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Abstract
OBJECTIVE Schizophrenia (SCZ) is a debilitating disease with a complex genetic cause in which age at onset may reflect genetic vulnerability. Though there has been some association between genetic polymorphisms and age of onset, there has been little exploration of the role of epigenetic processes. We sought to explore the influence of DNA methylation, a key epigenetic mechanism, and its association with the age of onset of illness. METHODS One hundred thirty-eight participants aged 18-75 years and previously diagnosed with SCZ spectrum disorders by the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders (SCID DSM-5) were recruited. Venous blood was collected and genome-wide DNA methylation was quantified using the Illumina Infinium HumanMethylation450 BeadChip array. Individual CpG sites and regions of differential methylation were explored by the age of onset; covariates included age, sex, as well as white blood cell composition. RESULTS Binary grouping (early vs. late onset) revealed four intergenic CpG sites on chromosome 2 that were above the expected P-value threshold, with hypermethylation of the CpG site cg10392614 most strongly associated with early-onset SCZ. The four most strongly associated CpG sites, including cg 10392614, were intergenic. Continuous analysis revealed the top CpG site to be cg11723066 , which is linked to the JAM3 gene, with hypomethylation associated with earlier onset; however, results were below the expected P-value threshold. CONCLUSION Studies on DNA methylation in the first-episode psychosis population may help further our understanding of the role of epigenetics in the age of onset of SCZ.
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C. Chi G, Liu Y, MacDonald JW, M. Reynolds L, Enquobahrie DA, L. Fitzpatrick A, Kerr KF, J. Budoff M, Lee SI, Siscovick D, D. Kaufman J. Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. Epigenetics 2022; 17:297-313. [PMID: 33818294 PMCID: PMC8920186 DOI: 10.1080/15592294.2021.1900028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Air pollution might affect atherosclerosis through DNA methylation changes in cells crucial to atherosclerosis, such as monocytes. We conducted an epigenome-wide study of DNA methylation in CD14+ monocytes and long-term ambient air pollution exposure in adults participating in the Multi-Ethnic Study of Atherosclerosis (MESA). We also assessed the association between differentially methylated signals and cis-gene expression. Using spatiotemporal models, one-year average concentrations of outdoor fine particulate matter (PM2.5) and oxides of nitrogen (NOX) were estimated at participants' homes. We assessed DNA methylation and gene expression using Illumina 450k and HumanHT-12 v4 Expression BeadChips, respectively (n = 1,207). We used bump hunting and site-specific approaches to identify differentially methylated signals (false discovery rate of 0.05) and used linear models to assess associations between differentially methylated signals and cis-gene expression. Four differentially methylated regions (DMRs) located on chromosomes 5, 6, 7, and 16 (within or near SDHAP3, ZFP57, HOXA5, and PRM1, respectively) were associated with PM2.5. The DMRs on chromosomes 5 and 6 also associated with NOX. The DMR on chromosome 5 had the smallest p-value for both PM2.5 (p = 1.4×10-6) and NOX (p = 7.7×10-6). Three differentially methylated CpGs were identified for PM2.5, and cg05926640 (near TOMM20) had the smallest p-value (p = 5.6×10-8). NOX significantly associated with cg11756214 within ZNF347 (p = 5.6×10-8). Several differentially methylated signals were also associated with cis-gene expression. The DMR located on chromosome 7 was associated with the expression of HOXA5, HOXA9, and HOXA10. The DMRs located on chromosomes 5 and 16 were associated with expression of MRPL36 and DEXI, respectively. The CpG cg05926640 was associated with expression of ARID4B, IRF2BP2, and TOMM20. We identified differential DNA methylation in monocytes associated with long-term air pollution exposure. Methylation signals associated with gene expression might help explain how air pollution contributes to cardiovascular disease.
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Affiliation(s)
- Gloria C. Chi
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,CONTACT Gloria C. Chi 1 DNA Way, South San Francisco, CA 94080
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Lindsay M. Reynolds
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Daniel A. Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Annette L. Fitzpatrick
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Family Medicine, School of Medicine, University of Washington, Seattle, Washington, USA,Department of Global Health, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Kathleen F. Kerr
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Matthew J. Budoff
- Division of Cardiology, Los Angeles Biomedical Research Institute at Harbor–UCLA Medical Center, Torrance, California, USA
| | - Su-in Lee
- Department of Computer Science & Engineering, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Joel D. Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
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Adanty C, Shakeri A, Strauss J, Graff A, De Luca V. Head-to-head comparison of various antipsychotic agents on genome-wide methylation in schizophrenia. Pharmacogenomics 2021; 23:5-14. [PMID: 34787483 DOI: 10.2217/pgs-2021-0113] [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] Open
Abstract
Aim: To explore possible differences in genome-wide methylation between schizophrenia patients who consume various antipsychotics. Methods: We compared DNA methylation in leukocytes between the following cohorts: clozapine (n = 19) versus risperidone (n = 19), clozapine (n = 12) versus olanzapine (n = 12), clozapine (n = 9) versus quetiapine (n = 9) and clozapine (n = 33) versus healthy controls (n = 33). Subjects were matched for age, sex, ethnicity, smoking status and leukocyte proportions. Results: No single CpG site reached genome-wide significance for clozapine versus risperidone/olanzapine/quetiapine. For clozapine versus quetiapine, one significantly differentially methylated region was found - ch5: 176797920-176798049 (fwer = 0.075). Clozapine versus healthy controls yielded thousands of significantly differentially methylated CpG sites. Conclusions: Establishing antipsychotic induced genome-wide methylation patterns will further elucidate the biological and clinical effects of antipsychotic administration.
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Affiliation(s)
| | - Ahmad Shakeri
- Centre for Addiction & Mental Health, Toronto, Canada
| | - John Strauss
- Centre for Addiction & Mental Health, Toronto, Canada
| | - Ariel Graff
- Centre for Addiction & Mental Health, Toronto, Canada
| | - Vincenzo De Luca
- Centre for Addiction & Mental Health, Toronto, Canada.,St Michael's Hospital, Toronto, Canada
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Praticò AD, Falsaperla R, Polizzi A, Ruggieri M. Monogenic Epilepsies: Channelopathies, Synaptopathies, mTorpathies, and Otheropathies. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractEpilepsy has been historically defined as the recurrence of two or more seizures, together with typical electroencephalogram (EEG) changes, and significant comorbidities, including cardiac and autonomic changes, injuries, intellectual disability, permanent brain damage, and higher mortality risk. Epilepsy may be the consequence of several causes, including genetic anomalies, structural brain malformations, hypoxic–ischemic encephalopathy, brain tumors, drugs, and all contributing factors to the imbalance between excitatory and inhibitory neurons and modulatory interneurons which in turn provoke abnormal, simultaneous electric discharge(s) involving part, or all the brain. In the pregenetic, pregenomic era, in most cases, the exact cause of such neuronal/interneuronal disequilibrium remained unknown and the term “idiopathic epilepsy” was used to define all the epilepsies without cause. At the same time, some specific epileptic syndromes were indicated by the eponym of the first physician who originally described the condition (e.g., the West syndrome, Dravet syndrome, Ohtahara syndrome, and Lennox–Gastaut syndrome) or by some characteristic clinical features (e.g., nocturnal frontal lobe epilepsy, absence epilepsy, and epilepsy and mental retardation limited to females). In many of these occurrences, the distinct epileptic syndrome was defined mainly by its most relevant clinical feature (e.g., seizure semiology), associated comorbidities, and EEGs patterns. Since the identification of the first epilepsy-associated gene (i.e., CHRNA4 gene: cholinergic receptor neuronal nicotinic α polypeptide 4), one of the genes responsible for autosomal dominant nocturnal frontal lobe epilepsy (currently known as sleep-related hypermotor epilepsy) in 1995, the field of epilepsy and the history of epilepsy gene discoveries have gone through at least three different stages as follows: (1) an early stage of relentless gene discovery in monogenic familial epilepsy syndromes; (2) a relatively quiescent and disappointing period characterized by largely negative genome-wide association candidate gene studies; and (3) a genome-wide era in which large-scale molecular genetic studies have led to the identification of several novel epilepsy genes, especially in sporadic forms of epilepsy. As of 2021, more than 150 epilepsy-associated genes or loci are listed in the Online Mendelian Inheritance in Man database.
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Affiliation(s)
- Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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Ahmadi Z, Fathi-Hafshejani P, Kayali E, Beidaghi M, Mahjouri-Samani M. Rapid laser nanomanufacturing and direct patterning of 2D materials on flexible substrates-2DFlex. NANOTECHNOLOGY 2021; 32:055302. [PMID: 33075755 DOI: 10.1088/1361-6528/abc285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Direct synthesis, large-scale integration, and patterning of two-dimensional (2D) quantum materials (e.g. MoS2, WSe2) on flexible and transparent substrates are of high interest for flexible and conformal device applications. However, the growth temperatures (e.g. 850 °C) of the emerging 2D materials in the common gas-phase synthesis methods are well beyond the tolerances limit of flexible substrates, such as polydimethylsiloxane (PDMS). In addition, random nucleation and growth process in most growth systems limits the predicted integration and patterning freedoms. Here, we report a rapid direct laser crystallization and mask-free large-scale patterning of MoS2 and WSe2 crystals on PDMS substrates. A thin layer of stoichiometric amorphous 2D film is first laser-deposited via pulsed laser deposition (PLD) system onto the flexible substrates followed by a controlled crystallization and direct writing process using a tunable nanosecond laser (1064 nm). The influences of pulse duration, number of pulses, and the thickness of the deposited amorphous 2D layer on the crystallization of 2D materials are discussed. Optical spectroscopy and electrical characterizations are performed to confirm the quality of crystallized 2D materials on flexible substrates. This novel method opens up a new opportunity for the crystallization of complex patterns directly from computer-aided design models for the future 2D materials-based wearable, transparent, and flexible devices.
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Affiliation(s)
- Zabihollah Ahmadi
- Department of Electrical and Computer Engineering, Auburn University, Auburn, AL, 36849, United States of America
| | - Parvin Fathi-Hafshejani
- Department of Electrical and Computer Engineering, Auburn University, Auburn, AL, 36849, United States of America
| | - Emre Kayali
- Department of Mechanical and Material Engineering, Auburn University, Auburn, AL, 36849, United States of America
| | - Majid Beidaghi
- Department of Mechanical and Material Engineering, Auburn University, Auburn, AL, 36849, United States of America
| | - Masoud Mahjouri-Samani
- Department of Electrical and Computer Engineering, Auburn University, Auburn, AL, 36849, United States of America
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