Publications by authors named "Matt Silver"

Worldwide trends to delay childbearing have increased parental ages at birth. Older parental age may harm offspring health, but mechanisms remain unclear. Alterations in offspring DNA methylation (DNAm) patterns could play a role as aging has been associated with methylation changes in gametes of older individuals.

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Higher birth order is associated with altered risk of many disease states. Changes in placentation and exposures to in utero growth factors with successive pregnancies may impact later life disease risk via persistent DNA methylation alterations. We investigated birth order with Illumina DNA methylation array data in each of 16 birth cohorts (8164 newborns) with European, African, and Latino ancestries from the Pregnancy and Childhood Epigenetics Consortium.

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Article Synopsis
  • Metastable epialleles (MEs) are DNA regions where methylation levels vary among individuals but remain consistent across different tissues in the same person, potentially influenced by environmental factors.
  • This review covers the definition of MEs, techniques for identifying them in humans, and their genetic characteristics.
  • It also examines research connecting DNA methylation at these MEs to early environmental influences and later health outcomes.
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  • Seasonal variations at birth can influence DNA methylation, which may affect health outcomes over a person’s lifetime.
  • A study involving multiple cohorts discovered specific DNA methylation patterns linked to different birth seasons, revealing 26 differentially methylated regions (DMRs) at birth and 32 in childhood.
  • Results suggested that geographic latitude plays a role in these associations, linking certain genes to conditions like schizophrenia and asthma, particularly in infants born in higher latitudes (≥50°N).
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  • Human height is primarily determined by genetics, but this study explores how modifiable epigenetic factors, specifically blood DNA methylation, influence child height in low and middle-income countries (LMIC).
  • The research identifies a significant link between DNA methylation in the SOCS3 gene and child height, with findings replicating in a high-income country cohort, showing that this effect is independent of genetic factors.
  • Analysis reveals that SOCS3 methylation explains up to 9.5% of height variance in mid-childhood and is influenced by prenatal maternal folate and socio-economic status, highlighting the potential role of epigenetic modifications in child growth in LMIC.
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DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues.

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  • Increasing evidence suggests that epigenetic changes, particularly DNA methylation of the POMC gene, can increase the risk of obesity, with a notable 1.4-fold risk linked to specific hypermethylation patterns.
  • A human embryonic stem cell model was used to study how these methylation states are established early in development, showing that reduced DNA methylation is associated with the formation of hypothalamic neurons that express the POMC gene.
  • Treatment with an MC4R agonist in individuals with hypermethylation resulted in an average body weight reduction of about 4.66% over several months, highlighting a potential therapeutic approach for addressing this epigenetic obesity risk variant.
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  • The study examined DNA methylation across 30 datasets with 3474 individuals from various tissues and ethnicities, identifying 4143 highly variable methylation sites (hvCpGs).
  • These hvCpGs were influenced by genetic factors but were not solely determined by them, nor were they significantly affected by factors like age, sex, or cell differences.
  • The hvCpGs showed patterns linking to retrovirus elements and were associated with early environmental factors, making them important for studying how early DNA methylation may affect long-term health.
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  • DNA methylation patterns from parents are mostly erased after fertilization, which influences the embryo's development and marks for gene expression.* -
  • A study in rural Gambia analyzed data from children conceived in different seasons, finding 259 specific DNA regions (CpGs) linked to the season of conception (SoC), especially evident in early infancy.* -
  • These findings suggest that the environment around conception plays a significant role in shaping long-lasting epigenetic changes that may impact health throughout life.*
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Background: The prevalence of cardiometabolic disease (CMD) is rising globally, with environmentally induced epigenetic changes suggested to play a role. Few studies have investigated epigenetic associations with CMD risk factors in children from low- and middle-income countries. We sought to identify associations between DNA methylation (DNAm) and CMD risk factors in children from India and The Gambia.

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PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that 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.

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Background: Many nutrients have powerful immunomodulatory actions with the potential to alter susceptibility to coronavirus disease 2019 (COVID-19) infection, progression to symptoms, likelihood of severe disease, and survival.

Objective: The aim was to review the latest evidence on how malnutrition across all its forms (under- and overnutrition and micronutrient status) may influence both susceptibility to, and progression of, COVID-19.

Methods: We synthesized information on 13 nutrition-related components and their potential interactions with COVID-19: overweight, obesity, and diabetes; protein-energy malnutrition; anemia; vitamins A, C, D, and E; PUFAs; iron; selenium; zinc; antioxidants; and nutritional support.

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Background: Maternal nutrition in pregnancy has been linked to offspring health in early and later life, with changes to DNA methylation (DNAm) proposed as a mediating mechanism.

Objective: We investigated intervention-associated DNAm changes in children whose mothers participated in 2 randomized controlled trials of micronutrient supplementation before and during pregnancy, as part of the EMPHASIS (Epigenetic Mechanisms linking Preconceptional nutrition and Health Assessed in India and sub-Saharan Africa) study (ISRCTN14266771).

Design: We conducted epigenome-wide association studies with blood samples from Indian (n = 698) and Gambian (n = 293) children using the Illumina EPIC array and a targeted study of selected loci not on the array.

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Early life exposures are important predictors of adult disease risk. Although the underlying mechanisms are largely unknown, telomere maintenance may be involved. This study investigated the relationship between seasonal differences in parental exposures at time of conception and leukocyte telomere length (LTL) in their offspring.

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The link between poor maternal nutrition and suboptimal outcomes in offspring is well established, but underlying mechanisms are not well understood. Modifications to the offspring epigenome are a plausible mechanism for the transmission of intergenerational signals that could extend to effects of paternal nutrition mediated by epigenetic modifications in sperm. The epigenome is extensively remodeled in the early embryo.

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Background: Infant DNA methylation profiles are associated with their mother's periconceptional nutritional status. DNA methylation relies on nutritional inputs for one-carbon metabolic pathways, including the efficient recycling of homocysteine. This randomised controlled trial in nonpregnant women in rural Gambia tests the efficacy of a novel nutritional supplement designed to improve one-carbon-related nutrient status by reducing plasma homocysteine, and assesses its potential future use in preconception trials.

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Article Synopsis
  • DNA methylation plays a key role in human phenotypic variation, but its impact has been difficult to measure due to its specificity to different cell types.
  • Researchers identified 9,926 genomic regions (CoRSIVs) demonstrating consistent interindividual DNA methylation variation across three germ layer tissues—thyroid, heart, and brain.
  • These CoRSIVs are linked to human disease and phenotypes, offering a valuable resource for studying how epigenetic differences may influence individual health risks in the future.
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  • Birthweight is linked to health outcomes throughout life, and DNA methylation may play a significant role, as shown in a meta-analysis involving 8,825 neonates.
  • The study identified 914 DNA methylation sites in neonatal blood associated with birthweight, revealing a weight difference from -183 to 178 grams per 10% increase in methylation.
  • Although some of the methylation changes related to birthweight were also seen in childhood, they did not persist into adulthood, suggesting the need for further research to clarify the causal relationships involved.
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Background: Mounting evidence suggests that nutritional exposures during pregnancy influence the fetal epigenome, and that these epigenetic changes can persist postnatally, with implications for disease risk across the life course.

Methods: We review human intergenerational studies using a three-part search strategy. Search 1 investigates associations between preconceptional or pregnancy nutritional exposures, focusing on one-carbon metabolism, and offspring DNA methylation.

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Article Synopsis
  • - The study explores how women's nutrition before conception affects their children's DNA methylation, specifically at metastable epialleles (MEs), which are unique genomic regions that vary in methylation patterns.
  • - Researchers conducted a genome-wide analysis identifying 687 MEs, revealing irregular methylation changes during critical developmental stages in IVF embryos, indicating potential responsiveness to environmental influences.
  • - In a case study from rural Gambia, MEs associated with seasonal conception displayed similar unusual methylation patterns, suggesting that these epigenetic markers are shaped by both genetic factors and the pre-conception environment, potentially impacting offspring traits.
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  • Monozygotic twins are often studied to understand the role of genetics and epigenetics in their phenotypic similarities, which are thought to be mainly due to their identical genetics.
  • Recent research shows that monozygotic twins have greater epigenetic similarity than expected, due to specific epigenetic changes happening before the embryo splits, a phenomenon called "epigenetic supersimilarity."
  • This epigenetic similarity is linked to environmental factors and is associated with a higher risk of developing certain cancers, suggesting early embryonic epigenetic changes can influence health later in life.
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Background: Animal studies have shown that nutritional exposures during pregnancy can modify epigenetic marks regulating fetal development and susceptibility to later disease, providing a plausible mechanism to explain the developmental origins of health and disease. Human observational studies have shown that maternal peri-conceptional diet predicts DNA methylation in offspring. However, a causal pathway from maternal diet, through changes in DNA methylation, to later health outcomes has yet to be established.

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Epigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account.

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The prenatal environment can alter an individual's developmental trajectory with long-lasting effects on health. Animal models demonstrate that the impact of the early life environment extends to subsequent generations, but there is a paucity of data from human populations on intergenerational transmission of environmentally induced phenotypes. Here we investigated the association of parental exposure to energy and nutrient restriction on their children's growth in rural Gambia.

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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.

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