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Angelin M, Gopinath P, Raghavan V, Thara R, Ahmad F, Munirajan AK, Sudesh R. Global DNA and RNA Methylation Signature in Response to Antipsychotic Treatment in First-Episode Schizophrenia Patients. Neuropsychiatr Dis Treat 2024; 20:1435-1444. [PMID: 39049939 PMCID: PMC11268744 DOI: 10.2147/ndt.s466502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Background Schizophrenia is a heterogeneous chronic psychiatric disorder influenced by genetic and environmental factors. Environmental factors can alter epigenetic marks, which regulate gene expression and cause an array of systemic changes. Several studies have demonstrated the association of epigenetic modulations in schizophrenia, which can influence clinical course, symptoms, and even treatment. Based on this, we have examined the global DNA methylation patterns, namely the 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC); and the global RNA modification N6-methyladenosine (m6A) RNA methylation status in peripheral blood cells. First-Episode Psychosis (FEP) patients who were diagnosed with Schizophrenia (SCZ) and undergoing treatment were stratified as Treatment-Responsive (TR) and Treatment-Non-Responsive (TNR). Age- and sex-matched healthy subjects served as controls. Results The methylation pattern of 5mC and 5hmC showed significant increases in patients in comparison to controls. Further, when patients were classified based on their response to treatment, there was a statistically significant increase in methylation patterns in the treatment non-responder group. 5fC and m6A levels did not show any statistical significance across the groups. Further, gender-based stratification did not yield any significant difference for the markers. Conclusion The study highlights the increased global methylation pattern in SCZ patients and a significant difference between the TR versus TNR groups. Global 5mC and 5hmC epigenetic marks suggest their potential roles in schizophrenia pathology, and also in the treatment response to antipsychotics. Since not many studies were available on the treatment response, further validation and the use of more sensitive techniques to study methylation status could unravel the potential of these epigenetic modifications as biomarkers for SCZ as well as distinguishing the antipsychotic treatment response in patients.
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Affiliation(s)
- Mary Angelin
- Department of Genetics, University of Madras, Dr ALM PG Institute of Basic Medical Sciences, Taramani Campus, Chennai, Tamil Nadu, 600 113, India
| | - Padmavathi Gopinath
- Department of Genetics, University of Madras, Dr ALM PG Institute of Basic Medical Sciences, Taramani Campus, Chennai, Tamil Nadu, 600 113, India
| | - Vijaya Raghavan
- Department of Genetics, University of Madras, Dr ALM PG Institute of Basic Medical Sciences, Taramani Campus, Chennai, Tamil Nadu, 600 113, India
- Schizophrenia Research Foundation, Chennai, Tamil Nadu, 600 101, India
| | - Rangaswamy Thara
- Schizophrenia Research Foundation, Chennai, Tamil Nadu, 600 101, India
| | - Faraz Ahmad
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Arasamabattu Kannan Munirajan
- Department of Genetics, University of Madras, Dr ALM PG Institute of Basic Medical Sciences, Taramani Campus, Chennai, Tamil Nadu, 600 113, India
| | - Ravi Sudesh
- Department of Biomedical Sciences, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
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Gore S, Meche B, Shao D, Ginnett B, Zhou K, Azad RK. DiseaseNet: a transfer learning approach to noncommunicable disease classification. BMC Bioinformatics 2024; 25:107. [PMID: 38468193 PMCID: PMC10926612 DOI: 10.1186/s12859-024-05734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such as DNA methylation, have emerged as potential indicators for NCDs. These have previously been exploited in other contexts within the framework of neural network models that capture complex relationships within the data. Applications of neural networks have led to significant breakthroughs in various biological or biomedical fields but these have not yet been effectively applied to NCD modeling. This is, in part, due to limited datasets that are not amenable to building of robust neural network models. In this work, we leveraged a neural network trained on one class of NCDs, cancer, as the basis for a transfer learning approach to non-cancer NCD modeling. Our results demonstrate promising performance of the model in predicting three NCDs, namely, arthritis, asthma, and schizophrenia, for the respective blood samples, with an overall accuracy (f-measure) of 94.5%. Furthermore, a concept based explanation method called Testing with Concept Activation Vectors (TCAV) was used to investigate the importance of the sample sources and understand how future training datasets for multiple NCD models may be improved. Our findings highlight the effectiveness of transfer learning in developing accurate diagnostic and predictive models for NCDs.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Bailey Meche
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Danyang Shao
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Benjamin Ginnett
- Department of Engineering, Eastern Arizona College, Thatcher, AZ, USA
| | - Kelly Zhou
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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Rowbal T, Kajy M, Burghardt KJ. Epigenome-wide studies of antipsychotics: a systematic review and pathway meta-analysis. Epigenomics 2023; 15:1085-1094. [PMID: 37933568 PMCID: PMC10663877 DOI: 10.2217/epi-2023-0222] [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: 06/20/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
Background & methods: Researchers have aimed to understand the mechanisms of antipsychotics through epigenetics to inform interindividual response rates. However, findings have widely varied across studies, making advancement in the field difficult. Materials & methods: A systematic review was performed to include all epigenome-wide studies of antipsychotic treatment in humans. Methylation sites were used for a pathway and enrichment map analysis was conducted. Results & conclusion: Seven studies were included and 82 methylation sites were used for the exploratory pathway meta-analysis that identified six pathway clusters. The findings here demonstrate that studies of the epigenome and antipsychotic treatment are highly heterogeneous in nature and could inform future work to target cross-cutting gene sets and pathways.
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Affiliation(s)
- Thomas Rowbal
- Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48202, USA
| | - Megan Kajy
- Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48202, USA
| | - Kyle J Burghardt
- Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48202, USA
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Rimawi I, Yanai S, Turgeman G, Yanai J. Whole transcriptome analysis in offspring whose fathers were exposed to a developmental insult: a novel avian model. Sci Rep 2023; 13:16499. [PMID: 37779136 PMCID: PMC10543553 DOI: 10.1038/s41598-023-43593-x] [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: 03/31/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
Although the effects of paternal exposure to insults on the offspring received limited attention in the past, it is currently gaining interest especially after understanding the mechanisms which may mediate such exposure effects. In the current study, the well-controlled avian model (Fayoumi) was utilized to investigate the effects of paternal exposure to the developmental insult, chlorpyrifos on the offspring's gene expression via mRNA and small RNA sequencing. Numerous mRNA gene expression changes were detected in the offspring after paternal exposure to the developmental insult, especially in genes related to neurogenesis, learning and memory. qPCR analysis of several genes, that were significantly changed in mRNA sequencing, confirmed the results obtained in mRNA sequencing. On the other hand, small RNA sequencing did not identify significant microRNA genes expression changes in the offspring after paternal exposure to the developmental insult. The effects of the paternal exposure were more pronounced in the female offspring compared to the male offspring. The results identified expression alterations in major genes (some of which were pertinent to the functional changes observed in other forms of early developmental exposure) after paternal insult exposure and provided a direction for future studies involving the most affected genes.
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Affiliation(s)
- Issam Rimawi
- The Ross Laboratory for Studies in Neural Birth Defects, Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, P.O. Box 12272, 91120, Jerusalem, Israel
| | - Sunny Yanai
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gadi Turgeman
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Joseph Yanai
- The Ross Laboratory for Studies in Neural Birth Defects, Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, P.O. Box 12272, 91120, Jerusalem, Israel.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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Iqbal MA, Hadlich F, Reyer H, Oster M, Trakooljul N, Murani E, Perdomo‐Sabogal A, Wimmers K, Ponsuksili S. RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken. Evol Appl 2023; 16:1135-1153. [PMID: 37360029 PMCID: PMC10286233 DOI: 10.1111/eva.13557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/28/2023] Open
Abstract
Recent advances in the selective breeding of broilers and layers have made poultry production one of the fastest-growing industries. In this study, a transcriptome variant calling approach from RNA-seq data was used to determine population diversity between broilers and layers. In total, 200 individuals were analyzed from three different chicken populations (Lohmann Brown (LB), n = 90), Lohmann Selected Leghorn (LSL, n = 89), and Broiler (BR, n = 21). The raw RNA-sequencing reads were pre-processed, quality control checked, mapped to the reference genome, and made compatible with Genome Analysis ToolKit for variant detection. Subsequently, pairwise fixation index (F ST) analysis was performed between broilers and layers. Numerous candidate genes were identified, that were associated with growth, development, metabolism, immunity, and other economically significant traits. Finally, allele-specific expression (ASE) analysis was performed in the gut mucosa of LB and LSL strains at 10, 16, 24, 30, and 60 weeks of age. At different ages, the two-layer strains showed significantly different allele-specific expressions in the gut mucosa, and changes in allelic imbalance were observed across the entire lifespan. Most ASE genes are involved in energy metabolism, including sirtuin signaling pathways, oxidative phosphorylation, and mitochondrial dysfunction. A high number of ASE genes were found during the peak of laying, which were particularly enriched in cholesterol biosynthesis. These findings indicate that genetic architecture as well as biological processes driving particular demands relate to metabolic and nutritional requirements during the laying period shape allelic heterogeneity. These processes are considerably affected by breeding and management, whereby elucidating allele-specific gene regulation is an essential step towards deciphering the genotype to phenotype map or functional diversity between the chicken populations. Additionally, we observed that several genes showing significant allelic imbalance also colocalized with the top 1% of genes identified by the FST approach, suggesting a fixation of genes in cis-regulatory elements.
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Affiliation(s)
| | - Frieder Hadlich
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Henry Reyer
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Michael Oster
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Nares Trakooljul
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Eduard Murani
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | | | - Klaus Wimmers
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
- Faculty of Agricultural and Environmental SciencesUniversity RostockRostockGermany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
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Micale V, Di Bartolomeo M, Di Martino S, Stark T, Dell'Osso B, Drago F, D'Addario C. Are the epigenetic changes predictive of therapeutic efficacy for psychiatric disorders? A translational approach towards novel drug targets. Pharmacol Ther 2023; 241:108279. [PMID: 36103902 DOI: 10.1016/j.pharmthera.2022.108279] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
The etiopathogenesis of mental disorders is not fully understood and accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, the study of these mechanisms may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
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Affiliation(s)
- Vincenzo Micale
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Tibor Stark
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Scientific Core Unit Neuroimaging, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences 'Luigi Sacco', University of Milan, Milan, Italy, Department of Mental Health, ASST Fatebenefratelli-Sacco, Milan, Italy; "Aldo Ravelli" Research Center for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan Medical School, Milan, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Aytac HM, Oyaci Y, Pehlivan M, Pehlivan S. DNA Methylation Pattern of Gene Promoters of MB-COMT, DRD2, and NR3C1 in Turkish Patients Diagnosed with Schizophrenia. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE : THE OFFICIAL SCIENTIFIC JOURNAL OF THE KOREAN COLLEGE OF NEUROPSYCHOPHARMACOLOGY 2022; 20:685-693. [PMID: 36263643 PMCID: PMC9606422 DOI: 10.9758/cpn.2022.20.4.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 01/25/2023]
Abstract
OBJECTIVE We aim to evaluate the methylation status of membrane-bound catechol-O-methyltransferase (MB-COMT) promotor, dopamine receptor D2 (DRD2), and nuclear receptor subfamily 3 group C member 1 (NR3C1) gene in pa- tients with SCZ by comparing healthy controls. METHODS A sample of 110 patients with SCZ and 100 age- and sex-matched healthy volunteers was included in the study. The interview was started by filling out data forms that included sociodemographic and clinical information. The Structured Clinical Interview for DSM-IV Axis I Disorders was used to confirming the diagnosis according to DSM-IV-TR criteria. Then the patients were evaluated with the Positive and Negative Symptoms Scale in terms of symp- tom severity. Methylation-specific polymerase chain reaction was used to determine the methylation status of MB-COMT promotor, DRD2 , and NR3C1 gene from DNA material. RESULTS When we compared the percentages of MB-COMT promotor, DRD2, and NR3C1 gene methylation status in SCZ patients with the healthy control group, the percentages of MB-COMT promotor (OR: 0.466; 95% CI: 0.268- 0.809; p = 0.006), DRD2 (OR: 0.439; 95% CI: 0.375-0.514; p < 0.001), and NR3C1 (OR: 0.003; 95% CI: 0.001- 0.011; p < 0.001) gene methylation status of SCZ was found to be significantly different from the control group. Whereas unmethylation of MB-COMT promotor and NR3C1 genes were associated with SCZ, the partial methylation of the DRD2 gene was related to the SCZ. CONCLUSION The MB-COMT promotor, DRD2, and NR3C1 gene methylation status may be associated with the SCZ in the Turkish population.
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Affiliation(s)
- Hasan Mervan Aytac
- Department of Psychiatry, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey,Address for correspondence: Hasan Mervan Aytac Department of Psychiatry, Basaksehir Cam and Sakura City Hospital, G-434 Street, No: 2L, Basaksehir, Istanbul 34944, Turkey, E-mail: , ORCID: https://orcid.org/0000-0002-1053-6808
| | - Yasemin Oyaci
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mustafa Pehlivan
- Department of Hematology, Gaziantep University, Faculty of Medicine, Gaziantep, Turkey
| | - Sacide Pehlivan
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Li L, Rami FZ, Lee BM, Kim WS, Kim SW, Lee BJ, Yu JC, Lee KY, Won SH, Lee SH, Kim SH, Kang SH, Kim E, Chung YC. Three-year outcomes and predictors for full recovery in patients with early-stage psychosis. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:87. [PMID: 36302861 PMCID: PMC9613771 DOI: 10.1038/s41537-022-00301-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/15/2022] [Indexed: 05/19/2023]
Abstract
In the present study, various outcomes over 3-year period in patients with early stage psychosis including remission, recovery, relapse and medication adherence were investigated. Predictor for full recovery at year 3 was also examined. Three-year follow-up data in 534 patients with schizophrenia spectrum disorders (SSD) and psychotic disorder not otherwise specified (PNOS) were examined for overall outcome trajectories. The data of completers at year 3 (n = 157) were used to identify predictors for recovery using logistic regression. The rates of symptomatic remission and full recovery at 6-, 12-, 24-, and 36-month follow-up were 76.10, 69.20, 79.50, and 79.10%, and 22.80, 26.40, 28.60, and 39.60%, respectively. The rates of drop-out and relapse at 6-, 12-, 24-, and 36-month follow-up were 25.4, 29.5, 38.6, and 51.1%, and 3.7, 8.9, 19.0, and 38.9%, respectively. The rates of good adherence and prescription of Long-Acting Injectable Antipsychotics (LAIA) at 6-, 12-, 24- and 36-month follow-up were 87.8, 88.0, 91.9, and 93.9%, and 18.3, 21.7, 22.0, and 25.5%, respectively. Significant predictors for full recovery were duration of untreated psychosis (DUP), family intimacy and physical activity. We observed similar or better results on remission, recovery, and relapse rates compared to other previous studies. Effective psychosocial intervention should be provided to shorten the gap between remission and recovery rates and to address DUP, family issues, and exercise to enhance recovery.
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Affiliation(s)
- Ling Li
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Fatima Zahra Rami
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Bo Mi Lee
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Woo-Sung Kim
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Bong Ju Lee
- Department of Psychiatry, Inje University Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Je-Chun Yu
- Department of Psychiatry, Eulji University School of Medicine, Eulji University Hospital, Daejeon, Republic of Korea
| | - Kyu Young Lee
- Department of Psychiatry, Eulji University School of Medicine, Eulji General Hospital, Seoul, Republic of Korea
| | - Seung-Hee Won
- Department of Psychiatry, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Seung-Hwan Lee
- Department of Psychiatry, Inje University College of Medicine, Goyang, Republic of Korea
| | - Seung-Hyun Kim
- Department of Psychiatry, Korea University College of Medicine, Guro Hospital, Seoul, Republic of Korea
| | - Shi Hyun Kang
- Department of Social Psychiatry and Rehabilitation, National Center for Mental Health, Seoul, Republic of Korea
| | - Euitae Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Young-Chul Chung
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Republic of Korea.
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea.
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Piao YH, Cui Y, Rami FZ, Li L, Karamikheirabad M, Kang SH, Kim SW, Kim JJ, Lee BJ, Chung YC. Methylome-wide Association Study of Patients with Recent-onset Psychosis. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2022; 20:462-473. [PMID: 35879030 PMCID: PMC9329103 DOI: 10.9758/cpn.2022.20.3.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022]
Abstract
Objective Dysregulation of gene expression through epigenetic mechanisms may have a vital role in the pathogenesis of schizophrenia (SZ). In this study, we investigated the association of altered methylation patterns with SZ symptoms and early trauma in patients and healthy controls. Methods The present study was conducted to identify methylation changes in CpG sites in peripheral blood associated with recent-onset (RO) psychosis using methylome-wide analysis. Lifestyle factors, such as smoking, alcohol, exercise, and diet, were controlled. Results We identified 2,912 differentially methylated CpG sites in patients with RO psychosis compared to controls. Most of the genes associated with the top 20 differentially methylated sites had not been reported in previous methylation studies and were involved in apoptosis, autophagy, axonal growth, neuroinflammation, protein folding, etc. The top 15 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways included the oxytocin signaling pathway, long-term depression pathway, axon guidance, endometrial cancer, long-term potentiation, mitogen-activated protein kinase signaling pathway, and glutamatergic pathway, among others. In the patient group, significant associations of novel methylated genes with early trauma and psychopathology were observed. Conclusion Our results suggest an association of differential DNA methylation with the pathophysiology of psychosis and early trauma. Blood DNA methylation signatures show promise as biomarkers of future psychosis.
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Affiliation(s)
- Yan-Hong Piao
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Yin Cui
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Fatima Zahra Rami
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Ling Li
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Maryam Karamikheirabad
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Shi Hyun Kang
- Department of Social Psychiatry and Rehabilitation, National Center for Mental Health, Seoul, Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Jung Jin Kim
- Department of Psychiatry, The Catholic University of Korea, Seoul St. Mary’s Hospital, Seoul, Korea
| | - Bong Ju Lee
- Department of Psychiatry, Inje University Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Young-Chul Chung
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
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McKinney BC, McClain LL, Hensler CM, Wei Y, Klei L, Lewis DA, Devlin B, Wang J, Ding Y, Sweet RA. Schizophrenia-associated differential DNA methylation in brain is distributed across the genome and annotated to MAD1L1, a locus at which DNA methylation and transcription phenotypes share genetic variation with schizophrenia risk. Transl Psychiatry 2022; 12:340. [PMID: 35987687 PMCID: PMC9392724 DOI: 10.1038/s41398-022-02071-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
DNA methylation (DNAm), the addition of a methyl group to a cytosine in DNA, plays an important role in the regulation of gene expression. Single-nucleotide polymorphisms (SNPs) associated with schizophrenia (SZ) by genome-wide association studies (GWAS) often influence local DNAm levels. Thus, DNAm alterations, acting through effects on gene expression, represent one potential mechanism by which SZ-associated SNPs confer risk. In this study, we investigated genome-wide DNAm in postmortem superior temporal gyrus from 44 subjects with SZ and 44 non-psychiatric comparison subjects using Illumina Infinium MethylationEPIC BeadChip microarrays, and extracted cell-type-specific methylation signals by applying tensor composition analysis. We identified SZ-associated differential methylation at 242 sites, and 44 regions containing two or more sites (FDR cutoff of q = 0.1) and determined a subset of these were cell-type specific. We found mitotic arrest deficient 1-like 1 (MAD1L1), a gene within an established GWAS risk locus, harbored robust SZ-associated differential methylation. We investigated the potential role of MAD1L1 DNAm in conferring SZ risk by assessing for colocalization among quantitative trait loci for methylation and gene transcripts (mQTLs and tQTLs) in brain tissue and GWAS signal at the locus using multiple-trait-colocalization analysis. We found that mQTLs and tQTLs colocalized with the GWAS signal (posterior probability >0.8). Our findings suggest that alterations in MAD1L1 methylation and transcription may mediate risk for SZ at the MAD1L1-containing locus. Future studies to identify how SZ-associated differential methylation affects MAD1L1 biological function are indicated.
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Affiliation(s)
- Brandon C McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Lora L McClain
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher M Hensler
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yue Wei
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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11
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DNA Methylation Profiles of the DRD2 and NR3C1 Genes in Patients with Recent-Onset Psychosis. DISEASE MARKERS 2022; 2022:2172564. [PMID: 35968502 PMCID: PMC9365600 DOI: 10.1155/2022/2172564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/25/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023]
Abstract
Objectives Dopamine receptor D2 gene (DRD2) and glucocorticoid receptor gene (NR3C1) are implicated in the development of psychosis. We investigated methylation levels of DRD2 and NR3C1 in peripheral blood of patients with recent-onset (RO) psychosis using bisulfite pyrosequencing as well as its association with childhood trauma and rumination. Methods In all, 51 individuals with RO psychosis and 47 healthy controls were recruited. DNA methylation levels in the targeted regions of two genes were analyzed and compared. Childhood trauma and rumination were evaluated using the Early Trauma Inventory Self-Report Short Form (ETI-SF) and Brooding Scale (BS), respectively. Correlations between the scores of the ETI-SF and BS and methylation levels were explored. Results For DRD2, we found no significant differences between groups in terms of methylation level or association with childhood trauma or rumination. For NR3C1, we found a trend level significance for average value of all CpG sites and significant hypermethylation or hypomethylation at specific sites. There was also a significant positive correlation between the methylation level at the CpG8 site of NR3C1 exon 1F and negative symptom subscale score of the PANSS (PANSS-N). Conclusion Epigenetic alterations of NR3C1 are associated with the pathophysiology of psychosis. Further epigenetic studies will elucidate the molecular mechanisms underpinning the pathophysiology of psychosis.
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12
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Alameda L, Trotta G, Quigley H, Rodriguez V, Gadelrab R, Dwir D, Dempster E, Wong CCY, Forti MD. Can epigenetics shine a light on the biological pathways underlying major mental disorders? Psychol Med 2022; 52:1645-1665. [PMID: 35193719 PMCID: PMC9280283 DOI: 10.1017/s0033291721005559] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/30/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
A significant proportion of the global burden of disease can be attributed to mental illness. Despite important advances in identifying risk factors for mental health conditions, the biological processing underlying causal pathways to disease onset remain poorly understood. This represents a limitation to implement effective prevention and the development of novel pharmacological treatments. Epigenetic mechanisms have emerged as mediators of environmental and genetic risk factors which might play a role in disease onset, including childhood adversity (CA) and cannabis use (CU). Particularly, human research exploring DNA methylation has provided new and promising insights into the role of biological pathways implicated in the aetio-pathogenesis of psychiatric conditions, including: monoaminergic (Serotonin and Dopamine), GABAergic, glutamatergic, neurogenesis, inflammatory and immune response and oxidative stress. While these epigenetic changes have been often studied as disease-specific, similarly to the investigation of environmental risk factors, they are often transdiagnostic. Therefore, we aim to review the existing literature on DNA methylation from human studies of psychiatric diseases (i) to identify epigenetic modifications mapping onto biological pathways either transdiagnostically or specifically related to psychiatric diseases such as Eating Disorders, Post-traumatic Stress Disorder, Bipolar and Psychotic Disorder, Depression, Autism Spectrum Disorder and Anxiety Disorder, and (ii) to investigate a convergence between some of these epigenetic modifications and the exposure to known risk factors for psychiatric disorders such as CA and CU, as well as to other epigenetic confounders in psychiatry research.
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Affiliation(s)
- Luis Alameda
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Departamento de Psiquiatría, Centro Investigación Biomedica en Red de Salud Mental (CIBERSAM), Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Sevilla, Spain
| | - Giulia Trotta
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Harriet Quigley
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Victoria Rodriguez
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Romayne Gadelrab
- Centre for Affective Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Daniella Dwir
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, UK
| | - Chloe C. Y. Wong
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Marta Di Forti
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
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13
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Chuang TD, Quintanilla D, Boos D, Khorram O. Differential Expression of Super-Enhancer-Associated Long Non-coding RNAs in Uterine Leiomyomas. Reprod Sci 2022; 29:2960-2976. [PMID: 35641855 PMCID: PMC9537225 DOI: 10.1007/s43032-022-00981-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
Super-enhancer-associated long non-coding RNAs (SE-lncRNAs) are a specific set of lncRNAs transcribed from super-enhancer (SE) genomic regions. Recent studies have revealed that SE-lncRNAs play essential roles in tumorigenesis through the regulation of oncogenes. The objective of this study was to elucidate the expression profile of SE-lncRNAs with concurrent assessment of associated mRNAs in leiomyomas and paired myometrium. Arraystar SE-lncRNAs arrays were used to systematically profile the differentially expressed SE-lncRNAs along with the corresponding SE-regulated protein coding genes in eight leiomyomas and paired myometrium. The analysis indicated 7680 SE-lncRNAs were expressed, of which 721 SE-lncRNAs were overexpressed, while 247 SE-lncRNAs were underexpressed by 1.5-fold or greater in leiomyoma. Thirteen novel SE-lncRNAs and their corresponding protein coding genes were selected, and their expression was confirmed in eighty-one paired leiomyoma tissues by quantitative real-time PCR. The thirteen pairs of SE-lncRNAs and their corresponding protein coding genes included RP11-353N14.2/CBX4, SOCS2-AS1/SOCS2, RP1-170O19.14/HOXA11, CASC15/PRL, EGFLAM-AS1/EGFLAM, RP11-225H22/NEURL1, RP5-1086K13.1/CD58, AC092839.3/SPTBN1, RP11-69I8.3/CTGF, TM4SF1-AS1/TM4SF1, RP11-373D23/FOSL2, RP11-399K21.11/COMTD1, and CTB-113P19.1/SPARC. Among these SE-lncRNAs, the expression of SOCS2-AS1/SOCS2, RP11-353N14.2/CBX4, RP1-170O19.14/HOXA11, and RP11-225H22/NEURL1 was significantly higher in African Americans as compared with Caucasians. The expression of RP11-353N14.2/CBX4, SOCS2-AS1/SOCS2, CASC15/PRL, and CTB-113P19.1/SPARC was significantly higher in tumors with MED12-mutation-positive as compared with MED12-mutation-negative tumors. Collectively, our results indicate that the differential expression of SE in leiomyomas is another mechanism contributing to dysregulation of protein coding genes in leiomyomas and that race and MED12 mutation can influence the expression of a select group of SE.
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Affiliation(s)
- Tsai-Der Chuang
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, CA, 90502, USA
| | - Derek Quintanilla
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, CA, 90502, USA
| | - Drake Boos
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, CA, 90502, USA
| | - Omid Khorram
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, CA, 90502, USA.
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14
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Zhang X, Lee J, Goh WWB. An Investigation of How Normalisation and Local Modelling Techniques Confound Machine Learning Performance In a Mental Health Study. Heliyon 2022; 8:e09502. [PMID: 35663731 PMCID: PMC9156999 DOI: 10.1016/j.heliyon.2022.e09502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/12/2022] [Accepted: 05/16/2022] [Indexed: 01/12/2023] Open
Abstract
Machine learning (ML) is increasingly deployed on biomedical studies for biomarker development (feature selection) and diagnostic/prognostic technologies (classification). While different ML techniques produce different feature sets and classification performances, less understood is how upstream data processing methods (e.g., normalisation) impact downstream analyses. Using a clinical mental health dataset, we investigated the impact of different normalisation techniques on classification model performance. Gene Fuzzy Scoring (GFS), an in-house developed normalisation technique, is compared against widely used normalisation methods such as global quantile normalisation, class-specific quantile normalisation and surrogate variable analysis. We report that choice of normalisation technique has strong influence on feature selection. with GFS outperforming other techniques. Although GFS parameters are tuneable, good classification model performance (ROC-AUC > 0.90) is observed regardless of the GFS parameter settings. We also contrasted our results against local modelling, which is meant to improve the resolution and meaningfulness of classification models built on heterogeneous data. Local models, when derived from non-biologically meaningful subpopulations, perform worse than global models. A deep dive however, revealed that the factors driving cluster formation has little to do with the phenotype-of-interest. This finding is critical, as local models are often seen as a superior means of clinical data modelling. We advise against such naivete. Additionally, we have developed a combinatorial reasoning approach using both global and local paradigms: This helped reveal potential data quality issues or underlying factors causing data heterogeneity that are often overlooked. It also assists to explain the model as well as provides directions for further improvement.
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Affiliation(s)
- Xinxin Zhang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jimmy Lee
- North Region & Department of Psychosis, Institute of Mental Health, 539747, Singapore
- Corresponding author.
| | - Wilson Wen Bin Goh
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 636921, Singapore
- Centre for Biomedical Informatics, Nanyang Technological University, 636921, Singapore
- Corresponding author.
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15
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Lockwood L, Miller B, Youssef NA. Epigenetics and first-episode psychosis: A systematic review. Psychiatry Res 2022; 307:114325. [PMID: 34896847 DOI: 10.1016/j.psychres.2021.114325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Schizophrenia has a large disease burden globally. Early intervention in psychosis, and therefore a decreased duration of untreated psychosis, has a positive clinical impact. There are several recognized risk factors for psychosis, including trauma history and substance use. This systematic review examined the literature for studies related to epigenetic changes in first-episode psychosis, with the goal of identifying future research directions. METHODS A literature review was conducted from inception to October 3, 2021 using MedLine/PubMed, Web of Science, and PsycInfo searches with the keywords ("first-episode schizophrenia" OR "first-episode psychosis" OR "drug-naive schizophrenia" OR "drug-naive psychosis") AND (epigenetic OR methylation OR hydroxymethylation OR "histone modification" OR "miRNA") as well as a search of the bibliography of the identified papers. RESULTS Seventeen studies that examined various portions of the genome were included in this systematic review. There were two studies that showed hypomethylation at the LINE-1 portion of the genome and two that showed hypermethylation at LINE-1. Additionally, two studies showed hypomethylation specifically at the GRIN2B promoter (part of LINE-1). CONCLUSIONS Although sample sizes were small, these studies provide evidence for epigenetic alterations in early psychosis. Further research in this area is warranted for more definitive epigenetic correlations.
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Affiliation(s)
| | - Brian Miller
- Department of Psychiatry and Health Behavior, Medical College of Georgia, Augusta, GA, USA
| | - Nagy A Youssef
- Department of Psychiatry and Health Behavior, Ohio State University, Columbus, OH, USA
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16
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Westhoff MLS, Ladwig J, Heck J, Schülke R, Groh A, Deest M, Bleich S, Frieling H, Jahn K. Early Detection and Prevention of Schizophrenic Psychosis-A Review. Brain Sci 2021; 12:11. [PMID: 35053755 PMCID: PMC8774083 DOI: 10.3390/brainsci12010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Psychotic disorders often run a chronic course and are associated with a considerable emotional and social impact for patients and their relatives. Therefore, early recognition, combined with the possibility of preventive intervention, is urgently warranted since the duration of untreated psychosis (DUP) significantly determines the further course of the disease. In addition to established diagnostic tools, neurobiological factors in the development of schizophrenic psychoses are increasingly being investigated. It is shown that numerous molecular alterations already exist before the clinical onset of the disease. As schizophrenic psychoses are not elicited by a single mutation in the deoxyribonucleic acid (DNA) sequence, epigenetics likely constitute the missing link between environmental influences and disease development and could potentially serve as a biomarker. The results from transcriptomic and proteomic studies point to a dysregulated immune system, likely evoked by epigenetic alterations. Despite the increasing knowledge of the neurobiological mechanisms involved in the development of psychotic disorders, further research efforts with large population-based study designs are needed to identify suitable biomarkers. In conclusion, a combination of blood examinations, functional imaging techniques, electroencephalography (EEG) investigations and polygenic risk scores should be considered as the basis for predicting how subjects will transition into manifest psychosis.
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Affiliation(s)
- Martin Lennart Schulze Westhoff
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Johannes Ladwig
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Johannes Heck
- Institute for Clinical Pharmacology, Hannover Medical School, D-30625 Hannover, Germany;
| | - Rasmus Schülke
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Adrian Groh
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Maximilian Deest
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Stefan Bleich
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
| | - Kirsten Jahn
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, D-30625 Hannover, Germany; (J.L.); (R.S.); (A.G.); (M.D.); (S.B.); (H.F.); (K.J.)
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17
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Pedrazzi JFC, Sales AJ, Guimarães FS, Joca SRL, Crippa JAS, Del Bel E. Cannabidiol prevents disruptions in sensorimotor gating induced by psychotomimetic drugs that last for 24-h with probable involvement of epigenetic changes in the ventral striatum. Prog Neuropsychopharmacol Biol Psychiatry 2021; 111:110352. [PMID: 34015384 DOI: 10.1016/j.pnpbp.2021.110352] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023]
Abstract
Cannabidiol (CBD), a major non-psychotomimetic component of the Cannabis sativa plant, shows therapeutic potential in several psychiatric disorders, including schizophrenia. The molecular mechanisms underlying the antipsychotic-like effects of CBD are not fully understood. Schizophrenia and antipsychotic treatment can modulate DNA methylation in the blood and brain, resulting in altered expression of diverse genes associated with this complex disorder. However, to date, the possible involvement of DNA methylation in the antipsychotic-like effects of CBD has not been investigated. Therefore, this study aimed at evaluating in mice submitted to the prepulse inhibition (PPI) model: i) the effects of a single injection of CBD or clozapine followed by AMPH or MK-801 on PPI and global DNA methylation changes in the ventral striatum and prefrontal cortex (PFC); and ii). if the acute antipsychotic-like effects of CBD would last for 24-h. AMPH (5 mg/kg) and MK-801 (0.5 mg/kg) impaired PPI. CBD (30 and 60 mg/kg), similar to clozapine (5 mg/kg), attenuated AMPH- and MK801-induced PPI disruption. AMPH, but not MK-801, increased global DNA methylation in the ventral striatum, an effect prevented by CBD. CBD and clozapine increased, by themselves, DNA methylation in the prefrontal cortex. The acute effects of CBD (30 or 60 mg/kg) on the PPI impairment induced by AMPH or MK-801 was also detectable 24 h later. Altogether, the results show that CBD induces acute antipsychotic-like effects that last for 24-h. It also modulates DNA methylation in the ventral striatum, suggesting a new potential mechanism for its antipsychotic-like effects.
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Affiliation(s)
- João F C Pedrazzi
- Department of Neurosciences and Behavioral Sciences, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Amanda J Sales
- Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Francisco S Guimarães
- Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Sâmia R L Joca
- Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil; Departament of Biomedicine, Aarhus University, Denmark
| | - José A S Crippa
- Department of Neurosciences and Behavioral Sciences, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Elaine Del Bel
- Department of Morphology, Physiology, and Basic Pathology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
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18
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Zhang YH, Li Z, Zeng T, Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One 2021; 16:e0250032. [PMID: 33886611 PMCID: PMC8062050 DOI: 10.1371/journal.pone.0250032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Pregnancy is a complicated and long procedure during one or more offspring development inside a woman. A short period of oxygen shortage after birth is quite normal for most babies and does not threaten their health. However, if babies have to suffer from a long period of oxygen shortage, then this condition is an indication of pathological fetal intolerance, which probably causes their death. The identification of the pathological fetal intolerance from the physical oxygen shortage is one of the important clinical problems in obstetrics for a long time. The clinical syndromes typically manifest five symptoms that indicate that the baby may suffer from fetal intolerance. At present, liquid biopsy combined with high-throughput sequencing or mass spectrum techniques provides a quick approach to detect real-time alteration in the peripheral blood at multiple levels with the rapid development of molecule sequencing technologies. Gene methylation is functionally correlated with gene expression; thus, the combination of gene methylation and expression information would help in screening out the key regulators for the pathogenesis of fetal intolerance. We combined gene methylation and expression features together and screened out the optimal features, including gene expression or methylation signatures, for fetal intolerance prediction for the first time. In addition, we applied various computational methods to construct a comprehensive computational pipeline to identify the potential biomarkers for fetal intolerance dependent on the liquid biopsy samples. We set up qualitative and quantitative computational models for the prediction for fetal intolerance during pregnancy. Moreover, we provided a new prospective for the detailed pathological mechanism of fetal intolerance. This work can provide a solid foundation for further experimental research and contribute to the application of liquid biopsy in antenatal care.
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Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Margarita Gamarra
- Department of Computational Science and Electronic, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Romany F. Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga, Egypt
| | - José Escorcia-Gutierrez
- Electronic and Telecommunicacions Program, Universidad Autónoma del Caribe, Barranquilla, Colombia
- * E-mail: (JEG); (TH); (YDC)
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
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Molecular characterization of the stress network in individuals at risk for schizophrenia. Neurobiol Stress 2021; 14:100307. [PMID: 33644266 PMCID: PMC7893486 DOI: 10.1016/j.ynstr.2021.100307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 01/24/2023] Open
Abstract
The biological mechanisms underlying inter-individual differences in human stress reactivity remain poorly understood. We aimed to identify the molecular underpinning of aberrant neural stress sensitivity in individuals at risk for schizophrenia. Linking mRNA expression data from the Allen Human Brain Atlas to task-based fMRI revealed 201 differentially expressed genes in cortex-specific brain regions differentially activated by stress in individuals with low (healthy siblings of schizophrenia patients) or high (healthy controls) stress sensitivity. These genes are associated with stress-related psychiatric disorders (e.g. schizophrenia and anxiety) and include markers for specific neuronal populations (e.g. ADCYAP1, GABRB1, SSTR1, and TNFRSF12A), neurotransmitter receptors (e.g. GRIN3A, SSTR1, GABRB1, and HTR1E), and signaling factors that interact with the corticosteroid receptor and hypothalamic-pituitary-adrenal axis (e.g. ADCYAP1, IGSF11, and PKIA). Overall, the identified genes potentially underlie altered stress reactivity in individuals at risk for schizophrenia and other psychiatric disorders and play a role in mounting an adaptive stress response in at-risk individuals, making them potentially druggable targets for stress-related diseases.
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Epigenomic Dysregulation in Schizophrenia: In Search of Disease Etiology and Biomarkers. Cells 2020; 9:cells9081837. [PMID: 32764320 PMCID: PMC7463953 DOI: 10.3390/cells9081837] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
Schizophrenia is a severe psychiatric disorder with a complex array of signs and symptoms that causes very significant disability in young people. While schizophrenia has a strong genetic component, with heritability around 80%, there is also a very significant range of environmental exposures and stressors that have been implicated in disease development and neuropathology, such as maternal immune infection, obstetric complications, childhood trauma and cannabis exposure. It is postulated that epigenetic factors, as well as regulatory non-coding RNAs, mediate the effects of these environmental stressors. In this review, we explore the most well-known epigenetic marks, including DNA methylation and histone modification, along with emerging RNA mediators of epigenomic state, including miRNAs and lncRNAs, and discuss their collective potential for involvement in the pathophysiology of schizophrenia implicated through the postmortem analysis of brain tissue. Given that peripheral tissues, such as blood, saliva, and olfactory epithelium have the same genetic composition and are exposed to many of the same environmental exposures, we also examine some studies supporting the application of peripheral tissues for epigenomic biomarker discovery in schizophrenia. Finally, we provide some perspective on how these biomarkers may be utilized to capture a signature of past events that informs future treatment.
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21
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Smigielski L, Jagannath V, Rössler W, Walitza S, Grünblatt E. Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings. Mol Psychiatry 2020; 25:1718-1748. [PMID: 31907379 DOI: 10.1038/s41380-019-0601-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/26/2022]
Abstract
Schizophrenia and other psychotic disorders are highly debilitating psychiatric conditions that lack a clear etiology and exhibit polygenic inheritance underlain by pleiotropic genes. The prevailing explanation points to the interplay between predisposing genes and environmental exposure. Accumulated evidence suggests that epigenetic regulation of the genome may mediate dynamic gene-environment interactions at the molecular level by modulating the expression of psychiatric phenotypes through transcription factors. This systematic review summarizes the current knowledge linking schizophrenia and other psychotic disorders to epigenetics, based on PubMed and Web of Science database searches conducted according to the PRISMA guidelines. Three groups of mechanisms in case-control studies of human tissue (i.e., postmortem brain and bio-fluids) were considered: DNA methylation, histone modifications, and non-coding miRNAs. From the initial pool of 3,204 records, 152 studies met our inclusion criteria (11,815/11,528, 233/219, and 2,091/1,827 cases/controls for each group, respectively). Many of the findings revealed associations with epigenetic modulations of genes regulating neurotransmission, neurodevelopment, and immune function, as well as differential miRNA expression (e.g., upregulated miR-34a, miR-7, and miR-181b). Overall, actual evidence moderately supports an association between epigenetics and schizophrenia and other psychotic disorders. However, heterogeneous results and cross-tissue extrapolations call for future work. Integrating epigenetics into systems biology may critically enhance research on psychosis and thus our understanding of the disorder. This may have implications for psychiatry in risk stratification, early recognition, diagnostics, precision medicine, and other interventional approaches targeting epigenetic fingerprints.
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Affiliation(s)
- Lukasz Smigielski
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland. .,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.
| | - Vinita Jagannath
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Merck Sharp & Dohme (MSD) R&D Innovation Centre, London, UK
| | - Wulf Rössler
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin, Berlin, Germany.,Laboratory of Neuroscience, Institute of Psychiatry, Universidade de São Paulo, São Paulo, Brazil
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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22
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Donegan JJ, Boley AM, Glenn JP, Carless MA, Lodge DJ. Developmental alterations in the transcriptome of three distinct rodent models of schizophrenia. PLoS One 2020; 15:e0232200. [PMID: 32497066 PMCID: PMC7272013 DOI: 10.1371/journal.pone.0232200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/09/2020] [Indexed: 11/25/2022] Open
Abstract
Schizophrenia is a debilitating disorder affecting just under 1% of the population. While the symptoms of this disorder do not appear until late adolescence, pathological alterations likely occur earlier, during development in utero. While there is an increasing literature examining transcriptome alterations in patients, it is not possible to examine the changes in gene expression that occur during development in humans that will develop schizophrenia. Here we utilize three distinct rodent developmental disruption models of schizophrenia to examine potential overlapping alterations in the transcriptome, with a specific focus on markers of interneuron development. Specifically, we administered either methylazoxymethanol acetate (MAM), Polyinosinic:polycytidylic acid (Poly I:C), or chronic protein malnutrition, on GD 17 and examined mRNA expression in the developing hippocampus of the offspring 18 hours later. Here, we report alterations in gene expression that may contribute to the pathophysiology of schizophrenia, including significant alterations in interneuron development and ribosome function.
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Affiliation(s)
- Jennifer J. Donegan
- Department of Pharmacology and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX, United States of America
| | - Angela M. Boley
- Department of Pharmacology and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX, United States of America
| | - Jeremy P. Glenn
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Melanie A. Carless
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Daniel J. Lodge
- Department of Pharmacology and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX, United States of America
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23
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Murata Y, Ikegame T, Koike S, Saito T, Ikeda M, Sasaki T, Iwata N, Kasai K, Bundo M, Iwamoto K. Global DNA hypomethylation and its correlation to the betaine level in peripheral blood of patients with schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2020; 99:109855. [PMID: 31911076 DOI: 10.1016/j.pnpbp.2019.109855] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/03/2019] [Accepted: 12/31/2019] [Indexed: 12/31/2022]
Abstract
Accumulating evidence suggests that aberrant epigenetic regulation is involved in the pathophysiology of major psychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BD). We previously showed that the plasma level of betaine (N,N,N-trimethylglycine), a methyl-group donor, was significantly decreased in patients with first episode schizophrenia (FESZ). In this study, we identified decrease of global DNA methylation level in FESZ (N = 24 patients vs N = 42 controls), and found that global DNA methylation level was inversely correlated with scores on the global assessment of functioning (GAF) scale, and positively correlated with plasma betaine level. Notably, correlations between levels of betaine and its metabolites (N,N-dimethylglycine and sarcosine, N-methylglycine) were lower or lost in FESZ plasma, but remained high in controls. We further examined global DNA methylation levels in patients with chronic SZ (N = 388) and BD (N = 414) as well as controls (N = 430), and confirmed significant hypomethylation and decreased betaine level in SZ. We also found that patients with BD type I, but not those with BD type II, showed significant global hypomethylation. These results suggest that global hypomethylation associated with decreased betaine level in blood cells is common to SZ and BD, and may reflect common pathophysiology such as psychotic symptoms.
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Affiliation(s)
- Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinsuke Koike
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeo Saito
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Tsukasa Sasaki
- Laboratory of Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; PRESTO Japan Science and Technology Agency, Saitama, Japan..
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
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24
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A multimodal attempt to follow-up linkage regions using RNA expression, SNPs and CpG methylation in schizophrenia and bipolar disorder kindreds. Eur J Hum Genet 2019; 28:499-507. [PMID: 31695175 DOI: 10.1038/s41431-019-0526-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/20/2019] [Accepted: 09/27/2019] [Indexed: 11/09/2022] Open
Abstract
The complexity of schizophrenia (SZ) and bipolar disorder (BD) has slowed down progress in understanding their genetic roots. Alternative genomic approaches are needed to bypass these difficulties. We attempted a multimodal approach to follow-up on reported linkage findings in SZ and BD from the Eastern Quebec kindreds in chromosomes 3q21, 4p34, 6p22, 8p21, 8p11, 13q11-q14, 15q13, 16p12, and 18q21. First, in 498 subjects, we measured RNA expression (47 K Illumina chips) in SZ and BD patients that we compared with their non-affected relatives (NARs) to identify, for each chromosomal region, genes showing the most significant differences in expression. Second, we performed SNP genotyping (700 K Illumina chips) and cis-eQTN analysis. Third, we measured DNA methylation on genes with RNA expression differences or eQTNs. We found a significant overexpression of the gene ITGB5 at 3q25 in SZ and BD after multiple testing p value adjustment. SPCS3 gene at 4q34, and FZD3 gene at 8p21, contained significant eQTNs after multiple testing corrections, while ITGB5 provided suggestive results. Methylation in associated genes did not explain the expression differences between patients and NARs. Our multimodal approach involving RNA expression, dense SNP genotyping and eQTN analyses, restricted to chromosomal regions having shown linkage, lowered the multiple testing burden and allowed for a deeper examination of candidate genes in SZ or BD.
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Jia P, Chen X, Xie W, Kendler KS, Zhao Z. Mega-analysis of Odds Ratio: A Convergent Method for a Deep Understanding of the Genetic Evidence in Schizophrenia. Schizophr Bull 2019; 45:698-708. [PMID: 29931221 PMCID: PMC6483587 DOI: 10.1093/schbul/sby085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Numerous high-throughput omics studies have been conducted in schizophrenia, providing an accumulated catalog of susceptible variants and genes. The results from these studies, however, are highly heterogeneous. The variants and genes nominated by different omics studies often have limited overlap with each other. There is thus a pressing need for integrative analysis to unify the different types of data and provide a convergent view of schizophrenia candidate genes (SZgenes). In this study, we collected a comprehensive, multidimensional dataset, including 7819 brain-expressed genes. The data hosted genome-wide association evidence in genetics (eg, genotyping data, copy number variations, de novo mutations), epigenetics, transcriptomics, and literature mining. We developed a method named mega-analysis of odds ratio (MegaOR) to prioritize SZgenes. Application of MegaOR in the multidimensional data resulted in consensus sets of SZgenes (up to 530), each enriched with dense, multidimensional evidence. We proved that these SZgenes had highly tissue-specific expression in brain and nerve and had intensive interactions that were significantly stronger than chance expectation. Furthermore, we found these SZgenes were involved in human brain development by showing strong spatiotemporal expression patterns; these characteristics were replicated in independent brain expression datasets. Finally, we found the SZgenes were enriched in critical functional gene sets involved in neuronal activities, ligand gated ion signaling, and fragile X mental retardation protein targets. In summary, MegaOR analysis reported consensus sets of SZgenes with enriched association evidence to schizophrenia, providing insights into the pathophysiology underlying schizophrenia.
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Affiliation(s)
- Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX
| | - Xiangning Chen
- Department of Psychology, University of Nevada Las Vegas, Las Vegas, NV,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Wei Xie
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX,Department of Psychiatry, The University of Texas Health Science Center at Houston, Houston, TX,To whom correspondence should be addressed; School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX 77030, USA; tel: 713-500-3631, fax: 713-500-3907, e-mail:
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26
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Roberts S, Suderman M, Zammit S, Watkins SH, Hannon E, Mill J, Relton C, Arseneault L, Wong CCY, Fisher HL. Longitudinal investigation of DNA methylation changes preceding adolescent psychotic experiences. Transl Psychiatry 2019; 9:69. [PMID: 30718501 PMCID: PMC6361958 DOI: 10.1038/s41398-019-0407-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/26/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Childhood psychotic experiences (PEs), such as seeing or hearing things that others do not, or extreme paranoia, are relatively common with around 1 in 20 children reporting them at age 12. Childhood PEs are often distressing and can be predictive of schizophrenia, other psychiatric disorders, and suicide attempts in adulthood, particularly if they persist during adolescence. Previous research has demonstrated that methylomic signatures in blood could be potential biomarkers of psychotic phenomena. This study explores the association between DNA methylation (DNAm) and the emergence, persistence, and remission of PEs in childhood and adolescence. DNAm profiles were obtained from the ALSPAC cohort at birth, age 7, and age 15/17 (n = 901). PEs were assessed through interviews with participants at ages 12 and 18. We identified PE-associated probes (p < 5 × 10-5) and regions (corrected p < 0.05) at ages 12 and 18. Several of the differentially methylated probes were also associated with the continuity of PEs across adolescence. One probe (cg16459265), detected consistently at multiple timepoints in the study sample, was replicated in an independent sample of twins (n = 1658). Six regions, including those spanning the HLA-DBP2 and GDF7 genes, were consistently differentially methylated at ages 7 and 15-17. Findings from this large, population-based study suggest that DNAm at multiple stages of development may be associated with PEs in late childhood and adolescence, though further replication is required. Research uncovering biomarkers associated with pre-clinical PEs is important as it has the potential to facilitate early identification of individuals at increased risk who could benefit from preventive interventions.
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Affiliation(s)
- Susanna Roberts
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Matthew Suderman
- 0000 0004 1936 7603grid.5337.2University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stanley Zammit
- University of Bristol, School of Medicine, Centre for Academic Mental Health, Bristol, UK ,Cardiff University School of Medicine, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff, UK
| | - Sarah H. Watkins
- University of Bristol, School of Medicine, Centre for Academic Mental Health, Bristol, UK
| | - Eilis Hannon
- 0000 0004 1936 8024grid.8391.3University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- 0000 0004 1936 8024grid.8391.3University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Caroline Relton
- 0000 0004 1936 7603grid.5337.2University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Louise Arseneault
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Chloe C. Y. Wong
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Helen L. Fisher
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
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Enhanced Molecular Appreciation of Psychiatric Disorders Through High-Dimensionality Data Acquisition and Analytics. Methods Mol Biol 2019; 2011:671-723. [PMID: 31273728 DOI: 10.1007/978-1-4939-9554-7_39] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The initial diagnosis, molecular investigation, treatment, and posttreatment care of major psychiatric disorders (schizophrenia and bipolar depression) are all still significantly hindered by the current inability to define these disorders in an explicit molecular signaling manner. High-dimensionality data analytics, using large datastreams from transcriptomic, proteomic, or metabolomic investigations, will likely advance both the appreciation of the molecular nature of major psychiatric disorders and simultaneously enhance our ability to more efficiently diagnose and treat these debilitating conditions. High-dimensionality data analysis in psychiatric research has been heterogeneous in aims and methods and limited by insufficient sample sizes, poorly defined case definitions, methodological inhomogeneity, and confounding results. All of these issues combine to constrain the conclusions that can be extracted from them. Here, we discuss possibilities for overcoming methodological challenges through the implementation of transcriptomic, proteomic, or metabolomics signatures in psychiatric diagnosis and offer an outlook for future investigations. To fulfill the promise of intelligent high-dimensionality data-based differential diagnosis in mental disease diagnosis and treatment, future research will need large, well-defined cohorts in combination with state-of-the-art technologies.
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Alfimova MV, Kondratiev NV, Golov AK, Golimbet VE. Methylation of the Reelin Gene Promoter in Peripheral Blood and Its Relationship with the Cognitive Function of Schizophrenia Patients. Mol Biol 2018. [DOI: 10.1134/s0026893318050023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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29
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Newton R, Rouleau A, Nylander AG, Loze JY, Resemann HK, Steeves S, Crespo-Facorro B. Diverse definitions of the early course of schizophrenia-a targeted literature review. NPJ SCHIZOPHRENIA 2018; 4:21. [PMID: 30323274 PMCID: PMC6189105 DOI: 10.1038/s41537-018-0063-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 01/07/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder and patients experience significant comorbidity, especially cognitive and psychosocial deficits, already at the onset of disease. Previous research suggests that treatment during the earlier stages of disease reduces disease burden, and that a longer time of untreated psychosis has a negative impact on treatment outcomes. A targeted literature review was conducted to gain insight into the definitions currently used to describe patients with a recent diagnosis of schizophrenia in the early course of disease ('early' schizophrenia). A total of 483 relevant English-language publications of clinical guidelines and studies were identified for inclusion after searches of MEDLINE, MEDLINE In-Process, relevant clinical trial databases and Google for records published between January 2005 and October 2015. The extracted data revealed a wide variety of terminology and definitions used to describe patients with 'early' or 'recent-onset' schizophrenia, with no apparent consensus. The most commonly used criteria to define patients with early schizophrenia included experience of their first episode of schizophrenia or disease duration of less than 1, 2 or 5 years. These varied definitions likely result in substantial disparities of patient populations between studies and variable population heterogeneity. Better agreement on the definition of early schizophrenia could aid interpretation and comparison of studies in this patient population and consensus on definitions should allow for better identification and management of schizophrenia patients in the early course of their disease.
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Affiliation(s)
- Richard Newton
- Austin Health, University of Melbourne, Melbourne, VIC, Australia.,Peninsula Health, Frankston, VIC, Australia
| | | | | | | | | | | | - Benedicto Crespo-Facorro
- Department of Medicine & Psychiatry, University Hospital Marqués de Valdecilla, IDIVAL, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
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30
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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31
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Nour El Huda AR, Norsidah KZ, Nabil Fikri MR, Hanisah MN, Kartini A, Norlelawati AT. DNA methylation of membrane-bound catechol-O-methyltransferase in Malaysian schizophrenia patients. Psychiatry Clin Neurosci 2018; 72:266-279. [PMID: 29160620 DOI: 10.1111/pcn.12622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/02/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022]
Abstract
AIM This study examined catechol-O-methyltransferase (COMT) DNA methylation in the peripheral blood of schizophrenia patients and also in healthy controls to investigate its potential use as a peripheral biomarker of schizophrenia and its relations with the clinical variables of schizophrenia patients. METHODS We examined the DNA methylation levels of COMT using genomic DNA from the peripheral blood of schizophrenia patients (n = 138) and healthy control participants (n = 132); all were Malaysian Malays. The extracted DNA was bisulfite converted, and the percentage methylation ratio value was calculated based on the results following a MethyLight protocol analysis. RESULTS The percentage methylation ratio of COMT was lower in schizophrenia than it was in the healthy controls (P < 0.001) and was different between the body mass index (P = 0.003) and antipsychotic (P = 0.004) groups. The COMT DNA methylation rate was lower in patients receiving atypical antipsychotics (P = 0.004) and risperidone (P = 0.049) as compared to typical antipsychotics. The Excitement and Depressed subdomains of the Positive and Negative Syndrome Scale were inversely related (P < 0.001) and therefore predictors (Excitement: b = -11.396, t = -4.760, P < 0.001; Depressed: b = -7.789, t = -3.487, P = 0.001) of COMT DNA methylation. CONCLUSION Our results suggested that the methylation level was affected by the severity of the clinical symptoms of schizophrenia and might also be influenced by pharmacological treatment. The epigenetic alteration of COMT in the peripheral blood could be a potential peripheral biomarker of schizophrenia.
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Affiliation(s)
- Abd Rahim Nour El Huda
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
| | - Ku Zaifah Norsidah
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
| | - Mohd Rahim Nabil Fikri
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
| | - Mohd Noor Hanisah
- Department of Psychiatry, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
| | - Abdullah Kartini
- Department of Psychiatry, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
| | - A Talib Norlelawati
- Department of Pathology and Laboratory Medicine, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, Malaysia
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32
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Kondratiev NV, Alfimova MV, Golimbet VE. [A search of target regions for association studies between DNA methylation and cognitive impairment in schizophrenia]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 117:72-75. [PMID: 28884721 DOI: 10.17116/jnevro20171178172-75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AIM To develop a strategy for the search for candidate genes and targets for epigenetic studies of cognitive impairments in patients with schizophrenia. MATERIAL AND METHODS A search for literature on epigenetics of schizophrenia and cognitive functions was performed. Single nucleotide polymorphisms (SNPs) that can create or abolish a site for DNA methylation or transcription factor sites were determined using a custom script. RESULTS AND CONCLUSION Eight candidate genes, including BDNF, COMT, RELN, SNRPN, PSMA4, FAM63B, IL-1RAP, MAD1L1, as well as 750 targets in CpG islands in the linkage regions identified in GWAS of schizophrenia and 406 targets in SNV located within transcription factor binding sites were selected.
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33
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Huang J, Zhu Q, Hao X, Shi X, Gao S, Xu X, Zhang D. Identifying Resting-State Multifrequency Biomarkers via Tree-Guided Group Sparse Learning for Schizophrenia Classification. IEEE J Biomed Health Inform 2018; 23:342-350. [PMID: 29994431 DOI: 10.1109/jbhi.2018.2796588] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The fractional amplitude of low-frequency fluctuations (fALFF) has been widely used as potential clinical biomarkers for resting-state functional-magnetic-resonance-imaging-based schizophrenia diagnosis. How-ever, previous studies usually measure the fALFF with specific bands from 0.01 to 0.08 Hz, which cannot fully delineate the complex variations of spontaneous fluctuations in the resting-state brain. In addition, fALFF data are intrinsically constrained by the brain structure, but most of the traditional methods have not consider it in feature selection. For addressing these problems, we propose a model to classify schizophrenia in multifrequency bands with tree-guided group sparse learning. In detail, we first acquire the fALFF data in multifrequency bands (i.e., slow-5: 0.01-0.027 Hz, slow-4: 0.027-0.073 Hz, slow-3: 0.073-0.198 Hz, and slow-2: 0.198-0.25 Hz). Then, we divide the whole brain into different candidate patches and select those significant patches related to schizophrenia using random forest-based important score. Moreover, we use tree-structured sparse learning method for feature selection with the above patch spatial constraint. Finally, considering biomarkers from multifrequency bands can reflect complementary information among multiple-frequency bands, we adopt the multikernel learning method to combine features of multifrequency bands for classification. Our experimental results show that these biomarkers from multifrequency bands can achieve a classification accuracy of 91.1% on 17 schizophrenia patients and 17 healthy controls, further demonstrating that the multifrequency bands analysis can better account for classification of schizophrenia.
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Tomassi S, Tosato S. Epigenetics and gene expression profile in first-episode psychosis: The role of childhood trauma. Neurosci Biobehav Rev 2017; 83:226-237. [PMID: 29056292 DOI: 10.1016/j.neubiorev.2017.10.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/02/2017] [Accepted: 10/18/2017] [Indexed: 11/24/2022]
Abstract
Childhood Trauma (CT) mediation of the epigenome and its impact on gene expression profile could provide a mechanism for the gene-environment interaction underling psychosis. We reviewed the evidence concerning epigenetic and gene expression modifications associated with CT in both First-Episode Psychosis (FEP) and healthy subjects. In order to explore the relative role of psychosis itself in determining these modifications, evidence about FEP and epigenetics/gene expression was also summarized. We performed a systematic search on PubMed, last updated in December 2016. Out of 2966 potentially relevant records, only 41 studies were included. CT resulted associated: in FEP subjects, with global DNA hypo-methylation and reduced BDNF gene-expression; in healthy subjects, with hyper-methylation of SLC6A4, NR3C1, KITLG, and OXTR; hypo-methylation of FKBP5, IL-6, and BDNF; increased IL1B, IL8, and PTGS gene expression; and decreased SLC6A4 gene expression. FEP showed global DNA hypo-methylation; increased methylation and reduced gene expression of GCH1; hyper-expression of MPB, NDEL1, AKT1, and DICER1; and hypo-expression of DROSHA, COMT, and DISC1 in comparison with healthy controls.
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Affiliation(s)
- Simona Tomassi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Psychiatry, University of Verona, Verona, Italy
| | - Sarah Tosato
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Psychiatry, University of Verona, Verona, Italy.
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The correlation between DNA methylation and transcriptional expression of human dopamine transporter in cell lines. Neurosci Lett 2017; 662:91-97. [PMID: 29030220 DOI: 10.1016/j.neulet.2017.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 01/03/2023]
Abstract
This study aims to investigate the relationship between DNA methylation and expression of human dopamine transporter (hDAT). We examined methylation status of hDAT in cells with various hDAT expression levels, including two dopaminergic neural cell lines (SK-N-AS and SH-SY-5Y) and one non-dopaminergic cell line (HEK293) by bisulfite sequencing PCR(BSP). The effects of DNA methyltransferase inhibitor 5-aza-dC or/and histone deacetylase inhibitor (HDACi, sodium butyrate, NaB) on the DNA methylation status and mRNA expression levels of hDAT were examined. The results revealed marked hypomethylation of the two promoter regions (-1214 to -856bp and -48 to 439bp, the first base of exon 1 was taken as +1 bp)of hDAT in SK-N-AS (4.7%±2.0mC and 3.5%±1.0mC, respectively) compared with SH-SY-5Y (88.0%±4.4%mC and 81.1%±8.8%mC) and HEK293 (90.7%±2.4mC and 84.4%±8.6% mC) cell lines, indicating a cell-specific methylation regulation of hDAT. 5-aza-dC and NaB decreased hypermethylation,while increase hDAT expression in SH-SY-5Y cells and recovered hDAT mRNA expression in HEK293 cells. DNA methylation enabled the cell-specific differential expression of the hDAT gene. hDAT silencing was reversed by the introduction of DNA hypomethylation via 5-aza-dC or/and NaB.
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Schmitt A, Martins-de-Souza D, Akbarian S, Cassoli JS, Ehrenreich H, Fischer A, Fonteh A, Gattaz WF, Gawlik M, Gerlach M, Grünblatt E, Halene T, Hasan A, Hashimoto K, Kim YK, Kirchner SK, Kornhuber J, Kraus TFJ, Malchow B, Nascimento JM, Rossner M, Schwarz M, Steiner J, Talib L, Thibaut F, Riederer P, Falkai P. Consensus paper of the WFSBP Task Force on Biological Markers: Criteria for biomarkers and endophenotypes of schizophrenia, part III: Molecular mechanisms. World J Biol Psychiatry 2017; 18:330-356. [PMID: 27782767 DOI: 10.1080/15622975.2016.1224929] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Despite progress in identifying molecular pathophysiological processes in schizophrenia, valid biomarkers are lacking for both the disease and treatment response. METHODS This comprehensive review summarises recent efforts to identify molecular mechanisms on the level of protein and gene expression and epigenetics, including DNA methylation, histone modifications and micro RNA expression. Furthermore, it summarises recent findings of alterations in lipid mediators and highlights inflammatory processes. The potential that this research will identify biomarkers of schizophrenia is discussed. RESULTS Recent studies have not identified clear biomarkers for schizophrenia. Although several molecular pathways have emerged as potential candidates for future research, a complete understanding of these metabolic pathways is required to reveal better treatment modalities for this disabling condition. CONCLUSIONS Large longitudinal cohort studies are essential that pair a thorough phenotypic and clinical evaluation for example with gene expression and proteome analysis in blood at multiple time points. This approach might identify biomarkers that allow patients to be stratified according to treatment response and ideally also allow treatment response to be predicted. Improved knowledge of molecular pathways and epigenetic mechanisms, including their potential association with environmental influences, will facilitate the discovery of biomarkers that could ultimately be effective tools in clinical practice.
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Affiliation(s)
- Andrea Schmitt
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany.,b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Daniel Martins-de-Souza
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil.,c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Schahram Akbarian
- d Division of Psychiatric Epigenomics, Departments of Psychiatry and Neuroscience , Mount Sinai School of Medicine , New York , USA
| | - Juliana S Cassoli
- c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Hannelore Ehrenreich
- e Clinical Neuroscience , Max Planck Institute of Experimental Medicine, DFG Centre for Nanoscale Microscopy & Molecular Physiology of the Brain , Göttingen , Germany
| | - Andre Fischer
- f Research Group for Epigenetics in Neurodegenerative Diseases , German Centre for Neurodegenerative Diseases (DZNE), Göttingen , Germany.,g Department of Psychiatry and Psychotherapy , University Medical Centre Göttingen , Germany
| | - Alfred Fonteh
- h Neurosciences , Huntington Medical Research Institutes , Pasadena , CA , USA
| | - Wagner F Gattaz
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Michael Gawlik
- i Department of Psychiatry and Psychotherapy , University of Würzburg , Germany
| | - Manfred Gerlach
- j Centre for Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy , University of Würzburg , Germany
| | - Edna Grünblatt
- i Department of Psychiatry and Psychotherapy , University of Würzburg , Germany.,k Department of Child and Adolescent Psychiatry and Psychotherapy , Psychiatric Hospital, University of Zürich , Switzerland.,l Neuroscience Centre Zurich , University of Zurich and the ETH Zurich , Switzerland.,m Zurich Centre for Integrative Human Physiology , University of Zurich , Switzerland
| | - Tobias Halene
- d Division of Psychiatric Epigenomics, Departments of Psychiatry and Neuroscience , Mount Sinai School of Medicine , New York , USA
| | - Alkomiet Hasan
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
| | - Kenij Hashimoto
- n Division of Clinical Neuroscience , Chiba University Centre for Forensic Mental Health , Chiba , Japan
| | - Yong-Ku Kim
- o Department of Psychiatry , Korea University, College of Medicine , Republic of Korea
| | | | - Johannes Kornhuber
- p Department of Psychiatry and Psychotherapy , Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | | | - Berend Malchow
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
| | - Juliana M Nascimento
- c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Moritz Rossner
- r Department of Psychiatry, Molecular and Behavioural Neurobiology , LMU Munich , Germany.,s Research Group Gene Expression , Max Planck Institute of Experimental Medicine , Göttingen , Germany
| | - Markus Schwarz
- t Institute for Laboratory Medicine, LMU Munich , Germany
| | - Johann Steiner
- u Department of Psychiatry , University of Magdeburg , Magdeburg , Germany
| | - Leda Talib
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Florence Thibaut
- v Department of Psychiatry , University Hospital Cochin (site Tarnier), University of Paris-Descartes, INSERM U 894 Centre Psychiatry and Neurosciences , Paris , France
| | - Peter Riederer
- w Center of Psychic Health; Department of Psychiatry, Psychosomatics and Psychotherapy , University Hospital of Würzburg , Germany
| | - Peter Falkai
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
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Chaumette B, Kebir O, Krebs MO. [Genetics and epigenetics of schizophrenia and other psychoses]. Biol Aujourdhui 2017; 211:69-82. [PMID: 28682228 DOI: 10.1051/jbio/2017015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Schizophrenia and other psychoses are categorical psychiatric diagnoses corresponding to frequent and heterogeneous disorders. Their physiopathology still remains largely unknown despite numerous recent advances. In particular, the last decade has identified different types of genetic variants, thanks to emergence of high-throughput methods. These methods allow both the identification of rare variants with a large effect such as punctual mutations or copy-number variants and the identification of frequent variants with a limited effect such as polymorphisms. Many impacted genes have been identified showing a very high genetic heterogeneity of psychoses. These genes are overrepresented in synaptic and neurotransmission pathways. Only a small fraction of psychoses could be easily explained by genetics but this screening in clinical practice is important as it can lead to therapeutic challenge or genetic counselling. Nowadays, it is clear that the pathophysiology of the psychoses can only be understood by an integrative approach taking into account the interaction between genes and environment. This interaction could be mediated by the epigenome defined as the modification of gene expression without changes in DNA sequence. Epigenome is stable but could be modified by environmental factors. Several epigenetic mechanisms have been studied in psychosis, in particular the DNA methylation, the modification of histones and the microRNA. All of these mechanisms are under regulation by genetic factors and variants in these epigenetic-involved genes and cofactors have been also associated with schizophrenia. Thus, pathophysiology of psychosis is complex and morestudiesare needed before definitive conclusions. Altogether, the recent advances in the genetics and epigenetics of psychosis are promising and could open the way to a recategorization of these disorders as well as the identification of new therapeutic targets.
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Affiliation(s)
- Boris Chaumette
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Oussama Kebir
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
| | - Marie-Odile Krebs
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
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Kebir O, Chaumette B, Rivollier F, Miozzo F, Lemieux Perreault LP, Barhdadi A, Provost S, Plaze M, Bourgin J, Gaillard R, Mezger V, Dubé MP, Krebs MO. Methylomic changes during conversion to psychosis. Mol Psychiatry 2017; 22:512-518. [PMID: 27113994 PMCID: PMC5378806 DOI: 10.1038/mp.2016.53] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 02/28/2016] [Accepted: 03/02/2016] [Indexed: 12/12/2022]
Abstract
The onset of psychosis is the consequence of complex interactions between genetic vulnerability to psychosis and response to environmental and/or maturational changes. Epigenetics is hypothesized to mediate the interplay between genes and environment leading to the onset of psychosis. We believe we performed the first longitudinal prospective study of genomic DNA methylation during psychotic transition in help-seeking young individuals referred to a specialized outpatient unit for early detection of psychosis and enrolled in a 1-year follow-up. We used Infinium HumanMethylation450 BeadChip array after bisulfite conversion and analyzed longitudinal variations in methylation at 411 947 cytosine-phosphate-guanine (CpG) sites. Conversion to psychosis was associated with specific methylation changes. Changes in DNA methylation were significantly different between converters and non-converters in two regions: one located in 1q21.1 and a cluster of six CpG located in GSTM5 gene promoter. Methylation data were confirmed by pyrosequencing in the same population. The 100 top CpGs associated with conversion to psychosis were subjected to exploratory analyses regarding the related gene networks and their capacity to distinguish between converters and non-converters. Cluster analysis showed that the top CpG sites correctly distinguished between converters and non-converters. In this first study of methylation during conversion to psychosis, we found that alterations preferentially occurred in gene promoters and pathways relevant for psychosis, including oxidative stress regulation, axon guidance and inflammatory pathways. Although independent replications are warranted to reach definitive conclusions, these results already support that longitudinal variations in DNA methylation may reflect the biological mechanisms that precipitate some prodromal individuals into full-blown psychosis, under the influence of environmental factors and maturational processes at adolescence.
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Affiliation(s)
- O Kebir
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - B Chaumette
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - F Rivollier
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - F Miozzo
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, Paris, France,Université Paris Diderot, Sorbonne Paris Cité, Paris, France,Département Hospitalo-Universitaire DHU PROTECT, Paris, France
| | - L P Lemieux Perreault
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - A Barhdadi
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - S Provost
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - M Plaze
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - J Bourgin
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | | | - R Gaillard
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - V Mezger
- CNRS, UMR7216 Épigénétique et Destin Cellulaire, Paris, France,Université Paris Diderot, Sorbonne Paris Cité, Paris, France,Département Hospitalo-Universitaire DHU PROTECT, Paris, France
| | - M-P Dubé
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - M-O Krebs
- Université Paris Descartes, PRES Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France,CNRS, GDR3557-Institut de Psychiatrie, Paris, France,Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France,Laboratoire de Physiopathologie de Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, Service Hospitalo-Universitaire, INSERM U894—Université Paris Descartes, 2 ter rue d'Alesia, Paris 75014, France. E-mail:
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Perkovic MN, Erjavec GN, Strac DS, Uzun S, Kozumplik O, Pivac N. Theranostic Biomarkers for Schizophrenia. Int J Mol Sci 2017; 18:E733. [PMID: 28358316 PMCID: PMC5412319 DOI: 10.3390/ijms18040733] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
Schizophrenia is a highly heritable, chronic, severe, disabling neurodevelopmental brain disorder with a heterogeneous genetic and neurobiological background, which is still poorly understood. To allow better diagnostic procedures and therapeutic strategies in schizophrenia patients, use of easy accessible biomarkers is suggested. The most frequently used biomarkers in schizophrenia are those associated with the neuroimmune and neuroendocrine system, metabolism, different neurotransmitter systems and neurotrophic factors. However, there are still no validated and reliable biomarkers in clinical use for schizophrenia. This review will address potential biomarkers in schizophrenia. It will discuss biomarkers in schizophrenia and propose the use of specific blood-based panels that will include a set of markers associated with immune processes, metabolic disorders, and neuroendocrine/neurotrophin/neurotransmitter alterations. The combination of different markers, or complex multi-marker panels, might help in the discrimination of patients with different underlying pathologies and in the better classification of the more homogenous groups. Therefore, the development of the diagnostic, prognostic and theranostic biomarkers is an urgent and an unmet need in psychiatry, with the aim of improving diagnosis, therapy monitoring, prediction of treatment outcome and focus on the personal medicine approach in order to improve the quality of life in patients with schizophrenia and decrease health costs worldwide.
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Affiliation(s)
| | | | - Dubravka Svob Strac
- Rudjer Boskovic Institute, Division of Molecular Medicine, 10000 Zagreb, Croatia.
| | - Suzana Uzun
- Clinic for Psychiatry Vrapce, 10090 Zagreb, Croatia.
| | | | - Nela Pivac
- Rudjer Boskovic Institute, Division of Molecular Medicine, 10000 Zagreb, Croatia.
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McKinney B, Ding Y, Lewis DA, Sweet RA. DNA methylation as a putative mechanism for reduced dendritic spine density in the superior temporal gyrus of subjects with schizophrenia. Transl Psychiatry 2017; 7:e1032. [PMID: 28195572 PMCID: PMC5438028 DOI: 10.1038/tp.2016.297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/13/2016] [Indexed: 01/11/2023] Open
Abstract
Reduced dendritic spine density (DSD) in cortical layer 3 of the superior temporal gyrus (STG), and multiple other brain regions, is consistently observed in postmortem studies of schizophrenia (SZ). Elucidating the molecular mechanisms of this intermediate phenotype holds promise for understanding SZ pathophysiology, identifying SZ treatment targets and developing animal models. DNA methylation (DNAm), the addition of a methyl group to a cytosine nucleotide, regulates gene transcription and is a strong candidate for such a mechanism. We tested the hypothesis that DNAm correlates with DSD in the human STG and that this relationship is disrupted in SZ. We used the Illumina Infinium HumanMethylation450 Beadchip Array to quantify DNAm on a genome-wide scale in the postmortem STG from 22 SZ subjects and matched non-psychiatric control (NPC) subjects; DSD measures were available for 17 of the 22 subject pairs. We found DNAm to correlate with DSD at more sites than expected by chance in NPC, but not SZ, subjects. In addition, we show that the slopes of the linear DNAm-DSD correlations differed between SZ and NPC subjects at more sites than expected by chance. From these data, we identified 2 candidate genes for mediating DSD abnormalities in SZ: brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2) and discs large, Drosophila, homolog of, 1 (DLG1). Together, these data suggest that altered DNAm in SZ may be a mechanism for SZ-related DSD reductions.
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Affiliation(s)
- B McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - D A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA,Mental Illness Research, Education, and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA,Department of Psychiatry, Neurology and VISN 4 Mental Illness Research, Education and Clinical Center (MIRECC), Biomedical Science Tower, Room W-1645, 3811 O'Hara Street, Pittsburgh, PA 15213, USA. E-mail:
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Fullard JF, Halene TB, Giambartolomei C, Haroutunian V, Akbarian S, Roussos P. Understanding the genetic liability to schizophrenia through the neuroepigenome. Schizophr Res 2016; 177:115-124. [PMID: 26827128 PMCID: PMC4963306 DOI: 10.1016/j.schres.2016.01.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 12/17/2022]
Abstract
The Psychiatric Genomics Consortium-Schizophrenia Workgroup (PGC-SCZ) recently identified 108 loci associated with increased risk for schizophrenia (SCZ). The vast majority of these variants reside within non-coding sequences of the genome and are predicted to exert their effects by affecting the mechanism of action of cis regulatory elements (CREs), such as promoters and enhancers. Although a number of large-scale collaborative efforts (e.g. ENCODE) have achieved a comprehensive mapping of CREs in human cell lines or tissue homogenates, it is becoming increasingly evident that many risk-associated variants are enriched for expression Quantitative Trait Loci (eQTLs) and CREs in specific tissues or cells. As such, data derived from previous research endeavors may not capture fully cell-type and/or region specific changes associated with brain diseases. Coupling recent technological advances in genomics with cell-type specific methodologies, we are presented with an unprecedented opportunity to better understand the genetics of normal brain development and function and, in turn, the molecular basis of neuropsychiatric disorders. In this review, we will outline ongoing efforts towards this goal and will discuss approaches with the potential to shed light on the mechanism(s) of action of cell-type specific cis regulatory elements and their putative roles in disease, with particular emphasis on understanding the manner in which the epigenome and CREs influence the etiology of SCZ.
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Affiliation(s)
- John F. Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA.
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Worsham MJ, Chen KM, Datta I, Stephen JK, Chitale D, Gothard A, Divine G. The biological significance of methylome differences in human papilloma virus associated head and neck cancer. Oncol Lett 2016; 12:4949-4956. [PMID: 28101231 PMCID: PMC5228097 DOI: 10.3892/ol.2016.5303] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/26/2016] [Indexed: 01/02/2023] Open
Abstract
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA). Using an identical experimental design of a 450K methylation platform, 7 of the 11 genes were detected to be significantly differentially methylated and all 11 genes were either hypo- or hypermethylated, which was in agreement with the results of a previous study. IPA's enriched networks analysis identified one network with msh homeobox 2 (MSX2) as a central node. Locally dense interactions between genes in networks tend to reflect significant biology; therefore MSX2 was selected as an important gene. Sequestration in the top four canonical pathways was noted for 5-hydroxytryptamine receptor 1E (serotonin signaling), collapsin response mediator protein 1 (semaphorin signaling) and paired like homeodomain 2 (bone morphogenic protein and transforming growth factor-β signaling). Placement of 9 of the 11 genes in highly ranked pathways and bionetworks identified key biological processes to further emphasize differences between HNSCC HPV positive and negative pathogenesis.
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Affiliation(s)
- Maria J Worsham
- Department of Otolaryngology/Head and Neck Research, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Kang Mei Chen
- Department of Otolaryngology/Head and Neck Research, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Indrani Datta
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Josena K Stephen
- Department of Otolaryngology/Head and Neck Research, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Dhananjay Chitale
- Department of Pathology, Henry Ford Hospital, Detroit, MI 48202, USA
| | | | - George Divine
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI 48202, USA
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Fisher HL, Murphy TM, Arseneault L, Caspi A, Moffitt TE, Viana J, Hannon E, Pidsley R, Burrage J, Dempster EL, Wong CCY, Pariante CM, Mill J. Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms. Epigenetics 2016; 10:1014-23. [PMID: 26479702 PMCID: PMC4867769 DOI: 10.1080/15592294.2015.1099797] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Childhood psychotic symptoms are associated with increased rates of schizophrenia, other psychiatric disorders, and suicide attempts in adulthood; thus, elucidating early risk indicators is crucial to target prevention efforts. There is considerable discordance for psychotic symptoms between monozygotic twins, indicating that child-specific non-genetic factors must be involved. Epigenetic processes may constitute one of these factors and have not yet been investigated in relation to childhood psychotic symptoms. Therefore, this study explored whether differences in DNA methylation at age 10 were associated with monozygotic twin discordance for psychotic symptoms at age 12. The Environmental Risk (E-Risk) Longitudinal Twin Study cohort of 2,232 children (1,116 twin pairs) was assessed for age-12 psychotic symptoms and 24 monozygotic twin pairs discordant for symptoms were identified for methylomic comparison. Children provided buccal samples at ages 5 and 10. DNA was bisulfite modified and DNA methylation was quantified using the Infinium HumanMethylation450 array. Differentially methylated positions (DMPs) associated with psychotic symptoms were subsequently tested in post-mortem prefrontal cortex tissue from adult schizophrenia patients and age-matched controls. Site-specific DNA methylation differences were observed at age 10 between monozygotic twins discordant for age-12 psychotic symptoms. Similar DMPs were not found at age 5. The top-ranked psychosis-associated DMP (cg23933044), located in the promoter of the C5ORF42 gene, was also hypomethylated in post-mortem prefrontal cortex brain tissue from schizophrenia patients compared to unaffected controls. These data tentatively suggest that epigenetic variation in peripheral tissue is associated with childhood psychotic symptoms and may indicate susceptibility to schizophrenia and other mental health problems.
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Affiliation(s)
- Helen L Fisher
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK
| | - Therese M Murphy
- b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
| | - Louise Arseneault
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK
| | - Avshalom Caspi
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK.,c Department of Psychology and Neuroscience ; Duke University ; Durham , NC , USA.,d Department of Psychiatry and Behavioral Sciences ; Duke University Medical School ; Durham , NC , USA
| | - Terrie E Moffitt
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK.,c Department of Psychology and Neuroscience ; Duke University ; Durham , NC , USA.,d Department of Psychiatry and Behavioral Sciences ; Duke University Medical School ; Durham , NC , USA
| | - Joana Viana
- b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
| | - Eilis Hannon
- b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
| | - Ruth Pidsley
- e Garvan Institute of Medical Research ; Darlinghurst , NSW , Australia
| | - Joe Burrage
- b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
| | - Emma L Dempster
- b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
| | - Chloe C Y Wong
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK
| | - Carmine M Pariante
- f Department of Psychological Medicine ; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK
| | - Jonathan Mill
- a MRC Social , Genetic & Developmental Psychiatry Center; Institute of Psychiatry , Psychology & Neuroscience; King's College London ; London , UK.,b University of Exeter Medical School; University of Exeter ; Exeter , Devon , UK
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44
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Alelú-Paz R, Carmona FJ, Sanchez-Mut JV, Cariaga-Martínez A, González-Corpas A, Ashour N, Orea MJ, Escanilla A, Monje A, Guerrero Márquez C, Saiz-Ruiz J, Esteller M, Ropero S. Epigenetics in Schizophrenia: A Pilot Study of Global DNA Methylation in Different Brain Regions Associated with Higher Cognitive Functions. Front Psychol 2016; 7:1496. [PMID: 27746755 PMCID: PMC5044511 DOI: 10.3389/fpsyg.2016.01496] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/20/2016] [Indexed: 12/29/2022] Open
Abstract
Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown. We found that altered DNA methylation is not restricted to a particular region, but includes others such as CpG shelves and gene bodies, indicating the presence of different DNA methylation signatures depending on the brain area analyzed. Our findings suggest that epimutations are not relatables between different tissues or even between tissues' regions, highlighting the need to adequately study brain samples to obtain reliable data concerning the epigenetics of schizophrenia.
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Affiliation(s)
- Raúl Alelú-Paz
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of AlcaláMadrid, Spain; Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of AlcaláMadrid, Spain; Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y CajalMadrid, Spain
| | - Francisco J Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - José V Sanchez-Mut
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - Ariel Cariaga-Martínez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana González-Corpas
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Nadia Ashour
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Maria J Orea
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana Escanilla
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | - Alfonso Monje
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | | | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y Cajal Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de LlobregatBarcelona, Spain; Institució Catalana de Recerca i Estudis AvançatsBarcelona, Spain; Department of Physiological Sciences II, School of Medicine, University of BarcelonaBarcelona, Spain
| | - Santiago Ropero
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
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Yoshino Y, Kawabe K, Mori T, Mori Y, Yamazaki K, Numata S, Nakata S, Yoshida T, Iga JI, Ohmori T, Ueno SI. Low methylation rates of dopamine receptor D2 gene promoter sites in Japanese schizophrenia subjects. World J Biol Psychiatry 2016; 17:449-56. [PMID: 27269479 DOI: 10.1080/15622975.2016.1197424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVES According to the dopamine hypothesis, several studies on the gene for the dopamine receptor D2 (DRD2) have been conducted. However, no trait biomarkers on DRD2 are available. We examined whether the methylation rates in the upstream region of DRD2 in leukocytes are different in schizophrenia (SCZ) subjects compared to control subjects. METHODS We selected seven CpG sites in the upstream region of DRD2 that may theoretically bind major transcription factors. The methylation rates in these regions of 50 medicated and 18 drug-naïve SCZ subjects were compared with those of age-matched control subjects. RESULTS The methylation rates were significantly lower in medicated (CpG2, P < 0.0001; CpG4, P = 0.013; CpG7, P < 0.0001; and average: 12.9 ± 1.8 vs. 14.1 ± 2.2, P = 0.005) and drug-naïve SCZ subjects (CpG1, P = 0.006; CpG2, P = 0.001; CpG3, P = 0.001; CpG5, P = 0.02; CpG6, P = 0.015; CpG7, P = 0.027; and average: 9.86 ± 0.9 vs. 11.2 ± 1.3, P = 0.002). CONCLUSIONS We confirmed low methylation rates in the upstream region of DRD2 in both medicated and drug-naïve SCZ subjects. Low methylation rates of DRD2 in leukocytes may be a trait biomarker for SCZ.
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Affiliation(s)
- Yuta Yoshino
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Kentaro Kawabe
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Takaaki Mori
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Yoko Mori
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Kiyohiro Yamazaki
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Shusuke Numata
- b Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences , The University of Tokushima Graduate School , Tokushima , Japan
| | - Shunsuke Nakata
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Taku Yoshida
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Jun-Ichi Iga
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
| | - Tetsuro Ohmori
- b Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences , The University of Tokushima Graduate School , Tokushima , Japan
| | - Shu-Ichi Ueno
- a Department of Neuropsychiatry, Molecules and Function , Ehime University Graduate School of Medicine , Toon , Ehime , Japan
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46
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Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". Curr Behav Neurosci Rep 2016; 3:264-274. [PMID: 28093577 DOI: 10.1007/s40473-016-0083-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Evidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages. RECENT FINDINGS Brain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important. SUMMARY Epigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Alycia Halladay
- Autism Science Foundation, New York City, New York, USA; Department of Pharmacology and Toxicology, Rutgers University, New Brunswick, New Jersey, USA
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK; Institute for Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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47
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Cariaga-Martinez A, Saiz-Ruiz J, Alelú-Paz R. From Linkage Studies to Epigenetics: What We Know and What We Need to Know in the Neurobiology of Schizophrenia. Front Neurosci 2016; 10:202. [PMID: 27242407 PMCID: PMC4862989 DOI: 10.3389/fnins.2016.00202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023] Open
Abstract
Schizophrenia is a complex psychiatric disorder characterized by the presence of positive, negative, and cognitive symptoms that lacks a unifying neuropathology. In the present paper, we will review the current understanding of molecular dysregulation in schizophrenia, including genetic and epigenetic studies. In relation to the latter, basic research suggests that normal cognition is regulated by epigenetic mechanisms and its dysfunction occurs upon epigenetic misregulation, providing new insights into missing heritability of complex psychiatric diseases, referring to the discrepancy between epidemiological heritability and the proportion of phenotypic variation explained by DNA sequence difference. In schizophrenia the absence of consistently replicated genetic effects together with evidence for lasting changes in gene expression after environmental exposures suggest a role of epigenetic mechanisms. In this review we will focus on epigenetic modifications as a key mechanism through which environmental factors interact with individual's genetic constitution to affect risk of psychotic conditions throughout life.
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Affiliation(s)
- Ariel Cariaga-Martinez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá University Madrid, Spain
| | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)Madrid, Spain
| | - Raúl Alelú-Paz
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá UniversityMadrid, Spain; Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain
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48
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Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, Idrizi A, Runarsson A, Berndsen B, Gur RC, Moore TM, Perry RT, Fugman D, Sabunciyan S, Yolken RH, Hyde TM, Kleinman JE, Sobell JL, Pato CN, Pato MT, Go RC, Nimgaonkar V, Weinberger DR, Braff D, Gur RE, Fallin MD, Feinberg AP. Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study. JAMA Psychiatry 2016; 73:506-14. [PMID: 27074206 PMCID: PMC6353566 DOI: 10.1001/jamapsychiatry.2016.0144] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE DNA methylation may play an important role in schizophrenia (SZ), either directly as a mechanism of pathogenesis or as a biomarker of risk. OBJECTIVE To scan genome-wide DNA methylation data to identify differentially methylated CpGs between SZ cases and controls. DESIGN, SETTING, AND PARTICIPANTS Epigenome-wide association study begun in 2008 using DNA methylation levels of 456 513 CpG loci measured on the Infinium HumanMethylation450 array (Illumina) in a consortium of case-control studies for initial discovery and in an independent replication set. Primary analyses used general linear regression, adjusting for age, sex, race/ethnicity, smoking, batch, and cell type heterogeneity. The discovery set contained 689 SZ cases and 645 controls (n = 1334), from 3 multisite consortia: the Consortium on the Genetics of Endophenotypes in Schizophrenia, the Project among African-Americans To Explore Risks for Schizophrenia, and the Multiplex Multigenerational Family Study of Schizophrenia. The replication set contained 247 SZ cases and 250 controls (n = 497) from the Genomic Psychiatry Cohort. MAIN OUTCOMES AND MEASURES Identification of differentially methylated positions across the genome in SZ cases compared with controls. RESULTS Of the 689 case participants in the discovery set, 477 (69%) were men and 258 (37%) were non-African American; of the 645 controls, 273 (42%) were men and 419 (65%) were non-African American. In our replication set, cases/controls were 76% male and 100% non-African American. We identified SZ-associated methylation differences at 923 CpGs in the discovery set (false discovery rate, <0.2). Of these, 625 showed changes in the same direction including 172 with P < .05 in the replication set. Some replicated differentially methylated positions are located in a top-ranked SZ region from genome-wide association study analyses. CONCLUSIONS AND RELEVANCE This analysis identified 172 replicated new associations with SZ after careful correction for cell type heterogeneity and other potential confounders. The overlap with previous genome-wide association study data can provide potential insights into the functional relevance of genetic signals for SZ.
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Affiliation(s)
- Carolina Montano
- Medical Scientist Training Program and Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eirikur Briem
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jason I. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rakel Trygvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arni Runarsson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Birna Berndsen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruben C. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tyler M. Moore
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rodney T. Perry
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | - Doug Fugman
- Rutgers University Cell and DNA Repository, Piscataway, New Jersey
| | - Sarven Sabunciyan
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Robert H. Yolken
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Janet L. Sobell
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Carlos N. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Michele T. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Rodney C. Go
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - David Braff
- Department of Psychiatry, University of California San Diego School of Medicine, La Jolla,VISN22, Mental Illness Research, Education, and Clinical Center, VA Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Raquel E. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Margaret Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland,Departments of Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, Maryland
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Lai CY, Scarr E, Udawela M, Everall I, Chen WJ, Dean B. Biomarkers in schizophrenia: A focus on blood based diagnostics and theranostics. World J Psychiatry 2016; 6:102-17. [PMID: 27014601 PMCID: PMC4804259 DOI: 10.5498/wjp.v6.i1.102] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/20/2015] [Accepted: 12/17/2015] [Indexed: 02/05/2023] Open
Abstract
Identifying biomarkers that can be used as diagnostics or predictors of treatment response (theranostics) in people with schizophrenia (Sz) will be an important step towards being able to provide personalized treatment. Findings from the studies in brain tissue have not yet been translated into biomarkers that are practical in clinical use because brain biopsies are not acceptable and neuroimaging techniques are expensive and the results are inconclusive. Thus, in recent years, there has been search for blood-based biomarkers for Sz as a valid alternative. Although there are some encouraging preliminary data to support the notion of peripheral biomarkers for Sz, it must be acknowledged that Sz is a complex and heterogeneous disorder which needs to be further dissected into subtype using biological based and clinical markers. The scope of this review is to critically examine published blood-based biomarker of Sz, focusing on possible uses for diagnosis, treatment response, or their relationship with schizophrenia-associated phenotype. We sorted the studies into six categories which include: (1) brain-derived neurotrophic factor; (2) inflammation and immune function; (3) neurochemistry; (4) oxidative stress response and metabolism; (5) epigenetics and microRNA; and (6) transcriptome and proteome studies. This review also summarized the molecules which have been conclusively reported as potential blood-based biomarkers for Sz in different blood cell types. Finally, we further discusses the pitfall of current blood-based studies and suggest that a prediction model-based, Sz specific, blood oriented study design as well as standardize blood collection conditions would be useful for Sz biomarker development.
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50
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Houseman EA, Kim S, Kelsey KT, Wiencke JK. DNA Methylation in Whole Blood: Uses and Challenges. Curr Environ Health Rep 2016; 2:145-54. [PMID: 26231364 DOI: 10.1007/s40572-015-0050-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to its convenience, the blood is commonly used in epigenomic studies, but its heterogeneous nature leads to interpretation difficulties, given the now widely recognized potential for confounding by cell composition effects. Many recent publications have reported significant associations between DNA methylation and a variety of health conditions or exposures. In this review, we summarize many of these recent publications, highlighting the findings in the context of potential cell composition effects, particularly findings that are indicative of immune response or inflammation. While there is substantial evidence for confounding by cell composition, there is nevertheless also evidence for differential DNA methylation suggestive of processes that are not cell mediated. We conclude that important biological insights still may be gained from studying DNA methylation in whole blood, either by investigating the cell composition effects themselves or processes that demonstrate associations even after adjusting for cell composition effects.
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Affiliation(s)
- E Andres Houseman
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA,
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