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Cell lineage-specific methylome and genome alterations in gout. Aging (Albany NY) 2021; 13:3843-3865. [PMID: 33493135 PMCID: PMC7906142 DOI: 10.18632/aging.202353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
In this study, we examined data from 69 gout patients and 1,455 non-gout controls using a MethylationEPIC BeadChip assay and Illumina HiSeq platform to identify lineage-specific epigenetic alterations and associated genetic factors that contributed to gouty inflammation. Cell lineage-specific differentially methylated sites were identified using CellDMC after adjusting for sex, age, alcohol drinking, smoking status, and smoking history (total pack-years). Different cell lineages displayed distinct differential methylation. Ingenuity Pathway Analysis and NetworkAnalyst indicated that many differential methylated sites were associated with interleukin-1β expression in monocytes. On the UCSC Genome Browser and WashU Epigenome Browser, metabolic trait, cis-methylation quantitative trait loci, genetic, and functional annotation analyses identified nine methylation loci located in interleukin-1β-regulating genes (PRKCZ, CIDEC, VDAC1, CPT1A, BIRC2, BRCA1, STK11, and NLRP12) that were associated specifically with gouty inflammation. All nine sites mapped to active regulatory elements in monocytes. MoLoTool and ReMap analyses indicated that the nine methylation loci overlapped with binding sites of several transcription factors that regulated interleukin-1β production and gouty inflammation. Decreases in PRKCZ and STK11 methylation were also associated with higher numbers of first-degree relatives who also had gout. The gouty-inflammation specific methylome and genome alterations could potentially aid in the identification of novel therapeutic targets.
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Ho AMC, Winham SJ, Armasu SM, Blacker CJ, Millischer V, Lavebratt C, Overholser JC, Jurjus GJ, Dieter L, Mahajan G, Rajkowska G, Vallender EJ, Stockmeier CA, Robertson KD, Frye MA, Choi DS, Veldic M. Genome-wide DNA methylomic differences between dorsolateral prefrontal and temporal pole cortices of bipolar disorder. J Psychiatr Res 2019; 117:45-54. [PMID: 31279243 PMCID: PMC6941851 DOI: 10.1016/j.jpsychires.2019.05.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/04/2019] [Accepted: 05/09/2019] [Indexed: 01/07/2023]
Abstract
Dorsolateral prefrontal cortex (DLPFC) and temporal pole (TP) are brain regions that display abnormalities in bipolar disorder (BD) patients. DNA methylation - an epigenetic mechanism both heritable and sensitive to the environment - may be involved in the pathophysiology of BD. To study BD-associated DNA methylomic differences in these brain regions, we extracted genomic DNA from the postmortem tissues of Brodmann Area (BA) 9 (DLPFC) and BA38 (TP) gray matter from 20 BD, ten major depression (MDD), and ten control age-and-sex-matched subjects. Genome-wide methylation levels were measured using the 850 K Illumina MethylationEPIC BeadChip. We detected striking differences between cortical regions, with greater numbers of between-brain-region differentially methylated positions (DMPs; i.e., CpG sites) in all groups, most pronounced in the BD group, and with substantial overlap across groups. The genes of DMPs common to both BD and MDD (hypothetically associated with their common features such as depression) and those distinct to BD (hypothetically associated with BD-specific features such as mania) were enriched in pathways involved in neurodevelopment including axon guidance. Pathways enriched only in the BD-MDD shared list pointed to GABAergic dysregulation, while those enriched in the BD-only list suggested glutamatergic dysregulation and greater impact on synaptogenesis and synaptic plasticity. We further detected group-specific between-brain-region gene expression differences in ODC1, CALY, GALNT2, and GABRD, which contained significant between-brain-region DMPs. In each brain region, no significant DMPs or differentially methylated regions (DMRs) were found between diagnostic groups. In summary, the methylation differences between DLPFC and TP may provide molecular targets for further investigations of genetic and environmental vulnerabilities associated with both unique and common features of various mood disorders and suggest directions of future development of individualized treatment strategies.
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Affiliation(s)
- Ada M.-C. Ho
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA,Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Health Science Research, Mayo Clinic,
Rochester, MN, USA
| | | | - Caren J. Blacker
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA
| | - Vincent Millischer
- Department for Molecular Medicine and Surgery (MMK),
Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University
Hospital, Stockholm, Sweden
| | - Catharina Lavebratt
- Department for Molecular Medicine and Surgery (MMK),
Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University
Hospital, Stockholm, Sweden
| | - James C. Overholser
- Department of Psychology, Case Western Reserve University,
Cleveland, OH, USA
| | - George J. Jurjus
- Department of Psychiatry, Case Western Reserve University,
Cleveland, OH, USA,Louis Stokes Cleveland VA Medical Center, Cleveland, OH,
USA
| | - Lesa Dieter
- Department of Psychology, Case Western Reserve University,
Cleveland, OH, USA
| | - Gouri Mahajan
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Grazyna Rajkowska
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Eric J. Vallender
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Craig A. Stockmeier
- Department of Psychiatry, Case Western Reserve University,
Cleveland, OH, USA,Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA
| | - Doo-Sup Choi
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA,Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Marin Veldic
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA.
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Keller S, Punzo D, Cuomo M, Affinito O, Coretti L, Sacchi S, Florio E, Lembo F, Carella M, Copetti M, Cocozza S, Balu DT, Errico F, Usiello A, Chiariotti L. DNA methylation landscape of the genes regulating D-serine and D-aspartate metabolism in post-mortem brain from controls and subjects with schizophrenia. Sci Rep 2018; 8:10163. [PMID: 29976992 PMCID: PMC6033866 DOI: 10.1038/s41598-018-28332-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/21/2018] [Indexed: 01/24/2023] Open
Abstract
The spatio-temporal regulation of genes involved in the synthesis and degradation of D-serine and D-aspartate such as serine racemase (SR), D-amino acid oxidase (DAO), G72 and D-aspartate oxidase (DDO), play pivotal roles in determining the correct levels of these D-amino acids in the human brain. Here we provide a comprehensive analysis of mRNA expression and DNA methylation status of these genes in post-mortem samples from hippocampus, dorsolateral prefrontal cortex, and cerebellum from patients with schizophrenia and non-psychiatric controls. DNA methylation analysis was performed at an ultradeep level, measuring individual epialleles frequency by single molecule approach. Differential CpG methylation and expression was detected across different brain regions, although no significant correlations were found with diagnosis. G72 showed the highest CpG and non-CpG methylation degree, which may explain the repression of G72 transcription in the brain regions considered here. Conversely, in line with the sustained SR mRNA expression in the analyzed areas, very low methylation levels were detected at this gene’s regulatory regions. Furthermore, for DAO and DDO, our single-molecule methylation approach demonstrated that analysis of epiallele distribution was able to detect differences in DNA methylation representing area-specific methylation signatures, which are likely not detectable with targeted or genome-wide classic methylation analyses.
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Affiliation(s)
- Simona Keller
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy
| | - Daniela Punzo
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145, Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Ornella Affinito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy
| | - Lorena Coretti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, 21100, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli studi dell'Insubria, 20131, Milano, Italy
| | - Ermanno Florio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy.,Department of Medicine, University of California, San Diego UCSD, La Jolla, 95000, CA, USA
| | - Francesca Lembo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Massimiliano Copetti
- Unit of Biostatistics, IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy
| | - Darrick T Balu
- Department of Psychiatry, Harvard Medical School, Boston, 02115, MA, USA.,Translational Psychiatry Laboratory, McLean Hospital, Belmont, 02478, MA, USA
| | - Francesco Errico
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145, Naples, Italy.,Department of Agricultural Sciences, University of Naples "Federico II", 80055, Portici, Italy
| | - Alessandro Usiello
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145, Naples, Italy. .,Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy.
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy. .,Endocrinology and Molecular Oncology Institute (I.E.O.S.), National Research Council (C.N.R.), 80131, Naples, Italy.
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