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Karunakaran KB, Amemori KI. Spatiotemporal expression patterns of anxiety disorder-associated genes. Transl Psychiatry 2023; 13:385. [PMID: 38092764 PMCID: PMC10719387 DOI: 10.1038/s41398-023-02693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Anxiety disorders (ADs) are the most common form of mental disorder that affects millions of individuals worldwide. Although physiological studies have revealed the neural circuits related to AD symptoms, how AD-associated genes are spatiotemporally expressed in the human brain still remains unclear. In this study, we integrated genome-wide association studies of four human AD subtypes-generalized anxiety disorder, social anxiety disorder, panic disorder, and obsessive-compulsive disorder-with spatial gene expression patterns. Our investigation uncovered a novel division among AD-associated genes, marked by significant and distinct expression enrichments in the cerebral nuclei, limbic, and midbrain regions. Each gene cluster was associated with specific anxiety-related behaviors, signaling pathways, region-specific gene networks, and cell types. Notably, we observed a significant negative correlation in the temporal expression patterns of these gene clusters during various developmental stages. Moreover, the specific brain regions enriched in each gene group aligned with neural circuits previously associated with negative decision-making and anxious temperament. These results suggest that the two distinct gene clusters may underlie separate neural systems involved in anxiety. As a result, our findings bridge the gap between genes and neural circuitry, shedding light on the mechanisms underlying AD-associated behaviors.
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Affiliation(s)
- Kalyani B Karunakaran
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ken-Ichi Amemori
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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Yin L, Chen Y, Fu T, Liu L, Xia Q. Identification of candidate blood biomarkers for the diagnosis of septicaemic melioidosis based on WGCNA. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2022; 50:252-259. [DOI: 10.1080/21691401.2022.2126490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Li Yin
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and The Second Affiliated Hospital, Hainan Medical University, Haikou, PR China
| | - Yuanyuan Chen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and The Second Affiliated Hospital, Hainan Medical University, Haikou, PR China
| | - Tingting Fu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and The Second Affiliated Hospital, Hainan Medical University, Haikou, PR China
| | - Lin Liu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and The Second Affiliated Hospital, Hainan Medical University, Haikou, PR China
| | - Qianfeng Xia
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and The Second Affiliated Hospital, Hainan Medical University, Haikou, PR China
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3
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Hemmings SMJ, Swart P, Womersely JS, Ovenden ES, van den Heuvel LL, McGregor NW, Meier S, Bardien S, Abrahams S, Tromp G, Emsley R, Carr J, Seedat S. RNA-seq analysis of gene expression profiles in posttraumatic stress disorder, Parkinson's disease and schizophrenia identifies roles for common and distinct biological pathways. DISCOVER MENTAL HEALTH 2022; 2:6. [PMID: 37861850 PMCID: PMC10501040 DOI: 10.1007/s44192-022-00009-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 10/21/2023]
Abstract
Evidence suggests that shared pathophysiological mechanisms in neuropsychiatric disorders (NPDs) may contribute to risk and resilience. We used single-gene and network-level transcriptomic approaches to investigate shared and disorder-specific processes underlying posttraumatic stress disorder (PTSD), Parkinson's disease (PD) and schizophrenia in a South African sample. RNA-seq was performed on blood obtained from cases and controls from each cohort. Gene expression and weighted gene correlation network analyses (WGCNA) were performed using DESeq2 and CEMiTool, respectively. Significant differences in gene expression were limited to the PTSD cohort. However, WGCNA implicated, amongst others, ribosomal expression, inflammation and ubiquitination as key players in the NPDs under investigation. Differential expression in ribosomal-related pathways was observed in the PTSD and PD cohorts, and focal adhesion and extracellular matrix pathways were implicated in PD and schizophrenia. We propose that, despite different phenotypic presentations, core transdiagnostic mechanisms may play important roles in the molecular aetiology of NPDs.
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Affiliation(s)
- Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa.
| | - Patricia Swart
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Jacqueline S Womersely
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Ellen S Ovenden
- Systems Genetics Working Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Leigh L van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Nathaniel W McGregor
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- Systems Genetics Working Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Stuart Meier
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
| | - Soraya Bardien
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shameemah Abrahams
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Robin Emsley
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
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de Oliveira KC, Camilo C, Gastaldi VD, Sant'Anna Feltrin A, Lisboa BCG, de Jesus Rodrigues de Paula V, Moretto AC, Lafer B, Hoexter MQ, Miguel EC, Maschietto M, Brentani H. Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation. BMC Genom Data 2021; 22:45. [PMID: 34717534 PMCID: PMC8557022 DOI: 10.1186/s12863-021-00993-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background Obsessive-compulsive disorder (OCD) is characterized by intrusive thoughts and repetitive actions, that presents the involvement of the cortico-striatal areas. The contribution of environmental risk factors to OCD development suggests that epigenetic mechanisms may contribute to its pathophysiology. DNA methylation changes and gene expression were evaluated in post-mortem brain tissues of the cortical (anterior cingulate gyrus and orbitofrontal cortex) and ventral striatum (nucleus accumbens, caudate nucleus and putamen) areas from eight OCD patients and eight matched controls. Results There were no differentially methylated CpG (cytosine-phosphate-guanine) sites (DMSs) in any brain area, nevertheless gene modules generated from CpG sites and protein-protein-interaction (PPI) showed enriched gene modules for all brain areas between OCD cases and controls. All brain areas but nucleus accumbens presented a predominantly hypomethylation pattern for the differentially methylated regions (DMRs). Although there were common transcriptional factors that targeted these DMRs, their targeted differentially expressed genes were different among all brain areas. The protein-protein interaction network based on methylation and gene expression data reported that all brain areas were enriched for G-protein signaling pathway, immune response, apoptosis and synapse biological processes but each brain area also presented enrichment of specific signaling pathways. Finally, OCD patients and controls did not present significant DNA methylation age differences. Conclusions DNA methylation changes in brain areas involved with OCD, especially those involved with genes related to synaptic plasticity and the immune system could mediate the action of genetic and environmental factors associated with OCD. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00993-0.
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Affiliation(s)
- Kátia Cristina de Oliveira
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil.,Center of Mathematics, Computation and Cognition, Federal University of ABC, São Bernardo do Campo, Brazil.,Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Caroline Camilo
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil.
| | - Vinícius Daguano Gastaldi
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil
| | - Arthur Sant'Anna Feltrin
- Center of Mathematics, Computation and Cognition, Federal University of ABC, São Bernardo do Campo, Brazil
| | - Bianca Cristina Garcia Lisboa
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil
| | - Vanessa de Jesus Rodrigues de Paula
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil
| | | | - Beny Lafer
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil
| | - Marcelo Queiroz Hoexter
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil.,Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Euripedes Constantino Miguel
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil.,Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | - Helena Brentani
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Rua Dr. Ovídio Pires de Campos, 785 - LIM23 (Térreo), São Paulo, 05403-010, Brazil.,Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
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Mahjani B, Bey K, Boberg J, Burton C. Genetics of obsessive-compulsive disorder. Psychol Med 2021; 51:2247-2259. [PMID: 34030745 PMCID: PMC8477226 DOI: 10.1017/s0033291721001744] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Obsessive-compulsive disorder (OCD) is a psychiatric disorder with multiple symptom dimensions (e.g. contamination, symmetry). OCD clusters in families and decades of twin studies clearly demonstrate an important role for genetics in the etiology of the disorder. METHODS In this review, we summarize the genetic epidemiology and molecular genetic studies of OCD and obsessive-compulsive symptoms. RESULTS OCD is a heritable, polygenic disorder with contributions from both common and rare variants, including de novo deleterious variations. Multiple studies have provided reliable support for a large additive genetic contribution to liability to OCD, with discrete OCD symptom dimensions having both shared and unique genetic risks. Genome-wide association studies have not produced significant results yet, likely because of small sample sizes, but larger meta-analyses are forthcoming. Both twin and genome-wide studies show that OCD shares genetic risk with its comorbid conditions (e.g. Tourette syndrome and anorexia nervosa). CONCLUSIONS Despite significant efforts to uncover the genetic basis of OCD, the mechanistic understanding of how genetic and environmental risk factors interact and converge at the molecular level to result in OCD's heterogeneous phenotype is still mostly unknown. Future investigations should increase ancestral genetic diversity, explore age and/or sex differences in genetic risk for OCD and expand the study of pharmacogenetics, gene expression, gene × environment interactions and epigenetic mechanisms for OCD.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Tics, Obsessive-Compulsive Disorder (OCD) and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Katharina Bey
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Julia Boberg
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Christie Burton
- Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Canada
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Karunakaran KB, Amemori S, Balakrishnan N, Ganapathiraju MK, Amemori KI. Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes. Sci Rep 2021; 11:18392. [PMID: 34526518 PMCID: PMC8443595 DOI: 10.1038/s41598-021-97418-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Mechanisms underlying anxiety disorders remain elusive despite the discovery of several associated genes. We constructed the protein-protein interaction networks (interactomes) of six anxiety disorders and noted enrichment for striatal expression among common genes in the interactomes. Five of these interactomes shared distinctive overlaps with the interactomes of genes that were differentially expressed in two striatal compartments (striosomes and matrix). Generalized anxiety disorder and social anxiety disorder interactomes showed exclusive and statistically significant overlaps with the striosome and matrix interactomes, respectively. Systematic gene expression analysis with the anxiety disorder interactomes constrained to contain only those genes that were shared with striatal compartment interactomes revealed a bifurcation among the disorders, which was influenced by the anterior cingulate cortex, nucleus accumbens, amygdala and hippocampus, and the dopaminergic signaling pathway. Our results indicate that the functionally distinct striatal pathways constituted by the striosome and the matrix may influence the etiological differentiation of various anxiety disorders.
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Affiliation(s)
- Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Satoko Amemori
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - N Balakrishnan
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA.
- Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, USA.
| | - Ken-Ichi Amemori
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.
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Predictive Potential of Circulating Ube2h mRNA as an E2 Ubiquitin-Conjugating Enzyme for Diagnosis or Treatment of Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21093398. [PMID: 32403399 PMCID: PMC7246987 DOI: 10.3390/ijms21093398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative disorders are caused by neuronal cell death, miscommunications between synapse, and abnormal accumulations of proteins in the brain. Alzheimer’s disease (AD) is one of the age-related disorders, which are the most common degenerative disorders today, and strongly affects memory consolidation and cognitive function in the brain. Amyloid-β and tau proteins are triggers for AD pathogenesis, and usually used as AD candidate biomarkers in the clinical research. Especially, clinical exam, brain imaging and molecular biological methods are being used to diagnosis for AD. Genome-wide association study (GWAS) is a new biomedical method, and its use contributes to understanding many human diseases, including brain diseases. Here, we identified ubiquitin conjugating enzyme E2 (Ube2) gene expression in neurons through GWAS. The subfamilies of Ube2’s genetic expression and inborn errors affect the ubiquitin proteasome system (UPS), leading to protein degradation in the brain. We found that only Ube2h mRNA transcription was significantly increased in the blood from AD, however we did not find any change of Ube2 subfamily genes’ expression in the blood and brain tissue. These data may provide information for diagnosis or clinical approach, and suggest that cell-free circulating Ube2h mRNA is a novel potential biomarker for AD.
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