1
|
Khoodoruth MAS, Chut-kai Khoodoruth WN, Al Alwani R. Exploring the epigenetic landscape: The role of 5-hydroxymethylcytosine in neurodevelopmental disorders. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e5. [PMID: 38699519 PMCID: PMC11062787 DOI: 10.1017/pcm.2024.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/18/2024] [Accepted: 03/16/2024] [Indexed: 05/05/2024]
Abstract
Recent advances in genetic and epigenetic research have underscored the significance of 5-hydroxymethylcytosine (5hmC) in neurodevelopmental disorders (NDDs), such as autism spectrum disorder (ASD) and intellectual disability (ID), revealing its potential as both a biomarker for early detection and a target for novel therapeutic strategies. This review article provides a comprehensive analysis of the role of 5hmC in NDDs by examining both animal models and human studies. By examining mouse models, studies have demonstrated that prenatal environmental challenges, such as maternal infection and food allergies, lead to significant epigenetic alterations in 5hmC levels, which were associated with NDDs in offspring, impacting social behavior, cognitive abilities and increasing ASD-like symptoms. In human studies, researchers have linked alterations in 5hmC levels NDDs through studies in individuals with ASD, fragile X syndrome, TET3 deficiency and ID, specifically identifying significant epigenetic modifications in genes such as GAD1, RELN, FMR1 and EN-2, suggesting that dysregulation of 5hmC played a critical role in the pathogenesis of these disorders and highlighted the potential for targeted therapeutic interventions. Moreover, we explore the implications of these findings for the development of epigenetic therapies aimed at modulating 5hmC levels. The review concludes with a discussion on future directions for research in this field, such as machine learning, emphasizing the need for further studies to elucidate the complex mechanisms underlying NDDs and to translate these findings into clinical practice. This paper not only advances our understanding of the epigenetic landscape of NDDs but also opens up new avenues for diagnosis and treatment, offering hope for individuals affected by these conditions.
Collapse
Affiliation(s)
- Mohamed Adil Shah Khoodoruth
- Department of Child and Adolescent Psychiatry, Hamad Medical Corporation, Doha, Qatar
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Rafaa Al Alwani
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| |
Collapse
|
2
|
Epigenetics in epilepsy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:249-269. [DOI: 10.1016/bs.pmbts.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
|
3
|
Levy G, Levin B. An Evolution-Based Model of Causation for Aging-Related Diseases and Intrinsic Mortality: Explanatory Properties and Implications for Healthy Aging. Front Public Health 2022; 10:774668. [PMID: 35252084 PMCID: PMC8894190 DOI: 10.3389/fpubh.2022.774668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/10/2022] [Indexed: 01/07/2023] Open
Abstract
Aging-related diseases are the most prevalent diseases in advanced countries nowadays, accounting for a substantial proportion of mortality. We describe the explanatory properties of an evolution-based model of causation (EBMC) applicable to aging-related diseases and intrinsic mortality. The EBMC takes the sufficient and component causes model of causation as a starting point and develops it using evolutionary and statistical theories. Genetic component causes are classified as “early-onset” or “late-onset” and environmental component causes as “evolutionarily conserved” or “evolutionarily recent.” Genetic and environmental component causes are considered to occur as random events following time-to-event distributions, and sufficient causes are classified according to whether or not their time-to-event distributions are “molded” by the declining force of natural selection with increasing age. We obtain for each of these two groups different time-to-event distributions for disease incidence or intrinsic mortality asymptotically (i.e., for a large number of sufficient causes). The EBMC provides explanations for observations about aging-related diseases concerning the penetrance of genetic risk variants, the age of onset of monogenic vs. sporadic forms, the meaning of “age as a risk factor,” the relation between frequency and age of onset, and the emergence of diseases associated with the modern Western lifestyle. The EBMC also provides an explanation of the Gompertz mortality model at the fundamental level of genetic causes and involving evolutionary biology. Implications for healthy aging are examined under the scenarios of health promotion and postponed aging. Most importantly from a public health standpoint, the EBMC implies that primary prevention through changes in lifestyle and reduction of environmental exposures is paramount in promoting healthy aging.
Collapse
Affiliation(s)
- Gilberto Levy
- Independent Researcher, Rio de Janeiro, Brazil
- *Correspondence: Gilberto Levy
| | - Bruce Levin
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, United States
| |
Collapse
|
4
|
Bani-Fatemi A, Raymond R, Adanty C, Dai N, Gerretsen P, Graff A, Nobrega JN, De Luca V. Global DNA methylation in suicidal ideation and suicide attempt in schizophrenia. Psychiatr Genet 2021; 31:65-71. [PMID: 33399315 DOI: 10.1097/ypg.0000000000000273] [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] [Indexed: 11/25/2022]
Abstract
Suicidal behavior is influenced by many risk factors such as childhood trauma, stressful life events, genetic factors, and severe mental illnesses. Suicidal ideation is present in 50% of schizophrenia patients and is associated with an elevated risk of suicide attempt. Studies have shown that epigenetic mechanisms are associated with suicidal behavior in schizophrenia. Although several studies have suggested the importance of epigenetic factors in suicidal ideation and behavior, no studies have investigated global methylation in association with these two phenotypes. This study investigated global methylation level/change in association with current and emergent suicidal ideation and also with suicide attempt. Forty-seven schizophrenia patients were assessed for the association between global methylation and suicide attempt, and a subsample of these patients (n = 27) was assessed for current suicidal ideation. Afterwards, we performed a longitudinal analysis in which global methylation changes during a 3-month follow-up were compared between patients with and without emergent suicidal ideation. This methylation analysis did not find evidence for a significant association between global methylation and suicidal ideation or suicide attempt. To date, there are no robust biomarkers predicting suicidal ideation or behavior in psychotic patients. This study is the first to investigate global methylation in predicting suicidal ideation and behavior. Although we did not find evidence for an association between global methylation and these phenotypes, our findings may offer novel insights into the molecular mechanisms linked to suicide. Future investigation may measure global methylation in association with suicidal ideation or behavior in larger samples.
Collapse
Affiliation(s)
- Ali Bani-Fatemi
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | |
Collapse
|
5
|
The black sheep of the family- whole-exome sequencing in family of lithium response discordant bipolar monozygotic twins. Eur Neuropsychopharmacol 2020; 34:19-27. [PMID: 32305265 DOI: 10.1016/j.euroneuro.2020.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/06/2020] [Indexed: 01/20/2023]
Abstract
Twin studies are among the most promising strategies for studying heritable disorders, including bipolar disorder (BD). The aim of the present study was to identify distinguishing genes between monozygotic (MZ) twins with different BD phenotype and compare them to their non-affected siblings. Whole-exome sequencing (WES) can identify rare and structural variants that could detect the polygenetic burden of complex disorders. WES was performed on a family composed of two MZ twins with BD, their unaffected brother and unaffected parents. The twins have a discordant response to lithium and distinct course of illness. Following WES, six genes of particular interest emerged: Neurofibromin type 1 (NF1), Biorientation of chromosomes in cell division 1 (BOD1), Golgi-associated gamma adaptin ear-containing ARF binding protein 3 (GGA3), Disrupted in schizophrenia 1 (DISC1), Neuromedin U receptor 2 (NMUR2), and Huntingtin interacting protein 1-related (HIP1R). Interestingly, many of these influence glutamatergic pathways and thus the findings may have therapeutical implications. These results may provide important insights to unveil genetic underpinnings of BD and the response to lithium.
Collapse
|
6
|
Zhan W, Li Y, Liu X, Zheng C, Fu Y. ZNF671 Inhibits the Proliferation and Metastasis of NSCLC via the Wnt/β-Catenin Pathway. Cancer Manag Res 2020; 12:599-610. [PMID: 32158264 PMCID: PMC6986545 DOI: 10.2147/cmar.s235933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/31/2019] [Indexed: 01/01/2023] Open
Abstract
Background Lung cancer is the most common cancer in the world and is the main cause of cancer-related death. Revealing the potential mechanism of malignant characteristics of lung cancer is urgent for treating this disease effectively. Zinc finger protein 671 (ZNF671) is a member of the largest transcription factor family in the human genome. The role of ZNF671 in non-small-cell lung cancer (NSCLC) remains unknown. The purpose of this study was to investigate the function and mechanism of ZNF671 in NSCLC. Methods ZNF671 expression in NSCLC cells and tissues were detected by Real-Time PCR, Western blot and TCGA databases. Then, we evaluated the prognostic value of ZNF671 expression in NSCLC using the Kaplan–Meier plotter (KM plotter) and TCGA databases. Moreover, the function of ZNF671 in the proliferation and metastasis of lung cancer was investigated by MTT assay, colony formation assay, in vivo experiment, EdU assay, wound healing assay, transwell assay, and 3D culture assay. Luciferase reporter and subcellular fractionation assays were performed to determine the underlying mechanism of ZNF671-mediated proliferation and metastasis of NSCLC. Results ZNF671 expression was significantly reduced in both NSCLC cell lines and clinical specimens compared to that in normal controls. The survival analysis results indicated that the downregulation of ZNF671 significantly correlates with poor prognosis and predicts a shorter overall survival and post-progression survival among NSCLC patients. Ectopic overexpression of ZNF671 dramatically restrains, whereas silencing ZNF671 enhanced, cell proliferation and metastasis of NSCLC. Mechanically, gene set enrichment analysis (GSEA) showed that the expression of ZNF671 was significantly correlated with Wnt/β-catenin signaling. Simultaneously, our results confirm that the overexpression of ZNF671 inhibits cell cycle progression and metastasis by weakening the Wnt/β-catenin pathway, and then downregulating the expression of downstream target genes CyclinD1 and MMP9. Conclusion This study found that the overexpression of ZNF671 restrains the proliferation and metastasis of lung cancer through inhibiting Wnt/β-catenin signaling pathway. Furthermore, our current results provide important insights into ZNF671 as an excellent predictive biomarker for NSCLC, thus providing a novel perspective for the treatment of NSCLC.
Collapse
Affiliation(s)
- Wei Zhan
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, People's Republic of China
| | - Yuzhe Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Lingnan Hospital, Guangzhou 510080, People's Republic of China
| | - Xuhui Liu
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, People's Republic of China
| | - Changlong Zheng
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, People's Republic of China
| | - Yongmei Fu
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, People's Republic of China
| |
Collapse
|
7
|
Mehl-Madrona L, McFarlane P, Mainguy B. Epigenetics, Gender, and Sex in the Diagnosis of Depression. CURRENT PSYCHIATRY RESEARCH AND REVIEWS 2020. [DOI: 10.2174/2666082215666191029141418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background :
A marked sexual dimorphism exists in psychiatric diagnoses. Culture derived
gender bias in diagnostic criteria is one explanation. Adverse childhood events, including sexual
and physical abuse, are more reliable and consistent predictors of later psychiatric diagnoses,
including depression and post-traumatic stress disorder. Some interesting interactions between genes
and experience have been uncovered, but the primary effect appears to be epigenetic with life experience
altering gene expression and being transmitted to subsequent generations.
Objectives :
To determine if reconceptualizing depression as encompassing both internalizing and
externalizing strategies would eliminate gender differences in the diagnosis of depression
Methods :
We reviewed 74 life stories of patients, collected during a study of the effect of physicians’
knowing patients’ life stories on the quality of the doctor-patient relationship. Looking at
diagnoses, the prevalence of women to men was 2.9 to 1. We redefined depression as a response to
being in a seemingly hopeless situation accompanied by despair, either externalizing ((more often
diagnosed as substance use disorders, impulse control disorders, antisocial personality disorder, or
bipolar disorder) or internalizing (the more standard diagnosis of depression). Then we reviewed
these life stories from that perspective to determine how many would be diagnosed as depressed.
Results :
With this reconceptualization of depression, the sex ratio changed to 1.2 to 1.
Conclusions:
From this perspective, men and women are equally likely to respond to hopelessness,
though men are more socialized to externalize and women to internalize. Considering depression in
this way may help to better identify men at risk for suicide.
Collapse
Affiliation(s)
- Lewis Mehl-Madrona
- Eastern Maine Medical Center Family Medicine Residency, Bangor, ME 04401, United States
| | - Patrick McFarlane
- Eastern Maine Medical Center Family Medicine Residency, Bangor, ME 04401, United States
| | | |
Collapse
|
8
|
Chang HI, Chang YT, Tsai SJ, Huang CW, Hsu SW, Liu ME, Chang WN, Lien CY, Huang SH, Lee CC, Chang CC. MAOA-VNTR Genotype Effects on Ventral Striatum-Hippocampus Network in Alzheimer's Disease: Analysis Using Structural Covariance Network and Correlation with Neurobehavior Performance. Mol Neurobiol 2018; 56:4518-4529. [PMID: 30338484 DOI: 10.1007/s12035-018-1394-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/11/2018] [Indexed: 01/22/2023]
Abstract
Functional polymorphisms in the promoter region of the monoamine oxidase A (MAOA) gene are associated with brain MAOA activity and transcriptional efficiency in patients with Alzheimer's disease (AD). This study investigated structural covariance networks mediated by MAOA-variable number tandem repeat (VNTR) genotypes in patients with AD, and assessed whether this effect was associated with sex. A total of 193 patients with AD were classified into four genotype groups based on MAOA transcriptional efficiency (female low [L], low-high + high activity groups [LH + H]; male L, male H groups). Structural covariance networks were constructed focusing on triple-network and striatal networks. Covariance strength was analyzed in the four groups, and the genotype and sex main effects and their interactions were analyzed. Significant peak cluster volumes were correlated with neurobehavioral scores to establish the clinical significance. MAOA genotypes mediated the structural covariance strength on the dorsolateral prefrontal cortex (dLPFC)-caudate axis in both sexes, but a higher covariance strength was shown in the female L group and male H group. The independent effect of male sex was related to higher covariance strength in the frontal medial superior region in the dLPFC, dorsal caudate (DC), and ventral superior striatum (VSs) seeds. In contrast, female sex had higher covariance strength in the frontal opercular areas anchored by the dLPFC, DC, and VSs seeds. Topographies showing higher covariance strength with sex interactions were found in the male H group and female L group in the dLPFC supplementary motor axis, DC-SMA, and DC-precentral axis. In our patients with AD, MAOA-VNTR polymorphisms and sex had independent and interactive effects on structural covariance networks, of which the dLPFC-, VSs-, and DC-anchored networks represented major endophenotypes that determined cognitive outcomes. The sex-genotype interaction model suggested that male high activity and female low activity may modulate brain morphometric connectivity and determine cognitive scores.
Collapse
Affiliation(s)
- Hsin-I Chang
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan
- Institute of Human Resource Management, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ya-Ting Chang
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan
| | - Shih-Jen Tsai
- Psychiatric Department of Taipei Veterans General Hospital, Taipei, Taiwan
- Psychiatric Division, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Wei Huang
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan
| | - Shih-Wei Hsu
- Department of Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Mu-En Liu
- Psychiatric Division, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Neng Chang
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan
| | - Chia-Yi Lien
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan
| | - Shu-Hua Huang
- Department of Nuclear Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chen-Chang Lee
- Department of Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Department of General Neurology, Cognitive and Aging Center, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, #123, Ta-Pei Road, Niaosung, Kaohsiung County, 833, Taiwan.
| |
Collapse
|
9
|
DNA methylation and clinical response to antidepressant medication in major depressive disorder: A review and recommendations. Neurosci Lett 2018; 669:14-23. [DOI: 10.1016/j.neulet.2016.12.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/28/2022]
|
10
|
Dogan MV, Grumbach IM, Michaelson JJ, Philibert RA. Integrated genetic and epigenetic prediction of coronary heart disease in the Framingham Heart Study. PLoS One 2018; 13:e0190549. [PMID: 29293675 PMCID: PMC5749823 DOI: 10.1371/journal.pone.0190549] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
An improved method for detecting coronary heart disease (CHD) could have substantial clinical impact. Building on the idea that systemic effects of CHD risk factors are a conglomeration of genetic and environmental factors, we use machine learning techniques and integrate genetic, epigenetic and phenotype data from the Framingham Heart Study to build and test a Random Forest classification model for symptomatic CHD. Our classifier was trained on n = 1,545 individuals and consisted of four DNA methylation sites, two SNPs, age and gender. The methylation sites and SNPs were selected during the training phase. The final trained model was then tested on n = 142 individuals. The test data comprised of individuals removed based on relatedness to those in the training dataset. This integrated classifier was capable of classifying symptomatic CHD status of those in the test set with an accuracy, sensitivity and specificity of 78%, 0.75 and 0.80, respectively. In contrast, a model using only conventional CHD risk factors as predictors had an accuracy and sensitivity of only 65% and 0.42, respectively, but with a specificity of 0.89 in the test set. Regression analyses of the methylation signatures illustrate our ability to map these signatures to known risk factors in CHD pathogenesis. These results demonstrate the capability of an integrated approach to effectively model symptomatic CHD status. These results also suggest that future studies of biomaterial collected from longitudinally informative cohorts that are specifically characterized for cardiac disease at follow-up could lead to the introduction of sensitive, readily employable integrated genetic-epigenetic algorithms for predicting onset of future symptomatic CHD.
Collapse
Affiliation(s)
- Meeshanthini V. Dogan
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
- Cardio Diagnostics LLC, Coralville, Iowa, United States of America
| | - Isabella M. Grumbach
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Iowa City Veterans Affairs Healthcare System, Iowa City, Iowa, United States of America
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert A. Philibert
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
- Behavioral Diagnostics LLC, Coralville, Iowa, United States of America
- * E-mail:
| |
Collapse
|
11
|
Peedicayil J. Epigenetic Drugs for Multiple Sclerosis. Curr Neuropharmacol 2016; 14:3-9. [PMID: 26813117 PMCID: PMC4787283 DOI: 10.2174/1570159x13666150211001600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/19/2015] [Accepted: 02/09/2015] [Indexed: 01/01/2023] Open
Abstract
There is increasing evidence that abnormalities in epigenetic mechanisms of gene expression contribute to the development of multiple sclerosis (MS). Advances in epigenetics have given rise to a new class of drugs, epigenetic drugs. Although many classes of epigenetic drugs are being investigated, at present most attention is being paid to two classes of epigenetic drugs: drugs that inhibit DNA methyltransferase (DNMTi) and drugs that inhibit histone deacetylase (HDACi). This paper discusses the potential use of epigenetic drugs in the treatment of MS, focusing on DNMTi and HDACi. Preclinical drug trials of DNMTi and HDACi for the treatment of MS are showing promising results. Epigenetic drugs could improve the clinical management of patients with MS.
Collapse
Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology Christian Medical College Vellore India.
| |
Collapse
|
12
|
Corwin EJ. The Concept of Epigenetics and Its Role in the Development of Cardiovascular Disease: Commentary on “New and Emerging Theories of Cardiovascular Disease”. Biol Res Nurs 2016; 6:11-6; discussion 21-3. [PMID: 15186703 DOI: 10.1177/1099800404264779] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Elizabeth J Corwin
- School of Nursing and Intercollege Physiology Program, Pennsylvania State University, 307C Health and Human Development East, University Park, PA 16802, USA.
| |
Collapse
|
13
|
Parr EB, Camera DM, Burke LM, Phillips SM, Coffey VG, Hawley JA. Circulating MicroRNA Responses between 'High' and 'Low' Responders to a 16-Wk Diet and Exercise Weight Loss Intervention. PLoS One 2016; 11:e0152545. [PMID: 27101373 PMCID: PMC4839646 DOI: 10.1371/journal.pone.0152545] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/16/2016] [Indexed: 01/24/2023] Open
Abstract
Background Interactions between diet, physical activity and genetic predisposition contribute to variable body mass changes observed in response to weight loss interventions. Circulating microRNAs (c-miRNAs) may act as ‘biomarkers’ that are associated with the rate of change in weight loss, and/or play a role in regulating the biological variation, in response to energy restriction. Objective To quantify targeted c-miRNAs with putative roles in energy metabolism and exercise adaptations following a 16 wk diet and exercise intervention in individuals with large (high responders; HiRes) versus small (low responders; LoRes) losses in body mass. Methods From 89 male and female overweight/obese participants who completed the intervention (energy restriction from diet, 250 kcal/d, and exercise, 250 kcal/d), subgroups of HiRes (>10% body mass loss, n = 22) and LoRes (<5% body mass loss, n = 18) were identified. From resting plasma samples collected after an overnight fast pre and post intervention, RNA was extracted, quantified and reverse transcribed. Thirteen c-miRNA selected a priori were analysed using a customised 96-well miScript miRNA PCR Array. Results Loss of body mass (-11.0 ± 2.3 kg vs. -3.0 ± 1.3 kg; P<0.01) and fat mass (-11.1 ± 2.6 kg vs. -3.9 ± 1.6 kg; P<0.01) was greater for HiRes than LoRes (P<0.001). Expression of c-miR-935 was higher in LoRes compared to HiRes pre- (~47%; P = 0.025) and post- (~100%; P<0.01) intervention and was the only c-miRNA differentially expressed at baseline between groups. The abundance of c-miR-221-3p and -223-3p increased pre- to post-intervention in both groups (~57–69% and ~25–90%, P<0.05). There was a post-intervention increase in c-miR-140 only in LoRes compared to HiRes (~23%, P = 0.016). Conclusion The differential expression and responses of selected c-miRNAs in overweight/obese individuals to an exercise and diet intervention suggests a putative role for these ‘biomarkers’ in the prediction or detection of individual variability to weight loss interventions.
Collapse
Affiliation(s)
- Evelyn B. Parr
- Mary MacKillop Institute for Health Research, Centre for Exercise and Nutrition, Australian Catholic University, Melbourne, Australia
| | - Donny M. Camera
- Mary MacKillop Institute for Health Research, Centre for Exercise and Nutrition, Australian Catholic University, Melbourne, Australia
| | - Louise M. Burke
- Mary MacKillop Institute for Health Research, Centre for Exercise and Nutrition, Australian Catholic University, Melbourne, Australia
- Department of Sports Nutrition, Australian Institute of Sport, Canberra, Australia
| | - Stuart M. Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Canada
| | - Vernon G. Coffey
- Bond Institute of Health and Sport and Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | - John A. Hawley
- Mary MacKillop Institute for Health Research, Centre for Exercise and Nutrition, Australian Catholic University, Melbourne, Australia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
- * E-mail:
| |
Collapse
|
14
|
Dahlen HG, Downe S, Wright ML, Kennedy HP, Taylor JY. Childbirth and consequent atopic disease: emerging evidence on epigenetic effects based on the hygiene and EPIIC hypotheses. BMC Pregnancy Childbirth 2016; 16:4. [PMID: 26762406 PMCID: PMC4712556 DOI: 10.1186/s12884-015-0768-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In most high and middle income countries across the world, at least 1:4 women give birth by cesarean section. Rates of labour induction and augmentation are rising steeply; and in some countries up to 50% of laboring women and newborns are given antibiotics. Governments and international agencies are increasingly concerned about the clinical, economic and psychosocial effects of these interventions. DISCUSSION There is emerging evidence that certain intrapartum and early neonatal interventions might affect the neonatal immune response in the longer term, and perhaps trans-generationally. Two theories lead the debate in this area. Those aligned with the hygiene (or 'Old Friends') hypothesis have examined the effect of gut microbiome colonization secondary to mode of birth and intrapartum/neonatal pharmacological interventions on immune response and epigenetic phenomena. Those working with the EPIIC (Epigenetic Impact of Childbirth) hypothesis are concerned with the effects of eustress and dys-stress on the epigenome, secondary to mode of birth and labour interventions. This paper examines the current and emerging findings relating to childbirth and atopic/autoimmune disease from the perspective of both theories, and proposes an alliance of research effort. This is likely to accelerate the discovery of important findings arising from both approaches, and to maximize the timely understanding of the longer-term consequences of childbirth practices.
Collapse
Affiliation(s)
- H G Dahlen
- School of Nursing and Midwifery, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia.
| | - S Downe
- University of Central Lancashire, Preston, PR3 2LE, Lancashire, UK.
| | - M L Wright
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
| | - H P Kennedy
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
| | - J Y Taylor
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
| |
Collapse
|
15
|
Guintivano J, Kaminsky ZA. Role of epigenetic factors in the development of mental illness throughout life. Neurosci Res 2016; 102:56-66. [DOI: 10.1016/j.neures.2014.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 07/31/2014] [Accepted: 08/04/2014] [Indexed: 12/15/2022]
|
16
|
Lee JW, Jaffar Z, Pinkerton KE, Porter V, Postma B, Ferrini M, Holian A, Roberts K, Cho YH. Alterations in DNA methylation and airway hyperreactivity in response to in utero exposure to environmental tobacco smoke. Inhal Toxicol 2015; 27:724-30. [PMID: 26525176 PMCID: PMC4760648 DOI: 10.3109/08958378.2015.1104402] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Growing evidence indicates that prenatal exposure to maternal smoking is a risk factor for the development of asthma in children. However, the effects of prenatal environmental tobacco smoke (ETS) exposure on the genome and lung immune cells are unclear. This study aims to determine whether in utero ETS exposure alters DNA methylation patterns and increases airway hyperreactivity (AHR) and inflammation. Pregnant C57BL/6 mice were exposed daily to a concentration of 1.0 mg/m(3) ETS. AHR was determined in the 6-week-old offspring by measurement of airway resistance. Global and gene promoter methylation levels in lung DNA from offspring were analyzed by luminometric methylation and pyrosequencing assays, respectively. Offspring exposed to ETS showed a marked increase in the number of alveolar macrophages in the bronchoalveolar lavage fluid and level of IL-13 in the airways compared with offspring of filtered-air exposed dams (controls). ETS exposure significantly augmented AHR compared with controls. In the methylation analysis, ETS-exposed offspring had a significantly lower level of global DNA methylation than the controls. We observed a significant increase in IFN-γ, and significant decrease in IL-13 methylation levels in the ETS group compared with controls. Collectively, these data suggest that in utero ETS exposure increases the risk of pulmonary inflammation and AHR through altered DNA methylation, but additional studies are needed to fully determine the causal link between changes in methylation and cytokines levels, as well as AHR.
Collapse
Affiliation(s)
- Joong Won Lee
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Zeina Jaffar
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Kent E. Pinkerton
- Department of Anatomy, Physiology and Cell Biology, Center for Health and the Environment, University of California, Davis, CA, USA
| | - Virginia Porter
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Britten Postma
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Maria Ferrini
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Andrij Holian
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Kevan Roberts
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, Center for Environmental Health Sciences, University of Montana, Missoula, MT, USA
| |
Collapse
|
17
|
Kojima A, Kobayashi T, Ito S, Murasawa A, Nakazono K, Yoshie H. Tumor necrosis factor-alpha gene promoter methylation in Japanese adults with chronic periodontitis and rheumatoid arthritis. J Periodontal Res 2015; 51:350-8. [PMID: 26247485 DOI: 10.1111/jre.12314] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND AND OBJECTIVE Over-expression of tumor necrosis factor-alpha (TNF-α) plays a pathological role in chronic periodontitis (CP) and rheumatoid arthritis (RA), which might be regulated by the epigenetic mechanism. The aim of the present study was to evaluate whether there is a unique methylation profile of the TNF-α gene promoter in blood cells of individuals with CP and RA. MATERIAL AND METHODS The study participants consisted of 30 Japanese adults with RA (RA group), 30 race-matched adults with CP only (CP group) and 30 race-matched healthy controls (H group). Genomic DNA isolated from peripheral blood was modified by sodium bisulfite and analyzed, by direct sequencing, to investigate DNA methylation of the TNF-α gene promoter region. The level of TNF-α produced in mononuclear cells stimulated with Porphyromonas gingivalis lipopolysaccharide was determined using ELISA. RESULTS Twelve cytosine-guanine dinucleotide (CpG) motifs were identified in the TNF-α promoter fragment from -343 to +57 bp. The CP group showed a significantly higher methylation rate and frequency at -72 bp than the H group (p < 0.01). The RA group exhibited significantly higher methylation rates at seven CpG motifs (-302, -163, -119, -72, -49, -38 and +10 bp), and significantly higher methylation frequencies at six CpG motifs (-163, -119, -72, -49, -38 and +10 bp), than the H group (p < 0.01 for all comparisons). The levels of TNF-α produced were significantly different between individuals with and without methylation at -163 bp (p = 0.03). CONCLUSION These results suggest that the hypermethylated status of CpG motifs in the TNF-α gene promoter in blood cells may be unique to Japanese adults with CP and RA.
Collapse
Affiliation(s)
- A Kojima
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Kobayashi
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,General Dentistry and Clinical Education Unit, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - S Ito
- Niigata Rheumatic Center, Shibata, Japan
| | - A Murasawa
- Niigata Rheumatic Center, Shibata, Japan
| | - K Nakazono
- Niigata Rheumatic Center, Shibata, Japan
| | - H Yoshie
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| |
Collapse
|
18
|
Abstract
Recent studies have shown an association between gene alterations by epigenetic mechanisms and suicidal behavior. These epigenetic mechanisms are mitotically, and in some cases meiotically, heritable changes in the genome through non-DNA sequence coding processes that alter gene expression as a result of variable changes in environmental stimuli. Genome-wide association studies have been inconsistent in elucidating the association between genes and suicidal behavior, thereby making the heritability of suicidal behavior is unclear. However, recent epigenetic studies have provided evidence that epigenetic mechanisms could deliver the missing link between the heritability of suicidal behavior and the interaction between environment and the genome. The present review provides an in-depth discussion of epigenetic mechanisms that may regulate gene expression in suicidal behavior. The findings of current epigenetic studies on suicidal behavior will also be discussed considering future epigenome-wide association studies on elucidating the contributions of environment and genome on suicidal behavior.
Collapse
Affiliation(s)
- Ali Bani-Fatemi
- a Group for Suicide Studies, CAMH, Department of Psychiatry , University of Toronto , Toronto , Canada
| | | | | |
Collapse
|
19
|
Mitsuya K, Singh N, Sooranna SR, Johnson MR, Myatt L. Epigenetics of human myometrium: DNA methylation of genes encoding contraction-associated proteins in term and preterm labor. Biol Reprod 2014; 90:98. [PMID: 24571989 DOI: 10.1095/biolreprod.113.113209] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Preterm birth involves the interaction of societal and environmental factors potentially modulating the length of gestation via the epigenome. An established form of epigenetic regulation is DNA methylation where promoter hypermethylation is associated with gene repression. We hypothesized we would find differences in DNA methylation in the myometrium of women with preterm labor of different phenotypes versus normal term labor. Myometrial tissue was obtained at cesarean section at term with or without labor, preterm without labor, idiopathic preterm labor, and twin gestations with labor. Genomic DNA was isolated, and samples in each group were combined and analyzed on a NimbleGen 2.1M human DNA methylation array. Differences in methylation from -8 to +3 kb of transcription start sites of 22 contraction-associated genes were determined. Cytosine methylation was not present in CpG islands of any gene but was present outside of CpG islands in shores and shelves in 19 genes. No differential methylation was found across the tissue groups for six genes (PTGES3L, PTGER2, PTGER4, PTGFRN, ESR2, and GJA1). For 13 genes, differential methylation occurred in several patterns between tissue groups. We find a correlation between hypomethylation and increased mRNA expression of PTGES/mPGES-1, indicating potential functional relevance of methylation, but no such correlation for PTGS2/COX-2, suggesting other regulatory mechanisms for PTGS2 at labor. The majority of differential DNA methylation of myometrial contraction-associated genes with different labor phenotypes occurs outside of CpG islands in gene promoters, suggesting that the entirety of DNA methylation across the genome should be considered.
Collapse
Affiliation(s)
- Kohzoh Mitsuya
- Center for Pregnancy and Newborn Research, Department of Obstetrics and Gynecology, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | | | | | | | | |
Collapse
|
20
|
Zamani AG, Acar A, Durakbasi-Dursun G, Yildirim MS, Ceylaner S, Tuncez E. Recurrent proximal 18p monosomy and 18q trisomy in a family due to a pericentric inversion. Am J Med Genet A 2014; 164A:1239-44. [PMID: 24478222 DOI: 10.1002/ajmg.a.36410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 11/10/2013] [Indexed: 11/08/2022]
Abstract
Here, we report on a family with pericentric inversion of chromosome 18 [inv(18)(p11.2q21)] and two recombinants with a duplication of q21 → qter and a deletion of p11.2 → pter regions in a four-generation family. This chromosomal abnormality was inherited in our first patient from the father, while it was transmitted to the second patient from the mother. Array-CGH analysis were used to better characterize duplicated and deleted chromosomal regions and showed no genomic copy number variation (CNV) differences between these two relatives. We discussed genotype-phenotype correlations including previously reported.
Collapse
Affiliation(s)
- Ayse Gul Zamani
- Meram Medical Faculty, Department of Medical Genetics, Necmettin Erbakan University, Konya, Turkey
| | | | | | | | | | | |
Collapse
|
21
|
Abstract
In humans, genomic DNA is organized in 23 chromosome pairs coding for roughly 25,000 genes. Not all of them are active at all times. During development, a broad range of different cell types needs to be generated in a highly ordered and reproducible manner, requiring selective gene expression programs. Epigenetics can be regarded as the information management system that is able to index or bookmark distinct regions in our genome to regulate the readout of DNA. It further comprises the molecular memory of any given cell, allowing it to store information of previously experienced external (e.g., environmental) or internal (e.g., developmental) stimuli, to learn from this experience and to respond. The underlying epigenetic mechanisms can be synergistic, antagonistic, or mutually exclusive and their large variety combined with the variability and interdependence is thought to provide the molecular basis for any phenotypic variation in physiological and pathological conditions. Thus, widespread reconfiguration of the epigenome is not only a key feature of neurodevelopment, brain maturation, and adult brain function but also disease.
Collapse
Affiliation(s)
- Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Schwabachanlage, Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Schwabachanlage, Erlangen, Germany.
| |
Collapse
|
22
|
Weaver ICG. Integrating early life experience, gene expression, brain development, and emergent phenotypes: unraveling the thread of nature via nurture. ADVANCES IN GENETICS 2014; 86:277-307. [PMID: 25172353 DOI: 10.1016/b978-0-12-800222-3.00011-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Adaptation to environmental changes is based on the perpetual generation of new phenotypes. Modern biology has focused on the role of epigenetic mechanisms in facilitating the adaptation of organisms to changing environments through alterations in gene expression. Inherited and/or acquired epigenetic factors are relatively stable and have regulatory roles in numerous genomic activities that translate into phenotypic outcomes. Evidence that dietary and pharmacological interventions have the potential to reverse environment-induced modification of epigenetic states (e.g., early life experience, nutrition, medication, infection) has provided an additional stimulus for understanding the biological basis of individual differences in cognitive abilities and disorders of the brain. It has been suggested that accurate quantification of the relative contribution of heritable genetic and epigenetic variation is essential for understanding phenotypic divergence and adaptation in changing environments, a process requiring stable modulation of gene expression. The main challenge for epigenetics in psychology and psychiatry is to determine how experiences and environmental cues, including the nature of our nurture, influence the expression of neuronal genes to produce long-term individual differences in behavior, cognition, personality, and mental health. To this end, focusing on DNA and histone modifications and their initiators, mediators and readers may provide new inroads for understanding the molecular basis of phenotypic plasticity and disorders of the brain. In this chapter, we review recent discoveries highlighting epigenetic aspects of normal brain development and mental illness, as well as discuss some future directions in the field of behavioral epigenetics.
Collapse
Affiliation(s)
- Ian C G Weaver
- Department of Psychology and Neuroscience, Dalhousie University, Nova Scotia, Canada; Department of Psychiatry, Dalhousie University, Nova Scotia, Canada
| |
Collapse
|
23
|
Abstract
The heritability of specific phenotypical traits relevant for physical performance has been extensively investigated and discussed by experts from various research fields. By deciphering the complete human DNA sequence, the human genome project has provided impressive insights into the genomic landscape. The hope that this information would reveal the origin of phenotypical traits relevant for physical performance or disease risks has proven overly optimistic, and it is still premature to refer to a 'post-genomic' era of biological science. Linking genomic regions with functions, phenotypical traits and variation in disease risk is now a major experimental bottleneck. The recent deluge of genome-wide association studies (GWAS) generates extensive lists of sequence variants and genes potentially linked to phenotypical traits, but functional insight is at best sparse. The focus of this review is on the complex mechanisms that modulate gene expression. A large fraction of these mechanisms is integrated into the field of epigenetics, mainly DNA methylation and histone modifications, which lead to persistent effects on the availability of DNA for transcription. With the exceptions of genomic imprinting and very rare cases of epigenetic inheritance, epigenetic modifications are not inherited transgenerationally. Along with their susceptibility to external influences, epigenetic patterns are highly specific to the individual and may represent pivotal control centers predisposing towards higher or lower physical performance capacities. In that context, we specifically review how epigenetics combined with classical genetics could broaden our knowledge of genotype-phenotype interactions. We discuss some of the shortcomings of GWAS and explain how epigenetic influences can mask the outcome of quantitative genetic studies. We consider epigenetic influences, such as genomic imprinting and epigenetic inheritance, as well as the life-long variability of epigenetic modification patterns and their potential impact on phenotype with special emphasis on traits related to physical performance. We suggest that epigenetic effects may also play a considerable role in the determination of athletic potential and these effects will need to be studied using more sophisticated quantitative genetic models. In the future, epigenetic status and its potential influence on athletic performance will have to be considered, explored and validated using well controlled model systems before we can begin to extrapolate new findings to complex and heterogeneous human populations. A combination of the fields of genomics, epigenomics and transcriptomics along with improved bioinformatics tools and precise phenotyping, as well as a precise classification of the test populations is required for future research to better understand the inter-relations of exercise physiology, performance traits and also susceptibility towards diseases. Only this combined input can provide the overall outlook necessary to decode the molecular foundation of physical performance.
Collapse
Affiliation(s)
- Tobias Ehlert
- Johannes Gutenberg-Universität Mainz, Department of Sports Medicine, Disease Prevention and Rehabilitation, Mainz, Germany
| | | | | |
Collapse
|
24
|
Abstract
BACKGROUND It has been well established that both genes and non-shared environment contribute substantially to the underlying aetiology of major depressive disorder (MDD). A comprehensive overview of genetic research in MDD is presented. Method Papers were retrieved from PubMed up to December 2011, using many keywords including: depression, major depressive disorder, genetics, rare variants, gene-environment, whole genome, epigenetics, and specific candidate genes and variants. These were combined in a variety of permutations. RESULTS Linkage studies have yielded some promising chromosomal regions in MDD. However, there is a continued lack of consistency in association studies, in both candidate gene and genome-wide association studies (GWAS). Numerous factors may account for variable results including the use of different diagnostic approaches, small samples in early studies, population stratification, epigenetic phenomena, copy number variation (CNV), rare variation, and phenotypic and allelic heterogeneity. The conflicting results are also probably, in part, a consequence of environmental factors not being considered or controlled for. CONCLUSIONS Each research group has to identify what issues their sample may best address. We suggest that, where possible, more emphasis should be placed on the environment in molecular behavioural genetics to identify individuals at environmental high risk in addition to genetic high risk. Sequencing should be used to identify rare and alternative variation that may act as a risk factor, and a systems biology approach including gene-gene interactions and pathway analyses would be advantageous. GWAS may require even larger samples with reliably defined (sub)phenotypes.
Collapse
Affiliation(s)
- S Cohen-Woods
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, UK.
| | | | | |
Collapse
|
25
|
Abstract
BACKGROUND Osteoarthritis (OA) is a frustrating disease for both patient and physician because neither cause nor cure is known and there are currently no disease-modifying drugs. OBJECTIVE To review current therapeutic approaches as well as new findings regarding OA pathoetiology that could form the basis of future direction for the development of drugs to prevent or slow down disease progression. METHODS After reviewing disease progression in human OA, as demonstrated by histological analyses, the reasons for cartilage erosion are explored and possible therapeutic approaches are highlighted. RESULTS/CONCLUSIONS OA may be an epigenetic disease. This new concept can explain many aspects of the disease and provide reasons why therapeutic approaches until now have met with little success.
Collapse
Affiliation(s)
- Helmtrud I Roach
- University of Southampton General Hospital, Bone & Joint Research Group, Southampton SO16 6YD, UK +44 023 8079 4316 ; +44 023 8079 5256 ;
| |
Collapse
|
26
|
Guintivano J, Arad M, Tamashiro KLK, Gould TD, Kaminsky ZA. BioTile, a Perl based tool for the identification of differentially enriched regions in tiling microarray data. BMC Bioinformatics 2013; 14:76. [PMID: 23452827 PMCID: PMC3599767 DOI: 10.1186/1471-2105-14-76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/22/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide tiling array experiments are increasingly used for the analysis of DNA methylation. Because DNA methylation patterns are tissue and cell type specific, the detection of differentially methylated regions (DMRs) with small effect size is a necessary feature of tiling microarray 'peak' finding algorithms, as cellular heterogeneity within a studied tissue may lead to a dilution of the phenotypically relevant effects. Additionally, the ability to detect short length DMRs is necessary as biologically relevant signal may occur in focused regions throughout the genome. RESULTS We present a free open-source Perl application, Binding Intensity Only Tile array analysis or "BioTile", for the identification of differentially enriched regions (DERs) in tiling array data. The application of BioTile to non-smoothed data allows for the identification of shorter length and smaller effect-size DERs, while correcting for probe specific variation by inversely weighting on probe variance through a permutation corrected meta-analysis procedure employed at identified regions. BioTile exhibits higher power to identify significant DERs of low effect size and across shorter genomic stretches as compared to other peak finding algorithms, while not sacrificing power to detect longer DERs. CONCLUSION BioTile represents an easy to use analysis option applicable to multiple microarray platforms, allowing for its integration into the analysis workflow of array data analysis.
Collapse
Affiliation(s)
- Jerry Guintivano
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | |
Collapse
|
27
|
Kobow K, Blümcke I. The emerging role of DNA methylation in epileptogenesis. Epilepsia 2013; 53 Suppl 9:11-20. [PMID: 23216575 DOI: 10.1111/epi.12031] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is a covalent chromatin modification, characterized by the biochemical addition of a methyl group (-CH3) to cytosine nucleotides via a DNA methyltransferase enzyme. 5'-Methylcytosine (5-mC), frequently called the fifth base, has been implicated in genome stability, silencing of transposable elements, and repression of gene expression. Through the latter, DNA methylation dynamics broadly influence brain development, function, and aging. Aberrant DNA methylation patterns, either localized to specific gene regions or scattered throughout the genome, are associated with many neurologic disorders. Herein, we discuss the emerging role of DNA methylation in epileptogenesis and the perspectives arising from epigenetic medicine as new therapeutic strategy in difficult-to-treat epilepsies.
Collapse
Affiliation(s)
- Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | | |
Collapse
|
28
|
Xu X, Li L, Dong X, Jin W, Melchinger AE, Chen S. Gametophytic and zygotic selection leads to segregation distortion through in vivo induction of a maternal haploid in maize. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1083-96. [PMID: 23349137 PMCID: PMC3580820 DOI: 10.1093/jxb/ers393] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Production of maternal haploids via a male inducer can greatly accelerate maize breeding and is an interesting biological phenomenon in double fertilization. However, the mechanism behind haploid induction remains elusive. Segregation distortion, which is increasingly recognized as a potentially powerful evolutionary force, has recently been observed during maternal haploid induction in maize. The results present here showed that both male gametophytic and zygotic selection contributed to severe segregation distortion of a locus, named segregation distortion 1 (sed1), during maternal haploid induction in maize. Interestingly, analysis of reciprocal crosses showed that sed1 is expressed in the male gametophyte. A novel mapping strategy based on segregation distortion has been used to fine-map this locus. Strong selection for the presence of the sed1 haplotype from inducers in kernels with haploid formation and defects could be detected in the segregating population. Dual-pollination experiments showed that viable pollen grains from inducers had poor pollen competitive ability against pollen from normal genotypes. Although defective kernels and haploids have different phenotypes, they are most probably caused by the sed1 locus, and possible mechanisms for production of maternal haploids and the associated segregation distortion are discussed. This research also provides new insights into the process of double fertilization.
Collapse
Affiliation(s)
- Xiaowei Xu
- National Maize Improvement Center, China Agricultural University, Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Liang Li
- National Maize Improvement Center, China Agricultural University, Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Xin Dong
- National Maize Improvement Center, China Agricultural University, Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Weiwei Jin
- National Maize Improvement Center, China Agricultural University, Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Albrecht E. Melchinger
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Shaojiang Chen
- National Maize Improvement Center, China Agricultural University, Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
29
|
Developmental genetics and psychopathology: Some new feathers for a fine old hat. Dev Psychopathol 2012; 24:1165-77. [DOI: 10.1017/s0954579412000624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractWithout even knowing of their existence, Mendel discovered how genes operate when they are completely penetrant, although they rarely are, at least with respect to human personality and psychopathology; yet quantitative genetics results have conclusively demonstrated their substantial macrolevel influence. Now we need to understand just how incompletely penetrant genes make their contributions to psychopathology. Exciting new developments in molecular genetics and epigenetics provide new insight into gene action in principle but have been of limited value so far in understanding the emergence of psychopathology. Some of the most helpful postulates might come from evolutionary and developmental biology and agricultural breeding experiments. I describe the all but forgotten evolutionary mechanisms articulated by Schmalhausen, a Russian evolutionary biologist whose work was suppressed by Stalin in the 1940s. I focus on Schmalhausen's law, the observation that organisms living in conditions at the boundary of their tolerance in any one aspect of existence will be vulnerable to expression of genetic liabilities related to all other aspects of existence. I show how Schmalhausen's ideas are relevant to the results of a century-long corn-breeding experiment and the current concepts of facilitated variation and cryptic genetic variation. I then discuss the relevance of all of these to understanding genetic influences on personality and psychopathology.
Collapse
|
30
|
Labrie V, Pai S, Petronis A. Epigenetics of major psychosis: progress, problems and perspectives. Trends Genet 2012; 28:427-35. [PMID: 22622229 PMCID: PMC3422438 DOI: 10.1016/j.tig.2012.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/26/2023]
Abstract
Understanding the origins of normal and pathological behavior is one of the most exciting opportunities in contemporary biomedical research. There is increasing evidence that, in addition to DNA sequence and the environment, epigenetic modifications of DNA and histone proteins may contribute to complex phenotypes. Inherited and/or acquired epigenetic factors are partially stable and have regulatory roles in numerous genomic activities, thus making epigenetics a promising research path in etiological studies of psychiatric disease. In this article, we review recent epigenetic studies examining the brain and other tissues, including those from individuals with schizophrenia (SCZ) and bipolar disorder (BPD). We also highlight heuristic aspects of the epigenetic theory of psychiatric disease and discuss the future directions of psychiatric epigenetics.
Collapse
Affiliation(s)
- Viviane Labrie
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ONT, M5T 1R8, Canada
| | | | | |
Collapse
|
31
|
Kaminsky Z, Tochigi M, Jia P, Pal M, Mill J, Kwan A, Ioshikhes I, Vincent JB, Kennedy JL, Strauss J, Pai S, Wang SC, Petronis A. A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. Mol Psychiatry 2012; 17:728-40. [PMID: 21647149 DOI: 10.1038/mp.2011.64] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.
Collapse
Affiliation(s)
- Z Kaminsky
- The Krembil Family Epigenetics Laboratory, Neuroscience Department, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Zhang C, Li R, Zhao R. A semi-quantitative assay of overall DNA methylation status using Methyl-CpG binding protein (MBD1). BMC Res Notes 2012; 5:234. [PMID: 22583687 PMCID: PMC3437204 DOI: 10.1186/1756-0500-5-234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 04/18/2012] [Indexed: 12/01/2022] Open
Abstract
Background In mammals, DNA methylation at the 5-position of cytosine is the most essential epigenetic modification. Changes in the level of genome-wide DNA methylation (also known as overall DNA methylation) are associated with alterations in gene expression, thereby contributing to the phenotypic and physiological diversity. Current technologies for detecting overall DNA methylation either suffer from low sensitivity or require sophisticated equipment. Studies on domestic animals are hampered by the lack of complete and annotated genomic information. Results Here we report a rapid slot blot method using methyl-CpG binding protein (MBD1) to exam the level of overall DNA methylation in pigs and chickens. Using this rapid approach, we determined the methylation status in various DNA samples of a Chinese indigenous (Erhualian) and a Western (Large White) breed of pigs. We also chose day 18 embryos (E18) and newly hatched chicks (D1) of a Chinese indigenous chicken breed (Wen’s yellow-feathered broiler chicken) for genome-wide DNA methylation analysis. The results revealed tissue- and breed-specific differences, as well as age-dependent variations, in the level of overall DNA methylation. Conclusion The results showed that the slot blot assay is a sensitive, highly specific and convenient method for semi-quantitative estimation of overall DNA methylation with no species specificity. This method does not require sophisticated equipment, such as high performance liquid chromatography (HPLC), or expensive technologies like sequencing, thus providing a useful tool for overall DNA methylation studies on domestic animals.
Collapse
Affiliation(s)
- Chunxiao Zhang
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | | | | |
Collapse
|
33
|
Chakraborty D, Bernal AJ, Schoch K, Howard TD, Ip EH, Hooper SR, Keshavan MS, Jirtle RL, Shashi V, Shashi V. Dysregulation of DGCR6 and DGCR6L: psychopathological outcomes in chromosome 22q11.2 deletion syndrome. Transl Psychiatry 2012; 2:e105. [PMID: 22832905 PMCID: PMC3337078 DOI: 10.1038/tp.2012.31] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11DS) is the most common microdeletion syndrome in humans. It is typified by highly variable symptoms, which might be explained by epigenetic regulation of genes in the interval. Using computational algorithms, our laboratory previously predicted that DiGeorge critical region 6 (DGCR6), which lies within the deletion interval, is imprinted in humans. Expression and epigenetic regulation of this gene have not, however, been examined in 22q11DS subjects. The purpose of this study was to determine if the expression levels of DGCR6 and its duplicate copy DGCR6L in 22q11DS subjects are associated with the parent-of-origin of the deletion and childhood psychopathologies. Our investigation showed no evidence of parent-of-origin-related differences in expression of both DGCR6 and DGCR6L. However, we found that the variability in DGCR6 expression was significantly greater in 22q11DS children than in age and gender-matched control individuals. Children with 22q11DS who had anxiety disorders had significantly lower DGCR6 expression, especially in subjects with the deletion on the maternal chromosome, despite the lack of imprinting. Our findings indicate that epigenetic mechanisms other than imprinting contribute to the dysregulation of these genes and the associated childhood psychopathologies observed in individuals with 22q11DS. Further studies are now needed to test the usefulness of DGCR6 and DGCR6L expression and alterations in the epigenome at these loci in predicting childhood anxiety and associated adult-onset pathologies in 22q11DS subjects.
Collapse
Affiliation(s)
- D Chakraborty
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - A J Bernal
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - K Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - T D Howard
- Center for Genomics & Personalized Medicine Research and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - E H Ip
- Center for Genomics & Personalized Medicine Research and Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - S R Hooper
- Department of Psychiatry and the Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - M S Keshavan
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - R L Jirtle
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - V Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA,Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Box 102857, DUMC, 595 LaSalle Street, Durham, NC 27710, USA. E-mail:
| | | |
Collapse
|
34
|
Zhang T, Wang M, Pan L, Ding W, Wang JG, Yang L, Liu M, Li W, Yan Z. Study of Gene Expression Profiles and Biological Mechanism of Cerebral Palsy Using a Monozygotic Twin Pair. Twin Res Hum Genet 2012; 10:496-507. [PMID: 17564508 DOI: 10.1375/twin.10.3.496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractThe gene expression profile of a normal-suffering monozygotic twin pair is investigated to explore biological mechanisms of spastic type cerebral palsy. Main works include following three aspects: First, a cDNA microarray test is carried out to get the differentially expressed genes of the patient with cerebral palsy compared to her monozygotic twin sister. Second, these differentially expressed genes are searched for their bioinformation within 4 biological databases: FatiGO, FatiGOPlus, KEGG, and SOURCE. Third, a set of special genes and gene families are screened out from the spastic type cerebral palsy patient. These biological analyses reveal that those genes for cell junction are mostly down-regulated, while those genes for metabolism are mostly up-regulated. The individual genes, gene family, and their associated biological functions can reflect the pathological and physiological characteristics of the cerebral palsy.
Collapse
Affiliation(s)
- Tiane Zhang
- Genetics Laboratory, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Urbán S V, Benevolenskaya E, Kiss J, Sági B, Hegyi B, Uher F. [Beyond genetics--the emerging role of epigenetics and its clinical aspects]. Orv Hetil 2012; 153:214-21. [PMID: 22296925 DOI: 10.1556/oh.2012.29301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Analysis of genomic sequences has clearly shown that the genomic differences among species do not explain the diversity of life. The genetic code itself serves as only a part of the dynamic complexity that results in the temporal and spatial changes in cell phenotypes during development. It has been concluded that the phenotype of a cell and of the organism as a whole is more influenced by environmentally-induced changes in gene activity than had been previously thought. The emerging field of epigenetics focuses on molecular marks on chromatin; called the epigenome, which serve as transmitters between the genome and the environment. These changes not only persist through multiple cell division cycles, but may also endure for multiple generations. Irregular alterations of the epigenome; called epimutations, may have a decisive role in the etiology of human pathologies such as malignancies and other complex human diseases. Epigenetics can provide the missing link between genetics, disease and the environment. Therefore, this field may have an increasing impact on future drug design and serve as a basis for new therapeutic/preventative approaches.
Collapse
|
36
|
Ettinger U, Schmechtig A, Toulopoulou T, Borg C, Orrells C, Owens S, Matsumoto K, van Haren NE, Hall MH, Kumari V, McGuire PK, Murray RM, Picchioni M. Prefrontal and striatal volumes in monozygotic twins concordant and discordant for schizophrenia. Schizophr Bull 2012; 38:192-203. [PMID: 20538831 PMCID: PMC3245600 DOI: 10.1093/schbul/sbq060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Frontostriatal networks mediating important cognitive and motor functions have been shown to be abnormal structurally and functionally in schizophrenia. However, the influence of genetic risk for schizophrenia on structural abnormalities in these areas is not well established. This study therefore aimed to investigate prefrontal and striatal volume alterations in schizophrenia and to define the extent to which they are dependent on genetic vulnerability for the condition. We employed structural magnetic resonance imaging (sMRI) in monozygotic (MZ) twins with or without schizophrenia. A sample of 129 twins completed sMRI, consisting of 21 MZ twin pairs concordant for schizophrenia, 17 MZ schizophrenic twins and 18 MZ nonschizophrenic twins drawn from 19 pairs discordant for schizophrenia, and 26 MZ control twin pairs without schizophrenia. Groups did not significantly differ in age, gender, handedness, height, level of education, parental socioeconomic status, and ethnicity. Using a region-of-interest approach, we measured the gray matter volumes (in cm(3)) of superior, middle, inferior, and orbital frontal cortices (SFC, MFC, IFC, and OFC, respectively); the caudate; and putamen. Covarying for whole-brain volume, age, and gender, we found that concordant but not discordant twins with schizophrenia had significantly lower volumes of MFC and OFC than control twins. In contrast, both patient groups had significantly lower SFC volumes than both groups of nonschizophrenic twins. There were no significant group differences in IFC and the striatum. We conclude that the prefrontal cortex shows a heterogeneous pattern of genetic influences on volumetric reductions in schizophrenia.
Collapse
Affiliation(s)
- Ulrich Ettinger
- Department of Psychiatry, Ludwig-Maximilians-University, Nussbaumstr. 7, 80336, Munich, Germany.
| | - Anne Schmechtig
- King's College London, Department of Neuroimaging, Institute of Psychiatry, London, UK
| | - Timothea Toulopoulou
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK
| | - Charmaine Borg
- King's College London, Department of Neuroimaging, Institute of Psychiatry, London, UK
| | - Claire Orrells
- King's College London, Department of Neuroimaging, Institute of Psychiatry, London, UK
| | - Sheena Owens
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK
| | - Kazunori Matsumoto
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK
| | - Neeltje E. van Haren
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mei-Hua Hall
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Boston, MA, USA
| | - Veena Kumari
- Department of Psychology, Institute of Psychiatry, King’s College London, London, UK
| | - Philip K. McGuire
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK
| | - Robin M. Murray
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK
| | - Marco Picchioni
- King's College London, Department of Psychosis Studies, Biomedical Research Centre, Institute of Psychiatry, London, UK,King’s College London, St Andrew’s Academic Centre, Institute of Psychiatry Northampton, UK
| |
Collapse
|
37
|
Gowers IR, Walters K, Kiss-Toth E, Read RC, Duff GW, Wilson AG. Age-related loss of CpG methylation in the tumour necrosis factor promoter. Cytokine 2011; 56:792-7. [PMID: 22004920 DOI: 10.1016/j.cyto.2011.09.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 09/12/2011] [Accepted: 09/19/2011] [Indexed: 11/29/2022]
Abstract
BACKGROUND Dysregulated production of TNF has been implicated in the pathogenesis and severity of inflammatory rheumatic diseases, many of which show age-related increased incidence. Ageing is also associated with changes in the immune system including higher systemic levels of pro-inflammatory cytokines. Methylation of DNA is an important regulator of gene expression and changes with age. OBJECTIVE In this study we investigated whether the DNA methylation status of the TNF promoter changed with age in peripheral blood leucocytes and macrophages. METHODS AND RESULTS Using pyrosequencing assays we detected age-related demethylation of CpG motifs (-304, -245 and -239) in the TNF promoter in human peripheral blood cells from 312 healthy controls (0.8% per decade, confidence interval (CI)=0.44-1.13%, p=1×10(-5)) and primary monocyte-derived macrophages (MDM) from a separate population of 78 healthy controls (1.4% per decade, CI=0.79-2.13%, p=7×10(-5)). Methylation a TNF promoter fragment (-345-+154) resulted in 78% reduction of reporter gene activity compared with the unmethylated promoter construct. CONCLUSIONS These data suggest a potential role of accrued changes in DNA methylation in the development of age-related inflammatory diseases, such as rheumatoid arthritis and polymyalgia rheumatica, in which TNF is a pivotal mediator.
Collapse
Affiliation(s)
- Isobel R Gowers
- Department of Infection & Immunity, Medical School, University of Sheffield, Sheffield S10 2RX, United Kingdom
| | | | | | | | | | | |
Collapse
|
38
|
Olden K, Freudenberg N, Dowd J, Shields AE. Discovering how environmental exposures alter genes could lead to new treatments for chronic illnesses. Health Aff (Millwood) 2011; 30:833-41. [PMID: 21555469 DOI: 10.1377/hlthaff.2011.0078] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Emerging research demonstrates that diet, pollution, and other environmental triggers can alter both the function and expression of human genes and lead to a heightened disease risk. These environment-gene interactions can cause so-called epigenetic changes in gene expression-patterns of which genes are switched "on" or "off"-that may account for the rising mortality from chronic diseases in industrialized nations. In this paper, we call for a new transdisciplinary approach to public health that would examine how environmental exposures, both physical and social, influence gene expression and a person's susceptibility to chronic disease. This initiative could lead to new ways to prevent and treat such illnesses.
Collapse
Affiliation(s)
- Kenneth Olden
- City University of New York School of Public Health at Hunter College, in New York City, USA.
| | | | | | | |
Collapse
|
39
|
Bollati V, Galimberti D, Pergoli L, Dalla Valle E, Barretta F, Cortini F, Scarpini E, Bertazzi PA, Baccarelli A. DNA methylation in repetitive elements and Alzheimer disease. Brain Behav Immun 2011; 25:1078-83. [PMID: 21296655 PMCID: PMC3742099 DOI: 10.1016/j.bbi.2011.01.017] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/13/2011] [Accepted: 01/26/2011] [Indexed: 11/19/2022] Open
Abstract
Epigenetics is believed to play a role in Alzheimer's disease (AD). DNA methylation, the most investigated epigenetic hallmark, is a reversible mechanism that modifies genome function and chromosomal stability through the addition of methyl groups to cytosine located in CpG dinucleotides to form 5 methylcytosine (5mC). Methylation status of repetitive elements (i.e. Alu, LINE-1 and SAT-α) is a major contributor of global DNA methylation patterns and has been investigated in relation to a variety of human diseases. However, the role of methylation of repetitive elements in blood of AD patients has never been investigated so far. In the present study, a quantitative bisulfite-PCR pyrosequencing method was used to evaluate methylation of Alu, LINE-1 and SAT-α sequences in 43 AD patients and 38 healthy donors. In multivariate analysis adjusting for age and gender, LINE-1 was increased in AD patients compared with healthy volunteers (ADs: 83.6%5mC, volunteers: 83.1%5mC, p-value: 0.05). The group with best performances in mini mental state examination (MMSE) showed higher levels of LINE-1 methylation compared to the group with worst performances (MMSE>22: 83.9%5mC; MMSE≤22: 83.2%5mC; p=0.05). Our data suggest that LINE-1 methylation may lead to a better understanding of AD pathogenesis and course, and may contribute to identify novel markers useful to assess risk stratification. Further prospective investigations are warranted to evaluate the dynamics of DNA methylation from early-stage AD to advanced phases of the disease.
Collapse
Affiliation(s)
- V Bollati
- Center of Molecular and Genetic Epidemiology, Department of Environmental and Occupational Health, University of Milan, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Park J, Oh H, Kim M, Kim G, Park E, Jang G, Lee B. Changes in the somatotrophic axis in genetically identical dogs. Cell Reprogram 2011; 13:451-7. [PMID: 21740269 DOI: 10.1089/cell.2011.0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Because cloned dogs are genetically identical, variations among these animals can be a useful tool to elucidate mechanisms underlying phenotypic differences. To estimate the influence of genetic factors on phenotypic variation, changes in concentration patterns of growth hormone (GH), insulin like growth factor-1 (IGF-1), and IGF binding protein 3 (IGFBP-3) were compared among cloned and age-matched control dogs. In addition, the concentrations of GH and IGF-1 following administration of growth hormone releasing hormone (GHRH) and somatostatin (SRIF) were measured in both groups. In comparing hormone profiles, the control dogs had larger standard deviations from the means for GH, IGF-1, and IGFBP-3 than the clones. Also, the mean concentration of IGFBP-3 in clones was significantly lower than in the controls between 7 to 12 months of age, whereas the IGFBP-3 changes in clones and controls followed the same pattern. GHRH induced increased serum growth hormone concentration both in clones and controls. However, the concentration of IGF-1 was lower in clones than in controls, and larger standard variations were noted in the control group. In conclusion, the measured traits were more homogeneous in cloned animals than in controls, so cloned animals could be valuable for assessing effects of genotype and environment interactions.
Collapse
Affiliation(s)
- JungEun Park
- Department of Theriogenology & Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
41
|
Yip L, Rufaut N, Sinclair R. Role of genetics and sex steroid hormones in male androgenetic alopecia and female pattern hair loss: an update of what we now know. Australas J Dermatol 2011; 52:81-8. [PMID: 21605090 DOI: 10.1111/j.1440-0960.2011.00745.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of genetic predisposition and the influence of sex steroid hormones are indisputable to the pathogenesis of male androgenetic alopecia (MAGA). The role of sex steroid hormones in female pattern hair loss (FPHL) is less known. A good knowledge of the pathophysiology underlying MAGA and FPHL empowers the clinician to confidently counsel patients and make informed therapeutic decisions. Vigorous research in recent years has provided greater insight into the role of genetics and sex steroids in physiological hair growth and cycling, as well as in hair follicle miniaturization, the histological hallmark of MAGA and FPHL. In the present review article directed towards clinicians, we discuss the current understanding of the role of androgens and oestrogens, as well as genetic associations with MAGA and FPHL. We also briefly discuss the interpretation of direct-to-consumer genetic testing for baldness to help clinicians understand the limitations of such tests.
Collapse
Affiliation(s)
- Leona Yip
- Department of Dermatology, St Vincent's Hospital, Melbourne, Victoria, Australia.
| | | | | |
Collapse
|
42
|
|
43
|
Oldehinkel AJ, Bouma EMC. Sensitivity to the depressogenic effect of stress and HPA-axis reactivity in adolescence: a review of gender differences. Neurosci Biobehav Rev 2010; 35:1757-70. [PMID: 21040743 DOI: 10.1016/j.neubiorev.2010.10.013] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 10/19/2010] [Accepted: 10/25/2010] [Indexed: 01/31/2023]
Abstract
Adolescence is characterized by major biological, psychological, and social challenges, as well as by an increase in depression rates. This review focuses on the association between stressful experiences and depression in adolescence, and the possible role of the hypothalamus-pituitary-adrenal cortex (HPA-)axis in this link. Adolescent girls have a higher probability to develop depressive symptoms than adolescent boys and preadolescents. Increasing evidence indicates that girls' higher risk of depression is partly brought about by an increased sensitivity for stressful life events, particularly interpersonal stressors, which are highly prevalent in adolescent girls. Genetic risk factors for depression, as well as those for stress sensitivity, are often expressed differently in girls and boys. Also environmental adversity tends to affect girls' stress responses more than those of boys. These gender-specific association patterns have been reported for both sensitivity to stressful life events and HPA-axis responses to social stress. Together, the findings suggest that girls are more malleable than boys in response to internal and external influences. This postulated greater malleability may be adaptive in many circumstances, but also brings along risk, such as an increased probability of depression.
Collapse
Affiliation(s)
- Albertine J Oldehinkel
- Interdisciplinary Center for Psychiatric Epidemiology, University Medical Center, University of Groningen, Groningen, The Netherlands.
| | | |
Collapse
|
44
|
Peerbooms OLJ, Wichers M, Jacobs N, Kenis G, Derom C, Vlietinck R, Thiery E, van Os J, Rutten BPF. No major role for X-inactivation in variations of intelligence and behavioral problems at middle childhood. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:1311-7. [PMID: 20593382 DOI: 10.1002/ajmg.b.31111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although members of monozygotic (MZ) twin pairs are identical in genomic sequence, epigenetic mechanisms may occasion difference in gene expression and, consequently, twin discordance in complex traits. Recent work suggests that the epigenetic process of X-inactivation in female individuals may impact on intelligence and child behavioral problems. The timing of X-inactivation has been linked to chorionic splitting in MZ twins. Dichorionic monozygotic (DC-MZ) twinning, unlike monochorionic monozygotic (MC-MZ) twinning, occurs prior to the time of X-inactivation in female organisms. Therefore, the hypothesis of a causal role of X-inactivation in intelligence and behavioral problems can be analyzed by modeling the statistical interaction between sex and chorion type for within-pair differences in these traits in MZ twins. In this study, the effect of X-inactivation on childhood behavioral problems, measured with the CBCL, was studied in a sample of 324 MZ twin pairs from the EFPTS and the effect of X-inactivation on IQ was studied in a sample of 272 twin pairs from the same twin survey. Information on chorion type, gestational age, and birth weight was additionally collated. No significant statistical interaction was found between sex and chorion type, indicating that X-inactivation is not likely involved in variations in intelligence or behavioral problems in middle childhood. Further studies are required to replicate these findings and may explore the role of X-inactivation at different ages or at the extreme scores in the spectrum of intelligence and behavioral problems or may focus on other epigenetic mechanisms.
Collapse
Affiliation(s)
- O L J Peerbooms
- Department of Psychiatry and Neuropsychology, Maastricht University, European Graduate School of Neuroscience, Maastricht, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Bengtson MB, Aamodt G, Vatn MH, Harris JR. Concordance for IBD among twins compared to ordinary siblings--a Norwegian population-based study. J Crohns Colitis 2010; 4:312-8. [PMID: 21122520 DOI: 10.1016/j.crohns.2009.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/10/2009] [Accepted: 12/10/2009] [Indexed: 02/08/2023]
Abstract
AIMS Comparing the risk to develop concordant disease among twins with inflammatory bowel disease (IBD) to ordinary siblings. Moreover, clinical characteristics of IBD and the association between perinatal factors and IBD, were evaluated. METHODS Patients with IBD, enrolled from an incidence study between 1990 and 1994, and the twins were identified from the Norwegian national birth registry, which was established in 1967. RESULTS Eight monozygotic and 16 dizygotic pairs, in which at least one twin reported a positive history of IBD were compared to 84 patients with Crohn's disease (CD) and 87 patients with ulcerative colitis (UC) from the incidence study. The relative risks for concordant disease in monozygotic pairs were estimated to 95.4 (95% CI: 76.3, 114.6) and 49.5 (95% CI: 35.7, 63.3) for CD and UC, respectively. The corresponding risks in dizygotic pairs were 42.4 (95% CI: 29.6, 55.2) and 0.0. Among ordinary siblings of CD and UC the risks for concordance were 22.7 (95% CI: 13.3, 32.1) and 4.6 (95% CI: 0.4, 8.7), respectively. Stricturing disease was significantly higher in twins with CD compared to incidental cases. The first-born twin in pairs discordant for disease, 12 out of 19 (63.2%), tended to be affected by IBD (p=0.10). CONCLUSION Genetic factors influence the development of IBD and fibrostenotic disease in CD. The increased risk for concordant disease among dizygotic twins compared to ordinary siblings, at least in CD, might underscore the importance of shared environment in utero or in childhood.
Collapse
|
46
|
Ollikainen M, Smith KR, Joo EJH, Ng HK, Andronikos R, Novakovic B, Abdul Aziz NK, Carlin JB, Morley R, Saffery R, Craig JM. DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum Mol Genet 2010; 19:4176-88. [PMID: 20699328 DOI: 10.1093/hmg/ddq336] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mounting evidence from both animal and human studies suggests that the epigenome is in constant drift over the life course in response to stochastic and environmental factors. In humans, this has been highlighted by a small number of studies that have demonstrated discordant DNA methylation patterns in adolescent or adult monozygotic (MZ) twin pairs. However, to date, it remains unclear when such differences emerge, and how prevalent they are across different tissues. To address this, we examined the methylation of four differentially methylated regions associated with the IGF2/H19 locus in multiple birth tissues derived from 91 twin pairs: 56 MZ and 35 dizygotic (DZ). Tissues included cord blood-derived mononuclear cells and granulocytes, human umbilical vein endothelial cells, buccal epithelial cells and placental tissue. Considerable variation in DNA methylation was observed between tissues and between unrelated individuals. Most interestingly, methylation discordance was also present within twin pairs, with DZ pairs showing greater discordance than MZ pairs. These data highlight the variable contribution of both intrauterine environmental exposures and underlying genetic factors to the establishment of the neonatal epigenome of different tissues and confirm the intrauterine period as a sensitive time for the establishment of epigenetic variability in humans. This has implications for the effects of maternal environment on the development of the newborn epigenome and supports an epigenetic mechanism for the previously described phenomenon of 'fetal programming' of disease risk.
Collapse
Affiliation(s)
- Miina Ollikainen
- Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Palermo GB. Biological and Environmental Correlates of Aggressive Behavior. JOURNAL OF FORENSIC PSYCHOLOGY PRACTICE 2010. [DOI: 10.1080/15228932.2010.481234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
48
|
Petronis A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 2010; 465:721-7. [PMID: 20535201 DOI: 10.1038/nature09230] [Citation(s) in RCA: 435] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Epigenetic modifications of DNA and histones might be crucial for understanding the molecular basis of complex phenotypes. One reason for this is that epigenetic factors are sometimes malleable and plastic enough to react to cues from the external and internal environments. Such induced epigenetic changes can be solidified and propagated during cell division, resulting in permanent maintenance of the acquired phenotype. In addition, the finding that there is partial epigenetic stability in somatic and germline cells allows insight into the molecular mechanisms of heritability. Epigenetics can provide a new framework for the search of aetiological factors in complex traits and diseases.
Collapse
Affiliation(s)
- Arturas Petronis
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario M5T 1R8, Canada.
| |
Collapse
|
49
|
Maremmani I, Stefania C, Pacini M, Maremmani AGI, Carlini M, Golia F, Deltito J, Dell'Osso L. Differential substance abuse patterns distribute according to gender in heroin addicts. J Psychoactive Drugs 2010; 42:89-95. [PMID: 20464810 DOI: 10.1080/02791072.2010.10399789] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This study attempts to analyse potential gender differences among a group of heroin addicts seeking treatment at a university-based medical centre. The central modality of treatment at this centre is the use of methadone maintenance. Among those patients entering this program there seems to be an emerging pattern of males who tend to use heroin as their opiate of choice, and are more likely to combine it with cannabis, while females are more likely to use to street methadone, with adjunctive use of ketamine, benzodiazepines, hypnotic drugs and/or amphetamines. Women are at higher risk of abusing opioids through a pathway of initial prescription painkiller use, and later to resort to street methadone to cope with prescription pain killer addiction. This latter pattern seems to result in an increased risk for fatal accidental overdoses. The use of these longer-acting agents in women may be influenced by psychosocial and hormonal factors.
Collapse
Affiliation(s)
- Icro Maremmani
- "Vincent P. Dole" Dual Diagnosis Unit, Santa Chiara University Hospital, Department of Psychiatry, NPB, University of Pisa, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Kloukina-Pantazidou I, Havaki S, Chrysanthou-Piterou M, Kontaxakis VP, Papadimitriou GN, Issidorides MR. Chromatin Alterations in Leukocytes of First-episode Schizophrenic Patients. Ultrastruct Pathol 2010; 34:106-16. [DOI: 10.3109/01913121003644781] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|