151
|
Liao P, Ostrom QT, Stetson L, Barnholtz-Sloan JS. Models of epigenetic age capture patterns of DNA methylation in glioma associated with molecular subtype, survival, and recurrence. Neuro Oncol 2018; 20:942-953. [PMID: 29432558 PMCID: PMC6007761 DOI: 10.1093/neuonc/noy003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Models of epigenetic aging (epigenetic clocks) have been implicated as potentially useful markers for cancer risk and prognosis. Using 2 previously published methods for modeling epigenetic age, Horvath's clock and epiTOC, we investigated epigenetic aging patterns related to World Health Organization grade and molecular subtype as well as associations of epigenetic aging with glioma survival and recurrence. Methods Epigenetic ages were calculated using Horvath's clock and epiTOC on 516 lower-grade glioma and 141 glioblastoma cases along with 136 nontumor (normal) brain samples. Associations of tumor epigenetic age with patient chronological age at diagnosis were assessed with correlation and linear regression, and associations were validated in an independent cohort of 203 gliomas. Contribution of epigenetic age to survival prediction was assessed using Cox proportional hazards modeling. Sixty-three samples from 18 patients with primary-recurrent glioma pairs were also analyzed and epigenetic age difference and rate of epigenetic aging of primary-recurrent tumors were correlated to time to recurrence. Results Epigenetic ages of gliomas were near-universally accelerated using both Horvath's clock and epiTOC compared with normal tissue. The 2 independent models of epigenetic aging were highly associated with each other and exhibited distinct aging patterns reflective of molecular subtype. EpiTOC was found to be a significant independent predictor of survival. Epigenetic aging of gliomas between primary and recurrent tumors was found to be highly variable and not significantly associated with time to recurrence. Conclusions We demonstrate that epigenetic aging reflects coherent modifications of the epigenome and can potentially provide additional prognostic power for gliomas.
Collapse
Affiliation(s)
- Peter Liao
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine
| | - Lindsay Stetson
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine
| | | |
Collapse
|
152
|
Pérez RF, Tejedor JR, Bayón GF, Fernández AF, Fraga MF. Distinct chromatin signatures of DNA hypomethylation in aging and cancer. Aging Cell 2018; 17:e12744. [PMID: 29504244 PMCID: PMC5946083 DOI: 10.1111/acel.12744] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2018] [Indexed: 12/21/2022] Open
Abstract
Cancer is an aging‐associated disease, but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, the similarity of the regions where this loss of DNA methylation occurs is currently not well characterized, and it is unknown if such regions also share a common chromatin signature in aging and cancer. To address this issue, we analyzed TCGA DNA methylation data from a total of 2,311 samples, including control and cancer cases from patients with breast, kidney, thyroid, skin, brain, and lung tumors and healthy blood, and integrated the results with histone, chromatin state, and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects. We identified 98,857 CpG sites differentially methylated in aging and 286,746 in cancer. Hyper‐ and hypomethylated changes in both processes each had a similar genomic distribution across tissues and displayed tissue‐independent alterations. The identified hypermethylated regions in aging and cancer shared a similar bivalent chromatin signature. In contrast, hypomethylated DNA sequences occurred in very different chromatin contexts. DNA hypomethylated sequences were enriched at genomic regions marked with the activating histone posttranslational modification H3K4me1 in aging, while in cancer, loss of DNA methylation was primarily associated with the repressive H3K9me3 mark. Our results suggest that the role of DNA methylation as a molecular link between aging and cancer is more complex than previously thought.
Collapse
Affiliation(s)
- Raúl F. Pérez
- Nanomedicine Group; Nanomaterials and Nanotechnology Research Center (CINN-CSIC); Universidad de Oviedo; El Entrego, Asturias Spain
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
- Cáncer Epigenetics Laboratory; Fundación para la Investigación Biosanitaria de Asturias (FINBA); Instituto de Investigación Sanitaria del Principado de Asturias (ISPA); Oviedo, Asturias Spain
| | - Gustavo F. Bayón
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
| | - Agustín F. Fernández
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
- Cáncer Epigenetics Laboratory; Fundación para la Investigación Biosanitaria de Asturias (FINBA); Instituto de Investigación Sanitaria del Principado de Asturias (ISPA); Oviedo, Asturias Spain
| | - Mario F. Fraga
- Nanomedicine Group; Nanomaterials and Nanotechnology Research Center (CINN-CSIC); Universidad de Oviedo; El Entrego, Asturias Spain
| |
Collapse
|
153
|
Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 2018; 23:239-254.e6. [PMID: 29617664 PMCID: PMC5961503 DOI: 10.1016/j.celrep.2018.03.076] [Citation(s) in RCA: 687] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.
Collapse
Affiliation(s)
| | - Linghua Wang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA; Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Feng
- TESARO Inc., Waltham, MA 02451, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase Miller
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Haoran Chen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Denise Wolf
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer, Houston, TX 77030, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Raymond J Monnat
- Departments of Pathology & Genome Sciences, University of Washington, Seattle, WA 98195-7705, USA.
| | | | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA; Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
| |
Collapse
|
154
|
Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
Collapse
Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
| |
Collapse
|
155
|
Smith RG, Hannon E, De Jager PL, Chibnik L, Lott SJ, Condliffe D, Smith AR, Haroutunian V, Troakes C, Al-Sarraj S, Bennett DA, Powell J, Lovestone S, Schalkwyk L, Mill J, Lunnon K. Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology. Alzheimers Dement 2018; 14:1580-1588. [PMID: 29550519 PMCID: PMC6438205 DOI: 10.1016/j.jalz.2018.01.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/07/2018] [Accepted: 01/26/2018] [Indexed: 01/05/2023]
Abstract
Introduction: Alzheimer’s disease is a neurodegenerative disorder that is hypothesized to involve epigenetic dysregulation of gene expression in the brain. Methods: We performed an epigenome-wide association study to identify differential DNA methylation associated with neuropathology in prefrontal cortex and superior temporal gyrus samples from 147 individuals, replicating our findings in two independent data sets (N = 117 and 740). Results: We identify elevated DNA methylation associated with neuropathology across a 48-kb region spanning 208 CpG sites within the HOXA gene cluster. A meta-analysis of the top-ranked probe within the HOXA3 gene (cg22962123) highlighted significant hypermethylation across all three cohorts (P = 3.11 × 10−18). Discussion: We present robust evidence for elevated DNA methylation associated with Alzheimer’s disease neuropathology spanning the HOXA gene cluster on chromosome 7. These data add to the growing evidence highlighting a role for epigenetic variation in Alzheimer’s disease, implicating the HOX gene family as a target for future investigation.
Collapse
Affiliation(s)
- Rebecca G Smith
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital Campus, Exeter, Devon, UK
| | - Eilis Hannon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital Campus, Exeter, Devon, UK
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Departments of Neurology and Psychiatry, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Columbia University College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Lori Chibnik
- Program in Translational NeuroPsychiatric Genomics, Departments of Neurology and Psychiatry, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Simon J Lott
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Adam R Smith
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital Campus, Exeter, Devon, UK
| | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA; JJ Peters VA Medical Center, Bronx, NY, USA
| | - Claire Troakes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - John Powell
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | | | - Jonathan Mill
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital Campus, Exeter, Devon, UK.
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital Campus, Exeter, Devon, UK.
| |
Collapse
|
156
|
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]
|
157
|
Abstract
Even though the importance of epigenetics was first recognized in light of its role in tissue development, an increasing amount of evidence has shown that it also plays an important role in the development and progression of many common diseases. We discuss some recent findings on one representative epigenetic modification, DNA methylation, in some common diseases. While many new risk factors have been identified through the population-based epigenetic epidemiologic studies on the role of epigenetics in common diseases, this relatively new field still faces many unique challenges. Here, we describe those promises and unique challenges of epigenetic epidemiological studies and propose some potential solutions.
Collapse
Affiliation(s)
| | - Yun Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
158
|
Doherty TS, Roth TL. Epigenetic Landscapes of the Adversity-Exposed Brain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:1-19. [PMID: 29933946 DOI: 10.1016/bs.pmbts.2017.11.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It is understood that adversity during development has the power to alter behavioral trajectories, and the role of the epigenome in that relationship is currently under intense investigation. Several studies in both nonhuman animals and humans have established a link between early adversity and epigenetic regulation of genes heavily implicated in the stress response, plasticity and cognition, and psychiatric disorders such as depression and anxiety. Thus the relatively recent surge of studies centering on the epigenetic outcomes of stress has great potential to inform treatments and interventions for psychiatric disorder precipitated by early adversity. Here we review what we know and what we do not know, and suggest approaches to help further elucidate the relationship between early adversity, epigenetics, and behavior.
Collapse
Affiliation(s)
| | - Tania L Roth
- University of Delaware, Newark, DE, United States.
| |
Collapse
|
159
|
Aging and nutrition induce tissue-specific changes on global DNA methylation status in rats. Mech Ageing Dev 2018; 174:47-54. [PMID: 29427568 DOI: 10.1016/j.mad.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 01/12/2023]
Abstract
A number of epigenetic studies have demonstrated that DNA methylation patterns exhibit a tissue specificity, but not much has been done to highlight the extent of this phenomenon. Moreover, it is unknown how external factors modulate the plasticity of the tissue specific epigenetic profile. We examined global DNA methylation profiles in tissues from rats of different age, fed with standard or low-calorie diet, and evaluated their association with aging and nutrition. Tissue-specific variations occur during aging with hyper-methylation taking place in all tissues except for liver. The expression of enzymes involved in methylation reactions (DNMTs and TETs) was consistent with the methylation patterns. Nutrition affects global DNA methylation status throughout lifespan. Interestingly, the differences among different tissues are magnified in 96 weeks old rats fed with low calorie diet. Moreover, the low-calorie diet appears to affect the offspring's epigenetic status more strongly if administered during the maternal pre-gestational period than the gestational and lactation time. Therefore, we propose that changes in the global DNA methylation status may represent an epigenetic mechanism by which age and nutrition intersect each other and, in turn, influence the aging plasticity.
Collapse
|
160
|
Ovenden ES, McGregor NW, Emsley RA, Warnich L. DNA methylation and antipsychotic treatment mechanisms in schizophrenia: Progress and future directions. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:38-49. [PMID: 29017764 DOI: 10.1016/j.pnpbp.2017.10.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Antipsychotic response in schizophrenia is a complex, multifactorial trait influenced by pharmacogenetic factors. With genetic studies thus far providing little biological insight or clinical utility, the field of pharmacoepigenomics has emerged to tackle the so-called "missing heritability" of drug response in disease. Research on psychiatric disorders has only recently started to assess the link between epigenetic alterations and treatment outcomes. DNA methylation, the best characterised epigenetic mechanism to date, is discussed here in the context of schizophrenia and antipsychotic treatment outcomes. The majority of published studies have assessed the influence of antipsychotics on methylation levels in specific neurotransmitter-associated candidate genes or at the genome-wide level. While these studies illustrate the epigenetic modifications associated with antipsychotics, very few have assessed clinical outcomes and the potential of differential DNA methylation profiles as predictors of antipsychotic response. Results from other psychiatric disorder studies, such as depression and bipolar disorder, provide insight into what may be achieved by schizophrenia pharmacoepigenomics. Other aspects that should be addressed in future research include methodological challenges, such as tissue specificity, and the influence of genetic variation on differential methylation patterns.
Collapse
Affiliation(s)
- Ellen S Ovenden
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Robin A Emsley
- Department of Psychiatry, Stellenbosch University, Tygerberg 7505, South Africa
| | - Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa.
| |
Collapse
|
161
|
Bustamante AC, Armstrong DL, Uddin M. Epigenetic profiles associated with major depression in the human brain. Psychiatry Res 2018; 260:439-442. [PMID: 29272728 DOI: 10.1016/j.psychres.2017.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/01/2017] [Accepted: 12/06/2017] [Indexed: 01/25/2023]
Abstract
We conducted an epigenome-wide association study of Major Depressive Disorder (MDD) in brain-derived DNA using two analytic approaches. DNA methylation data (GSE41826) was used in differential methylation (DM) analyses controlling for age, sex, suicide status, and post-mortem interval; and in weighted gene co-methylation network analyses (WGCNA) in probes mapping to transcription start sites. No probes in the DM analysis survived FDR correction. Nominally significant DM probes were enriched in synaptic function-related genes. WGCNA revealed one module correlated with MDD, enriched in genes associated with mitochondrial function. DM and WGCNA both showed enrichment of genes involved in transcription and DNA binding.
Collapse
Affiliation(s)
- Angela C Bustamante
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Don L Armstrong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Monica Uddin
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA; Department of Psychology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| |
Collapse
|
162
|
Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Yakovleva T, Hansson AC, Sommer WH, Spanagel R, Bakalkin G. Dynorphin and κ-Opioid Receptor Dysregulation in the Dopaminergic Reward System of Human Alcoholics. Mol Neurobiol 2018; 55:7049-7061. [PMID: 29383684 PMCID: PMC6061161 DOI: 10.1007/s12035-017-0844-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022]
Abstract
Molecular changes induced by excessive alcohol consumption may underlie formation of dysphoric state during acute and protracted alcohol withdrawal which leads to craving and relapse. A main molecular addiction hypothesis is that the upregulation of the dynorphin (DYN)/κ-opioid receptor (KOR) system in the nucleus accumbens (NAc) of alcohol-dependent individuals causes the imbalance in activity of D1- and D2 dopamine receptor (DR) expressing neural circuits that results in dysphoria. We here analyzed post-mortem NAc samples of human alcoholics to assess changes in prodynorphin (PDYN) and KOR (OPRK1) gene expression and co-expression (transcriptionally coordinated) patterns. To address alterations in D1- and D2-receptor circuits, we studied the regulatory interactions between these pathways and the DYN/KOR system. No significant differences in PDYN and OPRK1 gene expression levels between alcoholics and controls were evident. However, PDYN and OPRK1 showed transcriptionally coordinated pattern that was significantly different between alcoholics and controls. A downregulation of DRD1 but not DRD2 expression was seen in alcoholics. Expression of DRD1 and DRD2 strongly correlated with that of PDYN and OPRK1 suggesting high levels of transcriptional coordination between these gene clusters. The differences in expression and co-expression patterns were not due to the decline in neuronal proportion in alcoholic brain and thereby represent transcriptional phenomena. Dysregulation of DYN/KOR system and dopamine signaling through both alterations in co-expression patterns of opioid genes and decreased DRD1 gene expression may contribute to imbalance in the activity of D1- and D2-containing pathways which may lead to the negative affective state in human alcoholics.
Collapse
Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden.
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Anita C Hansson
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Wolfgang H Sommer
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Rainer Spanagel
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| |
Collapse
|
163
|
Jones MJ, Moore SR, Kobor MS. Principles and Challenges of Applying Epigenetic Epidemiology to Psychology. Annu Rev Psychol 2018; 69:459-485. [DOI: 10.1146/annurev-psych-122414-033653] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Meaghan J. Jones
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Sarah R. Moore
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
- Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
164
|
Abstract
The number of epigenetic studies is exponentially increasing. There is anticipation that DNA methylation may close gaps in our understanding of disease etiology, and how certain risk factors affect health and disease, but also that it has potential as a biomarker for disease. Human DNA methylation studies require careful considerations for design and analysis including population and tissue selection, population stratification, cell heterogeneity, confounding, temporality, sample size, appropriate statistical analysis, and validation of results. In this chapter, we discuss relevant aspects for the design of DNA methylation studies and delineate essential steps for their analysis. Specifically, we summarize methods used to extricate biologic signals from technical noise, and statistical approaches to capture meaningful variability based on the research hypothesis.
Collapse
Affiliation(s)
- Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Alexandra M Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| |
Collapse
|
165
|
Snijders C, Bassil KC, de Nijs L. Methodologies of Neuroepigenetic Research: Background, Challenges and Future Perspectives. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:15-27. [DOI: 10.1016/bs.pmbts.2018.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
166
|
Yang X, Gao L, Zhang S. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. Brief Bioinform 2017; 18:761-773. [PMID: 27436122 DOI: 10.1093/bib/bbw063] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 01/05/2023] Open
Abstract
Abnormal DNA methylation is an important epigenetic regulator involving tumorigenesis. Deciphering cancer common and specific DNA methylation patterns is essential for us to understand the mechanisms of tumor development. The Cancer Genome Atlas (TCGA) project provides a large number of samples of different cancers that enable a pan-cancer study of DNA methylation possible. Here we investigate cancer common and specific DNA methylation patterns among 5480 DNA methylation profiles of 15 cancer types from TCGA. We first define differentially methylated CpG sites (DMCs) in each cancer and then identify 5450 hyper- and 4433 hypomethylated pan-cancer DMCs (PDMCs). Intriguingly, three adjacent hypermethylated PDMC constitute an enhancer region, which potentially regulates two tumor suppressor genes BVES and PRDM1 negatively. Moreover, we identify six distinct motif clusters, which are enriched in hyper- or hypomethylated PDMCs and are associated with several well-known cancer hallmarks. We also observe that PDMCs relate to distinct transcriptional groups. Additionally, 55 hypermethylated and 7 hypomethylated PDMCs are significantly associated with patient survival. Lastly, we find that cancer-specific DMCs are enriched in known cancer genes and cell-type-specific super-enhancers. In summary, this study provides a comprehensive investigation and reveals meaningful cancer common and specific DNA methylation patterns.
Collapse
|
167
|
Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
Collapse
Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| |
Collapse
|
168
|
Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus. Nat Commun 2017; 8:1511. [PMID: 29142228 PMCID: PMC5688097 DOI: 10.1038/s41467-017-01818-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs. Cis-acting SNPs of hippocampal meQTLs and eQTLs significantly overlap schizophrenia-associated SNPs. Correlations of CpG methylation and RNA expression are found for 34 genes. Our comprehensive maps of cis-acting hippocampal meQTLs and eQTLs provide a link between disease-associated SNPs and the regulatory genome that will improve the functional interpretation of non-coding genetic variants in the molecular genetic dissection of brain disorders.
Collapse
|
169
|
Fortin JP, Triche TJ, Hansen KD. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics 2017; 33:558-560. [PMID: 28035024 PMCID: PMC5408810 DOI: 10.1093/bioinformatics/btw691] [Citation(s) in RCA: 414] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/04/2016] [Indexed: 02/06/2023] Open
Abstract
Summary The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data. Availability and Implementation The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project. Contact khansen@jhsph.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jean-Philippe Fortin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Timothy J Triche
- Jane Anne Nohl Division of Hematology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
170
|
Boström AE, Ciuculete DM, Attwood M, Krattinger R, Nikontovic L, Titova OE, Kullak-Ublick GA, Mwinyi J, Schiöth HB. A MIR4646 associated methylation locus is hypomethylated in adolescent depression. J Affect Disord 2017; 220:117-128. [PMID: 28618313 DOI: 10.1016/j.jad.2017.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/04/2017] [Accepted: 05/06/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Studies of epigenetics and transcriptional activity in adolescents may provide knowledge about possible preventive strategies of depression. METHODS We present a methylome-wide association study (MWAS) and cohort validation analysis of depression in adolescents, in two separate cohorts: discovery (n=93) and validation data set 1 (n=78). The genome-wide methylation pattern was measured from whole blood using the Illumina 450K array. A second validation cohort, validation data set 2, consists of post-mortem brain biopsies from depressed adults (n=58). We performed a MWAS by robust multiple linear regressions of methylation to a modified risk-score assessment of depression. Methylation levels of candidate CpG sites were correlated with expression levels of the associated gene in an independent cohort of 11 healthy volunteers. RESULTS The methylation state of two CpG sites reliably predicted ratings of depression in adolescents (cg13227623 and cg04102384) (p<10E-06). Cohort validation analysis confirmed cg04102384 - located in the promoter region of microRNA 4646 (MIR4646) - to be hypomethylated in both validation data set 1 and validation data set 2 (p<0.05). Cg04102384 was inversely correlated to expression levels of MIR4646-3p in healthy controls (p<0.05). LIMITATIONS MIR4646 was not differentially expressed in a subset of samples with adolescent depression measured by qRT-PCR measurements. CONCLUSION We identify a specific MIR4646 associated epigenetic risk site to be associated with depression in adolescents. Cg04102384 putatively regulates gene expression of MIR4646-3p. Target gene prediction and gene set overrepresentation analysis revealed involvement of this miRNA in fatty acid elongation, a process related to omega-3 fatty acids, previously associated with depression.
Collapse
Affiliation(s)
- Adrian E Boström
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden..
| | - Diana-Maria Ciuculete
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Misty Attwood
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Regina Krattinger
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Switzerland
| | - Lamia Nikontovic
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Olga E Titova
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Switzerland
| | - Jessica Mwinyi
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| |
Collapse
|
171
|
Viana J, Hannon E, Dempster E, Pidsley R, Macdonald R, Knox O, Spiers H, Troakes C, Al-Saraj S, Turecki G, Schalkwyk LC, Mill J. Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions. Hum Mol Genet 2017; 26:210-225. [PMID: 28011714 PMCID: PMC5351932 DOI: 10.1093/hmg/ddw373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/26/2016] [Indexed: 01/29/2023] Open
Abstract
Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular aetiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, which are not enriched in genomic regions identified in genetic studies of schizophrenia and do not reflect direct genetic effects on DNA methylation. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with aetiological variation in complex disease.
Collapse
Affiliation(s)
- Joana Viana
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ruby Macdonald
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Olivia Knox
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Helen Spiers
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Safa Al-Saraj
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Gustavo Turecki
- Douglas Mental Health Institute, McGill University, Montreal, QC, Canada and
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK.,Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| |
Collapse
|
172
|
Roubroeks JAY, Smith RG, van den Hove DLA, Lunnon K. Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases. J Neurochem 2017; 143:158-170. [PMID: 28805248 DOI: 10.1111/jnc.14148] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022]
Abstract
Recent studies have suggested a role for epigenetic mechanisms in the complex etiology of various neurodegenerative diseases. In this review, we discuss advances that have been made toward understanding the role of epigenetic processes in neurodegenerative disorders, with a particular focus on Alzheimer's disease, where the most extensive studies have been undertaken to date. We provide a brief overview of DNA modifications, followed by a summarization of studies of DNA modifications in Alzheimer's disease and other neurodegenerative diseases.
Collapse
Affiliation(s)
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Devon, UK
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands.,Laboratory of Translational Neuroscience, Division of Molecular Psychiatry, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Devon, UK
| |
Collapse
|
173
|
Epigenomics of Major Depressive Disorders and Schizophrenia: Early Life Decides. Int J Mol Sci 2017; 18:ijms18081711. [PMID: 28777307 PMCID: PMC5578101 DOI: 10.3390/ijms18081711] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/13/2022] Open
Abstract
Brain development is guided by the interactions between the genetic blueprint and the environment. Epigenetic mechanisms, especially DNA methylation, can mediate these interactions and may also trigger long-lasting adaptations in developmental programs that increase the risk of major depressive disorders (MDD) and schizophrenia (SCZ). Early life adversity is a major risk factor for MDD/SCZ and can trigger persistent genome-wide changes in DNA methylation at genes important to early, but also to mature, brain function, including neural proliferation, differentiation, and synaptic plasticity, among others. Moreover, genetic variations controlling dynamic DNA methylation in early life are thought to influence later epigenomic changes in SCZ. This finding corroborates the high genetic load and a neurodevelopmental origin of SCZ and shows that epigenetic responses to the environment are, at least in part, genetically controlled. Interestingly, genetic variants influencing DNA methylation are also enriched in risk variants from genome-wide association studies (GWAS) on SCZ supporting a role in neurodevelopment. Overall, epigenomic responses to early life adversity appear to be controlled to different degrees by genetics in MDD/SCZ, even though the potential reversibility of epigenomic processes may offer new hope for timely therapeutic interventions in MDD/SCZ.
Collapse
|
174
|
BECon: a tool for interpreting DNA methylation findings from blood in the context of brain. Transl Psychiatry 2017; 7:e1187. [PMID: 28763057 PMCID: PMC5611738 DOI: 10.1038/tp.2017.171] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented. Here, we aimed to provide a resource to the community to aid interpretation of blood-based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450 K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data, we have made available metrics on: the variability of cytosine-phosphate-guanine dinucleotides (CpGs) in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance; https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood-based human DNA methylation results, in the context of brain.
Collapse
|
175
|
Zheleznyakova GY, Piket E, Marabita F, Pahlevan Kakhki M, Ewing E, Ruhrmann S, Needhamsen M, Jagodic M, Kular L. Epigenetic research in multiple sclerosis: progress, challenges, and opportunities. Physiol Genomics 2017; 49:447-461. [PMID: 28754822 DOI: 10.1152/physiolgenomics.00060.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. MS likely results from a complex interplay between predisposing causal gene variants (the strongest influence coming from HLA class II locus) and environmental risk factors such as smoking, infectious mononucleosis, and lack of sun exposure/vitamin D. However, little is known about the mechanisms underlying MS development and progression. Moreover, the clinical heterogeneity and variable response to treatment represent additional challenges to a comprehensive understanding and efficient treatment of disease. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, integrate influences from the genes and the environment to regulate gene expression accordingly. Studying epigenetic modifications, which are stable and reversible, may provide an alternative approach to better understand and manage disease. We here aim to review findings from epigenetic studies in MS and further discuss the challenges and clinical opportunities arising from epigenetic research, many of which apply to other diseases with similar complex etiology. A growing body of evidence supports a role of epigenetic processes in the mechanisms underlying immune pathogenesis and nervous system dysfunction in MS. However, disparities between studies shed light on the need to consider possible confounders and methodological limitations for a better interpretation of the data. Nevertheless, translational use of epigenetics might offer new opportunities in epigenetic-based diagnostics and therapeutic tools for a personalized care of MS patients.
Collapse
Affiliation(s)
- Galina Y Zheleznyakova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Marabita
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
176
|
Caregiver maltreatment causes altered neuronal DNA methylation in female rodents. Dev Psychopathol 2017; 29:477-489. [PMID: 28401839 DOI: 10.1017/s0954579417000128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Negative experiences with a caregiver during infancy can result in long-term changes in brain function and behavior, but underlying mechanisms are not well understood. It is our central hypothesis that brain and behavior changes are conferred by early childhood adversity through epigenetic changes involving DNA methylation. Using a rodent model of early-life caregiver maltreatment (involving exposure to an adverse caregiving environment for postnatal days 1-7), we have previously demonstrated abnormal methylation of DNA associated with the brain-derived neurotrophic factor (Bdnf) gene in the medial prefrontal cortex (mPFC) of adult rats. The aim of the current study was to characterize Bdnf DNA methylation in specific cell populations within the mPFC. In the prefrontal cortex, there is approximately twice as many neurons as glia, and studies have recently shown differential and distinctive DNA methylation patterns in neurons versus nonneurons. Here, we extracted nuclei from the mPFC of adult animals that had experienced maltreatment and used fluorescence-activated cell sorting to isolate cell types before performing bisulfite sequencing to estimate methylation of cytosine-guanine sites. Our data indicate that early-life stress induced methylation of DNA associated with Bdnf IV in a cell-type and sex-specific manner. Specifically, females that experienced early-life maltreatment exhibited greater neuronal cytosine-guanine methylation compared to controls, while no changes were detected in Bdnf methylation in males regardless of cell type. These changes localize the specificity of our previous findings to mPFC neurons and highlight the capacity of maltreatment to cause methylation changes that are likely to have functional consequences for neuronal function.
Collapse
|
177
|
Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes (Basel) 2017; 8:genes8060152. [PMID: 28556790 PMCID: PMC5485516 DOI: 10.3390/genes8060152] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/21/2017] [Accepted: 05/25/2017] [Indexed: 12/30/2022] Open
Abstract
We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from control subjects who did not abuse illicit drugs and died of non-suicide causes (N = 28). We identified 1298 differentially methylated CpG sites (DMSs) between heroin users and controls, and 454 DMSs between suicide completers and controls (p < 0.001). DMSs and corresponding genes (DMGs) in heroin users showed significant differences in the preferential context of hyper and hypo DM. HyperDMSs were enriched in gene bodies and exons but depleted in promoters, whereas hypoDMSs were enriched in promoters and enhancers. In addition, hyperDMGs showed preference for genes expressed specifically by glutamatergic as opposed to GABAergic neurons and enrichment for axonogenesis- and synaptic-related gene ontology categories, whereas hypoDMGs were enriched for transcription factor activity- and gene expression regulation-related terms. Finally, we found that the DNAm-based “epigenetic age” of neurons from heroin users was younger than that in controls. Suicide-related results were more difficult to interpret. Collectively, these findings suggest that the observed DNAm differences could represent functionally significant marks of heroin-associated plasticity in the OFC.
Collapse
Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.
- Department of Biostatistics and Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | | | - Pasha Apontes
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
| | | | - Mihaela Barbu
- Hospital for Special Surgery, New York, NY 10021, USA.
| | - William Byne
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Yasmin L Hurd
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
- Department of Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
178
|
Genetic architecture of epigenetic and neuronal ageing rates in human brain regions. Nat Commun 2017; 8:15353. [PMID: 28516910 PMCID: PMC5454371 DOI: 10.1038/ncomms15353] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 03/23/2017] [Indexed: 12/21/2022] Open
Abstract
Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neurons. Locus 17q11.2 is significantly associated (P=4.5 × 10−9) with the ageing rate across five brain regions and harbours a cis-expression quantitative trait locus for EFCAB5 (P=3.4 × 10−20). Locus 1p36.12 is significantly associated (P=2.2 × 10−8) with epigenetic ageing of the prefrontal cortex, independent of the proportion of neurons. Our GWAS of the proportion of neurons identified two genome-wide significant loci (10q26 and 12p13.31) and resulted in a gene set that overlaps significantly with sets found by GWAS of age-related macular degeneration (P=1.4 × 10−12), ulcerative colitis (P<1.0 × 10−20), type 2 diabetes (P=2.8 × 10−13), hip/waist circumference in men (P=1.1 × 10−9), schizophrenia (P=1.6 × 10−9), cognitive decline (P=5.3 × 10−4) and Parkinson's disease (P=8.6 × 10−3). Studies on the ‘epigenetic clock', a recently identified ageing biomarker, suggest that pathology might be linked to tissue-specific accelerated ageing. Here, the authors investigate ageing in the human brain and identify genetic loci associated with accelerated ageing in different brain regions.
Collapse
|
179
|
Abstract
Alzheimer’s disease (AD) is a fatal neurodegenerative disease which is on the rise worldwide. Despite a wealth of information, genetic factors contributing to the emergence of AD still remain incompletely understood. Sporadic AD is polygenetic in nature and is associated with various environmental risks. Epigenetic mechanisms are well-recognized in the mediation of gene environment interactions, and analysis of epigenetic changes at the genome scale can offer new insights into the relationship between brain epigenomes and AD. In fact, recent epigenome-wide association studies (EWAS) indicate that changes in DNA methylation are an early event preceding clinical manifestation and are tightly associated with AD neuropathology. Further, candidate genes from EWAS interact with those from genome-wide association studies (GWAS) that can undergo epigenetic changes in their upstream gene regulatory elements. Functionally, AD-associated DNA methylation changes partially influence transcription of candidate genes involved in pathways relevant to AD. The timing of epigenomic changes in AD together with the genes affected indicate a critical role, however, further mechanistic insight is required to corroborate this hypothesis. In this respect, recent advances in neuronal reprogramming of patient-derived cells combined with new genome-editing techniques offer unprecedented opportunities to dissect the functional and mechanistic role of epigenomic changes in AD.
Collapse
|
180
|
McEwen LM, Morin AM, Edgar RD, MacIsaac JL, Jones MJ, Dow WH, Rosero-Bixby L, Kobor MS, Rehkopf DH. Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region. Epigenetics Chromatin 2017; 10:21. [PMID: 28465725 PMCID: PMC5408416 DOI: 10.1186/s13072-017-0128-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
Background The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population’s unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. Methods In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya (n = 48) and non-Nicoya (other Costa Rican regions, n = 47) using the Infinium HumanMethylation450 microarray. Results We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. Conclusions Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0128-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Alexander M Morin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - William H Dow
- School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Luis Rosero-Bixby
- Centro Centroamericano de Población, Universidad de Costa Rica, San José, Costa Rica
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - David H Rehkopf
- Division of General Medical Disciplines, Department of Medicine, School of Medicine, Stanford University, 1070 Arastradero Road, Suite 300, Palo Alto, CA 94304 USA
| |
Collapse
|
181
|
Johnson ND, Wiener HW, Smith AK, Nishitani S, Absher DM, Arnett DK, Aslibekyan S, Conneely KN. Non-linear patterns in age-related DNA methylation may reflect CD4 + T cell differentiation. Epigenetics 2017; 12:492-503. [PMID: 28387568 DOI: 10.1080/15592294.2017.1314419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA methylation (DNAm) is an important epigenetic process involved in the regulation of gene expression. While many studies have identified thousands of loci associated with age, few have differentiated between linear and non-linear DNAm trends with age. Non-linear trends could indicate early- or late-life gene regulatory processes. Using data from the Illumina 450K array on 336 human peripheral blood samples, we identified 21 CpG sites that associated with age (P<1.03E-7) and exhibited changing rates of DNAm change with age (P<1.94E-6). For 2 of these CpG sites (cg07955995 and cg22285878), DNAm increased with age at an increasing rate, indicating that differential DNAm was greatest among elderly individuals. We observed significant replication for both CpG sites (P<5.0E-8) in a second set of peripheral blood samples. In 8 of 9 additional data sets comprising samples of monocytes, T cell subtypes, and brain tissue, we observed a pattern directionally consistent with DNAm increasing with age at an increasing rate, which was nominally significant in the 3 largest data sets (4.3E-15<P<0.039). cg07955995 and cg22285878 reside in the promoter region of KLF14, which encodes a protein involved in immune cell differentiation via the repression of FOXP3. These findings may suggest a possible role for cg07955995 and cg22285878 in immunosenescence.
Collapse
Affiliation(s)
| | - Howard W Wiener
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Alicia K Smith
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Shota Nishitani
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Devin M Absher
- e HudsonAlpha Institute for Biotechnology , Huntsville , AL , USA
| | - Donna K Arnett
- f College of Public Health , University of Kentucky , Lexington , KY , USA
| | - Stella Aslibekyan
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Karen N Conneely
- a Department of Human Genetics , Emory University , Atlanta , GA , USA
| |
Collapse
|
182
|
Histone Acetylome-wide Association Study of Autism Spectrum Disorder. Cell 2017; 167:1385-1397.e11. [PMID: 27863250 DOI: 10.1016/j.cell.2016.10.031] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023]
Abstract
The association of histone modification changes with autism spectrum disorder (ASD) has not been systematically examined. We conducted a histone acetylome-wide association study (HAWAS) by performing H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) on 257 postmortem samples from ASD and matched control brains. Despite etiological heterogeneity, ≥68% of syndromic and idiopathic ASD cases shared a common acetylome signature at >5,000 cis-regulatory elements in prefrontal and temporal cortex. Similarly, multiple genes associated with rare genetic mutations in ASD showed common "epimutations." Acetylome aberrations in ASD were not attributable to genetic differentiation at cis-SNPs and highlighted genes involved in synaptic transmission, ion transport, epilepsy, behavioral abnormality, chemokinesis, histone deacetylation, and immunity. By correlating histone acetylation with genotype, we discovered >2,000 histone acetylation quantitative trait loci (haQTLs) in human brain regions, including four candidate causal variants for psychiatric diseases. Due to the relative stability of histone modifications postmortem, we anticipate that the HAWAS approach will be applicable to multiple diseases.
Collapse
|
183
|
Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol 2017. [PMID: 28340624 DOI: 10.1186/s13059-017-1182-6.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.
Collapse
Affiliation(s)
- Pavlo Lutsik
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123, Germany.,Present address: Division of Cancer Epigenetics, German Cancer Research Center, Im Neuenheimerfeld 280, Heidelberg, 69120, Germany
| | - Martin Slawski
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany.,Department of Statistics and Biostatistics, Department of Computer Science, Rutgers University, 110 Frelinghuysen Rd, Piscataway, 08854, NJ, USA.,Present address: Department of Statistics, Volgenau School of Engineering, George Mason University, 4400 University Drive, MS 4A7 Fairfax, Fairfax, VA 22030-4444, USA
| | - Gilles Gasparoni
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123, Germany
| | - Nikita Vedeneev
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany
| | - Matthias Hein
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany.
| | - Jörn Walter
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123, Germany.
| |
Collapse
|
184
|
Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol 2017; 18:55. [PMID: 28340624 PMCID: PMC5366155 DOI: 10.1186/s13059-017-1182-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/23/2017] [Indexed: 01/08/2023] Open
Abstract
It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.
Collapse
Affiliation(s)
- Pavlo Lutsik
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123 Germany
- Present address: Division of Cancer Epigenetics, German Cancer Research Center, Im Neuenheimerfeld 280, Heidelberg, 69120 Germany
| | - Martin Slawski
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany
- Department of Statistics and Biostatistics, Department of Computer Science, Rutgers University, 110 Frelinghuysen Rd, Piscataway, 08854 NJ USA
- Present address: Department of Statistics, Volgenau School of Engineering, George Mason University, 4400 University Drive, MS 4A7 Fairfax, Fairfax, VA 22030-4444 USA
| | - Gilles Gasparoni
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123 Germany
| | - Nikita Vedeneev
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany
| | - Matthias Hein
- Machine Learning Group, Saarland University, Campus E1.1, Saarbrücken66123, Germany
| | - Jörn Walter
- Department of EpiGenetics, Saarland University, Campus A2.4, Saarbrücken, 66123 Germany
| |
Collapse
|
185
|
Teschendorff AE, Zheng SC. Cell-type deconvolution in epigenome-wide association studies: a review and recommendations. Epigenomics 2017; 9:757-768. [PMID: 28517979 DOI: 10.2217/epi-2016-0153] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A major challenge faced by epigenome-wide association studies (EWAS) is cell-type heterogeneity. As many EWAS have already demonstrated, adjusting for changes in cell-type composition can be critical when analyzing and interpreting findings from such studies. Because of their importance, a great number of different statistical algorithms, which adjust for cell-type composition, have been proposed. Some of the methods are 'reference based' in that they require a priori defined reference DNA methylation profiles of cell types that are present in the tissue of interest, while other algorithms are 'reference free.' At present, however, it is unclear how best to adjust for cell-type heterogeneity, as this may also largely depend on the type of tissue and phenotype being considered. Here, we provide a critical review of the major existing algorithms for correcting cell-type composition in the context of Illumina Infinium Methylation Beadarrays, with the aim of providing useful recommendations to the EWAS community.
Collapse
Affiliation(s)
- Andrew E Teschendorff
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Women's Cancer, University College London, 74 Huntley Street, London WC1E 6AU, UK.,Statistical Cancer Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Shijie C Zheng
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
186
|
Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation. Acta Neuropathol 2017; 133:485-487. [PMID: 28097436 DOI: 10.1007/s00401-017-1675-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
|
187
|
Recent Progress in Functional Genomic Studies of Depression and Suicide. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
188
|
Sanchez-Mut JV, Heyn H, Vidal E, Delgado-Morales R, Moran S, Sayols S, Sandoval J, Ferrer I, Esteller M, Gräff J. Whole genome grey and white matter DNA methylation profiles in dorsolateral prefrontal cortex. Synapse 2017; 71. [PMID: 28105729 DOI: 10.1002/syn.21959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 12/11/2022]
Abstract
The brain's neocortex is anatomically organized into grey and white matter, which are mainly composed by neuronal and glial cells, respectively. The neocortex can be further divided in different Brodmann areas according to their cytoarchitectural organization, which are associated with distinct cortical functions. There is increasing evidence that brain development and function are governed by epigenetic processes, yet their contribution to the functional organization of the neocortex remains incompletely understood. Herein, we determined the DNA methylation patterns of grey and white matter of dorsolateral prefrontal cortex (Brodmann area 9), an important region for higher cognitive skills that is particularly affected in various neurological diseases. For avoiding interindividual differences, we analyzed white and grey matter from the same donor using whole genome bisulfite sequencing, and for validating their biological significance, we used Infinium HumanMethylation450 BeadChip and pyrosequencing in ten and twenty independent samples, respectively. The combination of these analysis indicated robust grey-white matter differences in DNA methylation. What is more, cell type-specific markers were enriched among the most differentially methylated genes. Interestingly, we also found an outstanding number of grey-white matter differentially methylated genes that have previously been associated with Alzheimer's, Parkinson's, and Huntington's disease, as well as Multiple and Amyotrophic lateral sclerosis. The data presented here thus constitute an important resource for future studies not only to gain insight into brain regional as well as grey and white matter differences, but also to unmask epigenetic alterations that might underlie neurological and neurodegenerative diseases.
Collapse
Affiliation(s)
- Jose Vicente Sanchez-Mut
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Brain Mind Institute, Lausanne, CH-1015, Switzerland
| | - Holger Heyn
- Single Cell Genomics Unit, Centre Nacional d'Anàlisi Genòmica, Barcelona, Catalonia, E-08028, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona E-08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raúl Delgado-Morales
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, Maastricht, MD 6200, The Netherlands
| | - Sebastian Moran
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain
| | - Sergi Sayols
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, D-55128, Germany
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Valencia, 46026, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Centre for Biomedical Research on Neurodegenerative Diseases (CIBERNED), E-08908 Hospitalet de Llobregat, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain
| | - Johannes Gräff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Brain Mind Institute, Lausanne, CH-1015, Switzerland
| |
Collapse
|
189
|
Iatrou A, Kenis G, Rutten BPF, Lunnon K, van den Hove DLA. Epigenetic dysregulation of brainstem nuclei in the pathogenesis of Alzheimer's disease: looking in the correct place at the right time? Cell Mol Life Sci 2017; 74:509-523. [PMID: 27628303 PMCID: PMC5241349 DOI: 10.1007/s00018-016-2361-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022]
Abstract
Even though the etiology of Alzheimer's disease (AD) remains unknown, it is suggested that an interplay among genetic, epigenetic and environmental factors is involved. An increasing body of evidence pinpoints that dysregulation in the epigenetic machinery plays a role in AD. Recent developments in genomic technologies have allowed for high throughput interrogation of the epigenome, and epigenome-wide association studies have already identified unique epigenetic signatures for AD in the cortex. Considerable evidence suggests that early dysregulation in the brainstem, more specifically in the raphe nuclei and the locus coeruleus, accounts for the most incipient, non-cognitive symptomatology, indicating a potential causal relationship with the pathogenesis of AD. Here we review the advancements in epigenomic technologies and their application to the AD research field, particularly with relevance to the brainstem. In this respect, we propose the assessment of epigenetic signatures in the brainstem as the cornerstone of interrogating causality in AD. Understanding how epigenetic dysregulation in the brainstem contributes to AD susceptibility could be of pivotal importance for understanding the etiology of the disease and for the development of novel diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- A Iatrou
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - G Kenis
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - B P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - K Lunnon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - D L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands.
- Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080, Würzburg, Germany.
| |
Collapse
|
190
|
McKinney B, Ding Y, Lewis DA, Sweet RA. DNA methylation as a putative mechanism for reduced dendritic spine density in the superior temporal gyrus of subjects with schizophrenia. Transl Psychiatry 2017; 7:e1032. [PMID: 28195572 PMCID: PMC5438028 DOI: 10.1038/tp.2016.297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/13/2016] [Indexed: 01/11/2023] Open
Abstract
Reduced dendritic spine density (DSD) in cortical layer 3 of the superior temporal gyrus (STG), and multiple other brain regions, is consistently observed in postmortem studies of schizophrenia (SZ). Elucidating the molecular mechanisms of this intermediate phenotype holds promise for understanding SZ pathophysiology, identifying SZ treatment targets and developing animal models. DNA methylation (DNAm), the addition of a methyl group to a cytosine nucleotide, regulates gene transcription and is a strong candidate for such a mechanism. We tested the hypothesis that DNAm correlates with DSD in the human STG and that this relationship is disrupted in SZ. We used the Illumina Infinium HumanMethylation450 Beadchip Array to quantify DNAm on a genome-wide scale in the postmortem STG from 22 SZ subjects and matched non-psychiatric control (NPC) subjects; DSD measures were available for 17 of the 22 subject pairs. We found DNAm to correlate with DSD at more sites than expected by chance in NPC, but not SZ, subjects. In addition, we show that the slopes of the linear DNAm-DSD correlations differed between SZ and NPC subjects at more sites than expected by chance. From these data, we identified 2 candidate genes for mediating DSD abnormalities in SZ: brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2) and discs large, Drosophila, homolog of, 1 (DLG1). Together, these data suggest that altered DNAm in SZ may be a mechanism for SZ-related DSD reductions.
Collapse
Affiliation(s)
- B McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - D A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA,Mental Illness Research, Education, and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA,Department of Psychiatry, Neurology and VISN 4 Mental Illness Research, Education and Clinical Center (MIRECC), Biomedical Science Tower, Room W-1645, 3811 O'Hara Street, Pittsburgh, PA 15213, USA. E-mail:
| |
Collapse
|
191
|
Chatterton Z, Hartley BJ, Seok MH, Mendelev N, Chen S, Milekic M, Rosoklija G, Stankov A, Trencevsja-Ivanovska I, Brennand K, Ge Y, Dwork AJ, Haghighi F. In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain. Epigenetics Chromatin 2017; 10:4. [PMID: 28149327 PMCID: PMC5270321 DOI: 10.1186/s13072-017-0111-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of cortical gray matter in childhood, indicating that prenatal exposure to tobacco may impact cortical development and manifest as behavioral problems. Cellular development is mediated by changes in epigenetic modifications such as DNA methylation, which can be affected by exposure to tobacco. Results In this study, we sought to ascertain how maternal smoking during pregnancy affects global DNA methylation profiles of the developing dorsolateral prefrontal cortex (DLPFC) during the second trimester of gestation. When DLPFC methylation profiles (assayed via Illumina, HM450) of smoking-exposed and unexposed fetuses were compared, no differentially methylated regions (DMRs) passed the false discovery correction (FDR ≤ 0.05). However, the most significant DMRs were hypomethylated CpG Islands within the promoter regions of GNA15 and SDHAP3 of smoking-exposed fetuses. Interestingly, the developmental up-regulation of SDHAP3 mRNA was delayed in smoking-exposed fetuses. Interaction analysis between gestational age and smoking exposure identified significant DMRs annotated to SYCE3, C21orf56/LSS, SPAG1 and RNU12/POLDIP3 that passed FDR. Furthermore, utilizing established methods to estimate cell proportions by DNA methylation, we found that exposed DLPFC samples contained a lower proportion of neurons in samples from fetuses exposed to maternal smoking. We also show through in vitro experiments that nicotine impedes the differentiation of neurons independent of cell death. Conclusions We found evidence that intrauterine smoking exposure alters the developmental patterning of DNA methylation and gene expression and is associated with reduced mature neuronal content, effects that are likely driven by nicotine. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0111-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zac Chatterton
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Brigham J Hartley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Man-Ho Seok
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Natalia Mendelev
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Sean Chen
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Maria Milekic
- Department of Psychiatry, Columbia University, New York, NY 10032 USA
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia.,School of Medicine, Skopje, Macedonia
| | | | | | - Kristen Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Fatemeh Haghighi
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| |
Collapse
|
192
|
A genome-wide profiling of brain DNA hydroxymethylation in Alzheimer's disease. Alzheimers Dement 2017; 13:674-688. [PMID: 28089213 DOI: 10.1016/j.jalz.2016.10.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 01/13/2023]
Abstract
INTRODUCTION DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology. RESULTS We identified 517 DhMRs significantly associated with neuritic plaques and 60 DhMRs associated with neurofibrillary tangles. DNA hydroxymethylation in gene bodies was predominantly positively correlated with cis-acting gene expression. Moreover, genes showing differential hydroxymethylation were significantly enriched in neurobiological processes and clustered in functional gene ontology categories. DISCUSSION Our results reveal a critical role of DNA hydroxymethylation in AD pathology and provide mechanistic insight into the molecular mechanisms underlying AD.
Collapse
|
193
|
Abstract
Schizophrenia is a highly heritable psychiatric condition that displays a complex phenotype. A multitude of genetic susceptibility loci have now been identified, but these fail to explain the high heritability estimates of schizophrenia. In addition, epidemiologically relevant environmental risk factors for schizophrenia may lead to permanent changes in brain function. In conjunction with genetic liability, these environmental risk factors-likely through epigenetic mechanisms-may give rise to schizophrenia, a clinical syndrome characterized by florid psychotic symptoms and moderate to severe cognitive impairment. These pathophysiological features point to the involvement of epigenetic processes. Recently, a wave of studies examining aberrant DNA modifications in schizophrenia was published. This chapter aims to comprehensively review the current findings, from both candidate gene studies and genome-wide approaches, on DNA methylation changes in schizophrenia.
Collapse
|
194
|
Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide. Transl Psychiatry 2017; 7:e989. [PMID: 28045465 PMCID: PMC5545719 DOI: 10.1038/tp.2016.249] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/16/2016] [Indexed: 02/06/2023] Open
Abstract
Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25)). Analyses focused on identifying differentially methylated regions (DMRs) associated with suicidal depression and epigenetic variation were explored in the context of polygenic risk scores for major depression and suicide. Weighted gene co-methylation network analysis was used to identify modules of co-methylated loci associated with depressed suicide completers and polygenic burden for MDD and suicide attempt. We identified a DMR upstream of the PSORS1C3 gene, subsequently validated using bisulfite pyrosequencing and replicated in a second set of suicide samples, which is characterised by significant hypomethylation in both cortical brain regions in MDD suicide cases. We also identified discrete modules of co-methylated loci associated with polygenic risk burden for suicide attempt, but not major depression. Suicide-associated co-methylation modules were enriched among gene networks implicating biological processes relevant to depression and suicidality, including nervous system development and mitochondria function. Our data suggest that there are coordinated changes in DNA methylation associated with suicide that may offer novel insights into the molecular pathology associated with depressed suicide completers.
Collapse
|
195
|
Smith RG, Lunnon K. DNA Modifications and Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:303-319. [PMID: 28523553 DOI: 10.1007/978-3-319-53889-1_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting millions of people worldwide. While a number of studies have focused on identifying genetic variants that contribute to the development and progression of late-onset AD, the majority of these only have a relatively small effect size. There are also a number of other risk factors, for example, age, gender, and other comorbidities; however, how these influence disease risk is not known. Therefore, in recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we discuss the current state of play for research into DNA modifications in AD, the most well studied being 5-methylcytosine (5-mC). We describe the earlier studies of candidate genes and global measures of DNA modifications in human AD samples, in addition to studies in mouse models of AD. We focus on recent epigenome-wide association studies (EWAS) in human AD, using microarray technology, examining a number of key study design issues pertinent to such studies. Finally, we discuss how new technological advances could further progress the research field.
Collapse
Affiliation(s)
- Rebecca G Smith
- University of Exeter Medical School, RILD, Barrack Road, Exeter, Devon, UK
| | - Katie Lunnon
- University of Exeter Medical School, RILD, Barrack Road, Exeter, Devon, UK.
| |
Collapse
|
196
|
The Future is The Past: Methylation QTLs in Schizophrenia. Genes (Basel) 2016; 7:genes7120104. [PMID: 27886132 PMCID: PMC5192480 DOI: 10.3390/genes7120104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have remarkably advanced insight into the genetic basis of schizophrenia (SCZ). Still, most of the functional variance in disease risk remains unexplained. Hence, there is a growing need to map genetic variability-to-genes-to-functions for understanding the pathophysiology of SCZ and the development of better treatments. Genetic variation can regulate various cellular functions including DNA methylation, an epigenetic mark with important roles in transcription and the mediation of environmental influences. Methylation quantitative trait loci (meQTLs) are derived by mapping levels of DNA methylation in genetically different, genotyped individuals and define loci at which DNA methylation is influenced by genetic variation. Recent evidence points to an abundance of meQTLs in brain tissues whose functional contributions to development and mental diseases are still poorly understood. Interestingly, fetal meQTLs reside in regulatory domains affecting methylome reconfiguration during early brain development and are enriched in loci identified by GWAS for SCZ. Moreover, fetal meQTLs are preserved in the adult brain and could trace early epigenomic deregulation during vulnerable periods. Overall, these findings highlight the role of fetal meQTLs in the genetic risk for and in the possible neurodevelopmental origin of SCZ.
Collapse
|
197
|
An integrative review of methylation at the serotonin transporter gene and its dialogue with environmental risk factors, psychopathology and 5-HTTLPR. Neurosci Biobehav Rev 2016; 72:190-209. [PMID: 27880876 DOI: 10.1016/j.neubiorev.2016.11.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/04/2016] [Accepted: 11/06/2016] [Indexed: 11/24/2022]
Abstract
Gene-environment (G×E) interactions have largely been regarded as the root of many complex disorders, including several psychiatric disorders. In this regard, it has been hypothesized that epigenetic mechanisms may be the main mediators of such interactions. Of particular interest is the previously described interaction between psychosocial stress and genetic variability of the serotonin transporter gene (SLC6A4) in its polymorphic region 5-HTTLPR. Here we review the literature concerning SLC6A4 methylation in association with environmental, clinical or genetic variables. While SLC6A4 hypermethylation has typically been described to be independently associated with both early life stress and depressive disorders, only a few papers address whether methylation could mediate the interaction between stress and 5-HTTLPR in predicting psychopathological risk. Nevertheless, research preliminarily indicates a methylation-driven increased vulnerability of carriers of the short allele of 5-HTTLPR to psychiatric disorders when exposed to early stress or soon after exposure to stress.
Collapse
|
198
|
Li M, Weinberger DR. RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
Collapse
Affiliation(s)
- Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
| |
Collapse
|
199
|
Klein HU, Bennett DA, De Jager PL. The epigenome in Alzheimer's disease: current state and approaches for a new path to gene discovery and understanding disease mechanism. Acta Neuropathol 2016; 132:503-14. [PMID: 27573688 DOI: 10.1007/s00401-016-1612-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/14/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023]
Abstract
The advent of new technologies and analytic approaches is beginning to provide an unprecedented look at features of the human genome that affect RNA expression. These "epigenomic" features are found in a number of different forms: they include DNA methylation, covalent modifications of histone proteins and non-coding RNAs. Some of these features have now been implicated in Alzheimer's disease (AD). Here, we focus on recent studies that have identified robust observations relating to DNA methylation and chromatin in human brain tissue; these findings will ground the next generation of studies and provide a model for the design of such studies. Stemming from observations that compounds with histone deacetylase activity may be beneficial in AD, epigenome-wide studies in cortical samples from large numbers of human subjects have now shown that AD-associated epigenomic changes are reproducible, are not driven by genetic risk factors, and are widespread at specific locations in the genome. A fundamental question of whether such changes are causal remains to be demonstrated, but it is already clear that well-powered investigations of the human epigenome in the target organ of a neurodegenerative disease are feasible, are implicating new areas of the genome in the disease, and will be an important tool for future studies. We are now at an inflection point: as genome-wide association studies of genetic variants come to an end, a new generation of studies exploring the epigenome will provide an important new layer of information with which to enrich our understanding of AD pathogenesis and to possibly guide development of new therapeutic targets.
Collapse
Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
200
|
Corley MJ, Dye C, D'Antoni ML, Byron MM, Yo KLA, Lum-Jones A, Nakamoto B, Valcour V, SahBandar I, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment. Sci Rep 2016; 6:33310. [PMID: 27629381 PMCID: PMC5024304 DOI: 10.1038/srep33310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022] Open
Abstract
Monocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
Collapse
Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Christian Dye
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Michelle L D'Antoni
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Mary Margaret Byron
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Kaahukane Leite-Ah Yo
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Beau Nakamoto
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ivo SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Cecilia M Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA.,Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| |
Collapse
|