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Nishizawa Y, Thompson KC, Yamanashi T, Wahba NE, Saito T, Marra PS, Nagao T, Nishiguchi T, Shibata K, Yamanishi K, Hughes CG, Pandharipande P, Cho H, Howard MA, Kawasaki H, Toda H, Kanazawa T, Iwata M, Shinozaki G. Epigenetic signals associated with delirium replicated across four independent cohorts. Transl Psychiatry 2024; 14:275. [PMID: 38965205 PMCID: PMC11224347 DOI: 10.1038/s41398-024-02986-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Delirium is risky and indicates poor outcomes for patients. Therefore, it is crucial to create an effective delirium detection method. However, the epigenetic pathophysiology of delirium remains largely unknown. We aimed to discover reliable and replicable epigenetic (DNA methylation: DNAm) markers that are associated with delirium including post-operative delirium (POD) in blood obtained from patients among four independent cohorts. Blood DNA from four independent cohorts (two inpatient cohorts and two surgery cohorts; 16 to 88 patients each) were analyzed using the Illumina EPIC array platform for genome-wide DNAm analysis. We examined DNAm differences in blood between patients with and without delirium including POD. When we compared top CpG sites previously identified from the initial inpatient cohort with three additional cohorts (one inpatient and two surgery cohorts), 11 of the top 13 CpG sites showed statistically significant differences in DNAm values between the delirium group and non-delirium group in the same directions as found in the initial cohort. This study demonstrated the potential value of epigenetic biomarkers as future diagnostic tools. Furthermore, our findings provide additional evidence of the potential role of epigenetics in the pathophysiology of delirium including POD.
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Affiliation(s)
- Yoshitaka Nishizawa
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Psychiatry, Osaka Medical and Pharmaceutical University School of Medicine, Osaka, Japan
| | - Kaitlyn C Thompson
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | - Takehiko Yamanashi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago-shi, Tottori, Japan
| | - Nadia E Wahba
- Department of Psychiatry, Oregon Health and Science University, School of Medicine, Portland, OR, USA
| | - Taku Saito
- Department of Psychiatry, National Defense Medical College School of Medicine, Tokorozawa, Saitama, Japan
| | - Pedro S Marra
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Takaaki Nagao
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Department of Neurosurgery (Sakura), Toho University School of Medicine Faculty of Medicine, Sakura-shi, Chiba, Japan
| | - Tsuyoshi Nishiguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago-shi, Tottori, Japan
| | - Kazuki Shibata
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- Sumitomo Pharma Co, Ltd, Osaka, Osaka, Japan
| | - Kyosuke Yamanishi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Neuropsychiatry, Hyogo Medical University, College of Medicine, Nishinomiya, Hyogo, Japan
| | - Christopher G Hughes
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pratik Pandharipande
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hyunkeun Cho
- University of Iowa, College of Public Health, Iowa City, IA, USA
| | - Matthew A Howard
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Hiroyuki Toda
- Department of Psychiatry, National Defense Medical College School of Medicine, Tokorozawa, Saitama, Japan
| | - Tetsufumi Kanazawa
- Department of Psychiatry, Osaka Medical and Pharmaceutical University School of Medicine, Osaka, Japan
| | - Masaaki Iwata
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago-shi, Tottori, Japan
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA.
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
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Hodge KM, Zhabotynsky V, Burt AA, Carter BS, Fry RC, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, DellaGrotta SA, Dansereau LM, Lester BM, Marsit CJ, O'Shea TM, Everson TM. Epigenetic associations in HPA axis genes related to bronchopulmonary dysplasia and antenatal steroids. Pediatr Res 2024:10.1038/s41390-024-03116-4. [PMID: 38480856 DOI: 10.1038/s41390-024-03116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/26/2024] [Accepted: 02/17/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD), a common morbidity among very preterm infants, is associated with chronic disease and neurodevelopmental impairments. A hypothesized mechanism for these outcomes lies in altered glucocorticoid (GC) activity. We hypothesized that BPD and its treatments may result in epigenetic differences in the hypothalamic-pituitary-adrenal (HPA) axis, which is modulated by GC, and could be ascertained using an established GC risk score and DNA methylation (DNAm) of HPA axis genes. METHODS DNAm was quantified from buccal tissue (ECHO-NOVI) and from neonatal blood spots (ELGAN ECHO) via the EPIC microarray. Prenatal maternal characteristics, pregnancy complication, and neonatal medical complication data were collected from medical record review and maternal interviews. RESULTS The GC score was not associated with steroid exposure or BPD. However, six HPA genes involved in stress response regulation demonstrated differential methylation with antenatal steroid exposure; two CpGs within FKBP5 and POMC were differentially methylated with BPD severity. These findings were sex-specific in both cohorts; males had greater magnitude of differential methylation within these genes. CONCLUSIONS These findings suggest that BPD severity and antenatal steroids are associated with DNAm at some HPA genes in very preterm infants and the effects appear to be sex-, tissue-, and age-specific. IMPACT This study addresses bronchopulmonary dysplasia (BPD), an important health outcome among preterm neonates, and interrogates a commonly studied pathway, the hypothalamic-pituitary-adrenal (HPA) axis. The combination of BPD, the HPA axis, and epigenetic markers has not been previously reported. In this study, we found that BPD itself was not associated with epigenetic responses in the HPA axis in infants born very preterm; however, antenatal treatment with steroids was associated with epigenetic responses.
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Affiliation(s)
- Kenyaita M Hodge
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Vasyl Zhabotynsky
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amber A Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Elisabeth C McGowan
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, USA
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Barry M Lester
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Pahl MC, Liu L, Pippin JA, Wagley Y, Boehm K, Hankenson KD, Wells AD, Yang W, Grant SFA. Variant to gene mapping for carpal tunnel syndrome risk loci implicates skeletal muscle regulatory elements. EBioMedicine 2024; 101:105038. [PMID: 38417377 PMCID: PMC10909706 DOI: 10.1016/j.ebiom.2024.105038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Carpal tunnel syndrome (CTS) is a common disorder caused by compression of the median nerve in the wrist, resulting in pain and numbness throughout the hand and forearm. While multiple behavioural and physiological factors influence CTS risk, a growing body of evidence supports a strong genetic contribution. Recent genome-wide association study (GWAS) efforts have reported 53 independent signals associated with CTS. While GWAS can identify genetic loci conferring risk, it does not determine which cell types drive the genetic aetiology of the trait, which variants are "causal" at a given signal, and which effector genes correspond to these non-coding variants. These obstacles limit interpretation of potential disease mechanisms. METHODS We analysed CTS GWAS findings in the context of chromatin conformation between gene promoters and accessible chromatin regions across cellular models of bone, skeletal muscle, adipocytes and neurons. We identified proxy variants in high LD with the lead CTS sentinel SNPs residing in promoter connected open chromatin in the skeletal muscle and bone contexts. FINDINGS We detected significant enrichment for heritability in skeletal muscle myotubes, as well as a weaker correlation in human mesenchymal stem cell-derived osteoblasts. In myotubes, our approach implicated 117 genes contacting 60 proxy variants corresponding to 20 of the 53 GWAS signals. In the osteoblast context we implicated 30 genes contacting 24 proxy variants coinciding with 12 signals, of which 19 genes shared. We subsequently prioritized BZW2 as a candidate effector gene in CTS and implicated it as novel gene that perturbs myocyte differentiation in vitro. INTERPRETATION Taken together our results suggest that the CTS genetic component influences the size, integrity, and organization of multiple tissues surrounding the carpal tunnel, in particular muscle and bone, to predispose the nerve to being compressed in this disease setting. FUNDING This work was supported by NIH Grant UM1 DK126194 (SFAG and WY), R01AG072705 (SFAG & KDH) and the Center for Spatial and Functional Genomics at CHOP (SFAG & ADW). SFAG is supported by the Daniel B. Burke Endowed Chair for Diabetes Research. WY is supported by the Perelman School of Medicine of the University of Pennsylvania.
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Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lin Liu
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA19104, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yadav Wagley
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kurt D Hankenson
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA, USA
| | - Wenli Yang
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA19104, USA.
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Hubers N, Hagenbeek FA, Pool R, Déjean S, Harms AC, Roetman PJ, van Beijsterveldt CEM, Fanos V, Ehli EA, Vermeiren RRJM, Bartels M, Hottenga JJ, Hankemeier T, van Dongen J, Boomsma DI. Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32955. [PMID: 37534875 DOI: 10.1002/ajmg.b.32955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores [PGSs]), epigenomics, and metabolomics data in a multi-omics framework to identify biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases = 14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein family TMEM, show that the DNA methylation of the MAD1L1 gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of the STAP2 gene. However, out-of-sample prediction in NTR participants (N = 258, cases = 14.3%) and in a clinical sample (N = 145, cases = 51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGSs, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
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Affiliation(s)
- Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219, University of Toulouse, CNRS, Toulouse, France
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Peter J Roetman
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Robert R J M Vermeiren
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
- Youz, Parnassia Group, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
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Niehues A, de Visser C, Hagenbeek FA, Kulkarni P, Pool R, Karu N, Kindt ASD, Singh G, Vermeiren RRJM, Boomsma DI, van Dongen J, ’t Hoen PAC, van Gool AJ. A multi-omics data analysis workflow packaged as a FAIR Digital Object. Gigascience 2024; 13:giad115. [PMID: 38217405 PMCID: PMC10787363 DOI: 10.1093/gigascience/giad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/14/2023] [Accepted: 12/10/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Applying good data management and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines. Practical examples can help promote the adoption of FAIR practices for computational workflows in the research community. We developed a multi-omics data analysis workflow implementing FAIR practices to share it as a FAIR Digital Object. FINDINGS We conducted a case study investigating shared patterns between multi-omics data and childhood externalizing behavior. The analysis workflow was implemented as a modular pipeline in the workflow manager Nextflow, including containers with software dependencies. We adhered to software development practices like version control, documentation, and licensing. Finally, the workflow was described with rich semantic metadata, packaged as a Research Object Crate, and shared via WorkflowHub. CONCLUSIONS Along with the packaged multi-omics data analysis workflow, we share our experiences adopting various FAIR practices and creating a FAIR Digital Object. We hope our experiences can help other researchers who develop omics data analysis workflows to turn FAIR principles into practice.
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Affiliation(s)
- Anna Niehues
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Casper de Visser
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Purva Kulkarni
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Alida S D Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Gurnoor Singh
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Robert R J M Vermeiren
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, 2342 AK Oegstgeest, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Peter A C ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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Sint Jago SC, Bahabry R, Schreiber AM, Homola J, Ngyuen T, Meijia F, Allendorfer JB, Lubin FD. Aerobic exercise alters DNA hydroxymethylation levels in an experimental rodent model of temporal lobe epilepsy. Epilepsy Behav Rep 2023; 25:100642. [PMID: 38323091 PMCID: PMC10844942 DOI: 10.1016/j.ebr.2023.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/24/2023] [Accepted: 12/26/2023] [Indexed: 02/08/2024] Open
Abstract
The therapeutic potential of aerobic exercise in mitigating seizures and cognitive issues in temporal lobe epilepsy (TLE) is recognized, yet the underlying mechanisms are not well understood. Using a rodent TLE model induced by Kainic acid (KA), we investigated the impact of a single bout of exercise (i.e., acute) or 4 weeks of aerobic exercise (i.e., chronic). Blood was processed for epilepsy-associated serum markers, and DNA methylation (DNAme), and hippocampal area CA3 was assessed for gene expression levels for DNAme-associated enzymes. While acute aerobic exercise did not alter serum Brain-Derived Neurotrophic Factor (BDNF) or Interleukin-6 (IL-6), chronic exercise resulted in an exercise-specific decrease in serum BDNF and an increase in serum IL-6 levels in epileptic rats. Additionally, whole blood DNAme levels, specifically 5-hydroxymethylcytosine (5-hmC), decreased in epileptic animals following chronic exercise. Hippocampal CA3 5-hmC levels and ten-eleven translocation protein (TET1) expression mirrored these changes. Furthermore, immunohistochemistry analysis revealed that most 5-hmC changes in response to chronic exercise were neuron-specific within area CA3 of the hippocampus. Together, these findings suggest that DNAme mechanisms in the rodent model of TLE are responsive to chronic aerobic exercise, with emphasis on neuronal 5-hmC DNAme in the epileptic hippocampus.
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Affiliation(s)
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | | | - Julia Homola
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Tram Ngyuen
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Fernando Meijia
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Jane B. Allendorfer
- Department of Neurobiology, University of Alabama at Birmingham, United States
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Farah D. Lubin
- Department of Neurobiology, University of Alabama at Birmingham, United States
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Epigenetic differences in stress response gene FKBP5 among children with abusive vs accidental injuries. Pediatr Res 2023:10.1038/s41390-022-02441-w. [PMID: 36624283 DOI: 10.1038/s41390-022-02441-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/08/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Survivors of child abuse experience high rates of adverse physical and mental health outcomes. Epigenetic alterations in the stress response system, the FKBP5 gene specifically, have been implicated as one mechanism that may link abuse to lifelong health issues. Prior studies primarily included older individuals with a remote history of maltreatment; our objective was to test for differential methylation of FKBP5 in children with abusive vs accidental injuries at the time of diagnosis. METHODS We conducted a cross-sectional pilot study of acutely injured children <4 years old at two children's hospitals (n = 82). Research personnel collected injury histories, buccal swabs (n = 65), and blood samples (n = 25) to measure DNA methylation. An expert panel classified the injuries as abusive, accidental, or indeterminate. RESULTS Children with abusive as compared to accidental injuries had lower methylation of the FKBP5 promoter in buccal and blood cells, even after controlling for injury severity, socioeconomic status, and psychosocial risk factors. CONCLUSION These findings suggest that epigenetic variation in FKBP5 may occur at the earliest indication of abuse and may be associated with delayed resolution of the HPA axis stress response. Additional testing for epigenetic differences in larger sample sizes is needed to further verify these findings. IMPACT Children (<4 years old) with abusive compared to accidental injuries showed lower methylation of the FKBP5 promoter in buccal and blood cells at the time of initial diagnosis even after controlling for injury severity, socioeconomic status, and psychosocial risk factors. Early childhood physical abuse may impact the epigenetic regulation of the stress response system, including demethylation within promoters and enhancers of the FKBP5 gene, even at the earliest indication of abuse. The findings are important because unmitigated stress is associated with adverse health outcomes throughout the life-course.
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Hagenbeek FA, van Dongen J, Pool R, Roetman PJ, Harms AC, Hottenga JJ, Kluft C, Colins OF, van Beijsterveldt CEM, Fanos V, Ehli EA, Hankemeier T, Vermeiren RRJM, Bartels M, Déjean S, Boomsma DI. Integrative Multi-omics Analysis of Childhood Aggressive Behavior. Behav Genet 2023; 53:101-117. [PMID: 36344863 PMCID: PMC9922241 DOI: 10.1007/s10519-022-10126-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
This study introduces and illustrates the potential of an integrated multi-omics approach in investigating the underlying biology of complex traits such as childhood aggressive behavior. In 645 twins (cases = 42%), we trained single- and integrative multi-omics models to identify biomarkers for subclinical aggression and investigated the connections among these biomarkers. Our data comprised transmitted and two non-transmitted polygenic scores (PGSs) for 15 traits, 78,772 CpGs, and 90 metabolites. The single-omics models selected 31 PGSs, 1614 CpGs, and 90 metabolites, and the multi-omics model comprised 44 PGSs, 746 CpGs, and 90 metabolites. The predictive accuracy for these models in the test (N = 277, cases = 42%) and independent clinical data (N = 142, cases = 45%) ranged from 43 to 57%. We observed strong connections between DNA methylation, amino acids, and parental non-transmitted PGSs for ADHD, Autism Spectrum Disorder, intelligence, smoking initiation, and self-reported health. Aggression-related omics traits link to known and novel risk factors, including inflammation, carcinogens, and smoking.
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Affiliation(s)
- Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Peter J. Roetman
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands
| | - Amy C. Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands
| | | | - Olivier F. Colins
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Department Special Needs Education, Ghent University, Ghent, Belgium
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota USA
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Robert R. J. M. Vermeiren
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Youz, Parnassia Psychiatric Institute, The Hague, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, University of Toulouse, CNRS, Toulouse, France
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
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9
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Yamanashi T, Crutchley KJ, Wahba NE, Nagao T, Marra PS, Akers CC, Sullivan EJ, Iwata M, Howard MA, Cho HR, Kawasaki H, Hughes CG, Pandharipande PP, Hefti MM, Shinozaki G. The genome-wide DNA methylation profiles among neurosurgery patients with and without post-operative delirium. Psychiatry Clin Neurosci 2023; 77:48-55. [PMID: 36266784 PMCID: PMC9812874 DOI: 10.1111/pcn.13495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 01/07/2023]
Abstract
AIMS There is no previous study demonstrating the differences of genome-wide DNA methylation (DNAm) profiles between patients with and without postoperative delirium (POD). We aimed to discover epigenetic (DNAm) markers that are associated with POD in blood obtained from patients before and after neurosurgery. METHODS Pre- and post-surgical blood DNA samples from 37 patients, including 10 POD cases, were analyzed using the Illumina EPIC array genome-wide platform. We examined DNAm differences in blood from patients with and without POD. Enrichment analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes terms were also conducted. RESULTS When POD cases were tested for DNAm change before and after surgery, enrichment analyses showed many relevant signals with statistical significance in immune response related-pathways and inflammatory cytokine related-pathways such as "cellular response to cytokine stimulus", "regulation of immune system process", "regulation of cell activation", and "regulation of cytokine production". Furthermore, after excluding the potential effect of common factors related to surgery and anesthesia between POD cases and non-POD controls, the enrichment analyses showed significant signals such as "immune response" and "T cell activation", which are same pathways previously identified from an independent non-surgical inpatient cohort. CONCLUSIONS Our first genome-wide DNAm investigation of POD showed promising signals related to immune response, inflammatory response and other relevant signals considered to be associated with delirium pathophysiology. Our data supports the hypothesis that epigenetics play an important role in the pathophysiological mechanism of delirium and suggest the potential usefulness of an epigenetics-based biomarker of POD.
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Affiliation(s)
- Takehiko Yamanashi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California, USA.,Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Neuropsychiatry, Tottori University Faculty of Medicine, Tottori, Japan
| | - Kaitlyn J Crutchley
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nadia E Wahba
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Takaaki Nagao
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Neurosurgery (Sakura), Toho University School of Medicine Faculty of Medicine, Chiba, Japan
| | - Pedro S Marra
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Cade C Akers
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eleanor J Sullivan
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Masaaki Iwata
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Tottori, Japan
| | - Mathew A Howard
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Hyunkeun R Cho
- College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Christopher G Hughes
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Pratik P Pandharipande
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California, USA.,Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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10
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van der Linden EL, Halley A, Meeks KAC, Chilunga F, Hayfron-Benjamin C, Venema A, Garrelds IM, Danser AHJ, van den Born BJ, Henneman P, Agyemang C. An explorative epigenome-wide association study of plasma renin and aldosterone concentration in a Ghanaian population: the RODAM study. Clin Epigenetics 2022; 14:159. [PMID: 36457109 PMCID: PMC9714193 DOI: 10.1186/s13148-022-01378-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The epigenetic regulation of the renin-angiotensin-aldosterone system (RAAS) potentially plays a role in the pathophysiology underlying the high burden of hypertension in sub-Saharan Africans (SSA). Here we report the first epigenome-wide association study (EWAS) of plasma renin and aldosterone concentrations and the aldosterone-to-renin ratio (ARR). METHODS Epigenome-wide DNA methylation was measured using the Illumina 450K array on whole blood samples of 68 Ghanaians. Differentially methylated positions (DMPs) were assessed for plasma renin concentration, aldosterone, and ARR using linear regression models adjusted for age, sex, body mass index, diabetes mellitus, hypertension, and technical covariates. Additionally, we extracted methylation loci previously associated with hypertension, kidney function, or that were annotated to RAAS-related genes and associated these with renin and aldosterone concentration. RESULTS We identified one DMP for renin, ten DMPs for aldosterone, and one DMP associated with ARR. Top DMPs were annotated to the PTPRN2, SKIL, and KCNT1 genes, which have been reported in relation to cardiometabolic risk factors, atherosclerosis, and sodium-potassium handling. Moreover, EWAS loci previously associated with hypertension, kidney function, or RAAS-related genes were also associated with renin, aldosterone, and ARR. CONCLUSION In this first EWAS on RAAS hormones, we identified DMPs associated with renin, aldosterone, and ARR in a SSA population. These findings are a first step in understanding the role of DNA methylation in regulation of the RAAS in general and in a SSA population specifically. Replication and translational studies are needed to establish the role of these DMPs in the hypertension burden in SSA populations.
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Affiliation(s)
- Eva L. van der Linden
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.7177.60000000084992262Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Adrienne Halley
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Karlijn A. C. Meeks
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Felix Chilunga
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Charles Hayfron-Benjamin
- grid.8652.90000 0004 1937 1485Department of Physiology, University of Ghana Medical School, Accra, Ghana ,grid.415489.50000 0004 0546 3805Department of Anesthesia and Critical Care, Korle Bu Teaching Hospital, Accra, Ghana
| | - Andrea Venema
- grid.7177.60000000084992262Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Ingrid M. Garrelds
- grid.5645.2000000040459992XDivision of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Amsterdam, The Netherlands
| | - A. H. Jan Danser
- grid.5645.2000000040459992XDivision of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Amsterdam, The Netherlands
| | - Bert-Jan van den Born
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.7177.60000000084992262Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Peter Henneman
- grid.7177.60000000084992262Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
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11
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Wiegand A, Munk MHJ, Drohm S, Fallgatter AJ, MacIsaac JL, Kobor MS, Nieratschker V, Kreifelts B. Neural correlates of attentional control in social anxiety disorder: the impact of early-life adversity and DNA methylation. J Psychiatry Neurosci 2021; 46:E663-E674. [PMID: 34916236 PMCID: PMC8687622 DOI: 10.1503/jpn.210064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/10/2021] [Accepted: 10/10/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Social anxiety disorder is characterized by intense fear and avoidance of social interactions and scrutiny by others. Although alterations in attentional control seem to play a central role in the psychopathology of social anxiety disorder, the neural underpinnings in prefrontal brain regions have not yet been fully clarified. METHODS The present study used functional MRI in participants (age 18-50 yr) with social anxiety disorder (n = 42, 31 female) and without (n = 58, 33 female). It investigated the interrelation of the effects of social anxiety disorder and early-life adversity (a main environmental risk factor of social anxiety disorder) on brain activity during an attentional control task. We applied DNA methylation analysis to determine whether epigenetic modulation in the gene encoding the glucocorticoid receptor, NR3C1, might play a mediating role in this process. RESULTS We identified 2 brain regions in the left and medial prefrontal cortex that exhibited an interaction effect of social anxiety disorder and early-life adversity. In participants with low levels of early-life adversity, neural activity in response to disorder-related stimuli was increased in association with social anxiety disorder. In participants with high levels of early-life adversity, neural activity was increased only in participants without social anxiety disorder. NR3C1 DNA methylation partly mediated the effect of social anxiety disorder on brain activity as a function of early-life adversity. LIMITATIONS The absence of behavioural correlates associated with social anxiety disorder limited functional interpretation of the results. CONCLUSION These findings demonstrate that the neurobiological processes that underlie social anxiety disorder might be fundamentally different depending on experiences of early-life adversity. Long-lasting effects of early-life adversity might be encoded in NR3C1 DNA methylation and entail alterations in social anxiety disorder-related activity patterns in the neural network of attentional control.
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Affiliation(s)
- Ariane Wiegand
- From the Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, Eberhard Karls University of Tübingen, Tübingen, Germany (Wiegand, Munk, Drohm, Fallgatter, Nieratschker, Kreifelts); the International Max Planck Research School for Cognitive and Systems Neuroscience, University of Tübingen, Tübingen, Germany (Wiegand); the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany (Munk); the Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC (MacIsaac, Kobor); and the Werner Reichardt Centre for Integrative Neuroscience, Tübingen, Germany (Nieratschker)
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12
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Yamanashi T, Nagao T, Wahba NE, Marra PS, Crutchley KJ, Meyer AA, Andreasen AJ, Hellman MM, Jellison SS, Hughes CG, Pandharipande PP, Howard, III MA, Kawasaki H, Iwata M, Hefti MM, Shinozaki G. DNA methylation in the inflammatory genes after neurosurgery and diagnostic ability of post-operative delirium. Transl Psychiatry 2021; 11:627. [PMID: 34887385 PMCID: PMC8660911 DOI: 10.1038/s41398-021-01752-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
The pathophysiological mechanisms of postoperative delirium (POD) are still not clear, and no reliable biomarker is available to differentiate those with and without POD. Pre- and post-surgery blood from epilepsy subjects undergoing neurosurgery were collected. DNA methylation (DNAm) levels of the TNF gene, IL1B gene, and IL6 gene by the Illumina EPIC array method, and DNAm levels of the TNF gene by pyrosequencing, were analyzed. Blood from 37 subjects were analyzed by the EPIC array method, and blood from 27 subjects were analyzed by pyrosequencing. Several CpGs in the TNF gene in preoperative blood showed a negative correlation between their DNAm and age both in the POD group and in the non-POD group. However, these negative correlations were observed only in the POD group after neurosurgery. Neurosurgery significantly altered DNAm levels at 17 out of 24 CpG sites on the TNF gene, 8 out of 14 CpG sites on the IL1B gene, and 4 out of 14 CpG sites on the IL6 gene. Furthermore, it was found that the Inflammatory Methylation Index (IMI), which was based on the post-surgery DNAm levels at the selected five CpG sites, can be a potential detection tool for delirium with moderate accuracy; area under the curve (AUC) value was 0.84. The moderate accuracy of this IMI was replicated using another cohort from our previous study, in which the AUC was 0.79. Our findings provide further evidence of the potential role of epigenetics and inflammation in the pathophysiology of delirium.
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Affiliation(s)
- Takehiko Yamanashi
- Stanford University School of Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, USA. .,University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA. .,Tottori University Faculty of Medicine, Department of Neuropsychiatry, Yonago-shi, Tottori, Japan.
| | - Takaaki Nagao
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Neurosurgery, Iowa City, IA USA ,grid.265050.40000 0000 9290 9879Toho University School of Medicine Faculty of Medicine, Department of Neurosurgery (Sakura), Sakura-shi, Chiba Japan
| | - Nadia E. Wahba
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Pedro S. Marra
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Kaitlyn J. Crutchley
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Alissa A. Meyer
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Ally J. Andreasen
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Mandy M. Hellman
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Sydney S. Jellison
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA USA
| | - Christopher G. Hughes
- grid.412807.80000 0004 1936 9916Vanderbilt University Medical Center, Department of anesthesiology, Nashville, TN USA
| | - Pratik P. Pandharipande
- grid.412807.80000 0004 1936 9916Vanderbilt University Medical Center, Department of anesthesiology, Nashville, TN USA
| | - Matthew A. Howard, III
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Neurosurgery, Iowa City, IA USA
| | - Hiroto Kawasaki
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Neurosurgery, Iowa City, IA USA
| | - Masaaki Iwata
- grid.265107.70000 0001 0663 5064Tottori University Faculty of Medicine, Department of Neuropsychiatry, Yonago-shi, Tottori Japan
| | - Marco M. Hefti
- grid.214572.70000 0004 1936 8294University of Iowa Carver College of Medicine, Department of Pathology, Iowa City, IA USA
| | - Gen Shinozaki
- Stanford University School of Medicine, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, USA. .,University of Iowa Carver College of Medicine, Department of Psychiatry, Iowa City, IA, USA.
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13
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Liu W, Mohan SP, Nagaraj NR, Sundar Jaganathan S, Wen Y, Ramasubramanyan S, Irudayaraj J. Epigenetic alterations associated with dexamethasone sodium phosphate through DNMT and TET in RPE cells. Mol Vis 2021; 27:643-655. [PMID: 34924744 PMCID: PMC8645185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To elucidate the mechanism behind epigenetic alteration associated with dexamethasone (DEX) sodium phosphate treatment. METHODS We performed enzyme-linked immunosorbent assay to quantify changes in global DNA methylation and hydroxymethylation, quantitative real-time PCR (qRT-PCR) of the DNA methylation- and hydroxymethylation-related gene, in vitro DNA methyltransferase (DNMT) enzymatic activity assays with purified DNMTs, and DNA hydroxymethylation pattern with super-resolution imaging. RESULTS We identified global DNA hypomethylation and hyper-hydroxymethylation upon DEX treatment, associated with aberrant mRNA expression levels of DNMT and ten-eleven translocation (TET) proteins. Additionally, DEX exposure could directly hinder DNMT activities. CONCLUSIONS We showed that DEX-induced epigenetic alterations are linked to aberrant DNMT and TET expression, potentially through an essential role of DNMT.
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Affiliation(s)
- Wenjie Liu
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sruthi Priya Mohan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | | | - Shyam Sundar Jaganathan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Yi Wen
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sharada Ramasubramanyan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Joseph Irudayaraj
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
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14
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Wiegand A, Blickle A, Brückmann C, Weller S, Nieratschker V, Plewnia C. Dynamic DNA Methylation Changes in the COMT Gene Promoter Region in Response to Mental Stress and Its Modulation by Transcranial Direct Current Stimulation. Biomolecules 2021; 11:1726. [PMID: 34827724 PMCID: PMC8615564 DOI: 10.3390/biom11111726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
Changes in epigenetic modifications present a mechanism how environmental factors, such as the experience of stress, can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. We investigated dynamic DNA methylation changes in whole blood of 42 healthy male individuals in response to a stressful cognitive task, its association with concentration changes in cortisol, and its modulation by transcranial direct current stimulation (tDCS). We observed a continuous increase in COMT promotor DNA methylation which correlated with higher saliva cortisol levels and was still detectable one week later. However, this lasting effect was suppressed by concurrent activity-enhancing anodal tDCS to the dorsolateral prefrontal cortex. Our findings support the significance of gene-specific DNA methylation in whole blood as potential biomarkers for stress-related effects. Moreover, they suggest alternative molecular mechanisms possibly involved in lasting behavioral effects of tDCS.
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Affiliation(s)
- Ariane Wiegand
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Molecular Psychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (A.B.); (C.B.); (V.N.)
- International Max Planck Research School for Cognitive and Systems Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Arne Blickle
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Molecular Psychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (A.B.); (C.B.); (V.N.)
| | - Christof Brückmann
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Molecular Psychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (A.B.); (C.B.); (V.N.)
| | - Simone Weller
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Neurophysiology & Interventional Neuropsychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (S.W.); (C.P.)
| | - Vanessa Nieratschker
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Molecular Psychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (A.B.); (C.B.); (V.N.)
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Christian Plewnia
- Tübingen Center for Mental Health, Department of Psychiatry and Psychotherapy, Neurophysiology & Interventional Neuropsychiatry, University Hospital Tübingen, Calwerstraße 14, 72076 Tübingen, Germany; (S.W.); (C.P.)
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15
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Lin YL, Wei CW, Lerdall TA, Nhieu J, Wei LN. Crabp1 Modulates HPA Axis Homeostasis and Anxiety-like Behaviors by Altering FKBP5 Expression. Int J Mol Sci 2021; 22:12240. [PMID: 34830120 PMCID: PMC8619219 DOI: 10.3390/ijms222212240] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/22/2022] Open
Abstract
Retinoic acid (RA), the principal active metabolite of vitamin A, is known to be involved in stress-related disorders. However, its mechanism of action in this regard remains unclear. This study reports that, in mice, endogenous cellular RA binding protein 1 (Crabp1) is highly expressed in the hypothalamus and pituitary glands. Crabp1 knockout (CKO) mice exhibit reduced anxiety-like behaviors accompanied by a lowered stress induced-corticosterone level. Furthermore, CRH/DEX tests show an increased sensitivity (hypersensitivity) of their feedback inhibition in the hypothalamic-pituitary-adrenal (HPA) axis. Gene expression studies show reduced FKBP5 expression in CKO mice; this would decrease the suppression of glucocorticoid receptor (GR) signaling thereby enhancing their feedback inhibition, consistent with their dampened corticosterone level and anxiety-like behaviors upon stress induction. In AtT20, a pituitary gland adenoma cell line elevating or reducing Crabp1 level correspondingly increases or decreases FKBP5 expression, and its endogenous Crabp1 level is elevated by GR agonist dexamethasone or RA treatment. This study shows, for the first time, that Crabp1 regulates feedback inhibition of the the HPA axis by modulating FKBP5 expression. Furthermore, RA and stress can increase Crabp1 level, which would up-regulate FKBP5 thereby de-sensitizing feedback inhibition of HPA axis (by decreasing GR signaling) and increasing the risk of stress-related disorders.
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Affiliation(s)
| | | | | | | | - Li-Na Wei
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; (Y.-L.L.); (C.-W.W.); (T.A.L.); (J.N.)
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16
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Yamanashi T, Saito T, Yu T, Alario A, Comp K, Crutchley KJ, Sullivan EJ, Anderson ZEM, Marra PS, Chang G, Wahba NE, Jellison SS, Meyer AA, Mathur S, Pandharipande P, Yoshino A, Kaneko K, Lee S, Toda H, Iwata M, Shinozaki G. DNA methylation in the TNF-alpha gene decreases along with aging among delirium inpatients. Neurobiol Aging 2021; 105:310-317. [PMID: 34192631 DOI: 10.1016/j.neurobiolaging.2021.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
It has been suggested that aging and inflammation play key roles in the development of delirium. In the present study, we investigated the differences of the DNAm patterns in the TNF gene between patients with delirium and without. The data and samples derived from previous and ongoing cohort studies were analyzed. DNAm levels of the TNF gene were analyzed using the Illumina EPIC array genome-wide method and pyrosequencing method. Correlations between age and DNAm levels of each CpG were calculated. Several CpG in the TNF gene in blood showed negative correlation between their DNAm and age in delirium cases both with the EPIC array and by the pyrosequencing method. However, there was no CpG that had significant correlation between their DNAm and age regardless of delirium status among buccal samples. On the other hand, among peripheral blood mononuclear cells samples, it was found that several CpG showed negative correlation between their DNAm and age in delirium cases. The evidence of DNAm change in the TNF gene among delirious subjects was demonstrated.
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Affiliation(s)
- Takehiko Yamanashi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA; Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Taku Saito
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA; Department of Psychiatry, National Defense Medical College School of Medicine, Tokorozawa, Saitama, Japan
| | - Tong Yu
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Alexandra Alario
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Katie Comp
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Kaitlyn J Crutchley
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Eleanor J Sullivan
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Zoe-Ella M Anderson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Pedro S Marra
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Gloria Chang
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Nadia E Wahba
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Sydney S Jellison
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Alissa A Meyer
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Srishti Mathur
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Pratik Pandharipande
- Department of anesthesiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aihide Yoshino
- Department of Psychiatry, National Defense Medical College School of Medicine, Tokorozawa, Saitama, Japan
| | - Koichi Kaneko
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Sangil Lee
- Department of Emergency Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Hiroyuki Toda
- Department of Psychiatry, National Defense Medical College School of Medicine, Tokorozawa, Saitama, Japan
| | - Masaaki Iwata
- Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
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17
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Bound Together: How Psychoanalysis Diminishes Inter-generational DNA Trauma. Am J Psychoanal 2020; 80:196-218. [PMID: 32488025 DOI: 10.1057/s11231-020-09247-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concept of intergenerational transmission of trauma plays a fundamental role in psychoanalysis. While it is known that intergenerational trauma can be transmitted through attachment relationships, a new branch of genetics (epigenetics) has emerged to study the interaction between human behavior and changes in DNA expression. Therefore, psychoanalysis, which has proven to reduce the intergenerational transmission of trauma from a behavioral perspective, can play a positive role in regulating DNA changes caused by environmental stress. The present paper focuses on recent research suggesting a direct correlation between psychological trauma and DNA modifications. In particular, DNA changes caused by psychological trauma can be transmitted from generation to generation, validating the psychoanalytic concept of intergenerational transmission of trauma. This evidence not only supports the essential role psychoanalysis has in influencing human behavior, but also suggests that it affects not only the individuals who undergo it but their offspring, as well, via the epigenetic passage of DNA.
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18
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Differential DNA methylation in high-grade serous ovarian cancer (HGSOC) is associated with tumor behavior. Sci Rep 2019; 9:17996. [PMID: 31784612 PMCID: PMC6884482 DOI: 10.1038/s41598-019-54401-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
The epigenome offers an additional facet of cancer that can help categorize patients into those at risk of disease, recurrence, or treatment failure. We conducted a retrospective, nested, case-control study of advanced and recurrent high-grade serous ovarian cancer (HGSOC) patients in which we assessed epigenome-wide association using Illumina methylationEPIC arrays to characterize DNA methylation status and RNAseq to evaluate gene expression. Comparing HGSOC tumors with normal fallopian tube tissues we observe global hypomethylation but with skewing towards hypermethylation when interrogating gene promoters. In total, 5,852 gene interrogating probes revealed significantly different methylation. Within HGSOC, 57 probes highlighting 17 genes displayed significant differential DNA methylation between primary and recurrent disease. Between optimal vs suboptimal surgical outcomes 99 probes displayed significantly different methylation but only 29 genes showed an inverse correlation between methylation status and gene expression. Overall, differentially methylated genes point to several pathways including RAS as well as hippo signaling in normal vs primary HGSOC; valine, leucine, and isoleucine degradation and endocytosis in primary vs recurrent HGSOC; and pathways containing immune driver genes in optimal vs suboptimal surgical outcomes. Thus, differential DNA methylation identified numerous genes that could serve as potential biomarkers and/or therapeutic targets in HGSOC.
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Wang AL, Gruzieva O, Qiu W, Kebede Merid S, Celedón JC, Raby BA, Söderhäll C, DeMeo DL, Weiss ST, Melén E, Tantisira KG. DNA methylation is associated with inhaled corticosteroid response in persistent childhood asthmatics. Clin Exp Allergy 2019; 49:1225-1234. [PMID: 31187518 DOI: 10.1111/cea.13447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/19/2019] [Accepted: 05/18/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Response to inhaled corticosteroids is highly variable, and the association between DNA methylation and treatment response is not known. OBJECTIVE To examine the association between peripheral blood DNA methylation and inhaled corticosteroid response in children with persistent asthma. METHODS Epigenome-wide DNA methylation was analysed in individuals on inhaled corticosteroids in three independent and ethnically diverse cohorts-Childhood Asthma Management Program (CAMP); Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE); and Genetic Epidemiology of Asthma in Costa Rica Study (GACRS). Treatment response was evaluated using two definitions, the absence of emergency department visits and/or hospitalizations and the absence oral corticosteroid use while on inhaled corticosteroid therapy. CpG sites meeting nominal significance (P < 0.05) for each outcome were combined in a three-cohort meta-analysis with adjustment for multiple testing. DNA methylation was correlated with gene expression using Pearson and partial correlations. RESULTS In 154 subjects from CAMP, 72 from BAMSE, and 168 from GACRS, relative hypomethylation of cg00066816 (171 bases upstream of IL12B) was associated with the absence of emergency department visits and/or hospitalizations (Q = 0.03) in all cohorts and lower IL12B expression (ρ = 0.34, P = 0.01) in BAMSE. Relative hypermethylation of cg04256470 (688 bases upstream of CORT) was associated with the absence of oral corticosteroid use (Q = 0.04) in all cohorts and higher CORT expression (ρ = 0.20, P = 0.045) in CAMP. CONCLUSION AND CLINICAL RELEVANCE Differential DNA methylation of IL12B and CORT are associated with inhaled corticosteroid treatment response in persistent childhood asthmatics. Pharmaco-methylation can identify novel markers of treatment sensitivity in asthma.
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Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden.,Sachs' Children's Hospital, Stockholm, Sweden
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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