keyword
https://read.qxmd.com/read/36631879/systemic-interindividual-epigenetic-variation-in-humans-is-associated-with-transposable-elements-and-under-strong-genetic-control
#1
JOURNAL ARTICLE
Chathura J Gunasekara, Harry MacKay, C Anthony Scott, Shaobo Li, Eleonora Laritsky, Maria S Baker, Sandra L Grimm, Goo Jun, Yumei Li, Rui Chen, Joseph L Wiemels, Cristian Coarfa, Robert A Waterland
BACKGROUND: Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS: We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program...
January 12, 2023: Genome Biology
https://read.qxmd.com/read/36170368/sex-specific-epigenetic-development-in-the-mouse-hypothalamic-arcuate-nucleus-pinpoints-human-genomic-regions-associated-with-body-mass-index
#2
JOURNAL ARTICLE
Harry MacKay, Chathura J Gunasekara, Kit-Yi Yam, Dollada Srisai, Hari Krishna Yalamanchili, Yumei Li, Rui Chen, Cristian Coarfa, Robert A Waterland
Recent genome-wide association studies corroborate classical research on developmental programming indicating that obesity is primarily a neurodevelopmental disease strongly influenced by nutrition during critical ontogenic windows. Epigenetic mechanisms regulate neurodevelopment; however, little is known about their role in establishing and maintaining the brain's energy balance circuitry. We generated neuron and glia methylomes and transcriptomes from male and female mouse hypothalamic arcuate nucleus, a key site for energy balance regulation, at time points spanning the closure of an established critical window for developmental programming of obesity risk...
September 30, 2022: Science Advances
https://read.qxmd.com/read/34739318/dna-methylation-at-a-nutritionally-sensitive-region-of-the-pax8-gene-is-associated-with-thyroid-volume-and-function-in-gambian-children
#3
JOURNAL ARTICLE
Toby Candler, Noah J Kessler, Chathura J Gunasekara, Kate A Ward, Philip James, Eleonora Laritsky, Maria S Baker, Roger Dyer, Rajavel Elango, David Jeffries, Robert A Waterland, Sophie E Moore, Marian Ludgate, Andrew M Prentice, Matt J Silver
PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density...
November 5, 2021: Science Advances
https://read.qxmd.com/read/34341337/a-machine-learning-case-control-classifier-for-schizophrenia-based-on-dna-methylation-in-blood
#4
JOURNAL ARTICLE
Chathura J Gunasekara, Eilis Hannon, Harry MacKay, Cristian Coarfa, Andrew McQuillin, David St Clair, Jonathan Mill, Robert A Waterland
Epigenetic dysregulation is thought to contribute to the etiology of schizophrenia (SZ), but the cell type-specificity of DNA methylation makes population-based epigenetic studies of SZ challenging. To train an SZ case-control classifier based on DNA methylation in blood, therefore, we focused on human genomic regions of systemic interindividual epigenetic variation (CoRSIVs), a subset of which are represented on the Illumina Human Methylation 450K (HM450) array. HM450 DNA methylation data on whole blood of 414 SZ cases and 433 non-psychiatric controls were used as training data for a classification algorithm with built-in feature selection, sparse partial least squares discriminate analysis (SPLS-DA); application of SPLS-DA to HM450 data has not been previously reported...
August 3, 2021: Translational Psychiatry
https://read.qxmd.com/read/33680493/rationale-and-design-of-the-baylor-infant-twin-study-a-study-assessing-obesity-related-risk-factors-from-infancy
#5
JOURNAL ARTICLE
Shabnam R Momin, Mackenzie K Senn, Scott Buckley, Neil R M Buist, Manisha Gandhi, Amy B Hair, Sheryl O Hughes, Kelly R Hodges, William C Lange, Maria A Papaioannou, Mimi Phan, Robert A Waterland, Alexis C Wood
Background: Early childhood (0-3 years) is a critical period for obesity prevention, when tendencies in eating behaviors and physical activity are established. Yet, little is understood about how the environment shapes children's genetic predisposition for these behaviors during this time. The Baylor Infant Twin Study (BITS) is a two phase study, initiated to study obesity risk factors from infancy. Data collection has been completed for Phase 1 in which three sub-studies pilot central measures for Phase 2...
February 2021: Obesity Science & Practice
https://read.qxmd.com/read/33387539/perfluorooctanoic-acid-pfoa-or-perfluorooctane-sulfonate-pfos-and-dna-methylation-in-newborn-dried-blood-spots-in-the-upstate-kids-cohort
#6
JOURNAL ARTICLE
Sonia L Robinson, Xuehuo Zeng, Weihua Guan, Rajeshwari Sundaram, Pauline Mendola, Diane L Putnick, Robert A Waterland, Chathura J Gunasekara, Kurunthachalam Kannan, Chongjing Gao, Erin M Bell, Edwina H Yeung
Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are persistent organic pollutants which may alter prenatal development, potentially through epigenetic modifications. Prior studies examining PFOS/PFOA and DNA methylation have relatively few subjects (n<200) and inconsistent results. We examined relations of PFOA/PFOS with DNA methylation among 597 neonates in the Upstate KIDS cohort study. PFOA/PFOS were quantified in newborn dried blood spots (DBS) using high-performance liquid chromatography/tandem mass spectrometry...
December 30, 2020: Environmental Research
https://read.qxmd.com/read/32605651/identification-of-cell-type-specific-methylation-signals-in-bulk-whole-genome-bisulfite-sequencing-data
#7
JOURNAL ARTICLE
C Anthony Scott, Jack D Duryea, Harry MacKay, Maria S Baker, Eleonora Laritsky, Chathura J Gunasekara, Cristian Coarfa, Robert A Waterland
BACKGROUND: The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions). Variation limited to single or small numbers of CpGs has been assumed to reflect stochastic processes. To test this, we developed software, Cluster-Based analysis of CpG methylation (CluBCpG), and explored variation in read-level CpG methylation patterns in whole genome bisulfite sequencing data...
July 1, 2020: Genome Biology
https://read.qxmd.com/read/32584399/can-children-catch-up-from-the-consequences-of-undernourishment-evidence-from-child-linear-growth-developmental-epigenetics-and-brain-and-neurocognitive-development
#8
JOURNAL ARTICLE
Jef L Leroy, Edward A Frongillo, Pragya Dewan, Maureen M Black, Robert A Waterland
Recovery from nutritionally induced height deficits continues to garner attention. The current literature on catch-up growth, however, has 2 important limitations: wide-ranging definitions of catch-up growth are used, and it remains unclear whether children can recover from the broader consequences of undernutrition. We addressed these shortcomings by reviewing the literature on the criteria for catch-up in linear growth and on the potential to recover from undernutrition early in life in 3 domains: linear growth, developmental epigenetics, and child brain and neurocognitive development...
June 25, 2020: Advances in Nutrition
https://read.qxmd.com/read/31792207/dna-methylation-in-agrp-neurons-regulates-voluntary-exercise-behavior-in-mice
#9
JOURNAL ARTICLE
Harry MacKay, C Anthony Scott, Jack D Duryea, Maria S Baker, Eleonora Laritsky, Amanda E Elson, Theodore Garland, Marta L Fiorotto, Rui Chen, Yumei Li, Cristian Coarfa, Richard B Simerly, Robert A Waterland
DNA methylation regulates cell type-specific gene expression. Here, in a transgenic mouse model, we show that deletion of the gene encoding DNA methyltransferase Dnmt3a in hypothalamic AgRP neurons causes a sedentary phenotype characterized by reduced voluntary exercise and increased adiposity. Whole-genome bisulfite sequencing (WGBS) and transcriptional profiling in neuronal nuclei from the arcuate nucleus of the hypothalamus (ARH) reveal differentially methylated genomic regions and reduced expression of AgRP neuron-associated genes in knockout mice...
December 2, 2019: Nature Communications
https://read.qxmd.com/read/31729252/a-new-era-for-epigenetic-epidemiology
#10
EDITORIAL
Chathura J Gunasekara, Robert A Waterland
No abstract text is available yet for this article.
November 15, 2019: Epigenomics
https://read.qxmd.com/read/31528363/early-postnatal-overnutrition-accelerates-aging-associated-epigenetic-drift-in-pancreatic-islets
#11
JOURNAL ARTICLE
Ge Li, Tihomira D Petkova, Eleonora Laritsky, Noah Kessler, Maria S Baker, Shaoyu Zhu, Robert A Waterland
Pancreatic islets of type 2 diabetes patients have altered DNA methylation, contributing to islet dysfunction and the onset of type 2 diabetes. The cause of these epigenetic alterations is largely unknown. We set out to test whether (i) islet DNA methylation would change with aging and (ii) early postnatal overnutrition would persistently alter DNA methylation. We performed genome-scale DNA methylation profiling in islets from postnatally over-nourished (suckled in a small litter) and control male mice at both postnatal day 21 and postnatal day 180...
July 2019: Environmental Epigenetics
https://read.qxmd.com/read/31265437/s100a4-cre-mediated-deletion-of-patched1-causes-hypogonadotropic-hypogonadism-role-of-pituitary-hematopoietic-cells-in-endocrine-regulation
#12
JOURNAL ARTICLE
Yi Athena Ren, Teresa Monkkonen, Michael T Lewis, Daniel J Bernard, Helen C Christian, Carolina J Jorgez, Joshua A Moore, John D Landua, Haelee M Chin, Weiqin Chen, Swarnima Singh, Ik Sun Kim, Xiang H-F Zhang, Yan Xia, Kevin J Phillips, Harry MacKay, Robert A Waterland, M Cecilia Ljungberg, Pradip K Saha, Sean M Hartig, Tatiana Fiordelisio Coll, JoAnne S Richards
Hormones produced by the anterior pituitary gland regulate an array of important physiological functions, but pituitary hormone disorders are not fully understood. Herein we report that genetically-engineered mice with deletion of the hedgehog signaling receptor Patched1 by S100a4 promoter-driven Cre recombinase (S100a4-Cre;Ptch1fl/fl mutants) exhibit adult-onset hypogonadotropic hypogonadism and multiple pituitary hormone disorders. During the transition from puberty to adult, S100a4-Cre;Ptch1fl/fl mice of both sexes develop hypogonadism coupled with reduced gonadotropin levels...
July 2, 2019: JCI Insight
https://read.qxmd.com/read/30294432/patient-s-views-of-the-consent-process-for-groin-hernia-repair-use-of-consent-template-improves-compliance-with-best-practice-original-research
#13
JOURNAL ARTICLE
Saad U Khan, David J Bowrey, Robert N Williams, Jun Yi Soh, Aikaterini Peleki, Nazli Muhibullah, Peter W Waterland
BACKGROUND: Informed consent obtained for day case surgery has been historically incomplete. An assessment of consenting practice for groin hernia was performed relative to existing gold standards and patient's perception of the consent process was evaluated with a questionnaire. The aim of the study was to identify areas of improvement to comply with best practice. METHODS: A retrospective audit of adult patients undergoing groin hernia repair (June-November 2016) at a tertiary care centre was performed...
November 2018: Annals of Medicine and Surgery
https://read.qxmd.com/read/30009262/establishment-of-environmentally-sensitive-dna-methylation-states-in-the-very-early-human-embryo
#14
JOURNAL ARTICLE
Noah J Kessler, Robert A Waterland, Andrew M Prentice, Matt J Silver
The molecular mechanisms responsible for the developmental origins of later disease are currently unknown. We previously demonstrated that women's periconceptional nutrition predicts their offspring's DNA methylation at metastable epialleles (MEs). We present a genome-wide screen yielding 687 MEs and track their trajectories across nine developmental stages in human in vitro fertilization embryos. MEs exhibit highly unusual methylation dynamics across the implantation-gastrulation transition, producing a large excess of intermediate methylation states, suggesting the potential for differential programming in response to external signals...
July 2018: Science Advances
https://read.qxmd.com/read/29694043/rate-coefficient-measurements-and-theoretical-analysis-of-the-oh-e-cf-3-ch%C3%A2-chcf-3-reaction
#15
JOURNAL ARTICLE
Munkhbayar Baasandorj, Paul Marshall, Robert L Waterland, A R Ravishankara, James B Burkholder
Rate coefficients, k, for the gas-phase reaction of the OH radical with ( E)-CF3 CH═CHCF3 (( E)-1,1,1,4,4,4-hexafluoro-2-butene, HFO-1336mzz(E)) were measured over a range of temperatures (211-374 K) and bath gas pressures (20-300 Torr; He, N2 ) using a pulsed laser photolysis-laser-induced fluorescence (PLP-LIF) technique. k1 ( T) was independent of pressure over this range of conditions with k1 (296 K) = (1.31 ± 0.15) × 10-13 cm3 molecule-1 s-1 and k1 ( T) = (6.94 ± 0.80) × 10-13 exp[-(496 ± 10)/ T] cm3 molecule-1 s-1 , where the uncertainties are 2σ, and the pre-exponential term includes estimated systematic error...
May 17, 2018: Journal of Physical Chemistry. A
https://read.qxmd.com/read/29310692/epigenetic-supersimilarity-of-monozygotic-twin-pairs
#16
JOURNAL ARTICLE
Timothy E Van Baak, Cristian Coarfa, Pierre-Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S Baker, Noah J Kessler, Jianrong Dong, Jack D Duryea, Matt J Silver, Ayden Saffari, Andrew M Prentice, Sophie E Moore, Akram Ghantous, Michael N Routledge, Yun Yun Gong, Zdenko Herceg, Paolo Vineis, Gianluca Severi, John L Hopper, Melissa C Southey, Graham G Giles, Roger L Milne, Robert A Waterland
BACKGROUND: Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to be largely due to their genetic identity. RESULTS: Here, by analyzing data from a genome-scale study of DNA methylation in monozygotic and dizygotic twins, we identified genomic regions at which the epigenetic similarity of monozygotic twins is substantially greater than can be explained by their genetic identity...
January 9, 2018: Genome Biology
https://read.qxmd.com/read/28836271/roadmap-for-investigating-epigenome-deregulation-and-environmental-origins-of-cancer
#17
REVIEW
Zdenko Herceg, Akram Ghantous, Christopher P Wild, Athena Sklias, Lavinia Casati, Susan J Duthie, Rebecca Fry, Jean-Pierre Issa, Richard Kellermayer, Igor Koturbash, Yukata Kondo, Johanna Lepeule, Sheila C S Lima, Carmen J Marsit, Vardhman Rakyan, Richard Saffery, Jack A Taylor, Andrew E Teschendorff, Toshikazu Ushijima, Paolo Vineis, Cheryl Lyn Walker, Robert A Waterland, Joe Wiemels, Srikant Ambatipudi, Davide Degli Esposti, Hector Hernandez-Vargas
The interaction between the (epi)genetic makeup of an individual and his/her environmental exposure record (exposome) is accepted as a determinant factor for a significant proportion of human malignancies. Recent evidence has highlighted the key role of epigenetic mechanisms in mediating gene-environment interactions and translating exposures into tumorigenesis. There is also growing evidence that epigenetic changes may be risk factor-specific ("fingerprints") that should prove instrumental in the discovery of new biomarkers in cancer...
March 1, 2018: International Journal of Cancer. Journal International du Cancer
https://read.qxmd.com/read/28051947/early-life-effects-on-adult-physical-activity-concepts-relevance-and-experimental-approaches
#18
JOURNAL ARTICLE
Theodore Garland, Marcell D Cadney, Robert A Waterland
Locomotion is a defining characteristic of animal life and plays a crucial role in most behaviors. Locomotion involves physical activity, which can have far-reaching effects on physiology and neurobiology, both acutely and chronically. In human populations and in laboratory rodents, higher levels of physical activity are generally associated with positive health outcomes, although excessive exercise can have adverse consequences. Whether and how such relationships occur in wild animals is unknown. Behavioral variation among individuals arises from genetic and environmental factors and their interactions as well as from developmental programming (persistent effects of early-life environment)...
January 2017: Physiological and Biochemical Zoology: PBZ
https://read.qxmd.com/read/27568547/interindividual-variation-in-dna-methylation-at-a-putative-pomc-metastable-epiallele-is-associated-with-obesity
#19
JOURNAL ARTICLE
Peter Kühnen, Daniela Handke, Robert A Waterland, Branwen J Hennig, Matt Silver, Anthony J Fulford, Paula Dominguez-Salas, Sophie E Moore, Andrew M Prentice, Joachim Spranger, Anke Hinney, Johannes Hebebrand, Frank L Heppner, Lena Walzer, Carsten Grötzinger, Jörg Gromoll, Susanna Wiegand, Annette Grüters, Heiko Krude
The estimated heritability of human BMI is close to 75%, but identified genetic variants explain only a small fraction of interindividual body-weight variation. Inherited epigenetic variants identified in mouse models named "metastable epialleles" could in principle explain this "missing heritability." We provide evidence that methylation in a variably methylated region (VMR) in the pro-opiomelanocortin gene (POMC), particularly in postmortem human laser-microdissected melanocyte-stimulating hormone (MSH)-positive neurons, is strongly associated with individual BMI...
September 13, 2016: Cell Metabolism
https://read.qxmd.com/read/27037645/developmental-programming-state-of-the-science-and-future-directions-summary-from-a-pennington-biomedical-symposium
#20
REVIEW
Elizabeth F Sutton, L Anne Gilmore, David B Dunger, Bas T Heijmans, Marie-France Hivert, Charlotte Ling, J Alfredo Martinez, Susan E Ozanne, Rebecca A Simmons, Moshe Szyf, Robert A Waterland, Leanne M Redman, Eric Ravussin
OBJECTIVE: On December 8-9, 2014, the Pennington Biomedical Research Center convened a scientific symposium to review the state-of-the-science and future directions for the study of developmental programming of obesity and chronic disease. The objectives of the symposium were to discuss: (i) past and current scientific advances in animal models, population-based cohort studies, and human clinical trials, (ii) the state-of-the-science of epigenetic-based research, and (iii) considerations for future studies...
May 2016: Obesity
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