1
|
Taylor JY, Jones-Patten A, Prescott L, Potts-Thompson S, Joyce C, Tayo B, Saban K. The race-based stress reduction intervention (RiSE) study on African American women in NYC and Chicago: Design and methods for complex genomic analysis. PLoS One 2024; 19:e0295293. [PMID: 38598554 PMCID: PMC11006145 DOI: 10.1371/journal.pone.0295293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/19/2023] [Indexed: 04/12/2024] Open
Abstract
RiSE study aims to evaluate a race-based stress-reduction intervention as an effective strategy to improve coping and decrease stress-related symptoms, inflammatory burden, and modify DNA methylation of stress response-related genes in older AA women. This article will describe genomic analytic methods to be utilized in this longitudinal, randomized clinical trial of older adult AA women in Chicago and NYC that examines the effect of the RiSE intervention on DNAm pre- and post-intervention, and its overall influence on inflammatory burden. Salivary DNAm will be measured at baseline and 6 months following the intervention, using the Oragene-DNA kit. Measures of perceived stress, depressive symptoms, fatigue, sleep, inflammatory burden, and coping strategies will be assessed at 4 time points including at baseline, 4 weeks, 8 weeks, and 6 months. Genomic data analysis will include the use of pre-processed and quality-controlled methylation data expressed as beta (β) values. Association analyses will be performed to detect differentially methylated sites on the targeted candidate genes between the intervention and non-intervention groups using the Δβ (changes in methylation) with adjustment for age, health behaviors, early life adversity, hybridization batch, and top principal components of the probes as covariates. To account for multiple testing, we will use FDR adjustment with a corrected p-value of <0.05 regarded as statistically significant. To assess the relationship between inflammatory burden and Δβ among the study samples, we will repeat association analyses with the inclusion of individual inflammation protein measures. ANCOVA will be used because it is more statistically powerful to detect differences.
Collapse
Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Alexandria Jones-Patten
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Laura Prescott
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Stephanie Potts-Thompson
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Cara Joyce
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Bamidele Tayo
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Karen Saban
- Marcella Niehoff School of Nursing, Center for Translational Research and Education, Loyola University Chicago, Maywood, Illinois, United States of America
| |
Collapse
|
2
|
Mrug S, Barker-Kamps M, Goering M, Patki A, Tiwari HK. Neighborhood Disadvantage and Parenting in Early Adolescence Predict Epigenetic Aging and Mortality Risk in Adulthood. J Youth Adolesc 2024; 53:258-272. [PMID: 37715862 DOI: 10.1007/s10964-023-01863-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/04/2023] [Indexed: 09/18/2023]
Abstract
Youth who grow up in disadvantaged neighborhoods experience poorer health later in life, but little is known about the biological mechanisms underlying these effects and socioenvironmental factors that may protect youth from the biological embedding of neighborhood adversity. This study tests whether supportive and consistent parenting buffers associations between neighborhood disadvantage in early adolescence and epigenetic aging in adulthood. A community sample from Birmingham, Alabama, USA (N = 343; 57% female; 81% Black, 19% White) was assessed in early adolescence (T1; ages 11 and 13) and adulthood (T2; age 27). At T1, neighborhood poverty was derived from census data and neighborhood disorder was reported by caregivers. Both youth and parents reported on parental discipline and nurturance. At T2, methylation of salivary DNA was used to derive a mortality risk index and Hannum, Horvath, PhenoAge, and GrimAge epigenetic age estimators. Regression analyses revealed that neighborhood disadvantage was associated with accelerated epigenetic aging and/or mortality risk only when combined with high levels of harsh and inconsistent discipline and low child-reported parental nurturance. These findings identify epigenetic aging and mortality risk as relevant mechanisms through which neighborhood adversity experienced in adolescence may affect later health; they also point to the importance of supportive and consistent parenting for reducing the biological embedding of neighborhood adversity in early adolescence.
Collapse
Affiliation(s)
- Sylvie Mrug
- Department of Psychology, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, AL, 35294, USA.
| | - Malcolm Barker-Kamps
- Department of Psychology, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, AL, 35294, USA
| | - Marlon Goering
- Department of Psychology, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, AL, 35294, USA
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, AL, 35294, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, AL, 35294, USA
| |
Collapse
|
3
|
Nazzari S, Cagliero L, Grumi S, Pisoni E, Mallucci G, Bergamaschi R, Maccarini J, Giorda R, Provenzi L. Prenatal exposure to environmental air pollution and psychosocial stress jointly contribute to the epigenetic regulation of the serotonin transporter gene in newborns. Mol Psychiatry 2023; 28:3503-3511. [PMID: 37542161 DOI: 10.1038/s41380-023-02206-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
Antenatal exposures to maternal stress and to particulate matter with an aerodynamic diameter of less than 2.5 μm (PM2.5) have been independently associated with developmental outcomes in early infancy and beyond. Knowledge about their joint impact, biological mechanisms of their effects and timing-effects, is still limited. Both PM2.5 and maternal stress exposure during pregnancy might result in altered patterns of DNA methylation in specific stress-related genes, such as the serotonin transporter gene (SLC6A4 DNAm), that might, in turn, influence infant development across several domains, including bio-behavioral, cognitive and socio-emotional domains. Here, we investigated the independent and interactive influence of variations in antenatal exposures to maternal pandemic-related stress (PRS) and PM2.5 on SLC6A4 DNAm levels in newborns. Mother-infant dyads (N = 307) were enrolled at delivery during the COVID-19 pandemic. Infants' methylation status was assessed in 13 CpG sites within the SLC6A4 gene's region (chr17:28562750-28562958) in buccal cells at birth and women retrospectively report on PRS. PM2.5 exposure throughout the entire gestation and at each gestational trimester was estimated using a spatiotemporal model based on residential address. Among several potentially confounding socio-demographic and health-related factors, infant's sex was significantly associated with infants' SLC6A4 DNAm levels, thus hierarchical regression models were adjusted for infant's sex. Higher levels of SLC6A4 DNAm at 6 CpG sites were found in newborns born to mothers reporting higher levels of antenatal PRS and greater PM2.5 exposure across gestation, while adjusting for infant's sex. These effects were especially evident when exposure to elevated PM2.5 occurred during the second trimester of pregnancy. Several important brain processes (e.g., synaptogenesis and myelination) occur during mid-pregnancy, potentially making the second trimester a sensitive time window for the effects of stress-related exposures. Understanding the interplay between environmental and individual-level stressors has important implications for the improvement of mother-infant health during and after the pandemic.
Collapse
Affiliation(s)
- Sarah Nazzari
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Lucia Cagliero
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Developmental Psychobiology Lab, IRCCS Mondino Foundation, Pavia, Italy
| | - Serena Grumi
- Developmental Psychobiology Lab, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Pisoni
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Giulia Mallucci
- Multiple Sclerosis Center, Neurocenter of South of Switzerland, EOC, Lugano, Switzerland
| | | | - Julia Maccarini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Developmental Psychobiology Lab, IRCCS Mondino Foundation, Pavia, Italy
| | - Roberto Giorda
- Molecular Biology Lab, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Livio Provenzi
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
- Developmental Psychobiology Lab, IRCCS Mondino Foundation, Pavia, Italy.
| |
Collapse
|
4
|
Maternal and infant NR3C1 and SLC6A4 epigenetic signatures of the COVID-19 pandemic lockdown: when timing matters. Transl Psychiatry 2022; 12:386. [PMID: 36114180 PMCID: PMC9481531 DOI: 10.1038/s41398-022-02160-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/27/2022] Open
Abstract
Stress exposure during pregnancy is critically linked with maternal mental health and child development. The effects might involve altered patterns of DNA methylation in specific stress-related genes (i.e., glucocorticoid receptor gene, NR3C1, and serotonin transporter gene, SLC6A4) and might be moderated by the gestational timing of stress exposure. In this study, we report on NR3C1 and SLC6A4 methylation status in Italian mothers and infants who were exposed to the COVID-19 pandemic lockdown during different trimesters of pregnancy. From May 2020 to February 2021, 283 mother-infant dyads were enrolled at delivery. Within 24 h from delivery, buccal cells were collected to assess NR3C1 (44 CpG sites) and SLC6A4 (13 CpG sites) methylation status. Principal component (PC) analyses were used to reduce methylation data dimension to one PC per maternal and infant gene methylation. Mother-infant dyads were split into three groups based on the pregnancy trimester (first, second, third), during which they were exposed to the COVID-19 lockdown. Mothers and infants who were exposed to the lockdown during the first trimester of pregnancy had lower NR3C1 and SLC6A4 methylation when compared to counterparts exposed during the second or third trimesters. The effect remained significant after controlling for confounders. Women who were pregnant during the pandemic and their infants might present altered epigenetic biomarkers of stress-related genes. As these epigenetic marks have been previously linked with a heightened risk of maternal psychiatric problems and less-than-optimal child development, mothers and infants should be adequately monitored for psychological health during and after the pandemic.
Collapse
|
5
|
Robakis TK, Roth MC, King LS, Humphreys KL, Ho M, Zhang X, Chen Y, Li T, Rasgon NL, Watson KT, Urban AE, Gotlib IH. Maternal attachment insecurity, maltreatment history, and depressive symptoms are associated with broad DNA methylation signatures in infants. Mol Psychiatry 2022; 27:3306-3315. [PMID: 35577912 PMCID: PMC9666564 DOI: 10.1038/s41380-022-01592-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 04/05/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022]
Abstract
The early environment, including maternal characteristics, provides many cues to young organisms that shape their long-term physical and mental health. Identifying the earliest molecular events that precede observable developmental outcomes could help identify children in need of support prior to the onset of physical and mental health difficulties. In this study, we examined whether mothers' attachment insecurity, maltreatment history, and depressive symptoms were associated with alterations in DNA methylation patterns in their infants, and whether these correlates in the infant epigenome were associated with socioemotional and behavioral functioning in toddlerhood. We recruited 156 women oversampled for histories of depression, who completed psychiatric interviews and depression screening during pregnancy, then provided follow-up behavioral data on their children at 18 months. Buccal cell DNA was obtained from 32 of their infants for a large-scale analysis of methylation patterns across 5 × 106 individual CpG dinucleotides, using clustering-based significance criteria to control for multiple comparisons. We found that tens of thousands of individual infant CpGs were alternatively methylated in association with maternal attachment insecurity, maltreatment in childhood, and antenatal and postpartum depressive symptoms, including genes implicated in developmental patterning, cell-cell communication, hormonal regulation, immune function/inflammatory response, and neurotransmission. Density of DNA methylation at selected genes from the result set was also significantly associated with toddler socioemotional and behavioral problems. This is the first report to identify novel regions of the human infant genome at which DNA methylation patterns are associated longitudinally both with maternal characteristics and with offspring socioemotional and behavioral problems in toddlerhood.
Collapse
Affiliation(s)
- Thalia K Robakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Marissa C Roth
- Department of Psychology and Human Development, Peabody College of Vanderbilt University, Nashville, TN, USA
| | - Lucy S King
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Kathryn L Humphreys
- Department of Psychology and Human Development, Peabody College of Vanderbilt University, Nashville, TN, USA
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | | | - Natalie L Rasgon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Kathleen T Watson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA, USA
| |
Collapse
|
6
|
Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden. Sci Rep 2022; 12:12670. [PMID: 35879377 PMCID: PMC9310683 DOI: 10.1038/s41598-022-15924-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70–95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24) gene was found. This confirms a previous finding, where changes in expression of SLC25A24 were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3 can be monitored.
Collapse
|
7
|
Mrug S, Barker-Kamps M, Orihuela CA, Patki A, Tiwari HK. Childhood Neighborhood Disadvantage, Parenting, and Adult Health. Am J Prev Med 2022; 63:S28-S36. [PMID: 35725138 PMCID: PMC9219037 DOI: 10.1016/j.amepre.2022.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/04/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Growing up in disadvantaged neighborhoods is associated with poor adult health indicators. Consistent and supportive parenting plays a key role in life-long health, but it is not known whether positive parenting can mitigate the relationship between neighborhood adversity and poor health. This study examines parenting as a moderator of the links between childhood neighborhood characteristics and adult health indicators. METHODS A sample of 305 individuals (61% female; 82% African American, 18% Caucasian) were assessed in childhood (T1; age 11 years; 2003‒2004) and adulthood (T2; age 27 years; 2018‒2021). At T1, neighborhood poverty was derived from census data; neighborhood disorder was reported by parents. Children reported on parental harsh discipline, inconsistent discipline, and parental nurturance. At T2, health outcomes included BMI, serum cortisol and C-reactive protein (CRP), and salivary DNA methylation index related to CRP. Regression models predicted T2 health outcomes from T1 neighborhood and parenting variables and their interactions, adjusting for clustering and confounders. Data were analyzed in 2021. RESULTS Neighborhood poverty was associated with lower cortisol, whereas neighborhood disorder was linked with CRP‒related DNA methylation. Multiple interactions between neighborhood and parenting variables emerged, indicating that adverse neighborhood conditions were only related to poor adult health when combined with inconsistent discipline and low parental nurturance. By contrast, warm and supportive parenting, consistent discipline, and to a lesser extent harsh discipline buffered children from poor health outcomes associated with neighborhood disadvantage. CONCLUSIONS Interventions enhancing consistent and nurturing parenting may help to reduce the long-term associations of neighborhood disadvantage with poor health.
Collapse
Affiliation(s)
- Sylvie Mrug
- Department of Psychology, College of Arts and Sciences, The University of Alabama at Birmingham, Birmingham, Alabama.
| | - Malcolm Barker-Kamps
- Department of Psychology, College of Arts and Sciences, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Catheryn A Orihuela
- Department of Psychology, College of Arts and Sciences, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Amit Patki
- Department of Biostatistics, School of Public Health, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, The University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
8
|
Yamazaki J, Meagawa S, Jelinek J, Yokoyama S, Nagata N, Yuki M, Takiguchi M. Obese status is associated with accelerated DNA methylation change in peripheral blood of senior dogs. Res Vet Sci 2021; 139:193-199. [PMID: 34358922 DOI: 10.1016/j.rvsc.2021.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/29/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Obesity and its associated comorbidities constitute a major and growing health problem worldwide not only involved with people but also dogs and cats. Although few genetic mutations have been associated with obesity in dogs, molecular mechanism remains to be clearly understood. Given the fact that DNA methylation leads to gene expression variability and has plasticity affected by metabolic phenotypes such as obesity in human, the objective of this study is to identify obesity-associated differentially methylated cytosine-phosphate-guanine (CpG) dinucleotide sites in dogs. With genome-wide DNA methylation analysis using next-generation sequencing for blood samples from fourteen Miniature dachshunds with body condition score (BCS) 4-5 and BCS ≥6, over 100,000 sites could be analysed to identify genomic locations of differentially methylated CpG sites. As a result, 191 differentially methylated CpG sites (89 CpG sites were hypermethylated in BCS ≥6 and 102 were hypermethylated in BCS 4-5) were identified. These sites included promoter regions of Kisspeptin receptor (KISS1R) and Calcyphosine 2 (CAPS2) genes which were subsequently validated by bisulfite-pyrosequencing for another set of 157 dog blood samples. KISS1R methylation levels were found to be higher in BCS ≥6 group than BCS 4-5 in senior (>84 months) dogs. Especially male dogs but not female dogs as well as uncastrated male dogs but not castrated male dogs showed this trend. DNA methylation of KISS1R gene will be useful for understanding of comprehensive epigenetic change in obese dogs.
Collapse
Affiliation(s)
- Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan.
| | - Shinji Meagawa
- Department of Pediatrics, MD Anderson Cancer Center, Houston, Tx, USA
| | | | - Shoko Yokoyama
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Noriyuki Nagata
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Masashi Yuki
- Yuki Animal Hospital, 2-99 Kiba-cho, Minato-ku, Aichi, Japan
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| |
Collapse
|
9
|
Childebayeva A, Harman T, Weinstein J, Day T, Brutsaert TD, Bigham AW. Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek. Front Physiol 2021; 12:660906. [PMID: 34262470 PMCID: PMC8273439 DOI: 10.3389/fphys.2021.660906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
The individual physiological response to high-altitude hypoxia involves both genetic and non-genetic factors, including epigenetic modifications. Epigenetic changes in hypoxia factor pathway (HIF) genes are associated with high-altitude acclimatization. However, genome-wide epigenetic changes that are associated with short-term hypoxia exposure remain largely unknown. We collected a series of DNA samples from 15 participants of European ancestry trekking to Everest Base Camp to identify DNA methylation changes associated with incremental altitude ascent. We determined genome-wide DNA methylation levels using the Illumina MethylationEPIC chip comparing two altitudes: baseline 1,400 m (day 0) and elevation 4,240 m (day 7). The results of our epigenome-wide association study revealed 2,873 significant differentially methylated positions (DMPs) and 361 significant differentially methylated regions (DMRs), including significant positions and regions in hypoxia inducible factor (HIF) and the renin–angiotensin system (RAS) pathways. Our pathway enrichment analysis identified 95 significant pathways including regulation of glycolytic process (GO:0006110), regulation of hematopoietic stem cell differentiation (GO:1902036), and regulation of angiogenesis (GO:0045765). Lastly, we identified an association between the ACE gene insertion/deletion (I/D) polymorphism and oxygen saturation, as well as average ACE methylation. These findings shed light on the genes and pathways experiencing the most epigenetic change associated with short-term exposure to hypoxia.
Collapse
Affiliation(s)
- Ainash Childebayeva
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States.,Department of Environmental Sciences, School of Public Health, Ann Arbor, MI, United States.,Department of Archaeogenetics, Max Planck Institute for the Study of Human History, Jena, Germany
| | - Taylor Harman
- Department of Anthropology, Syracuse University, Syracuse, NY, United States
| | - Julien Weinstein
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States
| | - Trevor Day
- Department of Biology, Mount Royal University, Calgary, AB, Canada
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, United States
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
10
|
Salivary DNA Methylation as an Epigenetic Biomarker for Head and Neck Cancer. Part I: A Diagnostic Accuracy Meta-Analysis. J Pers Med 2021; 11:jpm11060568. [PMID: 34204396 PMCID: PMC8233749 DOI: 10.3390/jpm11060568] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/31/2022] Open
Abstract
DNA hypermethylation is an important epigenetic mechanism for gene expression inactivation in head and neck cancer (HNC). Saliva has emerged as a novel liquid biopsy representing a potential source of biomarkers. We performed a comprehensive meta-analysis to evaluate the overall diagnostic accuracy of salivary DNA methylation for detecting HNC. PubMed EMBASE, Web of Science, LILACS, and the Cochrane Library were searched. Study quality was assessed by the Quality Assessment for Studies of Diagnostic Accuracy-2, and sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (dOR), and their corresponding 95% confidence intervals (CIs) were calculated using a bivariate random-effect meta-analysis model. Meta-regression and subgroup analyses were performed to assess heterogeneity. Eighty-four study units from 18 articles with 8368 subjects were included. The pooled sensitivity and specificity of salivary DNA methylation were 0.39 and 0.87, respectively, while PLR and NLR were 3.68 and 0.63, respectively. The overall area under the curve (AUC) was 0.81 and the dOR was 8.34. The combination of methylated genes showed higher diagnostic accuracy (AUC, 0.92 and dOR, 36.97) than individual gene analysis (AUC, 0.77 and dOR, 6.02). These findings provide evidence regarding the potential clinical application of salivary DNA methylation for HNC diagnosis.
Collapse
|
11
|
Young JI, Slifer S, Hecht JT, Blanton SH. DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate. Front Cell Dev Biol 2021; 9:656865. [PMID: 34055787 PMCID: PMC8149607 DOI: 10.3389/fcell.2021.656865] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect. The etiology of NSCLP is complex with multiple genes and environmental factors playing causal roles. Although studies have identified numerous genetic markers associated with NSCLP, the role of epigenetic variation remains relatively unexplored. Because of their identical DNA sequences, monozygotic (MZ) twins discordant for NSCLP are an ideal model for examining the potential contribution of DNA methylation to non-syndromic orofacial clefting. In this study, we compared the patterns of whole genome DNA methylation in six MZ twin pairs discordant for NSCLP. Differentially methylated positions (DMPs) and regions (DMRs) were identified in NSCLP candidate genes, including differential methylation in MAFB and ZEB2 in two independent MZ twin pairs. In addition to DNA methylation differences in NSCLP candidate genes, we found common differential methylation in genes belonging to the Hippo signaling pathway, implicating this mechanosensory pathway in the etiology of NSCLP. The results of this novel approach using MZ twins discordant for NSCLP suggests that differential methylation is one mechanism contributing to NSCLP, meriting future studies on the role of DNA methylation in familial and sporadic NSCLP.
Collapse
Affiliation(s)
- Juan I. Young
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Susan Slifer
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Jacqueline T. Hecht
- McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| |
Collapse
|
12
|
Hannon E, Mansell G, Walker E, Nabais MF, Burrage J, Kepa A, Best-Lane J, Rose A, Heck S, Moffitt TE, Caspi A, Arseneault L, Mill J. Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology. PLoS Genet 2021; 17:e1009443. [PMID: 33739972 PMCID: PMC8011804 DOI: 10.1371/journal.pgen.1009443] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 03/31/2021] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated DNAm variation is specific to an individual cellular population. We collected three peripheral tissues (whole blood, buccal epithelial and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. We identified significant differences in both the level and variability of DNAm between different sample types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, although the proportion of variance explained was greater than that explained by either buccal or nasal epithelial samples. Covariation across sample types was much higher for DNAm sites influenced by genetic factors. Overall, we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites, however, variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight about EWAS findings. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and our data will facilitate the interpretation of findings in epigenetic epidemiology. As epigenetic variation is cell-type specific, an ongoing challenge in epigenetic epidemiology is how to interpret studies performed using bulk tissue (for example, whole blood) which comprises a mix of different cell types. In this study, we identified major differences in DNA methylation (DNAm) across multiple peripheral tissues and different blood cell types, with each sample type being characterized by a unique signature across multiple genomic loci. We demonstrate how these differences influence commonly used prediction scores derived from DNAm data for age and tobacco smoking, with estimates for the same individual being highly variable across tissues and cell types. Our results enabled us to assess the extent to which variable DNAm in each individual blood cell type relates to variation measured in whole blood. We found that although individual blood cell types predict more of the variation in DNAm in whole blood compared to buccal and nasal epithelial cells, the actual proportion of variance explained is relatively small, except for at sites where DNAm is under genetic control. Our data indicate that for most sites variation in multiple blood cell types additively combines to drive variation in DNAm measured in whole blood. Of note, for a subset of sites, variation in DNAm detected in whole blood can be attributed to a specific blood cell type, potentially facilitating the interpretation of EWAS findings.
Collapse
Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Emma Walker
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Marta F Nabais
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kepa
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Janis Best-Lane
- Section of Anaesthetics, Pain Medicine and Intensive Care Medicine, Department of Surgery and Cancer, Imperial College London and Imperial College Healthcare NHS Trust, London, United Kingdom
- Imperial Clinical Trials Unit, Imperial College London, London, United Kingdom
| | - Anna Rose
- BRC Flow Cytometry Platform, NIHR GSTT/KCL Comprehensive Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Suzanne Heck
- Biomedical Research Centre at Guy's and St Thomas' Hospitals and King's College London, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Terrie E Moffitt
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Avshalom Caspi
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
13
|
Berretta E, Guida E, Forni D, Provenzi L. Glucocorticoid receptor gene (NR3C1) methylation during the first thousand days: Environmental exposures and developmental outcomes. Neurosci Biobehav Rev 2021; 125:493-502. [PMID: 33689802 DOI: 10.1016/j.neubiorev.2021.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/07/2020] [Accepted: 03/03/2021] [Indexed: 02/08/2023]
Abstract
The first 1000 days from conception are a sensitive period for human development programming. During this period, environmental exposures may result in long-lasting epigenetic imprints that contribute to future developmental trajectories. The present review reports on the effects of adverse and protective environmental conditions occurring during the first 1000 days on glucocorticoid receptor gene (NR3C1) regulation in humans. Thirty-four studies were included. Wide variations emerged for biological tissues, number and position of analyzed CpG sites, and age at methylation and outcomes assessment. Increased NR3C1 methylation associated with first 1000 days stress exposures. Maternal caregiving behaviors significantly buffered precocious stress exposures. A less robust pattern of findings emerged for the association of NR3C1 methylation with physical health, neurobehavioral and neuroendocrine outcomes. Although drawing comprehensive conclusions is partially hindered by methodological limitations, the present review underlines the relevance of the first 1000 days from conception as a time window for developmental plasticity. Prospective cohort studies and epigenome-wide approaches may increase our understanding of dynamics epigenetic changes and their consequences for child development.
Collapse
Affiliation(s)
- Erica Berretta
- Experimental and Behavioral Neurophysiology Lab, Scientific Institute IRCCS Fondazione Santa Lucia, Roma, Italy
| | - Elena Guida
- 0-3 Center for the At-Risk Infant, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Livio Provenzi
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy.
| |
Collapse
|
14
|
Preliminary indications that the Attachment and Biobehavioral Catch-up Intervention alters DNA methylation in maltreated children. Dev Psychopathol 2020; 32:1486-1494. [PMID: 31854285 DOI: 10.1017/s0954579419001421] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Maltreatment during development is associated with epigenetic changes to the genome. Enhancing caregiving may mitigate these effects. Attachment and Biobehavioral Catch-Up (ABC) is an intervention that has been shown to improve parent-child relationships and a variety of biological and behavioral outcomes among children that are involved in Child Protective Services. This preliminary study, using a small sample size, explored whether children who received ABC exhibit different methylation patterns than those who received a control intervention. The participants included 23 children aged 6-21 months who were randomized to receive ABC (n = 12) or a control intervention (n = 11). While the children displayed similar methylation patterns preintervention, DNA methylation varied between the ABC and control groups at 14,828 sites postintervention. Functional pathway analyses indicated that these differences were associated with gene pathways that are involved in cell signaling, metabolism, and neuronal development. This study is one of the first to explore parenting intervention effects on children's DNA methylation at the whole genome level in infancy. These preliminary findings provide a basis for hypothesis generation in further research with larger-scale studies regarding the malleability of epigenetic states that are associated with maltreatment.
Collapse
|
15
|
Gottschalk MG, Domschke K, Schiele MA. Epigenetics Underlying Susceptibility and Resilience Relating to Daily Life Stress, Work Stress, and Socioeconomic Status. Front Psychiatry 2020; 11:163. [PMID: 32265751 PMCID: PMC7099635 DOI: 10.3389/fpsyt.2020.00163] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/20/2020] [Indexed: 02/05/2023] Open
Abstract
Susceptibility and resilience to mental disorders result from a complex choreography of gene-environment interactions with epigenetics at the intersection of external psychological stressors and internal biological systems. Increasing awareness of the growing disease burden influenced by daily life stress ("daily hassles"), work-related stress, and low socioeconomic status (SES) has resulted in a novel interest into their underlying molecular signatures. This review offers a brief outline of psychiatric epigenetics and a comprehensive overview of recent findings exploring the relationship of various occupational stressors and DNA methylation in epigenome-wide association studies (EWAS) and in candidate gene studies including the serotonin transporter (SLC6A4; 5-HTTLPR), melatonin receptor 1A (MTNR1A), brain-derived neurotrophic factor (BDNF), tyrosine hydroxylase (TH), and the protein family of DNA methyltransferases (DNMTs). Conceptual and methodological challenges of epigenetic investigations with a special focus on gene-environment interactions are highlighted and discussed. The findings are integrated into a pathophysiological framework featuring epigenetic plasticity factors and work-related stress as a possible central detrimental component targetable by workplace interventions. Finally, the potential of dynamic epigenetic biomarkers of treatment response to pharmacotherapy or psychotherapy is expanded upon.
Collapse
Affiliation(s)
- Michael G Gottschalk
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam A Schiele
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
16
|
Provenzi L, Brambilla M, Scotto di Minico G, Montirosso R, Borgatti R. Maternal caregiving and DNA methylation in human infants and children: Systematic review. GENES BRAIN AND BEHAVIOR 2019; 19:e12616. [DOI: 10.1111/gbb.12616] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/18/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Livio Provenzi
- Scientific Institute IRCCS E. Medea0‐3 Centre for the at‐Risk Infant Bosisio Parini Lecco Italy
| | - Maddalena Brambilla
- Scientific Institute IRCCS E. Medea0‐3 Centre for the at‐Risk Infant Bosisio Parini Lecco Italy
| | - Giunia Scotto di Minico
- Scientific Institute IRCCS E. Medea0‐3 Centre for the at‐Risk Infant Bosisio Parini Lecco Italy
| | - Rosario Montirosso
- Scientific Institute IRCCS E. Medea0‐3 Centre for the at‐Risk Infant Bosisio Parini Lecco Italy
| | - Renato Borgatti
- Scientific Institute IRCCS E. MedeaChild Neuropsychiatry and Neurorehabilitation Unit Bosisio Parini Lecco Italy
| |
Collapse
|
17
|
Childebayeva A, Harman T, Weinstein J, Goodrich JM, Dolinoy DC, Day TA, Bigham AW, Brutsaert TD. DNA Methylation Changes Are Associated With an Incremental Ascent to High Altitude. Front Genet 2019; 10:1062. [PMID: 31737045 PMCID: PMC6828981 DOI: 10.3389/fgene.2019.01062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic and nongenetic factors are involved in the individual ability to physiologically acclimatize to high-altitude hypoxia through processes that include increased heart rate and ventilation. High-altitude acclimatization is thought to have a genetic component, yet it is unclear if other factors, such as epigenetic gene regulation, are involved in acclimatization to high-altitude hypoxia in nonacclimatized individuals. We collected saliva samples from a group of healthy adults of European ancestry (n = 21) in Kathmandu (1,400 m; baseline) and three altitudes during a trek to the Everest Base Camp: Namche (3,440 m; day 3), Pheriche (4,240 m; day 7), and Gorak Shep (5,160 m; day 10). We used quantitative bisulfite pyrosequencing to determine changes in DNA methylation, a well-studied epigenetic marker, in LINE-1, EPAS1, EPO, PPARa, and RXRa. We found significantly lower DNA methylation between baseline (1,400 m) and high altitudes in LINE-1, EPO (at 4,240 m only), and RXRa. We found increased methylation in EPAS1 (at 4,240 m only) and PPARa. We also found positive associations between EPO methylation and systolic blood pressure and RXRa methylation and hemoglobin. Our results show that incremental exposure to hypoxia can affect the epigenome. Changes to the epigenome, in turn, could underlie the process of altitude acclimatization.
Collapse
Affiliation(s)
- Ainash Childebayeva
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States.,Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Taylor Harman
- Department of Exercise Science, Syracuse University, Syracuse, NY, United States
| | - Julien Weinstein
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.,Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Trevor A Day
- Department of Biology, Faculty of Science and Technology, Mount Royal University, Calgary, AB, Canada
| | - Abigail W Bigham
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States.,Department of Anthropology, University of California, Los Angeles, CA, United States
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, United States
| |
Collapse
|
18
|
Brown KM, Hui Q, Huang Y, Taylor JY, Prescott L, de Mendoza VB, Crusto C, Sun YV. Association Between Stress and Coping with DNA Methylation of Blood Pressure-Related Genes Among African American Women. CHRONIC STRESS 2019; 3. [PMID: 32395678 PMCID: PMC7213592 DOI: 10.1177/2470547019879088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Exposure to psychosocial stress and employment of high effort coping
strategies have been identified as risk factors that may partially explain
the high prevalence of hypertension among African Americans. One biological
mechanism through which stress and coping may affect risk of hypertension is
via epigenetic modifications (e.g., DNA methylation) in blood
pressure-related genes; however, this area remains understudied in African
Americans. Methods We used data from the ongoing Intergenerational Blood Pressure Study, a
longitudinal study designed to investigate factors that contribute to
hypertension risk in African American women (n = 120) and their young
children, to investigate the association between stress overload,
problem-solving coping, avoidance coping, and social support coping with DNA
methylation in 25 candidate genes related to blood pressure. Multivariable
linear regression and multilevel modeling were used to conduct methylation
site-level and gene-level analyses, respectively. Results In site-level analyses, stress overload, problem-solving coping, social
support coping, and avoidance coping were associated with 47, 63, 66, and 61
sites, respectively, at p < 0.05. However, no associations were
statistically significant after multiple testing correction. There were also
no significant associations in gene-level analyses. Conclusions As human social epigenomics is an emerging, evolving area of research, there
is much to be learned from studies with statistically significant findings
as well as studies with null findings. Factors such as characteristics of
the social stressor, source of DNA, and synchronization of exposure and
outcome are likely important considerations as we move the field
forward.
Collapse
Affiliation(s)
| | - Qin Hui
- Emory University (Atlanta, Georgia)
| | | | | | | | | | | | | |
Collapse
|
19
|
Murata Y, Fujii A, Kanata S, Fujikawa S, Ikegame T, Nakachi Y, Zhao Z, Jinde S, Kasai K, Bundo M, Iwamoto K. Evaluation of the usefulness of saliva for DNA methylation analysis in cohort studies. Neuropsychopharmacol Rep 2019; 39:301-305. [PMID: 31393092 PMCID: PMC7292296 DOI: 10.1002/npr2.12075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Introduction Epigenetic information such as DNA methylation is a useful biomarker that reflects complex gene‐environmental interaction. Peripheral tissues such as blood and saliva are commonly collected as the source of genomic DNA in cohort studies. Epigenetic studies mainly use blood, while a few studies have addressed the epigenetic characteristics of saliva. Methods The effects of methods for DNA extraction and purification from saliva on DNA methylation were surveyed using Illumina Infinium HumanMethylation450 BeadChip. Using 386 661 probes, DNA methylation differences between blood and saliva from 22 healthy volunteers, and their functional and structural characteristics were examined. CpG sites with DNA methylation levels showing large interindividual variations in blood were evaluated using saliva DNA methylation profiles. Results Genomic DNA prepared by simplified protocol from saliva showed a similar quality DNA methylation profile to that derived from the manufacturer provided protocol. Consistent with previous studies, the DNA methylation profiles of blood and saliva showed high correlations. Blood showed 1,514 hypomethylated and 2099 hypermethylated probes, suggesting source‐dependent DNA methylation patterns. CpG sites with large methylation difference between the two sources were underrepresented in the promoter regions and enriched within gene bodies. CpG sites with large interindividual methylation variations in blood also showed considerable variations in saliva. Conclusion In addition to high correlation in DNA methylation profiles, CpG sites showing large interindividual DNA methylation differences were similar between blood and saliva, ensuring saliva could be a suitable alternative source for genomic DNA in cohort studies. Consideration of source‐dependent DNA methylation differences will, however, be necessary. We compared quality of saliva methylome data collected by several DNA purification protocols and examined the characteristics of saliva methylome. Optimized protocol and identified characteristics such as common informative CpG sites to blood and unique epigenetic changes in saliva will contribute to promote the use of saliva for epigenetic studies in clinical settings and epidemiological cohort studies.![]()
Collapse
Affiliation(s)
- Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ayaka Fujii
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sho Kanata
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Psychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Shinya Fujikawa
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Zhilei Zhao
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan
| | - Seiichiro Jinde
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
20
|
Hearn NL, Coleman AS, Ho V, Chiu CL, Lind JM. Comparing DNA methylation profiles in saliva and intestinal mucosa. BMC Genomics 2019; 20:163. [PMID: 30819108 PMCID: PMC6394071 DOI: 10.1186/s12864-019-5553-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/21/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Altered epigenetic profiles are a feature of intestinal diseases, including ulcerative colitis and Crohn's disease. DNA methylation studies in these diseases have utilised intestinal mucosal tissue or blood which can be difficult to collect, particularly for large-scale research studies. Saliva is an attractive alternative for epigenetic studies as it is easy to collect and provides high quality methylation profiles. The aim of the study was to determine the utility of saliva as an alternative for DNA methylation studies of intestinal disorders. RESULTS DNA methylation in saliva and intestinal mucosa samples were compared in individuals (n = 10) undergoing endoscopies using the Illumina Infinium Methylation 450 K Beadchip array. We found that DNA methylation was correlated between tissue types within an individual (Pearson correlation co-efficient r = 0.92 to 0.95, p < 0.001). Of the 48,541 probes (approximately 11% of CpG sites) that were differentially methylated between saliva and intestinal mucosa (adjusted p < 0.001, |Δβ| ≥ 20%), these mapped to genes involved in tissue-specific pathways, including the apelin signalling and oxytocin pathways which are important in gastrointestinal cytoprotection and motility. CONCLUSIONS This study suggests that saliva has the potential to be used as an alternate DNA source to invasive intestinal mucosa for DNA methylation research into intestinal conditions.
Collapse
Affiliation(s)
- Nerissa L. Hearn
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Aaron S. Coleman
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Vincent Ho
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Christine L. Chiu
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Joanne M. Lind
- School of Medicine, Western Sydney University, Sydney, Australia
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| |
Collapse
|
21
|
Epigenetic variation at the SLC6A4 gene promoter in mother-child pairs with major depressive disorder. J Affect Disord 2019; 245:716-723. [PMID: 30447571 DOI: 10.1016/j.jad.2018.10.369] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 01/16/2023]
Abstract
BACKGROUND Genetic and epigenetic variations of the serotonin transporter gene (SLC6A4) have been related to the etiology of depression. The 5-HTTLPR polymorphism at the SLC6A4 promoter region has two variants, a short allele (S) and a long allele (L), in which the S allele results in lower gene transcription and has been associated with depression. The short S-allele of 5-HTTLPR polymorphism of this gene has been associated with depression. In addition to molecular mechanisms, exposure to early life risk factors such as maternal depression seems to affect the development of depression in postnatal life. The present study investigated the association of 5-HTTLPR polymorphism and CpG DNA methylation (5mC) levels of an AluJb repeat element at the SLC6A4 promoter region in mother-child pairs exposed to maternal depression. METHODS We analyzed DNA samples from 60 subjects (30 mother-child pairs) split into three groups, with and without major depression disorder (DSM-IV) among children and mothers. The genotyping of 5-HTTLPR polymorphism and quantification of 5mC levels was performed by qualitative PCR and methylation-sensitive restriction enzyme digestion, and real-time quantitative PCR (MSRED-qPCR), respectively. RESULTS The sample analyzed presented a higher frequency of S allele of 5-HTTLPR (67.5%). Despite the high frequency of this allele, we did not find statistically significant differences between individuals carrying at least one S allele between the depression and healthy control subjects, or among the mother-child pair groups with different patterns of occurrence of depression. In the group where the mother and child were both diagnosed with depression, we found a statistically significant decrease of the 5mC level at the SLC6A4 promoter region. LIMITATIONS The limitations are the relatively small sample size and lack of gene expression data available for comparison with methylation data. CONCLUSION In this study, we demonstrated a repeat element specific 5mC level reduction in mother-child pairs, concordant for the diagnosis of depression.
Collapse
|
22
|
Schulz H, Ruppert AK, Zara F, Madia F, Iacomino M, S Vari M, Balagura G, Minetti C, Striano P, Bianchi A, Marini C, Guerrini R, Weber YG, Becker F, Lerche H, Kapser C, Schankin CJ, Kunz WS, Møller RS, Oliver KL, Bellows ST, Mullen SA, Berkovic SF, Scheffer IE, Caglayan H, Ozbek U, Hoffmann P, Schramm S, Tsortouktzidis D, Becker AJ, Sander T. No evidence for a BRD2 promoter hypermethylation in blood leukocytes of Europeans with juvenile myoclonic epilepsy. Epilepsia 2019; 60:e31-e36. [PMID: 30719712 DOI: 10.1111/epi.14657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/31/2023]
Abstract
Juvenile myoclonic epilepsy (JME) is a common syndrome of genetic generalized epilepsies (GGEs). Linkage and association studies suggest that the gene encoding the bromodomain-containing protein 2 (BRD2) may increase risk of JME. The present methylation and association study followed up a recent report highlighting that the BRD2 promoter CpG island (CpG76) is differentially hypermethylated in lymphoblastoid cells from Caucasian patients with JME compared to patients with other GGE subtypes and unaffected relatives. In contrast, we found a uniform low average percentage of methylation (<4.5%) for 13 CpG76-CpGs in whole blood cells from 782 unrelated European Caucasians, including 116 JME patients, 196 patients with genetic absence epilepsies, and 470 control subjects. We also failed to confirm an allelic association of the BRD2 promoter single nucleotide polymorphism (SNP) rs3918149 with JME (Armitage trend test, P = 0.98), and we did not detect a substantial impact of SNP rs3918149 on CpG76 methylation in either 116 JME patients (methylation quantitative trait loci [meQTL], P = 0.29) or 470 German control subjects (meQTL, P = 0.55). Our results do not support the previous observation that a high DNA methylation level of the BRD2 promoter CpG76 island is a prevalent epigenetic motif associated with JME in Caucasians.
Collapse
Affiliation(s)
- Herbert Schulz
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Francesca Madia
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Michele Iacomino
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Maria S Vari
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Ganna Balagura
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Carlo Minetti
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Amedeo Bianchi
- Division of Neurology, Hospital San Donato Arezzo, Arezzo, Italy
| | - Carla Marini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Felicitas Becker
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany.,Department of Neurology, University of Ulm, Ulm, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- Department of Neurology, Großhadern Hospital, University of Munich, Munich, Germany
| | - Christoph J Schankin
- Department of Neurology, Großhadern Hospital, University of Munich, Munich, Germany.,Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Wolfram S Kunz
- Department of Epileptology, Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Rikke S Møller
- Danish Epilepsy Center, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Karen L Oliver
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Susannah T Bellows
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Saul A Mullen
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia
| | - Hande Caglayan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey.,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Ugur Ozbek
- Department of Medical Genetics, Faculty of Medicine, Acibadem University, Istanbul, Turkey
| | - Per Hoffmann
- Department of Genomics, Life and Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Sara Schramm
- Institute of Medical Informatics, Biometry, and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Despina Tsortouktzidis
- Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Albert J Becker
- Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| |
Collapse
|
23
|
Provenzi L, Brambilla M, Borgatti R, Montirosso R. Methodological Challenges in Developmental Human Behavioral Epigenetics: Insights Into Study Design. Front Behav Neurosci 2018; 12:286. [PMID: 30532698 PMCID: PMC6266797 DOI: 10.3389/fnbeh.2018.00286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/05/2018] [Indexed: 11/21/2022] Open
Abstract
Developmental human behavioral epigenetics (DHBE) holds potential for contributing to better understanding of how early life exposures contribute to human developmental trajectories and to inform clinical practice and early interventions. Nonetheless, DHBE research to date is challenged by two major issues: (a) the frequent use of retrospective study designs; and (b) the major focus on epigenetic variations associated with early life adversities, rather than protective care exposures. In order for DHBE research to maintain its promises, these issues need to be addressed in a systematic way according to a careful methodological planning of study design. In this contribution, we provide pragmatic insights on methodological aspects that should be dealt with while designing DHBE studies. We propose different study designs for the retrospective and prospective investigation of both adversity- and care-related epigenetic variations. Examples from available scientific literature are provided to better describe the advantages and the limitations of each study design.
Collapse
Affiliation(s)
- Livio Provenzi
- Scientific Institute, IRCCS Eugenio Medea, 0-3 Center for the at-Risk Infant, Bosisio Parini, Italy
| | - Maddalena Brambilla
- Scientific Institute, IRCCS Eugenio Medea, 0-3 Center for the at-Risk Infant, Bosisio Parini, Italy
| | - Renato Borgatti
- Scientific Institute, IRCCS Eugenio Medea, Neuropsychiatry and Neurorehabilitation Unit, Bosisio Parini, Italy
| | - Rosario Montirosso
- Scientific Institute, IRCCS Eugenio Medea, 0-3 Center for the at-Risk Infant, Bosisio Parini, Italy
| |
Collapse
|
24
|
Yamaguchi T, Hosomichi K, Takahashi M, Haga S, Nakawaki T, Hikita Y, Maki K, Tajima A. Orthognathic surgery induces genomewide changes longitudinally in DNA methylation in saliva. Oral Dis 2018; 25:508-514. [PMID: 30362655 DOI: 10.1111/odi.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 07/27/2018] [Accepted: 10/05/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Orthognathic surgery dramatically changes morphology of the maxillofacial deformity and improves the malocclusion morphologically and functionally. We investigated the influence of orthognathic surgery on genomewide DNA methylation in saliva. METHODS Saliva was obtained from nine patients undergoing orthognathic surgery and two healthy reference individuals before and 3 months after orthognathic surgery. Genomewide DNA methylation profiling of saliva (341,482 CpG dinucleotides) was conducted using Infinium HumanMethylation450 BeadChips. RESULTS Comparison between pre- and postsurgery saliva samples revealed significant changes in DNA methylation patterns at 2,381 CpG sites (p < 0.01) with suggestive significance. The differentially methylated probe sets were significantly associated with the cancer pathway (p = 2.8 × 10-7 ; a false discovery rate q-value = 3.7 × 10-4 ) and PI3K-Akt signalling pathway (p = 2.4 × 10-5 ; a false discovery rate q-value = 3.1 × 10-2 ). CONCLUSION Pathway enrichment analysis of genes with suggestive significance demonstrated that altered DNA methylation in saliva of patients undergoing orthognathic surgery, possibly as a response to surgical stress or bone injury. Further studies with a large sample size and long-term observation are needed to validate the phenomena identified in this study.
Collapse
Affiliation(s)
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | | | - Shugo Haga
- Department of Orthodontics, Showa University, Tokyo, Japan
| | | | - Yu Hikita
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Koutaro Maki
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| |
Collapse
|
25
|
Differentially Methylated Genes in Saliva are linked to Childhood Stress. Sci Rep 2018; 8:10785. [PMID: 30018309 PMCID: PMC6050255 DOI: 10.1038/s41598-018-29107-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/29/2018] [Indexed: 12/24/2022] Open
Abstract
Chronic and severe stress exposure in early childhood is associated with the development of psychiatric disorders. Yet, the molecular mechanisms underlying this relationship remain poorly understood. Here, we profile molecular marks (DNA methylation and gene expression) throughout the human genome to determine the associations between childhood stress exposure and gene regulation. To do so, we collected saliva tissue from prepubertal girls (mean age 10.9 ± 1.26 years) who had experienced different levels of childhood adversity, ranging from mild to severe. We found 122 differentially methylated genes (FDR P-value < 0.05) associated with high childhood stress exposures that affect brain development. Of these differentially methylated genes, 12 also differed in gene expression. To further investigate the potential effects of stress exposure on gene regulation, we examined the DNA sequences flanking all the differentially methylated loci. This analysis revealed enrichment of known binding sites for transcription factors, suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding on these genes. Together, these findings indicate a possible neuromolecular mechanism linking children’s social experiences with risk for anxiety and depressive disorders.
Collapse
|
26
|
Langie SAS, Moisse M, Szarc Vel Szic K, Van Der Plas E, Koppen G, De Prins S, Louwies T, Nelen V, Van Camp G, Lambrechts D, Schoeters G, Vanden Berghe W, De Boever P. GLI2 promoter hypermethylation in saliva of children with a respiratory allergy. Clin Epigenetics 2018; 10:50. [PMID: 29682088 PMCID: PMC5896137 DOI: 10.1186/s13148-018-0484-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background The prevalence of respiratory allergy in children is increasing. Epigenetic DNA methylation changes are plausible underlying molecular mechanisms. Results Saliva samples collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) were used to discover and confirm DNA methylation signatures that can differentiate individuals with respiratory allergy from healthy subjects. Genome-wide analysis with Illumina Methylation 450K BeadChips revealed 23 differentially methylated gene regions (DMRs) in saliva from 11y old allergic children (N=26) vs. controls (N=20) in FLEHS1. A subset of 7 DMRs was selected for confirmation by iPLEX MassArray analysis. First, iPLEX analysis was performed in the same 46 FLEHS1 samples for analytical confirmation of the findings obtained during the discovery phase. iPLEX results correlated significantly with the 450K array data (P <0.0001) and confirmed 4 out of the 7 DMRs. Aiming for additional biological confirmation, the 7 DMRs were analyzed using iPLEX in a substudy of an independent birth cohort (FLEHS2; N=19 cases vs. 20 controls, aged 5 years). One DMR in the GLI2 promoter region showed a consistent statistically significant hypermethylation in individuals with respiratory allergy across the two birth cohorts and technologies. In addition to its involvement in TGF-β signaling and T-helper differentiation, GLI2 has a regulating role in lung development. Conclusion GLI2 is considered an interesting candidate DNA methylation marker for respiratory allergy. Electronic supplementary material The online version of this article (10.1186/s13148-018-0484-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sabine A S Langie
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,2Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Matthieu Moisse
- 3Laboratory for Translational Genetics, Center for Cancer Biology, VIB and KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Katarzyna Szarc Vel Szic
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,4Proteinchemistry, Proteomics & Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ellen Van Der Plas
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,7Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Gudrun Koppen
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Sofie De Prins
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Tijs Louwies
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Vera Nelen
- Environment and Health unit, Provincial Institute of Hygiene, Antwerp, Belgium
| | - Guy Van Camp
- 6Center for Medical Genetics, University of Antwerp and Antwerp University hospital, Antwerp, Belgium
| | - Diether Lambrechts
- 3Laboratory for Translational Genetics, Center for Cancer Biology, VIB and KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Greet Schoeters
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,7Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,8Department of Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Wim Vanden Berghe
- 4Proteinchemistry, Proteomics & Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick De Boever
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,2Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
27
|
Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
28
|
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
29
|
Langie SAS, Moisse M, Declerck K, Koppen G, Godderis L, Vanden Berghe W, Drury S, De Boever P. Salivary DNA Methylation Profiling: Aspects to Consider for Biomarker Identification. Basic Clin Pharmacol Toxicol 2017; 121 Suppl 3:93-101. [PMID: 27901320 PMCID: PMC5644718 DOI: 10.1111/bcpt.12721] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/13/2022]
Abstract
Is it not more comfortable to spit saliva in a tube than to be pricked with a needle to draw blood to analyse your health and disease risk? Many patients, study participants and (parents of) young children undoubtedly prefer non-invasive and convenient procedures. Such procedures increase compliance rates especially for longitudinal prospective studies. Saliva is an attractive biofluid providing good quality DNA to study epigenetic mechanisms underlying disease across development. In this MiniReview, we will describe the different applications of saliva in the field of epigenetics, focusing on genomewide methylation analysis. Advantages of the use of saliva and its comparability with blood will be discussed, as will the challenges in data processing and interpretation. Knowledge gaps will be identified and suggestions given on how to improve the analysis, making saliva 'the' biofluid of choice for future biomarker initiatives in many different epidemiological and public health studies.
Collapse
Affiliation(s)
- Sabine A. S. Langie
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
- Faculty of SciencesHasselt UniversityDiepenbeekBelgium
| | | | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic SignalingDepartment of Biomedical SciencesUniversity of AntwerpWilrijkBelgium
| | - Gudrun Koppen
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
| | - Lode Godderis
- Centre Environment & HealthDepartment of Public Health and Primary CareKU LeuvenLeuvenBelgium
- IDEWEExternal Service for Prevention and Protection at WorkHeverleeBelgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic SignalingDepartment of Biomedical SciencesUniversity of AntwerpWilrijkBelgium
| | - Stacy Drury
- The Brain InstituteTulane UniversityNew OrleansLAUSA
- Department of Psychiatry and Behavioral ScienceTulane University School of MedicineNew OrleansLAUSA
| | - Patrick De Boever
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
- Faculty of SciencesHasselt UniversityDiepenbeekBelgium
| |
Collapse
|
30
|
Differentially methylated embryonal Fyn-associated substrate (EFS) gene as a blood-specific epigenetic marker and its potential application in forensic casework. Forensic Sci Int Genet 2017; 29:165-173. [DOI: 10.1016/j.fsigen.2017.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 04/08/2017] [Accepted: 04/14/2017] [Indexed: 12/19/2022]
|
31
|
Taniguchi I, Iwaya C, Ohnaka K, Shibata H, Yamamoto K. Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines. Hum Genomics 2017; 11:8. [PMID: 28499412 PMCID: PMC5429538 DOI: 10.1186/s40246-017-0106-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types of commonly used DNA bioresources, peripheral blood cells (PBCs) and EBV-transformed lymphoblastoid cell lines (LCLs), which are available for genetic epidemiological studies. Therefore, to extend our knowledge of the difference in DNA methylation status between LCLs and PBCs is important in human population studies that use these DNA sources to elucidate the epigenetic risks for multifactorial diseases. We analyzed the methylation status of the autosomes for 192 and 92 DNA samples that were obtained from PBCs and LCLs, respectively, using a human methylation 450 K array. After excluding SNP-associated methylation sites and low-call sites, 400,240 sites were subjected to analysis using a generalized linear model with cell type, sex, and age as the independent variables. RESULTS We found that the large proportion of sites showed lower methylation levels in LCLs compared with PBCs, which is consistent with previous reports. We also found that significantly different methylation sites tend to be located on the outside of the CpG island and in a region relatively far from the transcription start site. Additionally, we observed that the methylation change of the sites in the low-CpG promoter region was remarkable. Finally, it was shown that the correlation between the chronological age and ageing-associated methylation sites in ELOVL2 and FHL2 in the LCLs was weaker than that in the PBCs. CONCLUSIONS The methylation levels of highly methylated sites of the low-CpG-density promoters in PBCs decreased in the LCLs, suggesting that the methylation sites located in low-CpG-density promoters could be sensitive to demethylation in LCLs. Despite being generated from a single cell type, LCLs may not always be a proxy for DNA from PBCs in studies of epigenome-wide analysis attempting to elucidate the role of epigenetic change in disease risks.
Collapse
Affiliation(s)
- Itsuki Taniguchi
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Chihiro Iwaya
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keizo Ohnaka
- Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan.
| |
Collapse
|
32
|
Banlaki Z, Cimarelli G, Viranyi Z, Kubinyi E, Sasvari-Szekely M, Ronai Z. DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds. Mol Genet Genomics 2017; 292:685-697. [DOI: 10.1007/s00438-017-1305-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 03/02/2017] [Indexed: 12/26/2022]
|
33
|
Jones TI, Himeda CL, Perez DP, Jones PL. Large family cohorts of lymphoblastoid cells provide a new cellular model for investigating facioscapulohumeral muscular dystrophy. Neuromuscul Disord 2017; 27:221-238. [PMID: 28161093 PMCID: PMC5815870 DOI: 10.1016/j.nmd.2016.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/11/2016] [Indexed: 01/26/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite repeat. The resulting DNA hypomethylation and relaxation of epigenetic repression leads to increased expression of the deleterious DUX4-fl mRNA encoded within the distal D4Z4 repeat. With the typical late onset of muscle weakness, prevalence of asymptomatic individuals, and an autosomal dominant mode of inheritance, FSHD is often passed on from one generation to the next and affects multiple individuals within a family. Here we have characterized unique collections of 114 lymphoblastoid cell lines (LCLs) generated from 12 multigenerational FSHD families, including 56 LCLs from large, genetically homogeneous families in Utah. We found robust expression of DUX4-fl in most FSHD LCLs and a good correlation between DNA hypomethylation and repeat length. In addition, DUX4-fl levels can be manipulated using epigenetic drugs as in myocytes, suggesting that some epigenetic pathways regulating DUX4-fl in myocytes are maintained in LCLs. Overall, these FSHD LCLs provide an alternative cellular model in which to study many aspects of D4Z4, DUX4, and FSHD gene regulation in a background of low genetic variation. Significantly, these non-adherent immortal LCLs are amenable for high-throughput screening of potential therapeutics targeting DUX4-fl mRNA or protein expression.
Collapse
Affiliation(s)
- Takako I Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Charis L Himeda
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Daniel P Perez
- FSH Society, 450 Bedford Street, Lexington, MA 02420, USA.
| | - Peter L Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
| |
Collapse
|
34
|
Oelsner KT, Guo Y, To SBC, Non AL, Barkin SL. Maternal BMI as a predictor of methylation of obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity. BMC Genomics 2017; 18:57. [PMID: 28068899 PMCID: PMC5223358 DOI: 10.1186/s12864-016-3473-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 12/26/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children at-risk for obesity despite the relevance of this developmental stage to trajectories of weight gain. We hypothesized that salivary DNA methylation patterns of key obesogenic genes in Hispanic children would 1) correlate with maternal BMI and 2) allow for identification of pathways associated with children at-risk for obesity. RESULTS Genome-wide DNA methylation was conducted on 92 saliva samples collected from Hispanic preschool children using the Infinium Illumina HumanMethylation 450 K BeadChip (Illumina, San Diego, CA, USA), which interrogates >484,000 CpG sites associated with ~24,000 genes. The analysis was limited to 936 genes that have been associated with obesity in a prior GWAS Study. Child DNA methylation at 17 CpG sites was found to be significantly associated with maternal BMI, with increased methylation at 12 CpG sites and decreased methylation at 5 CpG sites. Pathway analysis revealed methylation at these sites related to homocysteine and methionine degradation as well as cysteine biosynthesis and circadian rhythm. Furthermore, eight of the 17 CpG sites reside in genes (FSTL1, SORCS2, NRF1, DLC1, PPARGC1B, CHN2, NXPH1) that have prior known associations with obesity, diabetes, and the insulin pathway. CONCLUSIONS Our study confirms that saliva is a practical human tissue to obtain in community settings and in pediatric populations. These salivary findings indicate potential epigenetic differences in Hispanic preschool children at risk for pediatric obesity. Identifying early biomarkers and understanding pathways that are epigenetically regulated during this critical stage of child development may present an opportunity for prevention or early intervention for addressing childhood obesity. TRIAL REGISTRATION The clinical trial protocol is available at ClinicalTrials.gov ( NCT01316653 ). Registered 3 March 2011.
Collapse
Affiliation(s)
- Kathryn Tully Oelsner
- College of Medicine, Medical University of South Carolina, 96 Jonathan Lucas St, Suite 601, MSC 617, Charleston, SC 29425 USA
| | - Yan Guo
- Center for Quantitative Research, School of Medicine, Vanderbilt University, 2220 Pierce Ave, 571 Preston Research Building, Nashville, TN USA
| | - Sophie Bao-Chieu To
- Department of Biological Sciences, Vanderbilt University, 1210 BSB, 465 21st Ave S, Nashville, TN USA
| | - Amy L. Non
- Department of Anthropology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Shari L. Barkin
- Department of Pediatrics, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
- Pediatric Obesity Research, Diabetes Research and Training Center, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
| |
Collapse
|
35
|
Provenzi L, Giorda R, Beri S, Montirosso R. SLC6A4 methylation as an epigenetic marker of life adversity exposures in humans: A systematic review of literature. Neurosci Biobehav Rev 2016; 71:7-20. [DOI: 10.1016/j.neubiorev.2016.08.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/18/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022]
|
36
|
Yeo S, Enoch MA, Gorodetsky E, Akhtar L, Schuebel K, Roy A, Goldman D. The influence of FKBP5 genotype on expression of FKBP5 and other glucocorticoid-regulated genes, dependent on trauma exposure. GENES BRAIN AND BEHAVIOR 2016; 16:223-232. [PMID: 27648526 DOI: 10.1111/gbb.12342] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/01/2016] [Accepted: 09/16/2016] [Indexed: 01/17/2023]
Abstract
The FK506 binding protein 51 (FKBP5), an intrinsic regulator of the glucocorticoid receptor, has been associated with pathological behaviors particularly in the context of childhood trauma (CT), via a putatively regulatory polymorphism, rs1360780. However, trans- and cis-acting effects of this locus and its interaction with CT are incompletely understood. To study its effects on the expression of glucocorticoid-regulated genes including FKBP5, we used lymphoblastoid cell lines (LCLs) derived from 16 CT-exposed patients with greater than two substance dependence/suicidal behavior diagnoses (casesCT+) and 13 non-CT-exposed controls (controlsCT-). This study in LCLs measures long-term trait-like differences attributable to genotype or lasting epigenetic modification. Through analysis of differential allelic expression (DAE) using an FKBP5 3'-UTR reporter single nucleotide polymorphism (SNP), rs3800373, that is in strong linkage disequilibrium with rs1360780, we confirmed that the rs1360780 risk allele (A) (or conceivably that of a linked SNP) leads to higher FKBP5 expression in controlsCT-. Intriguingly, casesCT+ did not show DAE, perhaps because of a genotype-predicted difference in FKBP5 DNA methylation restricted to casesCT+. Furthermore, through correlation analyses on FKBP5 expression at baseline and after induction by dexamethasone, we observed that casesCT+ had lower induction of FKBP5 expression, indicating that overall they may have strong ultra-short negative-feedback. Only casesCT+ showed an effect of rs1360780 genotype on expression of FKBP5 and other glucocorticoid-regulated genes. Together, these results confirm that the rs1360780 locus alters FKBP5 expression and further that in trans-fashion this locus affects the expression of other glucocorticoid-regulated genes after a glucocorticoid challenge. The CT exposure appears to be essential for trans-effects of rs1360780 on glucocorticoid-regulated genes.
Collapse
Affiliation(s)
- S Yeo
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - M-A Enoch
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - E Gorodetsky
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - L Akhtar
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - K Schuebel
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - A Roy
- Psychiatry Service, Department of Veterans Affairs, New Jersey VA Health Care System, East Orange, NJ, USA
| | - D Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| |
Collapse
|
37
|
Hannon E, Lunnon K, Schalkwyk L, Mill J. Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics 2016; 10:1024-32. [PMID: 26457534 PMCID: PMC4844197 DOI: 10.1080/15592294.2015.1100786] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Given the tissue-specific nature of epigenetic processes, the assessment of disease-relevant tissue is an important consideration for epigenome-wide association studies (EWAS). Little is known about whether easily accessible tissues, such as whole blood, can be used to address questions about interindividual epigenomic variation in inaccessible tissues, such as the brain. We quantified DNA methylation in matched DNA samples isolated from whole blood and 4 brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus, and cerebellum) from 122 individuals. We explored co-variation between tissues and the extent to which methylomic variation in blood is predictive of interindividual variation identified in the brain. For the majority of DNA methylation sites, interindividual variation in whole blood is not a strong predictor of interindividual variation in the brain, although the relationship with cortical regions is stronger than with the cerebellum. Variation at a subset of probes is strongly correlated across tissues, even in instances when the actual level of DNA methylation is significantly different between them. A substantial proportion of this co-variation, however, is likely to result from genetic influences. Our data suggest that for the majority of the genome, a blood-based EWAS for disorders where brain is presumed to be the primary tissue of interest will give limited information relating to underlying pathological processes. These results do not, however, discount the utility of using a blood-based EWAS to identify biomarkers of disease phenotypes manifest in the brain. We have generated a searchable database for the interpretation of data from blood-based EWAS analyses (http://epigenetics.essex.ac.uk/bloodbrain/).
Collapse
Affiliation(s)
- Eilis Hannon
- a University of Exeter Medical School; University of Exeter ; Devon , UK
| | - Katie Lunnon
- a University of Exeter Medical School; University of Exeter ; Devon , UK
| | - Leonard Schalkwyk
- b School of Biological Sciences; University of Essex ; Wivenhoe Park, Colchester , UK
| | - Jonathan Mill
- a University of Exeter Medical School; University of Exeter ; Devon , UK.,c Institute of Psychiatry; Psychology & Neuroscience; King's College London ; De Crespigny Park, London , UK
| |
Collapse
|
38
|
Abstract
The last decade has been marked by an increased interest in relating epigenetic mechanisms to complex human behaviors, although this interest has not been balanced, accentuating various types of affective and primarily ignoring cognitive functioning. Recent animal model data support the view that epigenetic processes play a role in learning and memory consolidation and help transmit acquired memories even across generations. In this review, we provide an overview of various types of epigenetic mechanisms in the brain (DNA methylation, histone modification, and noncoding RNA action) and discuss their impact proximally on gene transcription, protein synthesis, and synaptic plasticity and distally on learning, memory, and other cognitive functions. Of particular importance are observations that neuronal activation regulates the dynamics of the epigenome's functioning under precise timing, with subsequent alterations in the gene expression profile. In turn, epigenetic regulation impacts neuronal action, closing the circle and substantiating the signaling pathways that underlie, at least partially, learning, memory, and other cognitive processes.
Collapse
|
39
|
Vidaki A, Giangasparo F, Syndercombe Court D. Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing. Electrophoresis 2016; 37:2767-2779. [DOI: 10.1002/elps.201600261] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Athina Vidaki
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
| | - Federica Giangasparo
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science; King's College London; Franklin-Wilkins Building London UK
| |
Collapse
|
40
|
Grove TB, Burghardt KJ, Kraal AZ, Dougherty RJ, Taylor SF, Ellingrod VL. Oxytocin Receptor (OXTR) Methylation and Cognition in Psychotic Disorders. MOLECULAR NEUROPSYCHIATRY 2016; 2:151-160. [PMID: 27867940 DOI: 10.1159/000448173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/30/2016] [Indexed: 01/17/2023]
Abstract
Previous reports have identified an association between cognitive impairment and genetic variation in psychotic disorders. In particular, this association may be related to abnormal regulation of genes responsible for broad cognitive functions such as the oxytocin receptor (OXTR). Within psychotic disorders, it is unknown if OXTR methylation, which can have important implications for gene regulation, is related to cognitive function. The current study examined peripheral blood OXTR methylation and general cognition in people with schizophrenia, schizoaffective disorder, and psychotic disorder not otherwise specified (N = 101). Using hierarchical multiple regression analysis, methylation at the Chr3:8767638 site was significantly associated with composite cognitive performance independent of demographic and medication factors while controlling for multiple testing in this combined diagnostic sample (adjusted p = 0.023).
Collapse
Affiliation(s)
- Tyler B Grove
- Department of Psychology, University of Michigan, Ann Arbor, Mich., USA
| | - Kyle J Burghardt
- Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Mich., USA
| | - A Zarina Kraal
- Department of Psychology, University of Michigan, Ann Arbor, Mich., USA
| | - Ryan J Dougherty
- Luskin School of Public Affairs, University of California, Los Angeles, Los Angeles, Calif.,USA
| | - Stephan F Taylor
- Department of Psychology, University of Michigan, Ann Arbor, Mich., USA; Department of Psychiatry, University of Michigan, Ann Arbor, Mich., USA
| | - Vicki L Ellingrod
- Department of Psychology, University of Michigan, Ann Arbor, Mich., USA; Department of Psychiatry, University of Michigan, Ann Arbor, Mich., USA; College of Pharmacy, University of Michigan, Ann Arbor, Mich., USA
| |
Collapse
|
41
|
Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics Chromatin 2016; 9:12. [PMID: 27014370 PMCID: PMC4806452 DOI: 10.1186/s13072-016-0060-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
Background Fragile X syndrome (FXS) is caused by CGG expansion over 200 repeats at the 5′ UTR of the FMR1 gene and subsequent DNA methylation of both the expanded sequence and the CpGs of the promoter region. This epigenetic change causes transcriptional silencing of the gene. We have previously demonstrated that 5-aza-2-deoxycytidine (5-azadC) treatment of FXS lymphoblastoid cell lines reactivates the FMR1 gene, concomitant with CpG sites demethylation, increased acetylation of histones H3 and H4 and methylation of lysine 4 on histone 3. Results In order to check the specificity of the 5-azadC-induced DNA demethylation, now we performed bisulphite sequencing of the entire methylation boundary upstream the FMR1 promoter region, which is preserved in control wild-type cells. We did not observe any modification of the methylation boundary after treatment. Furthermore, methylation analysis by MS-MLPA of PWS/AS and BWS/SRS loci demonstrated that 5-azadC treatment has no demethylating effect on these regions. Genome-wide methylation analysis through Infinium 450K (Illumina) showed no significant enrichment of specific GO terms in differentially methylated regions after 5-azadC treatment. We also observed that reactivation of FMR1 transcription lasts up to a month after a 7-day treatment and that maximum levels of transcription are reached at 10–15 days after last administration of 5-azadC. Conclusions Taken together, these data demonstrate that the demethylating effect of 5-azadC on genomic DNA is not random, but rather restricted to specific regions, if not exclusively to the FMR1 promoter. Moreover, we showed that 5-azadC has a long-lasting reactivating effect on the mutant FMR1 gene. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0060-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elisabetta Tabolacci
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Giorgia Mancano
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Stella Lanni
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Federica Palumbo
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Martina Goracci
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Fabrizio Ferrè
- Department of Biology, Centre for Molecular Bioinformatics (CBM), University of Rome Tor Vergata, Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, Centre for Molecular Bioinformatics (CBM), University of Rome Tor Vergata, Rome, Italy
| | - Giovanni Neri
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| |
Collapse
|
42
|
Langie SAS, Szarc vel Szic K, Declerck K, Traen S, Koppen G, Van Camp G, Schoeters G, Vanden Berghe W, De Boever P. Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy. PLoS One 2016; 11:e0151109. [PMID: 26999364 PMCID: PMC4801358 DOI: 10.1371/journal.pone.0151109] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/22/2016] [Indexed: 12/17/2022] Open
Abstract
The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field of respiratory allergy.
Collapse
Affiliation(s)
- Sabine A. S. Langie
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- * E-mail:
| | - Katarzyna Szarc vel Szic
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Sophie Traen
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Gudrun Koppen
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Guy Van Camp
- Laboratory of Cancer Research and Clinical Oncology, Center for Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Greet Schoeters
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
- University of Southern Denmark, Institute of Public Health, Department of Environmental Medicine, Odense, Denmark
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick De Boever
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
43
|
Braithwaite EC, Kundakovic M, Ramchandani PG, Murphy SE, Champagne FA. Maternal prenatal depressive symptoms predict infant NR3C1 1F and BDNF IV DNA methylation. Epigenetics 2016; 10:408-17. [PMID: 25875334 DOI: 10.1080/15592294.2015.1039221] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Prenatal maternal psychological distress increases risk for adverse infant outcomes. However, the biological mechanisms underlying this association remain unclear. Prenatal stress can impact fetal epigenetic regulation that could underlie changes in infant stress responses. It has been suggested that maternal glucocorticoids may mediate this epigenetic effect. We examined this hypothesis by determining the impact of maternal cortisol and depressive symptoms during pregnancy on infant NR3C1 and BDNF DNA methylation. Fifty-seven pregnant women were recruited during the second or third trimester. Participants self-reported depressive symptoms and salivary cortisol samples were collected diurnally and in response to a stressor. Buccal swabs for DNA extraction and DNA methylation analysis were collected from each infant at 2 months of age, and mothers were assessed for postnatal depressive symptoms. Prenatal depressive symptoms significantly predicted increased NR3C1 1F DNA methylation in male infants (β = 2.147, P = 0.044). Prenatal depressive symptoms also significantly predicted decreased BDNF IV DNA methylation in both male and female infants (β = -3.244, P = 0.013). No measure of maternal cortisol during pregnancy predicted infant NR3C1 1F or BDNF promoter IV DNA methylation. Our findings highlight the susceptibility of males to changes in NR3C1 DNA methylation and present novel evidence for altered BDNF IV DNA methylation in response to maternal depression during pregnancy. The lack of association between maternal cortisol and infant DNA methylation suggests that effects of maternal depression may not be mediated directly by glucocorticoids. Future studies should consider other potential mediating mechanisms in the link between maternal mood and infant outcomes.
Collapse
Affiliation(s)
- E C Braithwaite
- a Department of Psychiatry; University of Oxford; Warneford Hospital ; Oxford , UK
| | | | | | | | | |
Collapse
|
44
|
Associations among child abuse, mental health, and epigenetic modifications in the proopiomelanocortin gene (POMC): A study with children in Tanzania. Dev Psychopathol 2016; 28:1401-1412. [PMID: 26753719 DOI: 10.1017/s0954579415001248] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Child abuse is associated with a number of emotional and behavioral problems. Nevertheless, it has been argued that these adverse consequences may not hold for societies in which many of the specific acts of abuse are culturally normed. Epigenetic modifications in the genes of the hypothalamus-pituitary-adrenal axis may provide a potential mechanism translating abuse into altered gene expression, which subsequently results in behavioral changes. Our investigation took place in Tanzania, a society in which many forms of abuse are commonly employed as disciplinary methods. We included 35 children with high exposure and compared them to 25 children with low exposure. Extreme group comparisons revealed that children with high exposure reported more mental health problems. Child abuse was associated with differential methylation in the proopiomelanocortin gene (POMC), measured both in saliva and in blood. Hierarchical clustering based on the methylation of the POMC gene found two distinct clusters. These corresponded with children's self-reported abuse, with two-thirds of the children allocated into their respective group. Our results emphasize the consequences of child abuse based on both molecular and behavioral grounds, providing further evidence that acts of abuse affect children, even when culturally acceptable. Furthermore, on a molecular level, our findings strengthen the credibility of children's self-reports.
Collapse
|
45
|
Lei MK, Beach SRH, Simons RL, Philibert RA. Neighborhood crime and depressive symptoms among African American women: Genetic moderation and epigenetic mediation of effects. Soc Sci Med 2015; 146:120-8. [PMID: 26513121 DOI: 10.1016/j.socscimed.2015.10.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/23/2015] [Accepted: 10/16/2015] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Social scientists have long recognized the important role that neighborhood crime can play in stress-related disease, but very little is known about potential biosocial mechanisms that may link the experience of living in high-crime neighborhoods with depression. OBJECTIVE The current study introduces an integrated model that combines neighborhood, genetic, and epigenetic factors. METHODS Hypotheses were tested with a sample of 99 African American women from the Family and Community Health Study (FACHS). RESULTS Allele variants of the serotonin transporter gene (5-HTT) interact with neighborhood crime to predict depressive symptoms in a manner consonant with the differential susceptibility perspective. Furthermore, this association is mediated by DNA methylation of the promoter region of the serotonin transporter gene. CONCLUSION The findings provide support for an integrated model in which changes in DNA methylation, resulting from neighborhood crime, can result in an increase or decrease in gene activity which, in turn, influences depressive symptoms.
Collapse
Affiliation(s)
- Man-Kit Lei
- Center for Family Research, University of Georgia, USA.
| | | | | | | |
Collapse
|
46
|
Suderman M, Pappas JJ, Borghol N, Buxton JL, McArdle WL, Ring SM, Hertzman C, Power C, Szyf M, Pembrey M. Lymphoblastoid cell lines reveal associations of adult DNA methylation with childhood and current adversity that are distinct from whole blood associations. Int J Epidemiol 2015; 44:1331-40. [PMID: 26351305 DOI: 10.1093/ije/dyv168] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Some cohort studies bank lymphoblastoid cell lines (LCLs) as a renewable source of participant DNA. However, although LCL DNA has proved valuable for genetic studies, its utility in epigenetic epidemiology research is unknown. METHODS To assess whether LCL DNA can be used for life-course environmental epigenomics, we carried out a pilot methylomic study (using the Illumina Infinium Human Methylation 450 BeadChip) of nil-passage, Epstein-Barr virus (EBV)-transformed LCLs (n = 42) and 28 matched whole-blood (WB) samples. These were from adult male participants of the British 1958 birth cohort, selected for extremes of social economic position (SEP) in childhood and adulthood, with additional information available on childhood abuse and prenatal tobacco exposure. RESULTS We identified a small number of weak associations between these exposures and methylation levels of both individual CpG sites and genomic regions in WB and LCLs. However, only one of the regional, and none of the individual CpG site associations were common to both sample types. The lack of overlap between the associations detected in LCL compared with those found in WB could either be due to the EBV-transformation process, or to the fact that, unlike WB, LCLs are essentially a single (CD19+) cell type. We provide evidence that the latter is the more potent explanation, by showing that CpG sites known to be differentially methylated between different types of blood cell have significantly lower correlations (R = 0.11) than average (R = 0.2) between WB and LCLs in our datasets, whereas sites known to be affected by EBV-transformation have significantly higher correlations (R = 0.3). CONCLUSIONS This small pilot study suggests that the DNA methylation profile of LCLs is more closely related to that of B cells than WB and, additionally, that LCLs may nevertheless be useful for life-course environmental epigenomics.
Collapse
Affiliation(s)
- Matthew Suderman
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK,
| | - Jane J Pappas
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada, Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Nada Borghol
- Department of Biochemistry, Faculty of Sciences I, Lebanese University, Beirut, Lebanon
| | - Jessica L Buxton
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Clyde Hertzman
- Human Early Learning Partnership, University of British Columbia, British Columbia, Canada
| | - Chris Power
- Population, Policy and Practice, UCL Institute of Child Health, London, UK
| | - Moshe Szyf
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada, Sackler Program for Epigenetics & Developmental Psychobiology, McGill University, Montreal, Quebec, Canada and
| | - Marcus Pembrey
- Genetics and Epigenetics in Health and Disease Section, UCL Institute of Child Health, UK
| |
Collapse
|
47
|
Delmonico L, Moreira ADS, Franco MF, Esteves EB, Scherrer L, Gallo CVDM, do Nascimento CM, Ornellas MHF, de Azevedo CM, Alves G. CDKN2A (p14(ARF)/p16(INK4a)) and ATM promoter methylation in patients with impalpable breast lesions. Hum Pathol 2015; 46:1540-7. [PMID: 26255234 DOI: 10.1016/j.humpath.2015.06.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022]
Abstract
Early detection of breast cancer increases the chances of cure, but the reliable identification of impalpable lesions is still a challenge. In spite of the advances in breast cancer detection, the molecular basis of impalpable lesions and the corresponding circulating biomarkers are not well understood. Impalpable lesions, classified by radiologists according to the Breast Imaging Reporting and Data System in the categories 3 and 4, can be either benign or malignant (slow growing or aggressive). In this article, we report the DNA methylation pattern in CDKN2A (p14(ARF)/p16(INK4a)) and in ATM gene promoters from 62 impalpable lesions, 39 peripheral blood samples, and 39 saliva samples, assessed by methylation-specific polymerase chain reaction method. ATM showed the greatest percentage of methylation in DNA from lesions (benign and malignant), blood (even with p16(INK4a)), and saliva, followed by p16(INK4a) and p14(ARF). Among the malignant cases, ATM promoter was the most hypermethylated in lesion DNA and in blood and saliva DNAs, and p14(ARF), the least. The highest percentage of p16(INK4a) methylation was found in the blood. Finally, our data are relevant because they were obtained using impalpable breast lesions from patients who were carefully recruited in 2 public hospitals of Rio de Janeiro.
Collapse
Affiliation(s)
- Lucas Delmonico
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Aline dos Santos Moreira
- Laboratório de Genômica Funcional de Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Marco Felipe Franco
- Serviço de Radiologia, Hospital Universitário Gaffrée-Guinle, Rio de Janeiro 20270-004, Brazil
| | | | - Luciano Scherrer
- Sociedade Brasileira Oncologia Clínica, Belo Horizonte, Minas Gerais 30120-010, Brazil
| | - Claúdia Vitória de Moura Gallo
- Departamento de Genética, Instituto de Biologia Roberto Alcântara Gomes, Universidade Estadual do Rio de Janeiro, Rio de Janeiro 20550-900, Brazil
| | | | - Maria Helena Faria Ornellas
- Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | | | - Gilda Alves
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil; Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil.
| |
Collapse
|
48
|
Chagnon YC, Potvin O, Hudon C, Préville M. DNA methylation and single nucleotide variants in the brain-derived neurotrophic factor (BDNF) and oxytocin receptor (OXTR) genes are associated with anxiety/depression in older women. Front Genet 2015; 6:230. [PMID: 26175754 PMCID: PMC4485183 DOI: 10.3389/fgene.2015.00230] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/15/2015] [Indexed: 12/16/2022] Open
Abstract
Background: Environmental effects and personal experiences could be expressed in individuals through epigenetic non-structural changes such as DNA methylation. This methylation could up- regulate or down-regulate corresponding gene expressions and modify related phenotypes. DNA methylation increases with aging and could be related to the late expression of some forms of mental disease. The objective of this study was to evaluate the association between anxiety disorders and/or depression in older women and DNA methylation for four genes related to anxiety or depression. Methods: Women aged 65 and older with (n = 19) or without (n = 24) anxiety disorders and/or major depressive episode (DSM-IV), were recruited. DNA methylation and single nucleotide variant (SNV) were evaluated from saliva, respectively by pyrosequencing and by PCR, for the following genes: brain-derived neurotrophic factor (BDNF; rs6265), oxytocin receptor (OXTR; rs53576), serotonin transporter (SLC6A4; rs25531), and apolipoprotein E (APOE; rs429358 and rs7412). Results: A greater BDNF DNA methylation was observed in subjects with anxiety/depression compared to control group subjects (Mean: 2.92 SD ± 0.74 vs. 2.34 ± 0.42; p= 0.0026). This difference was more pronounced in subjects carrying the BDNF rs6265 CT genotype (2.99 ± 0.41 vs. 2.27 ± 0.26; p= 0.0006) than those carrying the CC genotype (p= 0.0332); no subjects with the TT genotype were observed. For OXTR, a greater DNA methylation was observed in subjects with anxiety/depression, but only for those carrying the AA genotype of the OXTR rs53576 SNV, more particularly at one out of the seven CpGs studied (7.01 ± 0.94 vs. 4.44 ± 1.11; p= 0.0063). No significant differences were observed for APOE and SLC6A4. Conclusion: These results suggest that DNA methylation in interaction with SNV variations in BDNF and OXTR, are associated with the occurrence of anxiety/depression in older women.
Collapse
Affiliation(s)
- Yvon C Chagnon
- Department of Psychiatry and Neurosciences, Laval University, Quebec City QC, Canada ; Research Center: Institut Universitaire en Sante Mentale de Quebec, Quebec City QC, Canada
| | - Olivier Potvin
- Research Center: Institut Universitaire en Sante Mentale de Quebec, Quebec City QC, Canada
| | - Carol Hudon
- Research Center: Institut Universitaire en Sante Mentale de Quebec, Quebec City QC, Canada ; School of Psychology, Laval University, Quebec City QC, Canada
| | - Michel Préville
- Department of Sciences de la Santé Communautaire, Sherbrooke University, Sherbrooke QC, Canada
| |
Collapse
|
49
|
Global Methylation and Hydroxymethylation in DNA from Blood and Saliva in Healthy Volunteers. BIOMED RESEARCH INTERNATIONAL 2015; 2015:845041. [PMID: 26090450 PMCID: PMC4450276 DOI: 10.1155/2015/845041] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/27/2014] [Indexed: 12/15/2022]
Abstract
Aims. We describe a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify and compare simultaneously global methylation and hydroxymethylation in human DNA of different tissues. Materials and Methods. Blood and saliva DNA from fourteen volunteers was processed for epigenetic endpoints using LC-MS/MS and PCR-pyrosequencing technology. Results. Global DNA methylation was significantly lower in saliva (mean 4.61% ± 0.80%), compared to blood samples (5.70% ± 0.22%). In contrast, saliva (0.036% ± 0.011%) revealed significantly higher hydroxymethylation compared to blood samples (mean 0.027% ± 0.004%). Whereas we did not find significant correlations for both epigenetic measures between the tissues, a significant association was observed between global methylation and global hydroxymethylation in saliva DNA. Neither LINE-1 nor Alu elements of blood and saliva correlated, nor were they correlated with the DNA hydroxymethylation of blood or saliva, respectively. Conclusion. Global DNA methylation and hydroxymethylation of cytosine can be quantified simultaneously by LC-MS/MS. Saliva DNA cannot be considered as a surrogate for blood DNA to study epigenetic endpoints.
Collapse
|
50
|
Wren ME, Shirtcliff EA, Drury SS. Not all biofluids are created equal: chewing over salivary diagnostics and the epigenome. Clin Ther 2015; 37:529-39. [PMID: 25778408 DOI: 10.1016/j.clinthera.2015.02.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/08/2023]
Abstract
PURPOSE This article describes progress to date in the characterization of the salivary epigenome and considers the importance of previous work in the salivary microbiome, proteome, endocrine analytes, genome, and transcriptome. METHODS PubMed and Web of Science were used to extensively search the existing literature (original research and reviews) related to salivary diagnostics and biomarker development, of which 125 studies were examined. This article was derived from the most relevant 74 sources highlighting the recent state of the evolving field of salivary epigenomics and contributing significantly to the foundational work in saliva-based research. FINDINGS Validation of any new saliva-based diagnostic or analyte will require comparison to previously accepted standards established in blood. Careful attention to the collection, processing, and analysis of salivary analytes is critical for the development and implementation of newer applications that include genomic, transcriptomic, and epigenomic markers. All these factors must be integrated into initial study design. IMPLICATIONS This commentary highlights the appeal of the salivary epigenome for translational applications and its utility in future studies of development and the interface among environment, disease, and health.
Collapse
Affiliation(s)
- Michael E Wren
- Neuroscience Graduate Program, Tulane University, New Orleans, Louisiana; Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Stacy S Drury
- Neuroscience Graduate Program, Tulane University, New Orleans, Louisiana; Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, New Orleans, Louisiana.
| |
Collapse
|