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Choi YJ, Cho J, Hong YC, Lee DW, Moon S, Park SJ, Lee KS, Shin CH, Lee YA, Kim BN, Kaminsky Z, Kim JI, Lim YH. DNA methylation is associated with prenatal exposure to sulfur dioxide and childhood attention-deficit hyperactivity disorder symptoms. Sci Rep 2023; 13:3501. [PMID: 36859453 PMCID: PMC9977725 DOI: 10.1038/s41598-023-29843-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
Epigenetic influence plays a role in the association between exposure to air pollution and attention deficit hyperactivity disorder (ADHD); however, research regarding sulfur dioxide (SO2) is scarce. Herein, we investigate the associations between prenatal SO2 exposure and ADHD rating scale (ARS) at ages 4, 6 and 8 years repeatedly in a mother-child cohort (n = 329). Whole blood samples were obtained at ages 2 and 6 years, and genome-wide DNA methylation (DNAm) was analyzed for 51 children using the Illumina Infinium HumanMethylation BeadChip. We analyzed the associations between prenatal SO2 exposure and DNAm levels at ages 2 and 6, and further investigated the association between the DNAm and ARS at ages 4, 6 and 8. Prenatal SO2 exposure was associated with ADHD symptoms. From candidate gene analysis, DNAm levels at the 6 CpGs at age 2 were associated with prenatal SO2 exposure levels. Of the 6 CpGs, cg07583420 (INS-IGF2) was persistently linked with ARS at ages 4, 6 and 8. Epigenome-wide analysis showed that DNAm at 6733 CpG sites were associated with prenatal SO2 exposure, of which 58 CpGs involved in Notch signalling pathway were further associated with ARS at age 4, 6 and 8 years, persistently. DNAm at age 6 was not associated with prenatal SO2 exposure. Changes in DNAm levels associated with prenatal SO2 exposure during early childhood are associated with increases in ARS in later childhood.
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Affiliation(s)
- Yoon-Jung Choi
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jinwoo Cho
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Dong-Wook Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Healthcare Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sungji Moon
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo Jin Park
- Department of Surgery, Wonkwang University Sanbon Hospital, Gunpo, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Health Research Institute, National Medical Center, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Zachary Kaminsky
- Institute of Mental Health Research, University of Ottawa, Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Section of Environmental Epidemiology, Department of Public Health, University of Copenhagen, Østerster Farimagsgade 5, 1014, København K, Copenhagen, Denmark.
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Robillard R, Daros AR, Phillips JL, Porteous M, Saad M, Pennestri MH, Kendzerska T, Edwards JD, Solomonova E, Bhatla R, Godbout R, Kaminsky Z, Boafo A, Quilty LC. Emerging New Psychiatric Symptoms and the Worsening of Pre-existing Mental Disorders during the COVID-19 Pandemic: A Canadian Multisite Study: Nouveaux symptômes psychiatriques émergents et détérioration des troubles mentaux préexistants durant la pandémie de la COVID-19: une étude canadienne multisite. Can J Psychiatry 2021; 66:815-826. [PMID: 33464115 PMCID: PMC8504288 DOI: 10.1177/0706743720986786] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has caused global disruptions with serious psychological impacts. This study investigated the emergence of new psychiatric symptoms and the worsening of pre-existing mental disorders during the COVID-19 pandemic, identified factors associated with psychological worsening, and assessed changes in mental health service use. METHODS An online survey was circulated between April 3 and June 23, 2020. Respondents were asked to complete mental health questionnaires based on 2 time referents: currently (i.e., during the outbreak) and in the month preceding the outbreak. A total of 4,294 Canadians between 16 and 99 years of age were subdivided based on the presence of self-reported psychiatric diagnoses. RESULTS The proportion of respondents without prior psychiatric history who screened positive for generalized anxiety disorder and depression increased by 12% and 29%, respectively, during the outbreak. Occurrences of clinically important worsening in anxiety, depression, and suicidal ideation symptoms relative to pre-outbreak estimates were significantly higher in those with psychiatric diagnoses. Furthermore, 15% to 19% of respondents reported increased alcohol or cannabis use. Worse psychological changes relative to pre-outbreak estimate were associated with female sex, younger age, lower income, poorer coping skills, multiple psychiatric comorbidities, previous trauma exposure, deteriorating physical health, poorer family relationships, and lower exercising. Reductions in mental health care were associated with increased suicidal ideation. CONCLUSION The worsening in mental health symptoms and the decline in access to care call for the urgent development of adapted interventions targeting both new mental disorders and pre-existing psychiatric conditions affected by the COVID-19 pandemic.
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Affiliation(s)
- Rebecca Robillard
- The Royal’s Institute of Mental Health Research, Ottawa, Ontario, Canada
- School of Psychology, University of Ottawa, Ontario, Canada
| | | | - Jennifer L. Phillips
- The Royal’s Institute of Mental Health Research, Ottawa, Ontario, Canada
- Department of Psychiatry, University of Ottawa, Ontario, Canada
| | - Meggan Porteous
- The Royal’s Institute of Mental Health Research, Ottawa, Ontario, Canada
- School of Psychology, University of Ottawa, Ontario, Canada
| | - Mysa Saad
- The Royal’s Institute of Mental Health Research, Ottawa, Ontario, Canada
| | - Marie-Helene Pennestri
- Department of Educational and Counselling Psychology, McGill University, Montreal, Quebec, Canada
- Hopital en santé mentale Rivières-des-Prairies, CIUSSS du Nord-de-l’Ile-de-Montreal, Quebec, Canada
| | - Tetyana Kendzerska
- The Ottawa Hospital Research Institute, University of Ottawa, Ontario, Canada
| | - Jodi D. Edwards
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Elizaveta Solomonova
- Mind and Brain research group, Division of Social and Transcultural Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Rajiv Bhatla
- Department of Psychiatry, University of Ottawa, Ontario, Canada
- The Royal Ottawa Mental Health Centre, Ottawa, Ontario, Canada
| | - Roger Godbout
- Hopital en santé mentale Rivières-des-Prairies, CIUSSS du Nord-de-l’Ile-de-Montreal, Quebec, Canada
- Department of PSychiatry, Université de Montréal, Québec, Canada
| | - Zachary Kaminsky
- The Royal’s Institute of Mental Health Research, Ottawa, Ontario, Canada
| | - Addo Boafo
- The Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Lena C. Quilty
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Ontario, Canada
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3
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Policicchio S, Washer S, Viana J, Iatrou A, Burrage J, Hannon E, Turecki G, Kaminsky Z, Mill J, Dempster EL, Murphy TM. Genome-wide DNA methylation meta-analysis in the brains of suicide completers. Transl Psychiatry 2020; 10:69. [PMID: 32075955 PMCID: PMC7031296 DOI: 10.1038/s41398-020-0752-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
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Affiliation(s)
- Stefania Policicchio
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Sam Washer
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana Viana
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Artemis Iatrou
- grid.240684.c0000 0001 0705 3621Rush Alzheimer’s Neurodisease Center, Rush University Medical Center, 600 South Paulina Street, Chicago, IL 60612 USA
| | - Joe Burrage
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gustavo Turecki
- grid.14709.3b0000 0004 1936 8649Douglas Institute, Department of Psychiatry, McGill University, Verdun, QC H4H 1R3 Canada
| | - Zachary Kaminsky
- grid.21107.350000 0001 2171 9311Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L. Dempster
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Therese M. Murphy
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK ,grid.497880.aSchool of Biological and Health Sciences, Technological University Dublin, City Campus, Dublin, 2 Ireland
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Kimmel M, Clive M, Gispen F, Guintivano J, Brown T, Cox O, Beckmann MW, Kornhuber J, Fasching PA, Osborne LM, Binder E, Payne JL, Kaminsky Z. Oxytocin receptor DNA methylation in postpartum depression. Psychoneuroendocrinology 2016; 69:150-60. [PMID: 27108164 PMCID: PMC7152506 DOI: 10.1016/j.psyneuen.2016.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/07/2023]
Abstract
The oxytocin receptor (OXTR) is a key regulator of stress and anxiety and may be regulated by both psychosocial risk factors and gonadal hormones, making it an attractive candidate for study in postpartum depression (PPD). The objective of this study was to investigate both serum hormone and PPD specific DNA methylation variation in the OXTR. Illumina HM450 microarray data generated in a prospective PPD cohort identified significant associations (P=0.014) with PPD in an intronic region in the OXTR located 4bp proximal to an estrogen receptor (ER) binding region. Pyrosequencing confirmed moderate evidence for an interaction of CpGs in the region with childhood abuse status to mediate PPD. These CpGs located on chr3 at positions 8810078 and 8810069 exhibited significant associations with postpartum depression scores from an independent cohort of 240 women with no prior psychiatric history. Hormone analysis suggested a PPD specific negative correlation of DNA methylation in the region with serum estradiol levels. Estradiol levels and OXTR DNA methylation exhibited a significant interaction to associate with the ratio of allopregnanolone to progesterone. Cumulatively, the data corroborate our previous hypotheses of a PPD specific increased sensitivity of epigenetic reprogramming at estrogen target genes and suggests that OXTR epigenetic variation may be an important mediator of mood relevant neuroactive steroid production.
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Affiliation(s)
- Mary Kimmel
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA,Department of Psychiatry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Makena Clive
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Fiona Gispen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jerry Guintivano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tori Brown
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Olivia Cox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Lauren M. Osborne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Jennifer L. Payne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zachary Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA.
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5
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Osborne L, Clive M, Kimmel M, Gispen F, Guintivano J, Brown T, Cox O, Judy J, Meilman S, Braier A, Beckmann MW, Kornhuber J, Fasching PA, Goes F, Payne JL, Binder EB, Kaminsky Z. Replication of Epigenetic Postpartum Depression Biomarkers and Variation with Hormone Levels. Neuropsychopharmacology 2016; 41:1648-58. [PMID: 26503311 PMCID: PMC4832028 DOI: 10.1038/npp.2015.333] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/02/2015] [Accepted: 09/18/2015] [Indexed: 11/09/2022]
Abstract
DNA methylation variation at HP1BP3 and TTC9B is modified by estrogen exposure in the rodent hippocampus and was previously shown to be prospectively predictive of postpartum depression (PPD) when modeled in antenatal blood. The objective of this study was to replicate the predictive efficacy of the previously established model in women with and without a previous psychiatric diagnosis and to understand the effects of changing hormone levels on PPD biomarker loci. Using a statistical model trained on DNA methylation data from N=51 high-risk women, we prospectively predicted PPD status in an independent N=51 women using first trimester antenatal gene expression levels of HP1BP3 and TTC9B, with an area under the receiver operator characteristic curve (AUC) of 0.81 (95% CI: 0.69-0.92, p<5 × 10(-4)). Modeling DNA methylation of these genes in N=240 women without a previous psychiatric diagnosis resulted in a cross-sectional prediction of PPD status with an AUC of 0.81 (95% CI: 0.68-0.93, p=0.01). TTC9B and HP1BP3 DNA methylation at early antenatal time points showed moderate evidence for association to the change in estradiol and allopregnanolone over the course of pregnancy, suggesting that epigenetic variation at these loci may be important for mediating hormonal sensitivity. In addition both loci showed PPD-specific trajectories with age, possibly mediated by age-associated hormonal changes. The data add to the growing body of evidence suggesting that PPD is mediated by differential gene expression and epigenetic sensitivity to pregnancy hormones and that modeling proxies of this sensitivity enable accurate prediction of PPD.
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Affiliation(s)
- Lauren Osborne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Makena Clive
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary Kimmel
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fiona Gispen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jerry Guintivano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tori Brown
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olivia Cox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Judy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samantha Meilman
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aviva Braier
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Fernando Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer L Payne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Zachary Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA,The Mood Disorder Center, Johns Hopkins University, 720 Rutland Avenue, Ross Research Building 1070, Baltimore, MD 21205, USA, Tel: +1 443 287 0093, Fax: +1 410 502 0065,E-mail:
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6
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Affiliation(s)
- Mary Kimmel
- Johns Hopkins School of Medicine, Department of Psychiatry, 550 N Broadway, Suite 305, Baltimore, MD 21205, USA
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7
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Boks MP, Rutten BPF, Geuze E, Houtepen LC, Vermetten E, Kaminsky Z, Vinkers CH. SKA2 Methylation is Involved in Cortisol Stress Reactivity and Predicts the Development of Post-Traumatic Stress Disorder (PTSD) After Military Deployment. Neuropsychopharmacology 2016; 41:1350-6. [PMID: 26361058 PMCID: PMC4793119 DOI: 10.1038/npp.2015.286] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/18/2015] [Accepted: 08/28/2015] [Indexed: 02/04/2023]
Abstract
Genomic variation in the SKA2 gene has recently been identified as a promising suicide biomarker. In light of its role in glucocorticoid receptor transactivation, we investigated whether SKA2 DNA methylation influences cortisol stress reactivity and is involved in the development of post-traumatic stress disorder (PTSD). Increased SKA2 methylation was significantly associated with lower cortisol stress reactivity in 85 healthy individuals exposed to the Trier Social Stress Test (B=-173.40, t=-2.324, p-value=0.023). Next, we observed that longitudinal decreases in SKA2 methylation after deployment were associated with the emergence of post-deployment PTSD symptoms in a Dutch military cohort (N=93; B=-0.054, t=-3.706, p-value=3.66 × 10(-4)). In contrast, exposure to traumatic stress during deployment by itself resulted in longitudinal increases in SKA2 methylation (B=0.037, t=4.173, p-value=6.98 × 10(-5)). Using pre-deployment SKA2 methylation levels and childhood trauma exposure, we found that the previously published suicide prediction rule significantly predicted post-deployment PTSD symptoms (AUC=0.66, 95% CI: 0.53-0.79) with an optimal sensitivity of 0.81 and specificity of 0.91. Permutation analysis using random methylation loci supported these findings. Together, these data establish the importance of SKA2 for cortisol stress responsivity and the development of PTSD and provide further evidence that SKA2 is a promising biomarker for stress-related disorders including PTSD.
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Affiliation(s)
- Marco P Boks
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, HP. A.01.489, PO Box 85500, Utrecht, 3508 GA, The Netherlands, Tel: +31 88 7556370, Fax: +31 88 7555509, E-mail:
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Elbert Geuze
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands,Research Centre Military Mental Healthcare, Ministry of Defence, The Hague, The Netherlands
| | - Lotte C Houtepen
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Eric Vermetten
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands,Research Centre Military Mental Healthcare, Ministry of Defence, The Hague, The Netherlands,Department of Psychiatry, Leiden University Medical Center, Utrecht, The Netherlands,Arq Psychotrauma Expert Group, Diemen, The Netherlands
| | - Zachary Kaminsky
- Department of Psychiatry and Behavioral Sciences, The Mood Disorders Center, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christiaan H Vinkers
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands
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Kaminsky Z, Wilcox HC, Eaton WW, Van Eck K, Kilaru V, Jovanovic T, Klengel T, Bradley B, Binder EB, Ressler KJ, Smith AK. Epigenetic and genetic variation at SKA2 predict suicidal behavior and post-traumatic stress disorder. Transl Psychiatry 2015; 5:e627. [PMID: 26305478 PMCID: PMC4564560 DOI: 10.1038/tp.2015.105] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/14/2015] [Indexed: 11/09/2022] Open
Abstract
Traumatic stress results in hypothalamic pituitary adrenal (HPA) axis abnormalities and an increased risk to both suicidal behaviors and post-traumatic stress disorder (PTSD). Previous work out of our laboratory identified SKA2 DNA methylation associations with suicidal behavior in the blood and brain of multiple cohorts. Interaction of SKA2 with stress predicted suicidal behavior with ~80% accuracy. SKA2 is hypothesized to reduce the ability to suppress cortisol following stress, which is of potentially high relevance in traumatized populations. Our objective was to investigate the interaction of SKA2 and trauma exposure on HPA axis function, suicide attempt and PTSD. SKA2 DNA methylation at Illumina HM450 probe cg13989295 was assessed for association with suicidal behavior and PTSD metrics in the context of Child Trauma Questionnaire (CTQ) scores in 421 blood and 61 saliva samples from the Grady Trauma Project (GTP) cohort. Dexamethasone suppression test (DST) data were evaluated for a subset of 209 GTP subjects. SKA2 methylation interacted with CTQ scores to predict lifetime suicide attempt in saliva and blood with areas under the receiver operator characteristic curve (AUCs) of 0.76 and 0.73 (95% confidence interval (CI): 0.6-0.92, P = 0.003, and CI: 0.65-0.78, P < 0.0001) and to mediate the suppression of cortisol following DST (β = 0.5 ± 0.19, F = 1.51, degrees of freedom (df) = 12/167, P = 0.0096). Cumulatively, the data suggest that epigenetic variation at SKA2 mediates vulnerability to suicidal behaviors and PTSD through dysregulation of the HPA axis in response to stress.
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Affiliation(s)
- Z Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - H C Wilcox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - W W Eaton
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - K Van Eck
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - V Kilaru
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - T Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - T Klengel
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - B Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Mental Health Service Line, Department of Veterans Affairs Medical, Atlanta, GA, USA
| | - E B Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - K J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - A K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
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Vinkers CH, Kalafateli AL, Rutten BPF, Kas MJ, Kaminsky Z, Turner JD, Boks MPM. Traumatic stress and human DNA methylation: a critical review. Epigenomics 2015; 7:593-608. [DOI: 10.2217/epi.15.11] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Animal studies have identified persistent and functional effects of traumatic stress on the epigenome. This review discusses the clinical evidence for trauma-induced changes in DNA methylation across the life span in humans. Studies are reviewed based on reports of trauma exposure during the prenatal period (13 studies), early life (20 studies), and adulthood (ten studies). Even though it is apparent that traumatic stress influences the human epigenome, there are significant drawbacks in the existing human literature. These include a lack of longitudinal studies, methodological heterogeneity, selection of tissue type, and the influence of developmental stage and trauma type on methylation outcomes. These issues are discussed in order to present a way in which future studies can gain more insight into the functional relevance of trauma-related DNA methylation changes. Epigenetic studies investigating the detrimental effects of traumatic stress have great potential for an improved detection and treatment of trauma-related psychiatric disorders.
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Affiliation(s)
- Christiaan H Vinkers
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Aimilia Lydia Kalafateli
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, Utrecht, The Netherlands
- John B Pierce Laboratory, Department of Neurobiology, Yale Medical School, New Haven, CT 06519, USA
| | - Bart PF Rutten
- Department of Psychiatry & Neuropsychology, School for Mental Health & Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Martien J Kas
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, Utrecht, The Netherlands
| | - Zachary Kaminsky
- The Mood Disorders Center, Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, MD 21205, USA
| | - Jonathan D Turner
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Grand-Duchy of Luxembourg
| | - Marco PM Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
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10
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Kaminsky Z, Jones I, Verma R, Saleh L, Trivedi H, Guintivano J, Akman R, Zandi P, Lee RS, Potash JB. DNA methylation and expression of KCNQ3 in bipolar disorder. Bipolar Disord 2015; 17:150-9. [PMID: 25041603 DOI: 10.1111/bdi.12230] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/29/2014] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Accumulating evidence implicates the potassium voltage-gated channel, KQT-like subfamily, member 2 and 3 (KCNQ2 and KCNQ3) genes in the etiology of bipolar disorder (BPD). Reduced KCNQ2 or KCNQ3 gene expression might lead to a loss of inhibitory M-current and an increase in neuronal hyperexcitability in disease. The goal of the present study was to evaluate epigenetic and gene expression associations of the KCNQ2 and KCNQ3 genes with BPD. METHODS DNA methylation and gene expression levels of alternative transcripts of KCNQ2 and KCNQ3 capable of binding the ankyrin G (ANK3) gene were evaluated using bisulfite pyrosequencing and the quantitative real-time polymerase chain reaction in the postmortem prefrontal cortex of subjects with BPD and matched controls from the McLean Hospital. Replication analyses of DNA methylation findings were performed using prefrontal cortical DNA obtained from the Stanley Medical Research Institute. RESULTS Significantly lower expression was observed in KCNQ3, but not KCNQ2. DNA methylation analysis of CpGs within an alternative exonic region of KCNQ3 exon 11 demonstrated significantly lower methylation in BPD, and correlated significantly with KCNQ3 mRNA levels. Lower KCNQ3 exon 11 DNA methylation was observed in the Stanley Medical Research Institute replication cohort, although only after correcting for mood stabilizer status. Mood stabilizer treatment in rats resulted in a slight DNA methylation increase at the syntenic KCNQ3 exon 11 region, which subsequent analyses suggested could be the result of alterations in neuronal proportion. CONCLUSION The results of the present study suggest that epigenetic alterations in the KCNQ3 gene may be important in the etiopathogenesis of BPD and highlight the importance of controlling for medication and cellular composition-induced heterogeneity in psychiatric studies of the brain.
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Affiliation(s)
- Zachary Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
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11
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Lunnon K, Smith R, Hannon E, De Jager PL, Srivastava G, Volta M, Troakes C, Al-Sarraj S, Burrage J, Macdonald R, Condliffe D, Harries LW, Katsel P, Haroutunian V, Kaminsky Z, Joachim C, Powell J, Lovestone S, Bennett DA, Schalkwyk LC, Mill J. Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. Nat Neurosci 2014; 17:1164-70. [PMID: 25129077 PMCID: PMC4410018 DOI: 10.1038/nn.3782] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 07/07/2014] [Indexed: 02/08/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is characterized by progressive neuropathology and cognitive decline. We performed a cross-tissue analysis of methylomic variation in AD using samples from four independent human post-mortem brain cohorts. We identified a differentially methylated region in the ankyrin 1 (ANK1) gene that was associated with neuropathology in the entorhinal cortex, a primary site of AD manifestation. This region was confirmed as being substantially hypermethylated in two other cortical regions (superior temporal gyrus and prefrontal cortex), but not in the cerebellum, a region largely protected from neurodegeneration in AD, or whole blood obtained pre-mortem from the same individuals. Neuropathology-associated ANK1 hypermethylation was subsequently confirmed in cortical samples from three independent brain cohorts. This study represents, to the best of our knowledge, the first epigenome-wide association study of AD employing a sequential replication design across multiple tissues and highlights the power of this approach for identifying methylomic variation associated with complex disease.
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Affiliation(s)
- Katie Lunnon
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Rebecca Smith
- Institute of Psychiatry, King's College London, London, UK
| | - Eilis Hannon
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Philip L De Jager
- 1] Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, USA
| | - Gyan Srivastava
- 1] Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, USA
| | - Manuela Volta
- Institute of Psychiatry, King's College London, London, UK
| | - Claire Troakes
- Institute of Psychiatry, King's College London, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, King's College London, London, UK
| | - Joe Burrage
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Ruby Macdonald
- University of Exeter Medical School, Exeter University, Exeter, UK
| | | | - Lorna W Harries
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Pavel Katsel
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, USA
| | - Vahram Haroutunian
- 1] Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, USA. [2] Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, USA. [3] JJ Peters Virginia Medical Center, Bronx, New York, USA
| | - Zachary Kaminsky
- 1] Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Catharine Joachim
- Department of Neuropathology, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - John Powell
- Institute of Psychiatry, King's College London, London, UK
| | - Simon Lovestone
- 1] Institute of Psychiatry, King's College London, London, UK. [2] Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | | | - Jonathan Mill
- 1] University of Exeter Medical School, Exeter University, Exeter, UK. [2] Institute of Psychiatry, King's College London, London, UK. [3]
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12
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Affiliation(s)
- Zachary Kaminsky
- The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Payne
- The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,E-mail:
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13
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Kaminsky Z, Tochigi M, Jia P, Pal M, Mill J, Kwan A, Ioshikhes I, Vincent JB, Kennedy JL, Strauss J, Pai S, Wang SC, Petronis A. A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. Mol Psychiatry 2012; 17:728-40. [PMID: 21647149 DOI: 10.1038/mp.2011.64] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.
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Affiliation(s)
- Z Kaminsky
- The Krembil Family Epigenetics Laboratory, Neuroscience Department, Centre for Addiction and Mental Health, Toronto, ON, Canada
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14
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Cortese R, Kwan A, Lalonde E, Bryzgunova O, Bondar A, Wu Y, Gordevicius J, Park M, Oh G, Kaminsky Z, Tverkuviene J, Laurinavicius A, Jankevicius F, Sendorek DHS, Haider S, Wang SC, Jarmalaite S, Laktionov P, Boutros PC, Petronis A. Epigenetic markers of prostate cancer in plasma circulating DNA. Hum Mol Genet 2012; 21:3619-31. [PMID: 22619380 DOI: 10.1093/hmg/dds192] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers. To test this hypothesis, we investigated cirDNA modifications in prostate cancer patients with locally confined disease (n = 19), in patients with benign prostate hyperplasias (n = 20) and in men without any known prostate disease (n = 20). This initial discovery screen identified 39 disease-associated changes in cirDNA modification, and seven of these were validated using the sodium bisulfite-based mapping of modified cytosines in both the discovery cohort and an independent 38-patient validation cohort. In particular, we showed that the DNA modification of regions adjacent to the gene encoding ring finger protein 219 distinguished prostate cancer from benign hyperplasias with good sensitivity (61%) and specificity (71%). We also showed that repetitive sequences detected in this study were meaningful, as they indicated a highly statistically significant loss of DNA at the pericentromeric region of chromosome 10 in prostate cancer patients (p = 1.8 × 10(-6)). Based on these strong univariate results, we applied machine-learning techniques to develop a multi-locus biomarker that correctly distinguished prostate cancer samples from unaffected controls with 72% accuracy. Lastly, we used systems biology techniques to integrate our data with publicly available DNA modification and transcriptomic data from primary prostate tumors, thereby prioritizing genes for further studies. These data suggest that cirDNA epigenomics are promising source for non-invasive biomarkers.
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Affiliation(s)
- Rene Cortese
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
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15
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Abstract
As the role for epigenetic signals in genome regulation becomes increasingly understood, the ability to accurately measure levels of DNA methylation at individual cytosines throughout the genome is becoming increasingly important. In contrast to traditional methods for the quantification of cytosine methylation, such as cloning and sequencing of PCR fragments amplified from sodium bisulfite-modified DNA, recent developments have created a fast and effective alternative called methylation-sensitive single nucleotide primer extension (Ms-SNuPE). The following protocol outlines the steps necessary to design and perform Ms-SNuPE experiments using the SNaPshot chemistry and associated capillary electrophoresis platforms available through Applied Biosystems.
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Affiliation(s)
- Zachary Kaminsky
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Toronto, Ontario, Canada
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16
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Kaminsky Z, Petronis A, Wang SC, Levine B, Ghaffar O, Floden D, Feinstein A. Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior. Twin Res Hum Genet 2008; 11:1-11. [PMID: 18251670 DOI: 10.1375/twin.11.1.1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
DNA methylation differences between identical twins could account for phenotypic twin discordance of behavioral traits and diseases. High throughput epigenomic microarray profiling can be a strategy of choice for identification of epigenetic differences in phenotypically different monozygotic (MZ) twins. Epigenomic profiling of a pair of MZ twins with quantified measures of psychometric discordance identified several DNA methylation differences, some of which may have developmental and behavioral implications and are consistent with the contrasting psychometric profiles of the twins. In particular, differential methylation of CpG islands proximal to the homeobox DLX1 gene could modulate stress responses and risk taking behavior, and deserve further attention as a potential marker of aversion to danger. The epigenetic difference detected at DLX1 of approximately 1.2 fold change was used to evaluate experimental design issues such as the required numbers of technical replicates. It also enabled us to estimate the power this technique would have to detect a functionally relevant epigenetic difference given a range of 1 to 50 twin pairs. We found that use of epigenomic microarray profiling in a relatively small number (15-25) of phenotypically discordant twin pairs has sufficient power to detect 1.2 fold epigenetic changes.
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Affiliation(s)
- Zachary Kaminsky
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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17
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Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, Jia P, Assadzadeh A, Flanagan J, Schumacher A, Wang SC, Petronis A. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 2008; 82:696-711. [PMID: 18319075 DOI: 10.1016/j.ajhg.2008.01.008] [Citation(s) in RCA: 550] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 11/12/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022] Open
Abstract
Epigenetic misregulation is consistent with various non-Mendelian features of schizophrenia and bipolar disorder. To date, however, few studies have investigated the role of DNA methylation in major psychosis, and none have taken a genome-wide epigenomic approach. In this study we used CpG-island microarrays to identify DNA-methylation changes in the frontal cortex and germline associated with schizophrenia and bipolar disorder. In the frontal cortex we find evidence for psychosis-associated DNA-methylation differences in numerous loci, including several involved in glutamatergic and GABAergic neurotransmission, brain development, and other processes functionally linked to disease etiology. DNA-methylation changes in a significant proportion of these loci correspond to reported changes of steady-state mRNA level associated with psychosis. Gene-ontology analysis highlighted epigenetic disruption to loci involved in mitochondrial function, brain development, and stress response. Methylome network analysis uncovered decreased epigenetic modularity in both the brain and the germline of affected individuals, suggesting that systemic epigenetic dysfunction may be associated with major psychosis. We also report evidence for a strong correlation between DNA methylation in the MEK1 gene promoter region and lifetime antipsychotic use in schizophrenia patients. Finally, we observe that frontal-cortex DNA methylation in the BDNF gene is correlated with genotype at a nearby nonsynonymous SNP that has been previously associated with major psychosis. Our data are consistent with the epigenetic theory of major psychosis and suggest that DNA-methylation changes are important to the etiology of schizophrenia and bipolar disorder.
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18
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Mill J, Yazdanpanah S, Gückel E, Ziegler S, Kaminsky Z, Petronis A. Whole genome amplification of sodium bisulfite-treated DNA allows the accurate estimate of methylated cytosine density in limited DNA resources. Biotechniques 2006; 41:603-7. [PMID: 17140118 DOI: 10.2144/000112266] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sodium bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to sodium bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)—and compared with those obtained from bisulfite-treated DNA not subjected to WGA. Our data indicates that the DNA methylation profiles obtained from WGA of sodium bisulfite-treated DNA are consistent with those obtained from non-WGA DNA. The average difference in methylation percentage calculated from the two sets of template using MS-SNuPE was 4%. If our results are replicated on other genomic loci, WGA may become a useful technique in DNA methylation studies.
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Affiliation(s)
- Jonathan Mill
- Centre for Addiction and Mental Health, Toronto, ON, Canada
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19
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Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, Virtanen C, Winegarden N, Cheng J, Gingeras T, Petronis A. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 2006; 34:528-42. [PMID: 16428248 PMCID: PMC1345696 DOI: 10.1093/nar/gkj461] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA fractions are enriched using a series of treatments with methylation sensitive restriction enzymes, and interrogated on microarrays. We have investigated various aspects of the technology including its replicability, informativeness, sensitivity and optimal PCR conditions using microarrays containing oligonucleotides representing 100 kb of genomic DNA derived from the chromosome 22 COMT region in addition to 12 192 element CpG island microarrays. Several new aspects of methylation profiling are provided, including the parallel identification of confounding effects of DNA sequence variation, the description of the principles of microarray design for epigenomic studies and the optimal choice of methylation sensitive restriction enzymes. We also demonstrate the advantages of using the unmethylated DNA fraction versus the methylated one, which substantially improve the chances of detecting DNA methylation differences. We applied this methodology for fine-mapping of methylation patterns of chromosomes 21 and 22 in eight individuals using tiling microarrays consisting of over 340 000 oligonucleotide probe pairs. The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.
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Affiliation(s)
| | | | | | | | | | - Patrick Yau
- The Microarray Centre, The University Health Network200 Elizabeth Street, Toronto, ON, Canada M5G 2C4
| | - Carl Virtanen
- The Microarray Centre, The University Health Network200 Elizabeth Street, Toronto, ON, Canada M5G 2C4
| | - Neil Winegarden
- The Microarray Centre, The University Health Network200 Elizabeth Street, Toronto, ON, Canada M5G 2C4
| | | | | | - Arturas Petronis
- To whom correspondence should be addressed. The Krembil Family Epigenetics Laboratory, Room 28, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, Canada M4T 1R8. Tel: +1 416 5358501 4880; Fax: +1 416 979 4666;
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20
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Abstract
Gender differences in susceptibility to complex disease such as asthma, diabetes, lupus, autism and major depression, among numerous other disorders, represent one of the hallmarks of non-Mendelian biology. It has been generally accepted that endocrinological differences are involved in the sexual dimorphism of complex disease; however, specific molecular mechanisms of such hormonal effects have not been elucidated yet. This paper will review evidence that sex hormone action may be mediated via gene-specific epigenetic modifications of DNA and histones. The epigenetic modifications can explain sex effects at DNA sequence polymorphisms and haplotypes identified in gender-stratified genetic linkage and association studies. Hormone-induced DNA methylation and histone modification changes at specific gene regulatory regions may increase or reduce the risk of a disease. The epigenetic interpretation of sexual dimorphism fits well into the epigenetic theory of complex disease, which argues for the primary pathogenic role of inherited and/or acquired epigenetic misregulation rather than DNA sequence variation. The new experimental strategies, especially the high throughput microarray-based epigenetic profiling, can be used for testing the epigenetic hypothesis of gender effects in complex diseases.
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Affiliation(s)
- Zachary Kaminsky
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Canada
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21
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Engelender S, Kaminsky Z, Guo X, Sharp AH, Amaravi RK, Kleiderlein JJ, Margolis RL, Troncoso JC, Lanahan AA, Worley PF, Dawson VL, Dawson TM, Ross CA. Synphilin-1 associates with alpha-synuclein and promotes the formation of cytosolic inclusions. Nat Genet 1999; 22:110-4. [PMID: 10319874 DOI: 10.1038/8820] [Citation(s) in RCA: 352] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parkinson disease (PD) is a neurodegenerative disease characterized by tremor, bradykinesia, rigidity and postural instability. Post-mortem examination shows loss of neurons and Lewy bodies, which are cytoplasmic eosinophilic inclusions, in the substantia nigra and other brain regions. A few families have PD caused by mutations (A53T or A30P) in the gene SNCA (encoding alpha-synuclein). Alpha-synuclein is present in Lewy bodies of patients with sporadic PD, suggesting that alpha-synuclein may be involved in the pathogenesis of PD. It is unknown how alpha-synuclein contributes to the cellular and biochemical mechanisms of PD, and its normal functions and biochemical properties are poorly understood. To determine the protein-interaction partners of alpha-synuclein, we performed a yeast two-hybrid screen. We identified a novel interacting protein, which we term synphilin-1 (encoded by the gene SNCAIP). We found that alpha-synuclein interacts in vivo with synphilin-1 in neurons. Co-transfection of both proteins (but not control proteins) in HEK 293 cells yields cytoplasmic eosinophilic inclusions.
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Affiliation(s)
- S Engelender
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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22
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Wood JD, Yuan J, Margolis RL, Colomer V, Duan K, Kushi J, Kaminsky Z, Kleiderlein JJ, Sharp AH, Ross CA. Atrophin-1, the DRPLA gene product, interacts with two families of WW domain-containing proteins. Mol Cell Neurosci 1998; 11:149-60. [PMID: 9647693 DOI: 10.1006/mcne.1998.0677] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy (DRPLA). The normal function of atrophin-1 is unknown. We have identified five atrophin-1 interacting proteins (AIPs) which bind to atrophin-1 in the vicinity of the polyglutamine tract using the yeast two-hybrid system. Four of the interactions were confirmed using in vitro binding assays. All five interactors contained multiple WW domains. Two are novel. The AIPs can be divided into two distinct classes. AIP1 and AIP3/WWP3 are MAGUK-like multidomain proteins containing a number of protein-protein interaction modules, namely a guanylate kinase-like region, two WW domains, and multiple PDZ domains. AIP2/WWP2, AIP4, and AIP5/WWP1 are highly homologous, each having four WW domains and a HECT domain characteristic of ubiquitin ligases. These interactors are similar to recently isolated huntingtin-interacting proteins, suggesting possible commonality of function between two proteins responsible for very similar diseases.
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Affiliation(s)
- J D Wood
- Division of Neurobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205-2196, USA
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23
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Cooper JK, Schilling G, Peters MF, Herring WJ, Sharp AH, Kaminsky Z, Masone J, Khan FA, Delanoy M, Borchelt DR, Dawson VL, Dawson TM, Ross CA. Truncated N-terminal fragments of huntingtin with expanded glutamine repeats form nuclear and cytoplasmic aggregates in cell culture. Hum Mol Genet 1998; 7:783-90. [PMID: 9536081 DOI: 10.1093/hmg/7.5.783] [Citation(s) in RCA: 258] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by an expanding CAG repeat coding for polyglutamine in the huntingtin protein. Recent data have suggested the possibility that an N-terminal fragment of huntingtin may aggregate in neurons of patients with HD, both in the cytoplasm, forming dystrophic neurites, and in the nucleus, forming intranuclear neuronal inclusion bodies. An animal model of HD using the short N-terminal fragment of huntingtin has also been found to have intranuclear inclusions and this same fragment can aggregate in vitro . We have now developed a cell culture model demonstrating that N-terminal fragments of huntingtin with expanded glutamine repeats aggregate both in the cytoplasm and in the nucleus. Neuroblastoma cells transiently transfected with full-length huntingtin constructs with either a normal or expanded repeat had diffuse cytoplasmic localization of the protein. In contrast, cells transfected with truncated N-terminal fragments showed aggregation only if the glutamine repeat was expanded. The aggregates were often ubiquitinated. The shorter truncated product appeared to form more aggregates in the nucleus. Cells transfected with the expanded repeat construct but not the normal repeat construct showed enhanced toxicity to the apoptosis-inducing agent staurosporine. These data indicate that N-terminal truncated fragments of huntingtin with expanded glutamine repeats can aggregate in cells in culture and that this aggregation can be toxic to cells. This model will be useful for future experiments to test mechanisms of aggregation and toxicity and potentially for testing experimental therapeutic interventions.
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Affiliation(s)
- J K Cooper
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
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