients was related to blood folate, homocysteine and TNF-α in a transversal case-control study. We studied T1D patients (n 25, mean=13·7 years) and healthy control subjects (n 25, mean=31·1 years), without T1D and/or other autoimmune diseases or direct family history of these diseases...
November 28, 2016: British Journal of Nutrition
https://www.readbyqxmd.com/read/27889327/epigenetics-in-non-alcoholic-fatty-liver-disease
#15
REVIEW
Jooho Lee, Yuri Kim, Simonetta Friso, Sang-Woon Choi
Non-alcoholic fatty liver disease (NAFLD), a common hepatic disorder ranging from simple steatosis through steatohepatitis to fibrosis and cirrhosis, is an emerging health concern. NAFLD is a pathologic condition characterized by the buildup of extra fat in liver cells that is not caused by alcohol consumption. Excess hepatic fat accumulation results from increased delivery of triglycerides (TG) to the liver or conversion of surplus carbohydrates to TG. Importantly, a subgroup of NAFLD results in hepatocellular injury and inflammation, which is referred to as non-alcoholic steatohepatitis (NASH), and may progress to irreversible cirrhosis and hepatocellular carcinoma (HCC)...
November 23, 2016: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/27889100/epigenetic-regulation-of-an-adverse-metabolic-phenotype-in-polycystic-ovary-syndrome-the-impact-of-the-leukocyte-methylation-of-ppargc1a-promoter
#16
Hongcui Zhao, Yue Zhao, Yun Ren, Min Li, Tianjie Li, Rong Li, Yang Yu, Jie Qiao
OBJECTIVE: To investigate PPARGC1A promoter methylation and mitochondria DNA (mtDNA) content in the leukocytes of women with polycystic ovary syndrome (PCOS) and analyze the relationship between these indices and metabolic risk for women with PCOS. DESIGN: Cross-sectional study. SETTING: University hospital. PATIENT(S): A total of 175 women with PCOS and 127 healthy controls. INTERVENTION(S): None...
November 23, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27888347/different-phenotypes-in-identical-twins-with-cerebrotendinous-xanthomatosis-case-series
#17
Dénes Zádori, László Szpisjak, László Madar, Viktória Evelin Varga, Bernadett Csányi, Krisztina Bencsik, István Balogh, Mariann Harangi, Éva Kereszty, László Vécsei, Péter Klivényi
Cerebrotendinous xanthomatosis (CTX) is a rare, genetically determined error of metabolism. The characteristic clinical symptoms are diarrhea, juvenile cataracts, tendon xanthomas and neuropsychiatric alterations. The aim of this study is to present a pair of identical adult twins with considerable differences in the severity of phenotype. With regards to neuropsychiatric symptoms, the predominant features were severe Parkinsonism and moderate cognitive dysfunctions in the more-affected individual, whereas these alterations in the less-affected patient were only very mild and mild, respectively...
November 25, 2016: Neurological Sciences
https://www.readbyqxmd.com/read/27887750/chronic-kidney-disease
#18
REVIEW
Angela C Webster, Evi V Nagler, Rachael L Morton, Philip Masson
The definition and classification of chronic kidney disease (CKD) have evolved over time, but current international guidelines define this condition as decreased kidney function shown by glomerular filtration rate (GFR) of less than 60 mL/min per 1·73 m(2), or markers of kidney damage, or both, of at least 3 months duration, regardless of the underlying cause. Diabetes and hypertension are the main causes of CKD in all high-income and middle-income countries, and also in many low-income countries. Incidence, prevalence, and progression of CKD also vary within countries by ethnicity and social determinants of health, possibly through epigenetic influence...
November 22, 2016: Lancet
https://www.readbyqxmd.com/read/27884142/dna-methylation-patterns-associated-with-oxidative-stress-in-an-ageing-population
#19
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27882772/mirnas-differentially-expressed-by-next-generation-sequencing-in-cord-blood-buffy-coat-samples-of-boys-and-girls
#20
Daneida Lizarraga, Karen Huen, Mary Combs, Maria Escudero-Fung, Brenda Eskenazi, Nina Holland
AIM: Differences in children's development and susceptibility to diseases and exposures have been observed by sex, yet human studies of sex differences in miRNAs are limited. MATERIALS & METHODS: The genome-wide miRNA expression was characterized by sequencing-based EdgeSeq assay in cord blood buffy coats from 89 newborns, and 564 miRNAs were further analyzed. RESULTS: Differential expression of most miRNAs was higher in boys. Neurodevelopment, RNA metabolism and metabolic ontology terms were enriched among miRNA targets...
November 24, 2016: Epigenomics
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