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Campbell TL, Xie LY, Johnson RH, Hultman CM, van den Oord EJCG, Aberg KA. Investigating neonatal health risk variables through cell-type specific methylome-wide association studies. Clin Epigenetics 2024; 16:69. [PMID: 38778395 PMCID: PMC11112760 DOI: 10.1186/s13148-024-01681-3] [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: 11/06/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Adverse neonatal outcomes are a prevailing risk factor for both short- and long-term mortality and morbidity in infants. Given the importance of these outcomes, refining their assessment is paramount for improving prevention and care. Here we aim to enhance the assessment of these often correlated and multifaceted neonatal outcomes. To achieve this, we employ factor analysis to identify common and unique effects and further confirm these effects using criterion-related validity testing. This validation leverages methylome-wide profiles from neonatal blood. Specifically, we investigate nine neonatal health risk variables, including gestational age, Apgar score, three indicators of body size, jaundice, birth diagnosis, maternal preeclampsia, and maternal age. The methylomic profiles used for this research capture data from nearly all 28 million methylation sites in human blood, derived from the blood spot collected from 333 neonates, within 72 h post-birth. Our factor analysis revealed two common factors, size factor, that captured the shared effects of weight, head size, height, and gestational age and disease factor capturing the orthogonal shared effects of gestational age, combined with jaundice and birth diagnosis. To minimize false positives in the validation studies, validation was limited to variables with significant cumulative association as estimated through an in-sample replication procedure. This screening resulted in that the two common factors and the unique effects for gestational age, jaundice and Apgar were further investigated with full-scale cell-type specific methylome-wide association analyses. Highly significant, cell-type specific, associations were detected for both common effect factors and for Apgar. Gene Ontology analyses revealed multiple significant biologically relevant terms for the five fully investigated neonatal health risk variables. Given the established links between adverse neonatal outcomes and both immediate and long-term health, the distinct factor effects (representing the common and unique effects of the risk variables) and their biological profiles confirmed in our work, suggest their potential role as clinical biomarkers for assessing health risks and enhancing personalized care.
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Affiliation(s)
- Thomas L Campbell
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Ralen H Johnson
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA.
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Ren X, Feng Z, Ma X, Huo L, Zhou H, Bai A, Feng S, Zhou Y, Weng X, Fan C. m6A/m1A/m5C-Associated Methylation Alterations and Immune Profile in MDD. Mol Neurobiol 2024:10.1007/s12035-024-04042-6. [PMID: 38453794 DOI: 10.1007/s12035-024-04042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Major depressive disorder (MDD) is a prevalent psychiatric condition often accompanied by severe impairments in cognitive and functional capacities. This research was conducted to identify RNA modification-related gene signatures and associated functional pathways in MDD. Differentially expressed RNA modification-related genes in MDD were first identified. And a random forest model was developed and distinct RNA modification patterns were discerned based on signature genes. Then, comprehensive analyses of RNA modification-associated genes in MDD were performed, including functional analyses and immune cell infiltration. The study identified 29 differentially expressed RNA modification-related genes in MDD and two distinct RNA modification patterns. TRMT112, MBD3, NUDT21, and IGF2BP1 of the risk signature were detected. Functional analyses confirmed the involvement of RNA modification in pathways like phosphatidylinositol 3-kinase signaling and nucleotide oligomerization domain (NOD)-like receptor signaling in MDD. NUDT21 displayed a strong positive correlation with type 2 T helper cells, while IGF2BP1 negatively correlated with activated CD8 T cells, central memory CD4 T cells, and natural killer T cells. In summary, further research into the roles of NUDT21 and IGF2BP1 would be valuable for understanding MDD prognosis. The identified RNA modification-related gene signatures and pathways provide insights into MDD molecular etiology and potential diagnostic biomarkers.
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Affiliation(s)
- Xin Ren
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Zhuxiao Feng
- Department of Psychiatry, Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
| | - Xiaodong Ma
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Lijuan Huo
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Huiying Zhou
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Ayu Bai
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Shujie Feng
- Department of Rehabilitation Medicine, Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
| | - Ying Zhou
- Department of Psychiatry, Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
| | - Xuchu Weng
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, 55 Zhongshan Avenue West, Tianhe District, Guangzhou, 510631, China.
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China.
| | - Changhe Fan
- Department of Psychiatry, Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China.
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Zhuang Q, Zhang R, Li X, Ma D, Wang Y. Identification of the shared molecular mechanisms between major depressive disorder and COVID-19 from postmortem brain transcriptome analysis. J Affect Disord 2024; 346:273-284. [PMID: 37956829 DOI: 10.1016/j.jad.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/21/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVES This study aims to investigate the molecular mechanisms underlying the interaction of major depressive disorder (MDD) and COVID-19, and on this basis, diagnostic biomarkers and potential therapeutic drugs are further explored. METHODS Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) were employed to identify common key genes involved in the pathogenesis of COVID-19 and MDD. Correlations with clinical features were explored. Detailed mechanisms were further investigated through protein interaction networks, GSEA, and immune cell infiltration analysis. Finally, Enrichr's Drug Signature Database and Coremine Medical were used to predict the potential drugs associated with key genes. RESULTS The study identified 18 genes involved in both COVID-19 and MDD. Four key genes (MBP, CYP4B1, ERMN, and SLC26A7) were selected based on clinical relevance. A multi-gene prediction model showed good diagnostic efficiency for the two diseases: AUC of 0.852 for COVID-19 and 0.915 for MDD. GO and GSEA analyses identified specific biological functions and pathways associated with key genes in COVID-19 (axon guidance, metabolism, stress response) and MDD (neuron ensheathment, biosynthesis, glutamatergic neuron differentiation). The key genes also affected immune infiltration. Potential therapeutic drugs, including small molecules and traditional Chinese medicines, targeting these genes were identified. CONCLUSION This study provides insights into the complex biological mechanisms underlying COVID-19 and MDD, develops an effective diagnostic model, and predicts potential therapeutic drugs, which may contribute to the prevention and treatment of these two prevalent diseases.
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Affiliation(s)
- Qishuai Zhuang
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China; Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Rongqing Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China
| | - Xiaobing Li
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China
| | - Dapeng Ma
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China
| | - Yue Wang
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China; Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China.
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Patil CR, Suryakant Gawli C, Bhatt S. Targeting inflammatory pathways for treatment of the major depressive disorder. Drug Discov Today 2023; 28:103697. [PMID: 37422168 DOI: 10.1016/j.drudis.2023.103697] [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: 11/06/2022] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
Current treatments modalities for major depressive disorder (MDD) mainly target the monoaminergic neurotransmission. However, the therapeutic inadequacy and adverse effects confine the use of these conventional antidepressants to a limited subset of MDD patients. The classical antidepressants are increasingly proving unsatisfactory in tackling the treatment-resistant depression (TRD). Hence, the focus of treatment is shifting to alternative pathogenic pathways involved in depression. Preclinical and clinical evidences accumulated across the last decades have unequivocally affirmed the causative role of immuno-inflammatory pathways in the progression of depression. There is an upsurge in the clinical evaluations of the drugs having anti-inflammatory effects as antidepressants. This review highlights the molecular mechanisms connecting the inflammatory pathways to the MDD and current clinical status of inflammation modulating drugs in the treatment of MDD.
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Affiliation(s)
- Chandragauda R Patil
- Department of Pharmacology, R. C. Patel Institute of Pharmaceutical Education and Research, Karwand Naka, Shirpur 425405, Maharashtra, India
| | - Chandrakant Suryakant Gawli
- Department of Pharmacology, R. C. Patel Institute of Pharmaceutical Education and Research, Karwand Naka, Shirpur 425405, Maharashtra, India
| | - Shvetank Bhatt
- School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, Pune 411038, Maharashtra, India.
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Hettema JM, van den Oord EJCG, Zhao M, Xie LY, Copeland WE, Penninx BWJH, Aberg KA, Clark SL. Methylome-wide association study of anxiety disorders. Mol Psychiatry 2023; 28:3484-3492. [PMID: 37542162 PMCID: PMC10838347 DOI: 10.1038/s41380-023-02205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
Anxiety Disorders (ANX) such as panic disorder, generalized anxiety disorder, and phobias, are highly prevalent conditions that are moderately heritable. Evidence suggests that DNA methylation may play a role, as it is involved in critical adaptations to changing environments. Applying an enrichment-based sequencing approach covering nearly 28 million autosomal CpG sites, we conducted a methylome-wide association study (MWAS) of lifetime ANX in 1132 participants (618 cases/514 controls) from the Netherlands Study of Depression and Anxiety. Using epigenomic deconvolution, we performed MWAS for the main cell types in blood: granulocytes, T-cells, B-cells and monocytes. Cell-type specific analyses identified 280 and 82 methylome-wide significant associations (q-value < 0.1) in monocytes and granulocytes, respectively. Our top finding in monocytes was located in ZNF823 on chromosome 19 (p = 1.38 × 10-10) previously associated with schizophrenia. We observed significant overlap (p < 1 × 10-06) with the same direction of effect in monocytes (210 sites), T-cells (135 sites), and B-cells (727 sites) between this Discovery MWAS signal and a comparable replication dataset from the Great Smoky Mountains Study (N = 433). Overlapping Discovery-Replication MWAS signal was enriched for findings from published GWAS of ANX, major depression, and post-traumatic stress disorder. In monocytes, two specific sites in the FZR1 gene showed significant replication after Bonferroni correction with an additional 15 nominally replicated sites in monocytes and 4 in T-cells. FZR1 regulates neurogenesis in the hippocampus, and its knockout leads to impairments in associative fear memory and long-term potentiation in mice. In the largest and most extensive methylome-wide study of ANX, we identified replicable methylation sites located in genes of potential relevance for brain mechanisms of psychiatric conditions.
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Affiliation(s)
- John M Hettema
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, TX, USA
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center / GGZ inGeest, Amsterdam, 1081 HV, the Netherlands
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, TX, USA.
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van den Oord EJCG, Xie LY, Zhao M, Campbell TL, Turecki G, Kähler AK, Dean B, Mors O, Hultman CM, Staunstrup NH, Aberg KA. Genes implicated by a methylome-wide schizophrenia study in neonatal blood show differential expression in adult brain samples. Mol Psychiatry 2023; 28:2088-2094. [PMID: 37106120 DOI: 10.1038/s41380-023-02080-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Schizophrenia is a disabling disorder involving genetic predisposition in combination with environmental influences that likely act via dynamic alterations of the epigenome and the transcriptome but its detailed pathophysiology is largely unknown. We performed cell-type specific methylome-wide association study of neonatal blood (N = 333) from individuals who later in life developed schizophrenia and controls. Suggestively significant associations (P < 1.0 × 10-6) were detected in all cell-types and in whole blood with methylome-wide significant associations in monocytes (P = 2.85 × 10-9-4.87 × 10-9), natural killer cells (P = 1.72 × 10-9-7.82 × 10-9) and B cells (P = 3.8 × 10-9). Validation of methylation findings in post-mortem brains (N = 596) from independent schizophrenia cases and controls showed significant enrichment of transcriptional differences (enrichment ratio = 1.98-3.23, P = 2.3 × 10-3-1.0 × 10-5), with specific highly significant differential expression for, for example, BDNF (t = -6.11, P = 1.90 × 10-9). In addition, expression difference in brain significantly predicted schizophrenia (multiple correlation = 0.15-0.22, P = 3.6 × 10-4-4.5 × 10-8). In summary, using a unique design combining pre-disease onset (neonatal) blood methylomic data and post-disease onset (post-mortem) brain transcriptional data, we have identified genes of likely functional relevance that are associated with schizophrenia susceptibility, rather than confounding disease associated artifacts. The identified loci may be of clinical value as a methylation-based biomarker for early detection of increased schizophrenia susceptibility.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas L Campbell
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Gustavo Turecki
- Douglas Mental Health University Institute and McGill University, Montréal, Québec, Canada
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brian Dean
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital - Psychiatry, Risskov, Denmark
- Center for Genomics and Personalized Medicine, University of Aarhus, Aarhus, Denmark
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nicklas H Staunstrup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, University of Aarhus, Aarhus, Denmark
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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Meijer M, Franke B, Sandi C, Klein M. Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis. Neurosci Biobehav Rev 2023; 145:104997. [PMID: 36566803 DOI: 10.1016/j.neubiorev.2022.104997] [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: 08/08/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide association studies (EWAS) for externalizing behaviours have been limited in sample size, and, therefore, candidate genes and biomarkers with robust evidence are still lacking. We 1) performed a systematic literature review of EWAS of attention-deficit/hyperactivity disorder (ADHD)- and aggression-related behaviours conducted in peripheral tissue and cord blood and 2) combined the most strongly associated DNAm sites observed in individual studies (p < 10-3) to identify candidate genes and biological systems for ADHD and aggressive behaviours. We observed enrichment for neuronal processes and neuronal cell marker genes for ADHD. Astrocyte and granulocytes cell markers among genes annotated to DNAm sites were relevant for both ADHD and aggression-related behaviours. Only 1 % of the most significant epigenetic findings for ADHD/ADHD symptoms were likely to be directly explained by genetic factors involved in ADHD. Finally, we discuss how the field would greatly benefit from larger sample sizes and harmonization of assessment instruments.
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Affiliation(s)
- Mandy Meijer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92093, USA.
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Fries GR, Saldana VA, Finnstein J, Rein T. Molecular pathways of major depressive disorder converge on the synapse. Mol Psychiatry 2023; 28:284-297. [PMID: 36203007 PMCID: PMC9540059 DOI: 10.1038/s41380-022-01806-1] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023]
Abstract
Major depressive disorder (MDD) is a psychiatric disease of still poorly understood molecular etiology. Extensive studies at different molecular levels point to a high complexity of numerous interrelated pathways as the underpinnings of depression. Major systems under consideration include monoamines, stress, neurotrophins and neurogenesis, excitatory and inhibitory neurotransmission, mitochondrial dysfunction, (epi)genetics, inflammation, the opioid system, myelination, and the gut-brain axis, among others. This review aims at illustrating how these multiple signaling pathways and systems may interact to provide a more comprehensive view of MDD's neurobiology. In particular, considering the pattern of synaptic activity as the closest physical representation of mood, emotion, and conscience we can conceptualize, each pathway or molecular system will be scrutinized for links to synaptic neurotransmission. Models of the neurobiology of MDD will be discussed as well as future actions to improve the understanding of the disease and treatment options.
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Affiliation(s)
- Gabriel R. Fries
- grid.267308.80000 0000 9206 2401Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, Houston, TX 77054 USA ,grid.240145.60000 0001 2291 4776Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Ave, Houston, TX 77030 USA
| | - Valeria A. Saldana
- grid.262285.90000 0000 8800 2297Frank H. Netter MD School of Medicine at Quinnipiac University, 370 Bassett Road, North Haven, CT 06473 USA
| | - Johannes Finnstein
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Project Group Molecular Pathways of Depression, Max Planck Institute of Psychiatry, Kraepelinstr. 10, 80804 Munich, Germany
| | - Theo Rein
- Department of Translational Research in Psychiatry, Project Group Molecular Pathways of Depression, Max Planck Institute of Psychiatry, Kraepelinstr. 10, 80804, Munich, Germany.
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9
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Paoli C, Misztak P, Mazzini G, Musazzi L. DNA Methylation in Depression and Depressive-Like Phenotype: Biomarker or Target of Pharmacological Intervention? Curr Neuropharmacol 2022; 20:2267-2291. [PMID: 35105292 PMCID: PMC9890294 DOI: 10.2174/1570159x20666220201084536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 12/29/2022] Open
Abstract
Major depressive disorder (MDD) is a debilitating psychiatric disorder, the third leading global cause of disability. Regarding aetiopathogenetic mechanisms involved in the onset of depressive disorders, the interaction between genetic vulnerability traits and environmental factors is believed to play a major role. Although much is still to be elucidated about the mechanisms through which the environment can interact with genetic background shaping the disease risk, there is a general agreement about a key role of epigenetic marking. In this narrative review, we focused on the association between changes in DNA methylation patterns and MDD or depressive-like phenotype in animal models, as well as mechanisms of response to antidepressant drugs. We discussed studies presenting DNA methylation changes at specific genes of interest and profiling analyses in both patients and animal models of depression. Overall, we collected evidence showing that DNA methylation could not only be considered as a promising epigenetic biomarker of pathology but could also help in predicting antidepressant treatment efficacy. Finally, we discussed the hypothesis that specific changes in DNA methylation signature could play a role in aetiopathogenetic processes as well as in the induction of antidepressant effect.
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Affiliation(s)
- Caterina Paoli
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- School of Pharmacy, Pharmacy Unit, University of Camerino, 62032 Camerino, Italy
| | - Paulina Misztak
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Giulia Mazzini
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Laura Musazzi
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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10
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Transcriptome Profiling of the Dorsomedial Prefrontal Cortex in Suicide Victims. Int J Mol Sci 2022; 23:ijms23137067. [PMID: 35806070 PMCID: PMC9266666 DOI: 10.3390/ijms23137067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 01/27/2023] Open
Abstract
The default mode network (DMN) plays an outstanding role in psychiatric disorders. Still, gene expressional changes in its major component, the dorsomedial prefrontal cortex (DMPFC), have not been characterized. We used RNA sequencing in postmortem DMPFC samples to investigate suicide victims compared to control subjects. 1400 genes differed using log2FC > ±1 and adjusted p-value < 0.05 criteria between groups. Genes associated with depressive disorder, schizophrenia and impaired cognition were strongly overexpressed in top differentially expressed genes. Protein−protein interaction and co-expressional networks coupled with gene set enrichment analysis revealed that pathways related to cytokine receptor signaling were enriched in downregulated, while glutamatergic synaptic signaling upregulated genes in suicidal individuals. A validated differentially expressed gene, which is known to be associated with mGluR5, was the N-terminal EF-hand calcium-binding protein 2 (NECAB2). In situ hybridization histochemistry and immunohistochemistry proved that NECAB2 is expressed in two different types of inhibitory neurons located in layers II-IV and VI, respectively. Our results imply extensive gene expressional alterations in the DMPFC related to suicidal behavior. Some of these genes may contribute to the altered mental state and behavior of suicide victims.
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Schiele MA, Lipovsek J, Schlosser P, Soutschek M, Schratt G, Zaudig M, Berberich G, Köttgen A, Domschke K. Epigenome-wide DNA methylation in obsessive-compulsive disorder. Transl Psychiatry 2022; 12:221. [PMID: 35650177 PMCID: PMC9160220 DOI: 10.1038/s41398-022-01996-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/02/2023] Open
Abstract
In adult patients with obsessive-compulsive disorder (OCD), altered DNA methylation has been discerned in several candidate genes, while DNA methylation on an epigenome-wide level has been investigated in only one Chinese study so far. Here, an epigenome-wide association study (EWAS) was performed in a sample of 76 OCD patients of European ancestry (37 women, age ± SD: 33.51 ± 10.92 years) and 76 sex- and age-matched healthy controls for the first time using the Illumina MethylationEPIC BeadChip. After quality control, nine epigenome-wide significant quantitative trait methylation sites (QTMs) and 21 suggestive hits were discerned in the final sample of 68 patients and 68 controls. The top hit (cg24159721) and four other significant QTMs (cg11894324, cg01070250, cg11330075, cg15174812) map to the region of the microRNA 12136 gene (MIR12136). Two additional significant CpG sites (cg05740793, cg20450977) are located in the flanking region of the MT-RNR2 (humanin) like 8 gene (MT-RNRL8), while two further QTMs (cg16267121, cg15890734) map to the regions of the MT-RNR2 (humanin) like 3 (MT-RNRL3) and MT-RNR2 (humanin) like 2 (MT-RNRL2) genes. Provided replication of the present findings in larger samples, the identified QTMs might provide more biological insight into the pathogenesis of OCD and thereby could in the future serve as peripheral epigenetic markers of OCD risk with the potential to inform targeted preventive and therapeutic efforts.
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Affiliation(s)
- Miriam A. Schiele
- grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104 Freiburg, Germany
| | - Jan Lipovsek
- grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104 Freiburg, Germany ,grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany
| | - Pascal Schlosser
- grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany ,grid.21107.350000 0001 2171 9311Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD USA
| | - Michael Soutschek
- grid.5801.c0000 0001 2156 2780ETH Zurich–D-HEST, Institute for Neuroscience, Systems Neuroscience, Building Y17 L48, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Gerhard Schratt
- grid.5801.c0000 0001 2156 2780ETH Zurich–D-HEST, Institute for Neuroscience, Systems Neuroscience, Building Y17 L48, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Michael Zaudig
- Psychosomatic Hospital Windach, Schützenstraße 100, 86949 Windach, Germany
| | - Götz Berberich
- Psychosomatic Hospital Windach, Schützenstraße 100, 86949 Windach, Germany
| | - Anna Köttgen
- grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany. .,Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.
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12
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Guintivano J, Aberg KA, Clark SL, Rubinow DR, Sullivan PF, Meltzer-Brody S, van den Oord EJCG. Transcriptome-wide association study for postpartum depression implicates altered B-cell activation and insulin resistance. Mol Psychiatry 2022; 27:2858-2867. [PMID: 35365803 PMCID: PMC9156403 DOI: 10.1038/s41380-022-01525-7] [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: 09/29/2021] [Revised: 02/08/2022] [Accepted: 03/09/2022] [Indexed: 12/12/2022]
Abstract
Postpartum depression (PPD) affects 1 in 7 women and has negative mental health consequences for both mother and child. However, the precise biological mechanisms behind the disorder are unknown. Therefore, we performed the largest transcriptome-wide association study (TWAS) for PPD (482 cases, 859 controls) to date using RNA-sequencing in whole blood and deconvoluted cell types. No transcriptional changes were observed in whole blood. B-cells showed a majority of transcriptome-wide significant results (891 transcripts representing 789 genes) with pathway analyses implicating altered B-cell activation and insulin resistance. Integration of other data types revealed cell type-specific DNA methylation loci and disease-associated eQTLs (deQTLs), but not hormones/neuropeptides (estradiol, progesterone, oxytocin, BDNF), serve as regulators for part of the transcriptional differences between cases and controls. Further, deQTLs were enriched for several brain region-specific eQTLs, but no overlap with MDD risk loci was observed. Altogether, our results constitute a convergence of evidence for pathways most affected in PPD with data across different biological mechanisms.
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Affiliation(s)
- Jerry Guintivano
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, TX, USA
| | - David R Rubinow
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick F Sullivan
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Samantha Meltzer-Brody
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:ijms23105856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene–environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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15
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Clark SL, Chan RF, Zhao M, Xie LY, Copeland WE, Penninx BW, Aberg KA, van den Oord EJ. Dual methylation and hydroxymethylation study of alcohol use disorder. Addict Biol 2022; 27:e13114. [PMID: 34791764 PMCID: PMC8891051 DOI: 10.1111/adb.13114] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 09/16/2021] [Accepted: 10/30/2021] [Indexed: 12/11/2022]
Abstract
Using an integrative, multi-tissue design, we sought to characterize methylation and hydroxymethylation changes in blood and brain associated with alcohol use disorder (AUD). First, we used epigenomic deconvolution to perform cell-type-specific methylome-wide association studies within subpopulations of granulocytes/T-cells/B-cells/monocytes in 1132 blood samples. Blood findings were then examined for overlap with AUD-related associations with methylation and hydroxymethylation in 50 human post-mortem brain samples. Follow-up analyses investigated if overlapping findings mediated AUD-associated transcription changes in the same brain samples. Lastly, we replicated our blood findings in an independent sample of 412 individuals and aimed to replicate published alcohol methylation findings using our results. Cell-type-specific analyses in blood identified methylome-wide significant associations in monocytes and T-cells. The monocyte findings were significantly enriched for AUD-related methylation and hydroxymethylation in brain. Hydroxymethylation in specific sites mediated AUD-associated transcription in the same brain samples. As part of the most comprehensive methylation study of AUD to date, this work involved the first cell-type-specific methylation study of AUD conducted in blood, identifying and replicating a finding in DLGAP1 that may be a blood-based biomarker of AUD. In this first study to consider the role of hydroxymethylation in AUD, we found evidence for a novel mechanism for cognitive deficits associated with AUD. Our results suggest promising new avenues for AUD research.
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Affiliation(s)
| | - Robin F. Chan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | - Lin Y. Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | | | - Brenda W.J.H. Penninx
- Department of Psychiatry, University of Vermont,Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karolina A. Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
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Fulton S, Décarie-Spain L, Fioramonti X, Guiard B, Nakajima S. The menace of obesity to depression and anxiety prevalence. Trends Endocrinol Metab 2022; 33:18-35. [PMID: 34750064 DOI: 10.1016/j.tem.2021.10.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 02/07/2023]
Abstract
The incidence of depression and anxiety is amplified by obesity. Mounting evidence reveals that the psychiatric consequences of obesity stem from poor diet, inactivity, and visceral adipose accumulation. Resulting metabolic and vascular dysfunction, including inflammation, insulin and leptin resistance, and hypertension, have emerged as key risks to depression and anxiety development. Recent research advancements are exposing the important contribution of these different corollaries of obesity and their impact on neuroimmune status and the neural circuits controlling mood and emotional states. Along these lines, this review connects the clinical manifestations of depression and anxiety in obesity to our current understanding of the origins and biology of immunometabolic threats to central nervous system function and behavior.
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Affiliation(s)
- Stephanie Fulton
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Nutrition, Université de Montréal, Montréal, QC H3T1J4, Canada.
| | - Léa Décarie-Spain
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Neuroscience, Université de Montréal, Montréal, QC H3T1J4, Canada
| | - Xavier Fioramonti
- NutriNeuro, UMR 1286 INRAE, Bordeaux INP, Bordeaux University, Bordeaux, France
| | - Bruno Guiard
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), CNRS UMR5169, UPS, Université de Toulouse, Toulouse, France
| | - Shingo Nakajima
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Nutrition, Université de Montréal, Montréal, QC H3T1J4, Canada
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17
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DNA methylation of the KLK8 gene in depression symptomatology. Clin Epigenetics 2021; 13:200. [PMID: 34715912 PMCID: PMC8556955 DOI: 10.1186/s13148-021-01184-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022] Open
Abstract
Background Depression is a common, complex, and debilitating mental disorder estimated to be under-diagnosed and insufficiently treated in society. Liability to depression is influenced by both genetic and environmental risk factors, which are both capable of impacting DNA methylation (DNAm). Accordingly, numerous studies have researched for DNAm signatures of this disorder. Recently, an epigenome-wide association study of monozygotic twins identified an association between DNAm status in the KLK8 (neuropsin) promoter region and severity of depression symptomatology. Methods In this study, we aimed to investigate: (i) if blood DNAm levels, quantified by pyrosequencing, at two CpG sites in the KLK8 promoter are associated with depression symptomatology and depression diagnosis in an independent clinical cohort and (ii) if KLK8 DNAm levels are associated with depression, postpartum depression, and depression symptomatology in four independent methylomic cohorts, with blood and brain DNAm quantified by either MBD-seq or 450 k methylation array. Results DNAm levels in KLK8 were not significantly different between depression cases and controls, and were not significantly associated with any of the depression symptomatology scores after correction for multiple testing (minimum p value for KLK8 CpG1 = 0.12 for ‘Depressed mood,’ and for CpG2 = 0.03 for ‘Loss of self-confidence with other people’). However, investigation of the link between KLK8 promoter DNAm levels and depression-related phenotypes collected from four methylomic cohorts identified significant association (p value < 0.05) between severity of depression symptomatology and blood DNAm levels at seven CpG sites. Conclusions Our findings suggest that variance in blood DNAm levels in KLK8 promoter region is associated with severity of depression symptoms, but not depression diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01184-5.
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Abstract
Epigenetic mechanisms such as DNA methylation (DNAm) have been associated with stress responses and increased vulnerability to depression. Abnormal DNAm is observed in stressed animals and depressed individuals. Antidepressant treatment modulates DNAm levels and regulates gene expression in diverse tissues, including the brain and the blood. Therefore, DNAm could be a potential therapeutic target in depression. Here, we reviewed the current knowledge about the involvement of DNAm in the behavioural and molecular changes associated with stress exposure and depression. We also evaluated the possible use of DNAm changes as biomarkers of depression. Finally, we discussed current knowledge limitations and future perspectives.
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19
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Kendall KM, Van Assche E, Andlauer TFM, Choi KW, Luykx JJ, Schulte EC, Lu Y. The genetic basis of major depression. Psychol Med 2021; 51:2217-2230. [PMID: 33682643 DOI: 10.1017/s0033291721000441] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Major depressive disorder (MDD) is a common, debilitating, phenotypically heterogeneous disorder with heritability ranges from 30% to 50%. Compared to other psychiatric disorders, its high prevalence, moderate heritability, and strong polygenicity have posed major challenges for gene-mapping in MDD. Studies of common genetic variation in MDD, driven by large international collaborations such as the Psychiatric Genomics Consortium, have confirmed the highly polygenic nature of the disorder and implicated over 100 genetic risk loci to date. Rare copy number variants associated with MDD risk were also recently identified. The goal of this review is to present a broad picture of our current understanding of the epidemiology, genetic epidemiology, molecular genetics, and gene-environment interplay in MDD. Insights into the impact of genetic factors on the aetiology of this complex disorder hold great promise for improving clinical care.
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Affiliation(s)
- K M Kendall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - E Van Assche
- Department of Psychiatry, University of Muenster, Muenster, Germany
| | - T F M Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - K W Choi
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA02114, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA02115, USA
| | - J J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Outpatient Second Opinion Clinic, GGNet Mental Health, Warnsveld, The Netherlands
| | - E C Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Y Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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20
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Suh JS, Fiori LM, Ali M, Harkness KL, Ramonas M, Minuzzi L, Hassel S, Strother SC, Zamyadi M, Arnott SR, Farzan F, Foster JA, Lam RW, MacQueen GM, Milev R, Müller DJ, Parikh SV, Rotzinger S, Sassi RB, Soares CN, Uher R, Kennedy SH, Turecki G, Frey BN. Hypothalamus volume and DNA methylation of stress axis genes in major depressive disorder: A CAN-BIND study report. Psychoneuroendocrinology 2021; 132:105348. [PMID: 34229186 DOI: 10.1016/j.psyneuen.2021.105348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Dysfunction of the hypothalamic-pituitary-adrenal (HPA) axis is considered one of the mechanisms underlying the development of major depressive disorder (MDD), but the exact nature of this dysfunction is unknown. We investigated the relationship between hypothalamus volume (HV) and blood-derived DNA methylation in MDD. We obtained brain MRI, clinical and molecular data from 181 unmedicated MDD and 90 healthy control (HC) participants. MDD participants received a 16-week standardized antidepressant treatment protocol, as part of the first Canadian Biomarker Integration Network in Depression (CAN-BIND) study. We collected bilateral HV measures via manual segmentation by two independent raters. DNA methylation and RNA sequencing were performed for three key HPA axis-regulating genes coding for the corticotropin-binding protein (CRHBP), glucocorticoid receptor (NR3C1) and FK506 binding protein 5 (FKBP5). We used elastic net regression to perform variable selection and assess predictive ability of methylation variables on HV. Left HV was negatively associated with duration of current episode (ρ = -0.17, p = 0.035). We did not observe significant differences in HV between MDD and HC or any associations between HV and treatment response at weeks 8 or 16, overall depression severity, illness duration or childhood maltreatment. We also did not observe any differentially methylated CpG sites between MDD and HC groups. After assessing functionality by correlating methylation levels with RNA expression of the respective genes, we observed that the number of functionally relevant CpG sites differed between MDD and HC groups in FKBP5 (χ2 = 77.25, p < 0.0001) and NR3C1 (χ2 = 7.29, p = 0.007). Cross-referencing functionally relevant CpG sites to those that were highly ranked in predicting HV in elastic net modeling identified one site from FKBP5 (cg03591753) and one from NR3C1 (cg20728768) within the MDD group. Stronger associations between DNA methylation, gene expression and HV in MDD suggest a novel putative molecular pathway of stress-related sensitivity in depression. Future studies should consider utilizing the epigenome and ultra-high field MR data which would allow the investigation of HV sub-fields.
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Affiliation(s)
- Jee Su Suh
- Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada; Mood Disorders Program and Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, ON, Canada
| | - Laura M Fiori
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Mohammad Ali
- Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada; Mood Disorders Program and Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, ON, Canada
| | - Kate L Harkness
- Department of Psychology, Queen's University, Kingston, ON, Canada
| | - Milita Ramonas
- Juravinski Hospital and Cancer Centre, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Luciano Minuzzi
- Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada; Mood Disorders Program and Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, ON, Canada; Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Stefanie Hassel
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada
| | | | - Mojdeh Zamyadi
- Rotman Research Institute, Baycrest, Toronto, ON, Canada
| | | | - Faranak Farzan
- eBrain Lab, School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, BC, Canada
| | - Jane A Foster
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Raymond W Lam
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Glenda M MacQueen
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada
| | - Roumen Milev
- Departments of Psychiatry and Psychology, Queen's University, and Providence Care Hospital, Kingston, ON, Canada
| | - Daniel J Müller
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Centre for Addiction and Mental Health, Pharmacogenetics Research Clinic, Toronto, ON, Canada
| | - Sagar V Parikh
- University of Michigan Depression Center, Ann Arbor, MI, United States
| | - Susan Rotzinger
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Roberto B Sassi
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Claudio N Soares
- Departments of Psychiatry and Psychology, Queen's University, and Providence Care Hospital, Kingston, ON, Canada
| | - Rudolf Uher
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Sidney H Kennedy
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Centre for Depression and Suicide Studies, St. Michael's Hospital, Toronto, ON, Canada
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Benicio N Frey
- Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada; Mood Disorders Program and Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, ON, Canada; Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
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21
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van den Oord EJCG, Xie LY, Tran CJ, Zhao M, Aberg KA. A targeted solution for estimating the cell-type composition of bulk samples. BMC Bioinformatics 2021; 22:462. [PMID: 34565346 PMCID: PMC8474864 DOI: 10.1186/s12859-021-04385-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
Background To avoid false-positive findings and detect cell-type specific associations in methylation and transcription investigations with bulk samples, it is critical to know the proportions of the major cell-types. Results We present a novel approach that allows for precise estimation of cell-type proportions using only a few highly informative methylation markers. The most reliable estimates were obtained with 17 amplicons (34 CpGs) using the MuSiC estimator, for which the average correlations between the estimated and the true cell-type proportions were 0.889. Furthermore, the estimates were not significantly different from the true values (P = 0.95) indicating that the estimator is unbiased and the standard deviation of the estimates further indicate high precision. Moreover, the overall variability of the estimates as measured by the Root Mean Squared Error (RMSE), which is a function of both bias and precision, was low (mean RMSE = 0.038). Taken together, these results indicate that the approach produced reliable estimates that are both unbiased and highly precise. Conclusion This cost-effective approach for estimating cell-type proportions in bulk samples allows for enhanced targeted analysis, which in turn will minimize the risk of reporting false-positive findings and allowing for detection of cell-type specific associations. The approach is applicable across platforms and can be extended to assess cell-type proportions for various tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04385-0.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA
| | - Charles J Tran
- Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA.
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Rasmusson AJ, Gallwitz M, Soltanabadi B, Ciuculete DM, Mengel-From J, Christensen K, Nygaard M, Soerensen M, Boström AE, Fredriksson R, Freyhult E, Mwinyi J, Czamara D, Binder EB, Schiöth HB, Cunningham JL. Toll-like receptor 4 methylation grade is linked to depressive symptom severity. Transl Psychiatry 2021; 11:371. [PMID: 34226490 PMCID: PMC8257733 DOI: 10.1038/s41398-021-01481-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
This study explores potential associations between the methylation of promoter-associated CpG sites of the toll-like receptor (TLR)-family, plasma levels of pro-inflammatory proteins and depressive symptoms in young female psychiatric patients. Ratings of depressive symptoms and blood samples were obtained from 92 young women seeking psychiatric care. Methylation of 32 promoter-associated CpG sites in TLR1 to TLR10 was analysed using the Illumina Infinium Methylation EPIC BeadChip. Expression levels of 91 inflammatory proteins were determined by proximity extension assay. Statistical correlations between depressive state, TLR1-10 methylation and inflammatory proteins were investigated. Four additional cohorts were studied to evaluate the generalizability of the findings. In the discovery cohort, methylation grade of cg05429895 (TLR4) in blood was inversely correlated with depressive symptoms score in young adults. After correction for multiple testing, plasma levels of macrophage inflammatory protein 1β (MIP-1β/CCL4) were associated with both TLR4 methylation and depressive symptom severity. A similar inverse association between TLR4 methylation in blood and affective symptoms score was also found in a cohort of 148 both males and females (<40 years of age) from the Danish Twin Registry. These findings were not, however, replicated in three other external cohorts; which differed from the first two cohorts by a higher age and mixed ethnicities, thus limiting the generalizability of our findings. However, TLR4 methylation inversely correlated with TLR4 mRNA expression in the Danish Twin Study indicating a functional significance of methylation at this particular CpG. Higher depression scores in young Scandinavian adults was associated with decreased methylation of TLR4 in blood.
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Affiliation(s)
- Annica J Rasmusson
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala University Hospital, Entrance 10, Floor 3B, 751 85, Uppsala, Sweden
| | - Maike Gallwitz
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala University Hospital, Entrance 10, Floor 3B, 751 85, Uppsala, Sweden
| | - Bardia Soltanabadi
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala University Hospital, Entrance 10, Floor 3B, 751 85, Uppsala, Sweden
| | - Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Jonas Mengel-From
- The Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Marianne Nygaard
- The Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mette Soerensen
- The Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Adrian E Boström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, 75124, Uppsala, Sweden
| | - Eva Freyhult
- Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Darina Czamara
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
- Institute of Translational Medicine and Biotechnology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Janet L Cunningham
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala University Hospital, Entrance 10, Floor 3B, 751 85, Uppsala, Sweden.
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Afridi R, Seol S, Kang HJ, Suk K. Brain-immune interactions in neuropsychiatric disorders: Lessons from transcriptome studies for molecular targeting. Biochem Pharmacol 2021; 188:114532. [PMID: 33773976 DOI: 10.1016/j.bcp.2021.114532] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Understanding the pathophysiological mechanisms of neuropsychiatric disorders has been a challenging quest for neurobiologists. Recent years have witnessed enormous technological advances in the field of neuroimmunology, blurring boundaries between the central nervous system and the periphery. Consequently, the discipline has expanded to cover interactions between the nervous and immune systems in health and diseases. The complex interplay between the peripheral and central immune pathways in neuropsychiatric disorders has recently been documented in various studies, but the genetic determinants remain elusive. Recent transcriptome studies have identified dysregulated genes involved in peripheral immune cell activation, blood-brain barrier integrity, glial cell activation, and synaptic plasticity in major depressive disorder, bipolar disorder, autism spectrum disorder, and schizophrenia. Herein, the key transcriptomic techniques applied in investigating differentially expressed genes and pathways responsible for altered brain-immune interactions in neuropsychiatric disorders are discussed. The application of transcriptomics that can aid in identifying molecular targets in various neuropsychiatric disorders is highlighted.
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Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sihwan Seol
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyo Jung Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea.
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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24
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Microglia Diversity in Healthy and Diseased Brain: Insights from Single-Cell Omics. Int J Mol Sci 2021; 22:ijms22063027. [PMID: 33809675 PMCID: PMC8002227 DOI: 10.3390/ijms22063027] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
Microglia are the resident immune cells of the central nervous system (CNS) that have distinct ontogeny from other tissue macrophages and play a pivotal role in health and disease. Microglia rapidly react to the changes in their microenvironment. This plasticity is attributed to the ability of microglia to adapt a context-specific phenotype. Numerous gene expression profiling studies of immunosorted CNS immune cells did not permit a clear dissection of their phenotypes, particularly in diseases when peripheral cells of the immune system come to play. Only recent advances in single-cell technologies allowed studying microglia at high resolution and revealed a spectrum of discrete states both under homeostatic and pathological conditions. Single-cell technologies such as single-cell RNA sequencing (scRNA-seq) and mass cytometry (Cytometry by Time-Of-Flight, CyTOF) enabled determining entire transcriptomes or the simultaneous quantification of >30 cellular parameters of thousands of individual cells. Single-cell omics studies demonstrated the unforeseen heterogeneity of microglia and immune infiltrates in brain pathologies: neurodegenerative disorders, stroke, depression, and brain tumors. We summarize the findings from those studies and the current state of knowledge of functional diversity of microglia under physiological and pathological conditions. A precise definition of microglia functions and phenotypes may be essential to design future immune-modulating therapies.
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25
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Sales AJ, Maciel IS, Suavinha ACDR, Joca SRL. Modulation of DNA Methylation and Gene Expression in Rodent Cortical Neuroplasticity Pathways Exerts Rapid Antidepressant-Like Effects. Mol Neurobiol 2021; 58:777-794. [PMID: 33025509 DOI: 10.1007/s12035-020-02145-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Stress increases DNA methylation, primarily a suppressive epigenetic mechanism catalyzed by DNA methyltransferases (DNMT), and decreases the expression of genes involved in neuronal plasticity and mood regulation. Despite chronic antidepressant treatment decreases stress-induced DNA methylation, it is not known whether inhibition of DNMT would convey rapid antidepressant-like effects. AIM This work tested such a hypothesis and evaluated whether a behavioral effect induced by DNMT inhibitors (DNMTi) corresponds with changes in DNA methylation and transcript levels in genes consistently associated with the neurobiology of depression and synaptic plasticity (BDNF, TrkB, 5-HT1A, NMDA, and AMPA). METHODS Male Wistar rats received intraperitoneal (i.p.) injection of two pharmacologically different DNMTi (5-AzaD 0.2 and 0.6 mg/kg or RG108 0.6 mg/kg) or vehicle (1 ml/kg), 1 h or 7 days before the learned helplessness test (LH). DNA methylation in target genes and the correspondent transcript levels were measured in the hippocampus (HPC) and prefrontal cortex (PFC) using meDIP-qPCR. In parallel separate groups, the antidepressant-like effect of 5-AzaD and RG108 was investigated in the forced swimming test (FST). The involvement of cortical BDNF-TrkB-mTOR pathways was assessed by intra-ventral medial PFC (vmPFC) injections of rapamycin (mTOR inhibitor), K252a (TrkB receptor antagonist), or vehicle (0.2 μl/side). RESULTS We found that both 5-AzaD and RG108 acutely and 7 days before the test decreased escape failures in the LH. LH stress increased DNA methylation and decreased transcript levels of BDNF IV and TrkB in the PFC, effects that were not significantly attenuated by RG108 treatment. The systemic administration of 5-AzaD (0.2 mg/kg) and RG108 (0.2 mg/kg) induced an antidepressant-like effect in FST, which was, however, attenuated by TrkB and mTOR inhibition into the vmPFC. CONCLUSION These findings suggest that acute inhibition of stress-induced DNA methylation promotes rapid and sustained antidepressant effects associated with increased BDNF-TrkB-mTOR signaling in the PFC.
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Affiliation(s)
- Amanda J Sales
- Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
- FMRP-USP, Av Bandeirantes, 3900, Ribeirão Preto, SP, 14049-900, Brazil.
| | - Izaque S Maciel
- Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Angélica C D R Suavinha
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences 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.
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- FCFRP-USP, Av Café, sn, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Le-Niculescu H, Roseberry K, Gill SS, Levey DF, Phalen PL, Mullen J, Williams A, Bhairo S, Voegtline T, Davis H, Shekhar A, Kurian SM, Niculescu AB. Precision medicine for mood disorders: objective assessment, risk prediction, pharmacogenomics, and repurposed drugs. Mol Psychiatry 2021; 26:2776-2804. [PMID: 33828235 PMCID: PMC8505261 DOI: 10.1038/s41380-021-01061-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 12/23/2022]
Abstract
Mood disorders (depression, bipolar disorders) are prevalent and disabling. They are also highly co-morbid with other psychiatric disorders. Currently there are no objective measures, such as blood tests, used in clinical practice, and available treatments do not work in everybody. The development of blood tests, as well as matching of patients with existing and new treatments, in a precise, personalized and preventive fashion, would make a significant difference at an individual and societal level. Early pilot studies by us to discover blood biomarkers for mood state were promising [1], and validated by others [2]. Recent work by us has identified blood gene expression biomarkers that track suicidality, a tragic behavioral outcome of mood disorders, using powerful longitudinal within-subject designs, validated them in suicide completers, and tested them in independent cohorts for ability to assess state (suicidal ideation), and ability to predict trait (future hospitalizations for suicidality) [3-6]. These studies showed good reproducibility with subsequent independent genetic studies [7]. More recently, we have conducted such studies also for pain [8], for stress disorders [9], and for memory/Alzheimer's Disease [10]. We endeavored to use a similar comprehensive approach to identify more definitive biomarkers for mood disorders, that are transdiagnostic, by studying mood in psychiatric disorders patients. First, we used a longitudinal within-subject design and whole-genome gene expression approach to discover biomarkers which track mood state in subjects who had diametric changes in mood state from low to high, from visit to visit, as measured by a simple visual analog scale that we had previously developed (SMS-7). Second, we prioritized these biomarkers using a convergent functional genomics (CFG) approach encompassing in a comprehensive fashion prior published evidence in the field. Third, we validated the biomarkers in an independent cohort of subjects with clinically severe depression (as measured by Hamilton Depression Scale, (HAMD)) and with clinically severe mania (as measured by the Young Mania Rating Scale (YMRS)). Adding the scores from the first three steps into an overall convergent functional evidence (CFE) score, we ended up with 26 top candidate blood gene expression biomarkers that had a CFE score as good as or better than SLC6A4, an empirical finding which we used as a de facto positive control and cutoff. Notably, there was among them an enrichment in genes involved in circadian mechanisms. We further analyzed the biological pathways and networks for the top candidate biomarkers, showing that circadian, neurotrophic, and cell differentiation functions are involved, along with serotonergic and glutamatergic signaling, supporting a view of mood as reflecting energy, activity and growth. Fourth, we tested in independent cohorts of psychiatric patients the ability of each of these 26 top candidate biomarkers to assess state (mood (SMS-7), depression (HAMD), mania (YMRS)), and to predict clinical course (future hospitalizations for depression, future hospitalizations for mania). We conducted our analyses across all patients, as well as personalized by gender and diagnosis, showing increased accuracy with the personalized approach, particularly in women. Again, using SLC6A4 as the cutoff, twelve top biomarkers had the strongest overall evidence for tracking and predicting depression after all four steps: NRG1, DOCK10, GLS, PRPS1, TMEM161B, GLO1, FANCF, HNRNPDL, CD47, OLFM1, SMAD7, and SLC6A4. Of them, six had the strongest overall evidence for tracking and predicting both depression and mania, hence bipolar mood disorders. There were also two biomarkers (RLP3 and SLC6A4) with the strongest overall evidence for mania. These panels of biomarkers have practical implications for distinguishing between depression and bipolar disorder. Next, we evaluated the evidence for our top biomarkers being targets of existing psychiatric drugs, which permits matching patients to medications in a targeted fashion, and the measuring of response to treatment. We also used the biomarker signatures to bioinformatically identify new/repurposed candidate drugs. Top drugs of interest as potential new antidepressants were pindolol, ciprofibrate, pioglitazone and adiphenine, as well as the natural compounds asiaticoside and chlorogenic acid. The last 3 had also been identified by our previous suicidality studies. Finally, we provide an example of how a report to doctors would look for a patient with depression, based on the panel of top biomarkers (12 for depression and bipolar, one for mania), with an objective depression score, risk for future depression, and risk for bipolar switching, as well as personalized lists of targeted prioritized existing psychiatric medications and new potential medications. Overall, our studies provide objective assessments, targeted therapeutics, and monitoring of response to treatment, that enable precision medicine for mood disorders.
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Affiliation(s)
- H. Le-Niculescu
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN USA
| | - K. Roseberry
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - S. S. Gill
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - D. F. Levey
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.47100.320000000419368710Present Address: Department of Psychiatry, Yale University School of Medicine, New Haven, CT USA
| | - P. L. Phalen
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.411024.20000 0001 2175 4264Present Address: VA Maryland Health Care System/University of Maryland School of Medicine, Baltimore, MD USA
| | - J. Mullen
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - A. Williams
- grid.280828.80000 0000 9681 3540Indianapolis VA Medical Center, Indianapolis, IN USA
| | - S. Bhairo
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.280828.80000 0000 9681 3540Indianapolis VA Medical Center, Indianapolis, IN USA
| | - T. Voegtline
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.280828.80000 0000 9681 3540Indianapolis VA Medical Center, Indianapolis, IN USA
| | - H. Davis
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.280828.80000 0000 9681 3540Indianapolis VA Medical Center, Indianapolis, IN USA
| | - A. Shekhar
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.21925.3d0000 0004 1936 9000Present Address: Office of the Dean, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - S. M. Kurian
- grid.214007.00000000122199231Scripps Health and Department of Molecular Medicine, Scripps Research, La Jolla, CA USA
| | - A. B. Niculescu
- grid.257413.60000 0001 2287 3919Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN USA ,grid.280828.80000 0000 9681 3540Indianapolis VA Medical Center, Indianapolis, IN USA
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Figueroa-Hall LK, Paulus MP, Savitz J. Toll-Like Receptor Signaling in Depression. Psychoneuroendocrinology 2020; 121:104843. [PMID: 32911436 PMCID: PMC7883590 DOI: 10.1016/j.psyneuen.2020.104843] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/09/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Depression is one of the most prevalent, disabling, and costly mental illnesses currently affecting over 300 million people worldwide. A subset of depressed patients display inflammation as indicated by increased levels of proinflammatory mediators in the blood and cerebrospinal fluid. Longitudinal and experimental studies suggest that this inflammatory profile may causally contribute to the initiation, maintenance, or recurrence of depressive episodes in the context of major depressive disorder (MDD). While the mechanistic pathways that mediate these depressogenic effects have not yet been fully elucidated, toll-like receptor (TLR) signaling is one potential common inflammatory pathway. In this review, we focus on the role that inflammation plays in depression, TLR signaling and its plasticity as a candidate pathway, its regulation by micro ribonucleic acids (miRNAs), and their potential as diagnostic biomarkers for identification of inflammatory subtypes of depression. Pre-clinical and clinical studies have demonstrated that TLR expression and TLR signaling regulators are associated with MDD. Further, TLR expression and signaling is in-turn, regulated in part by miRNAs and some TLR-responsive miRNAs indirectly modulate pathways that are implicated in MDD pathophysiology. These data suggest an intersection between TLR signaling regulation and MDD-linked pathways. While these studies suggest that miRNAs play a role in the pathophysiology of MDD via their regulatory effects on TLR pathways, the utility of miRNAs as biomarkers and potential treatment targets remains to be determined. Developing new and innovative techniques or adapting established immunological approaches to mental health, should be at the forefront in moving the field forward, especially in terms of categorization of inflammatory subtypes in MDD.
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Affiliation(s)
| | - Martin P Paulus
- Laureate Institute for Brain Research, 6655 S. Yale Ave, Tulsa, OK, 74136, United States; Oxley College of Health Sciences, 1215 S. Boulder Ave W., The University of Tulsa, Tulsa, OK, 74199, United States.
| | - Jonathan Savitz
- Laureate Institute for Brain Research, 6655 S. Yale Ave, Tulsa, OK, 74136, United States; Oxley College of Health Sciences, 1215 S. Boulder Ave W., The University of Tulsa, Tulsa, OK, 74199, United States.
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28
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Nascimento C, Nunes PV, Suemoto CK, Rodriguez RD, Leite REP, Grinberg LT, Pasqualucci CA, Nitrini R, Jacob-Filho W, Brentani HP, Lafer B. Differential levels of inflammatory and neuroendocrine markers in the hippocampus and anterior cingulate cortex of bipolar disorder subjects: A post-mortem study. Brain Behav Immun 2020; 90:286-293. [PMID: 32949690 PMCID: PMC8549680 DOI: 10.1016/j.bbi.2020.08.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Camila Nascimento
- Bipolar Disorder Program (PROMAN), Department of Psychiatry, University of São Paulo Medical School, Sao Paulo, SP, Brazil.
| | - Paula Villela Nunes
- Bipolar Disorder Program (PROMAN), Department of Psychiatry, University of São Paulo Medical School, Sao Paulo, SP, Brazil
| | - Claudia Kimie Suemoto
- Biobank for Aging Studies, University of São Paulo Medical School, Sao Paulo, SP, Brazil
| | | | | | - Lea Tenenholz Grinberg
- Biobank for Aging Studies, University of São Paulo Medical School, Sao Paulo, SP, Brazil,Memory and Aging Center University of California, Department of Neurology, San Francisco, USA
| | | | - Ricardo Nitrini
- Biobank for Aging Studies, University of São Paulo Medical School, Sao Paulo, SP, Brazil
| | - Wilson Jacob-Filho
- Biobank for Aging Studies, University of São Paulo Medical School, Sao Paulo, SP, Brazil
| | - Helena Paula Brentani
- Department of Psychiatry, University of São Paulo Medical School, Sao Paulo, SP, Brazil
| | - Beny Lafer
- Bipolar Disorder Program (PROMAN), Department of Psychiatry, University of São Paulo Medical School, Sao Paulo, SP, Brazil
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29
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Single-cell mass cytometry of microglia in major depressive disorder reveals a non-inflammatory phenotype with increased homeostatic marker expression. Transl Psychiatry 2020; 10:310. [PMID: 32917850 PMCID: PMC7486938 DOI: 10.1038/s41398-020-00992-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Stress-induced disturbances of brain homeostasis and neuroinflammation have been implicated in the pathophysiology of mood disorders. In major depressive disorder (MDD), elevated levels of proinflammatory cytokines and chemokines can be found in peripheral blood, but very little is known about the changes that occur directly in the brain. Microglia are the primary immune effector cells of the central nervous system and exquisitely sensitive to changes in the brain microenvironment. Here, we performed the first single-cell analysis of microglia from four different post-mortem brain regions (frontal lobe, temporal lobe, thalamus, and subventricular zone) of medicated individuals with MDD compared to controls. We found no evidence for the induction of inflammation-associated molecules, such as CD11b, CD45, CCL2, IL-1β, IL-6, TNF, MIP-1β (CCL4), IL-10, and even decreased expression of HLA-DR and CD68 in microglia from MDD cases. In contrast, we detected increased levels of the homeostatic proteins P2Y12 receptor, TMEM119 and CCR5 (CD195) in microglia from all brain regions of individuals with MDD. We also identified enrichment of non-inflammatory CD206hi macrophages in the brains of MDD cases. In sum, our results suggest enhanced homeostatic functions of microglia in MDD.
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30
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Hüls A, Robins C, Conneely KN, De Jager PL, Bennett DA, Epstein MP, Wingo TS, Wingo AP. Association between DNA methylation levels in brain tissue and late-life depression in community-based participants. Transl Psychiatry 2020; 10:262. [PMID: 32733030 PMCID: PMC7393126 DOI: 10.1038/s41398-020-00948-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Major depressive disorder (MDD) arises from a combination of genetic and environmental risk factors and DNA methylation is one of the molecular mechanisms through which these factors can manifest. However, little is known about the epigenetic signature of MDD in brain tissue. This study aimed to investigate associations between brain tissue-based DNA methylation and late-life MDD. METHODS We performed a brain epigenome-wide association study (EWAS) of late-life MDD in 608 participants from the Religious Order Study and the Rush Memory and Aging Project (ROS/MAP) using DNA methylation profiles of the dorsal lateral prefrontal cortex generated using the Illumina HumanMethylation450 Beadchip array. We also conducted an EWAS of MDD in each sex separately. RESULTS We found epigenome-wide significant associations between brain tissue-based DNA methylation and late-life MDD. The most significant and robust association was found with altered methylation levels in the YOD1 locus (cg25594636, p value = 2.55 × 10-11; cg03899372, p value = 3.12 × 10-09; cg12796440, p value = 1.51 × 10-08, cg23982678, p value = 7.94 × 10-08). Analysis of differentially methylated regions (p value = 5.06 × 10-10) further confirmed this locus. Other significant loci include UGT8 (cg18921206, p value = 1.75 × 10-08), FNDC3B (cg20367479, p value = 4.97 × 10-08) and SLIT2 (cg10946669, p value = 8.01 × 10-08). Notably, brain tissue-based methylation levels were strongly associated with late-life MDD in men more than in women. CONCLUSIONS We identified altered methylation in the YOD1, UGT8, FNDC3B, and SLIT2 loci as new epigenetic factors associated with late-life MDD. Furthermore, our study highlights the sex-specific molecular heterogeneity of MDD.
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Affiliation(s)
- Anke Hüls
- Department of Epidemiology and Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Chloe Robins
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Philip L De Jager
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | | | - Thomas S Wingo
- Department of Human Genetics, Emory University, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Aliza P Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA.
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
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Kokkosis AG, Tsirka SE. Neuroimmune Mechanisms and Sex/Gender-Dependent Effects in the Pathophysiology of Mental Disorders. J Pharmacol Exp Ther 2020; 375:175-192. [PMID: 32661057 DOI: 10.1124/jpet.120.266163] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Innate and adaptive immune mechanisms have emerged as critical regulators of CNS homeostasis and mental health. A plethora of immunologic factors have been reported to interact with emotion- and behavior-related neuronal circuits, modulating susceptibility and resilience to mental disorders. However, it remains unclear whether immune dysregulation is a cardinal causal factor or an outcome of the pathologies associated with mental disorders. Emerging variations in immune regulatory pathways based on sex differences provide an additional framework for discussion in these psychiatric disorders. In this review, we present the current literature pertaining to the effects that disrupted immune pathways have in mental disorder pathophysiology, including immune dysregulation in CNS and periphery, microglial activation, and disturbances of the blood-brain barrier. In addition, we present the suggested origins of such immune dysregulation and discuss the gender and sex influence of the neuroimmune substrates that contribute to mental disorders. The findings challenge the conventional view of these disorders and open the window to a diverse spectrum of innovative therapeutic targets that focus on the immune-specific pathophenotypes in neuronal circuits and behavior. SIGNIFICANCE STATEMENT: The involvement of gender-dependent inflammatory mechanisms on the development of mental pathologies is gaining momentum. This review addresses these novel factors and presents the accumulating evidence introducing microglia and proinflammatory elements as critical components and potential targets for the treatment of mental disorders.
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Affiliation(s)
- Alexandros G Kokkosis
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Stella E Tsirka
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
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