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Das SC, Schulmann A, Callor WB, Jerominski L, Panicker MM, Christensen ED, Bunney WE, Williams ME, Coon H, Vawter MP. Altered transcriptomes, cell type proportions, and dendritic spine morphology in hippocampus of suicide decedents. J Affect Disord 2024; 367:118-128. [PMID: 39191313 DOI: 10.1016/j.jad.2024.08.144] [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: 10/23/2023] [Revised: 08/03/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND Suicide is a manner of death resulting from complex environmental and genetic risks that affect millions of people globally. Both structural and functional studies identified the hippocampus as one of the vulnerable brain regions contributing to suicide risk. METHODS We have identified the hippocampal tissue transcriptomes, gene ontology, cell type proportions, and dendritic spine morphology in controls (n = 28) and suicide decedents (n = 22). In addition, the transcriptomic signature in iPSC-derived neuronal precursor cells (NPCs) and neurons were also investigated in controls (n = 2) and suicide decedents (n = 2). RESULTS The hippocampal tissue transcriptomic data revealed that NPAS4 gene expression was downregulated while ALDH1A2, NAAA, and MLXIPL gene expressions were upregulated in hippocampal tissue of suicide decedents. The gene ontology identified 29 significant pathways including NPAS4-associated gene ontology terms "excitatory post-synaptic potential", "regulation of postsynaptic membrane potential" and "long-term memory" indicating alteration of glutamatergic synapses in the hippocampus of suicide decedents. The cell type deconvolution identified decreased excitatory neuron proportion and an increased inhibitory neuron proportion providing evidence of excitation/inhibition imbalance in the hippocampus of suicide decedents. In addition, suicide decedents had increased dendric spine density in the hippocampus, due to an increase of thin (relatively unstable) dendritic spines, compared to controls. The transcriptomes of iPSC-derived hippocampal-like NPCs and neurons revealed 31 and 33 differentially expressed genes in NPC and neurons, respectively, of suicide decedents. CONCLUSIONS Our findings will provide new insights into the hippocampal neuropathology of suicide.
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Affiliation(s)
- Sujan C Das
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA
| | | | - William B Callor
- Office of Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - Leslie Jerominski
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mitradas M Panicker
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, USA
| | - Erik D Christensen
- Office of Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - William E Bunney
- Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA
| | - Megan E Williams
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, UT, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Marquis P Vawter
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA.
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Agoston DV. Of artificial intelligence, machine learning, and the human brain. Celebrating Miklos Palkovits' 90th birthday. Front Neuroanat 2024; 18:1374864. [PMID: 38764486 PMCID: PMC11099251 DOI: 10.3389/fnana.2024.1374864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/25/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Denes V. Agoston
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, United States
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Arčan IŠ, Kouter K, Zupanc T, Paska AV. Epigenetics and suicide: investigating altered H3K14ac unveiled differential expression in ADORA2A, B4GALT2 and MMP14. Epigenomics 2024; 16:701-714. [PMID: 38545853 PMCID: PMC11318710 DOI: 10.2217/epi-2023-0351] [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: 10/06/2023] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Background: Environmental factors make an important contribution to suicide. Histone tails are prone to different modifications, leading to changes of chromatin (de)condensation and consequently gene expression. Materials & methods: Level of H3K14ac was studied with chromatin immunoprecipitation followed by high-throughput DNA sequencing. Genes were further validated with RT-qPCR; using hippocampal tissue. Results: We showed lowered H3K14ac levels in individuals who died by suicide. The genes ADORA2A, B4GALT2 and MMP14 showed differential expression in individuals who died by suicide. Identified genetic and protein interactions among genes show interactions with suicide-related genes. Conclusion: Further investigations of histone modifications in association with DNA methylation and miRNA are needed to expand our knowledge of the genes that could significantly contribute to suicide.
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Affiliation(s)
- Iris Šalamon Arčan
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Kouter
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Institute of Microbiology & Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Pereira CA, Reis-de-Oliveira G, Pierone BC, Martins-de-Souza D, Kaster MP. Depicting the molecular features of suicidal behavior: a review from an "omics" perspective. Psychiatry Res 2024; 332:115682. [PMID: 38198856 DOI: 10.1016/j.psychres.2023.115682] [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: 07/09/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Background Suicide is one of the leading global causes of death. Behavior patterns from suicide ideation to completion are complex, involving multiple risk factors. Advances in technologies and large-scale bioinformatic tools are changing how we approach biomedical problems. The "omics" field may provide new knowledge about suicidal behavior to improve identification of relevant biological pathways associated with suicidal behavior. Methods We reviewed transcriptomic, proteomic, and metabolomic studies conducted in blood and post-mortem brains from individuals who experienced suicide or suicidal behavior. Omics data were combined using systems biology in silico, aiming at identifying major biological mechanisms and key molecules associated with suicide. Results Post-mortem samples of suicide completers indicate major dysregulations in pathways associated with glial cells (astrocytes and microglia), neurotransmission (GABAergic and glutamatergic systems), neuroplasticity and cell survivor, immune responses and energy homeostasis. In the periphery, studies found alterations in molecules involved in immune responses, polyamines, lipid transport, energy homeostasis, and amino and nucleic acid metabolism. Limitations We included only exploratory, non-hypothesis-driven studies; most studies only included one brain region and whole tissue analysis, and focused on suicide completers who were white males with almost none confounding factors. Conclusions We can highlight the importance of synaptic function, especially the balance between the inhibitory and excitatory synapses, and mechanisms associated with neuroplasticity, common pathways associated with psychiatric disorders. However, some of the pathways highlighted in this review, such as transcriptional factors associated with RNA splicing, formation of cortical connections, and gliogenesis, point to mechanisms that still need to be explored.
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Affiliation(s)
- Caibe Alves Pereira
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bruna Caroline Pierone
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico E Tecnológico, São Paulo, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil; D'Or Institute for Research and Education (IDOR), São Paulo, Brazil; INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
| | - Manuella Pinto Kaster
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.
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Li YN, Hu DD, Cai XL, Wang Y, Yang C, Jiang J, Zhang QL, Tu T, Wang XS, Wang H, Tu E, Wang XP, Pan A, Yan XX, Wan L. Doublecortin-Expressing Neurons in Human Cerebral Cortex Layer II and Amygdala from Infancy to 100 Years Old. Mol Neurobiol 2023; 60:3464-3485. [PMID: 36879137 DOI: 10.1007/s12035-023-03261-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/04/2023] [Indexed: 03/08/2023]
Abstract
A cohort of morphologically heterogenous doublecortin immunoreactive (DCX +) "immature neurons" has been identified in the cerebral cortex largely around layer II and the amygdala largely in the paralaminar nucleus (PLN) among various mammals. To gain a wide spatiotemporal view on these neurons in humans, we examined layer II and amygdalar DCX + neurons in the brains of infants to 100-year-old individuals. Layer II DCX + neurons occurred throughout the cerebrum in the infants/toddlers, mainly in the temporal lobe in the adolescents and adults, and only in the temporal cortex surrounding the amygdala in the elderly. Amygdalar DCX + neurons occurred in all age groups, localized primarily to the PLN, and reduced in number with age. The small-sized DCX + neurons were unipolar or bipolar, and formed migratory chains extending tangentially, obliquely, and inwardly in layers I-III in the cortex, and from the PLN to other nuclei in the amygdala. Morphologically mature-looking neurons had a relatively larger soma and weaker DCX reactivity. In contrast to the above, DCX + neurons in the hippocampal dentate gyrus were only detected in the infant cases in parallelly processed cerebral sections. The present study reveals a broader regional distribution of the cortical layer II DCX + neurons than previously documented in human cerebrum, especially during childhood and adolescence, while both layer II and amygdalar DCX + neurons persist in the temporal lobe lifelong. Layer II and amygdalar DCX + neurons may serve as an essential immature neuronal system to support functional network plasticity in human cerebrum in an age/region-dependent manner.
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Affiliation(s)
- Ya-Nan Li
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Dan-Dan Hu
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Xiao-Lu Cai
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Yan Wang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Chen Yang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Juan Jiang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Qi-Lei Zhang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Tian Tu
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao-Sheng Wang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Hui Wang
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Ewen Tu
- Department of Neurology, Brain Hospital of Hunan Province, Changsha, 410007, Hunan, China
| | - Xiao-Ping Wang
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410031, Hunan, China
| | - Aihua Pan
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China.
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China
| | - Lily Wan
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, 410013, Hunan, China.
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Das SC, Schulmann A, Callor WB, Jerominski L, Panicker MM, Christensen ED, Bunney WE, Williams ME, Coon H, Vawter MP. Altered transcriptomes, cell type proportions, and dendritic spine morphology in hippocampus of suicide deaths. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.28.23285121. [PMID: 36778310 PMCID: PMC9915834 DOI: 10.1101/2023.01.28.23285121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Suicide is a condition resulting from complex environmental and genetic risks that affect millions of people globally. Both structural and functional studies identified the hippocampus as one of the vulnerable brain regions contributing to suicide risk. Here, we have identified the hippocampal transcriptomes, gene ontology, cell type proportions, dendritic spine morphology, and transcriptomic signature in iPSC-derived neuronal precursor cells (NPCs) and neurons in postmortem brain tissue from suicide deaths. The hippocampal tissue transcriptomic data revealed that NPAS4 gene expression was downregulated while ALDH1A2, NAAA, and MLXIPL gene expressions were upregulated in tissue from suicide deaths. The gene ontology identified 29 significant pathways including NPAS4-associated gene ontology terms "excitatory post-synaptic potential", "regulation of postsynaptic membrane potential" and "long-term memory" indicating alteration of glutamatergic synapses in the hippocampus of suicide deaths. The cell type deconvolution identified decreased excitatory neuron proportion and an increased inhibitory neuron proportion providing evidence of excitation/inhibition imbalance in the hippocampus of suicide deaths. In addition, suicide deaths had increased dendric spine density, due to an increase of thin (relatively unstable) dendritic spines, compared to controls. The transcriptomes of iPSC-derived hippocampal-like NPCs and neurons revealed 31 and 33 differentially expressed genes in NPC and neurons, respectively, of suicide deaths. The suicide-associated differentially expressed genes in NPCs were RELN, CRH, EMX2, OXTR, PARM1 and IFITM2 which overlapped with previously published results. The previously-known suicide-associated differentially expressed genes in differentiated neurons were COL1A1, THBS1, IFITM2, AQP1, and NLRP2. Together, these findings would help better understand the hippocampal neurobiology of suicide for identifying therapeutic targets to prevent suicide.
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Affiliation(s)
- Sujan C. Das
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA
| | | | - William B. Callor
- Utah State Office of Medical Examiner, Utah Department of Health, Salt Lake City, UT, USA
| | - Leslie Jerominski
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mitradas M. Panicker
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, USA
| | - Erik D. Christensen
- Utah State Office of Medical Examiner, Utah Department of Health, Salt Lake City, UT, USA
| | - William E. Bunney
- Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA
| | - Megan E. Williams
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, UT, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Marquis P. Vawter
- Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA, USA
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