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Martins D, Abbasi M, Egas C, Arrais JP. Enhancing schizophrenia phenotype prediction from genotype data through knowledge-driven deep neural network models. Genomics 2024; 116:110910. [PMID: 39111546 DOI: 10.1016/j.ygeno.2024.110910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024]
Abstract
This article explores deep learning model design, drawing inspiration from the omnigenic model and genetic heterogeneity concepts, to improve schizophrenia prediction using genotype data. It introduces an innovative three-step approach leveraging neural networks' capabilities to efficiently handle genetic interactions. A locally connected network initially routes input data from variants to their corresponding genes. The second step employs an Encoder-Decoder to capture relationships among identified genes. The final model integrates knowledge from the first two and incorporates a parallel component to consider the effects of additional genes. This expansion enhances prediction scores by considering a larger number of genes. Trained models achieved an average AUC of 0.83, surpassing other genotype-trained models and matching gene expression dataset-based approaches. Additionally, tests on held-out sets reported an average sensitivity of 0.72 and an accuracy of 0.76, aligning with schizophrenia heritability predictions. Moreover, the study addresses genetic heterogeneity challenges by considering diverse population subsets.
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Affiliation(s)
- Daniel Martins
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal; Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Maryam Abbasi
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal; Polytechnic Institute of Coimbra, Applied Research Institute, Coimbra, Portugal; Research Centre for Natural Resources Environment and Society (CERNAS), Polytechnic Institute of Coimbra, Coimbra, Portugal.
| | - Conceição Egas
- Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Biocant - Transfer Technology Association, Cantanhede, Portugal; CNC - CNC Center for Neuroscience and Cell Biology, Coimbra, Portugal
| | - Joel P Arrais
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal
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Bartošík V, Plucarová J, Laníková A, Janáčková Z, Padrta P, Jansen S, Vařečka V, Gruber T, Feller SM, Žídek L. Structural basis of binding the unique N-terminal domain of microtubule-associated protein 2c to proteins regulating kinases of signaling pathways. J Biol Chem 2024; 300:107551. [PMID: 39002671 PMCID: PMC11367651 DOI: 10.1016/j.jbc.2024.107551] [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: 04/23/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/15/2024] Open
Abstract
Isoforms of microtubule-associated protein 2 (MAP2) differ from their homolog Tau in the sequence and interactions of the N-terminal region. Binding of the N-terminal region of MAP2c (N-MAP2c) to the dimerization/docking domains of the regulatory subunit RIIα of cAMP-dependent protein kinase (RIIDD2) and to the Src-homology domain 2 (SH2) of growth factor receptor-bound protein 2 (Grb2) have been described long time ago. However, the structural features of the complexes remained unknown due to the disordered nature of MAP2. Here, we provide structural description of the complexes. We have solved solution structure of N-MAP2c in complex with RIIDD2, confirming formation of an amphiphilic α-helix of MAP2c upon binding, defining orientation of the α-helix in the complex and showing that its binding register differs from previous predictions. Using chemical shift mapping, we characterized the binding interface of SH2-Grb2 and rat MAP2c phosphorylated by the tyrosine kinase Fyn in their complex and proposed a model explaining differences between SH2-Grb2 complexes with rat MAP2c and phosphopeptides with a Grb2-specific sequence. The results provide the structural basis of a potential role of MAP2 in regulating cAMP-dependent phosphorylation cascade via interactions with RIIDD2 and Ras signaling pathway via interactions with SH2-Grb2.
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Affiliation(s)
- Viktor Bartošík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jitka Plucarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alice Laníková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Janáčková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Padrta
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Séverine Jansen
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtěch Vařečka
- Institute of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tobias Gruber
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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Nussinov R, Yavuz BR, Demirel HC, Arici MK, Jang H, Tuncbag N. Review: Cancer and neurodevelopmental disorders: multi-scale reasoning and computational guide. Front Cell Dev Biol 2024; 12:1376639. [PMID: 39015651 PMCID: PMC11249571 DOI: 10.3389/fcell.2024.1376639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
The connection and causality between cancer and neurodevelopmental disorders have been puzzling. How can the same cellular pathways, proteins, and mutations lead to pathologies with vastly different clinical presentations? And why do individuals with neurodevelopmental disorders, such as autism and schizophrenia, face higher chances of cancer emerging throughout their lifetime? Our broad review emphasizes the multi-scale aspect of this type of reasoning. As these examples demonstrate, rather than focusing on a specific organ system or disease, we aim at the new understanding that can be gained. Within this framework, our review calls attention to computational strategies which can be powerful in discovering connections, causalities, predicting clinical outcomes, and are vital for drug discovery. Thus, rather than centering on the clinical features, we draw on the rapidly increasing data on the molecular level, including mutations, isoforms, three-dimensional structures, and expression levels of the respective disease-associated genes. Their integrated analysis, together with chromatin states, can delineate how, despite being connected, neurodevelopmental disorders and cancer differ, and how the same mutations can lead to different clinical symptoms. Here, we seek to uncover the emerging connection between cancer, including pediatric tumors, and neurodevelopmental disorders, and the tantalizing questions that this connection raises.
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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, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | | | - M. Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Türkiye
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Türkiye
- School of Medicine, Koc University, Istanbul, Türkiye
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
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Martín-Guerrero SM, Martín-Estebané M, Lara Ordóñez AJ, Cánovas M, Martín-Oliva D, González-Maeso J, Cutillas PR, López-Giménez JF. Maternal Immune Activation imprints translational dysregulation and differential MAP2 phosphorylation in descendant neural stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597886. [PMID: 38895311 PMCID: PMC11185659 DOI: 10.1101/2024.06.07.597886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alterations induced by maternal immune activation (MIA) during gestation impact the subsequent neurodevelopment of progeny, a process that in humans, has been linked to the development of several neuropsychiatric conditions. To undertake a comprehensive examination of the molecular mechanisms governing MIA, we have devised an in vitro model based on neural stem cells (NSCs) sourced from fetuses carried by animals subjected to Poly I:C treatment. These neural progenitors demonstrate proliferative capacity and can be effectively differentiated into both neurons and glial cells. Transcriptomic, proteomic, and phosphoproteomic analyses conducted on these cellular models, in conjunction with counterparts from control treatments, revealed discernible shifts in the expression levels of a specific subset of proteins implicated in neuronal function. Noteworthy, we found an absence of congruence between these alterations at the transcriptomic level, suggesting that differences in protein translation contribute to the observed dysregulation. Furthermore, the phosphoproteomic data highlighted a discernible discrepancy in the basal phosphorylation of proteins between differentiated cells from both experimental groups, particularly within proteins associated with cytoskeletal architecture and synaptic functionality, notably those belonging to the MAP family. Observed alterations in MAP phosphorylation were found to potentially have functional consequences as they correlate with changes in neuronal plasticity and the establishment of neuronal synapses. Our data agrees with previous published observations and further underscore the importance of MAP2 phosphorylation state on its function and the impact that this protein has in neuronal structure and function.
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Martinez-Feduchi P, Jin P, Yao B. Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci 2024; 17:1398026. [PMID: 38726308 PMCID: PMC11079283 DOI: 10.3389/fnmol.2024.1398026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.
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Affiliation(s)
| | | | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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Reyes-Lizaola S, Luna-Zarate U, Tendilla-Beltrán H, Morales-Medina JC, Flores G. Structural and biochemical alterations in dendritic spines as key mechanisms for severe mental illnesses. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110876. [PMID: 37863171 DOI: 10.1016/j.pnpbp.2023.110876] [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: 08/01/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Severe mental illnesses (SMI) collectively affect approximately 20% of the global population, as estimated by the World Health Organization (WHO). Despite having diverse etiologies, clinical symptoms, and pharmacotherapies, these diseases share a common pathophysiological characteristic: the misconnection of brain areas involved in reality perception, executive control, and cognition, including the corticolimbic system. Dendritic spines play a crucial role in excitatory neurotransmission within the central nervous system. These small structures exhibit remarkable plasticity, regulated by factors such as neurotransmitter tone, neurotrophic factors, and innate immunity-related molecules, and other mechanisms - all of which are associated with the pathophysiology of SMI. However, studying dendritic spine mechanisms in both healthy and pathological conditions in patients is fraught with technical limitations. This is where animal models related to these diseases become indispensable. They have played a pivotal role in elucidating the significance of dendritic spines in SMI. In this review, the information regarding the potential role of dendritic spines in SMI was summarized, drawing from clinical and animal model reports. Also, the implications of targeting dendritic spine-related molecules for SMI treatment were explored. Specifically, our focus is on major depressive disorder and the neurodevelopmental disorders schizophrenia and autism spectrum disorder. Abundant clinical and basic research has studied the functional and structural plasticity of dendritic spines in these diseases, along with potential pharmacological targets that modulate the dynamics of these structures. These targets may be associated with the clinical efficacy of the pharmacotherapy.
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Affiliation(s)
- Sebastian Reyes-Lizaola
- Departamento de Ciencias de la Salud, Licenciatura en Medicina, Universidad Popular del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Ulises Luna-Zarate
- Departamento de Ciencias de la Salud, Licenciatura en Medicina, Universidad de las Américas Puebla (UDLAP), Puebla, Mexico
| | - Hiram Tendilla-Beltrán
- Laboratorio de Neuropsiquiatría, Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Julio César Morales-Medina
- Centro de Investigación en Reproducción Animal, CINVESTAV-Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Gonzalo Flores
- Laboratorio de Neuropsiquiatría, Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico.
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Shao Y, Cai Y, Chen T, Hao K, Luo B, Wang X, Guo W, Su X, Lv L, Yang Y, Li W. Impaired erythropoietin-producing hepatocellular B receptors signaling in the prefrontal cortex and hippocampus following maternal immune activation in male rats. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12863. [PMID: 37575018 PMCID: PMC10733575 DOI: 10.1111/gbb.12863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
An environmental risk factor for schizophrenia (SZ) is maternal infection, which exerts longstanding effects on the neurodevelopment of offspring. Accumulating evidence suggests that synaptic disturbances may contribute to the pathology of the disease, but the underlying molecular mechanisms remain poorly understood. Erythropoietin-producing hepatocellular B (EphB) receptor signaling plays an important role in synaptic plasticity by regulating the formation and maturation of dendritic spines and regulating excitatory neurotransmission. We examined whether EphB receptors and downstream associated proteins are susceptible to environmental risk factors implicated in the etiology of synaptic disturbances in SZ. Using an established rodent model, which closely imitates the characteristics of SZ, we observed the behavioral performance and synaptic structure of male offspring in adolescence and early adulthood. We then analyzed the expression of EphB receptors and associated proteins in the prefrontal cortex and hippocampus. Maternal immune activation offspring showed significantly progressive cognitive impairment and pre-pulse inhibition deficits together with an increase in the expression of EphB2 receptors and NMDA receptor subunits. We also found changes in EphB receptor downstream signaling, in particular, a decrease in phospho-cofilin levels which may explain the reduced dendritic spine density. Besides, we found that the AMPA glutamate, another glutamate ionic receptor associated with cofilin, decreased significantly in maternal immune activation offspring. Thus, alterations in EphB signaling induced by immune activation during pregnancy may underlie disruptions in synaptic plasticity and function in the prefrontal cortex and hippocampus associated with behavioral and cognitive impairment. These findings may provide insight into the mechanisms underlying SZ.
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Affiliation(s)
- Yiqian Shao
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Yaqi Cai
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Tengfei Chen
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Keke Hao
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Binbin Luo
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Xiujuan Wang
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
| | - Weiyun Guo
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
- Stem Cell and Biological Treatment Engineering Research Center of Henan, College of Life Science and TechnologyXinxiang Medical UniversityXinxiangChina
| | - Xi Su
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Prevention and Treatment of Mental DisorderXinxiang Medical UniversityXinxiangChina
| | - Luxian Lv
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Prevention and Treatment of Mental DisorderXinxiang Medical UniversityXinxiangChina
| | - Yongfeng Yang
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Prevention and Treatment of Mental DisorderXinxiang Medical UniversityXinxiangChina
| | - Wenqiang Li
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Prevention and Treatment of Mental DisorderXinxiang Medical UniversityXinxiangChina
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Sfera A, Andronescu L, Britt WG, Himsl K, Klein C, Rahman L, Kozlakidis Z. Receptor-Independent Therapies for Forensic Detainees with Schizophrenia-Dementia Comorbidity. Int J Mol Sci 2023; 24:15797. [PMID: 37958780 PMCID: PMC10647468 DOI: 10.3390/ijms242115797] [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: 08/31/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Forensic institutions throughout the world house patients with severe psychiatric illness and history of criminal violations. Improved medical care, hygiene, psychiatric treatment, and nutrition led to an unmatched longevity in this population, which previously lived, on average, 15 to 20 years shorter than the public at large. On the other hand, longevity has contributed to increased prevalence of age-related diseases, including neurodegenerative disorders, which complicate clinical management, increasing healthcare expenditures. Forensic institutions, originally intended for the treatment of younger individuals, are ill-equipped for the growing number of older offenders. Moreover, as antipsychotic drugs became available in 1950s and 1960s, we are observing the first generation of forensic detainees who have aged on dopamine-blocking agents. Although the consequences of long-term treatment with these agents are unclear, schizophrenia-associated gray matter loss may contribute to the development of early dementia. Taken together, increased lifespan and the subsequent cognitive deficit observed in long-term forensic institutions raise questions and dilemmas unencountered by the previous generations of clinicians. These include: does the presence of neurocognitive dysfunction justify antipsychotic dose reduction or discontinuation despite a lifelong history of schizophrenia and violent behavior? Should neurolipidomic interventions become the standard of care in elderly individuals with lifelong schizophrenia and dementia? Can patients with schizophrenia and dementia meet the Dusky standard to stand trial? Should neurocognitive disorders in the elderly with lifelong schizophrenia be treated differently than age-related neurodegeneration? In this article, we hypothesize that gray matter loss is the core symptom of schizophrenia which leads to dementia. We hypothesize further that strategies to delay or stop gray matter depletion would not only improve the schizophrenia sustained recovery, but also avert the development of major neurocognitive disorders in people living with schizophrenia. Based on this hypothesis, we suggest utilization of both receptor-dependent and independent therapeutics for chronic psychosis.
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Affiliation(s)
- Adonis Sfera
- Paton State Hospital, 3102 Highland Ave, Patton, CA 92369, USA; (L.A.); (K.H.)
- School of Behavioral Health, Loma Linda University, 11139 Anderson St., Loma Linda, CA 92350, USA
- Department of Psychiatry, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Luminita Andronescu
- Paton State Hospital, 3102 Highland Ave, Patton, CA 92369, USA; (L.A.); (K.H.)
| | - William G. Britt
- Department of Psychiatry, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA;
| | - Kiera Himsl
- Paton State Hospital, 3102 Highland Ave, Patton, CA 92369, USA; (L.A.); (K.H.)
| | - Carolina Klein
- California Department of State Hospitals, Sacramento, CA 95814, USA;
| | - Leah Rahman
- Department of Neuroscience, University of Oregon, 1585 E 13th Ave, Eugene, OR 97403, USA;
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, 69366 Lyon Cedex, France;
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DeGiosio RA, Needham PG, Andrews OA, Tristan H, Grubisha MJ, Brodsky JL, Camacho C, Sweet RA. Differential regulation of MAP2 by phosphorylation events in proline-rich versus C-terminal domains. FASEB J 2023; 37:e23194. [PMID: 37702880 PMCID: PMC10539048 DOI: 10.1096/fj.202300486r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/31/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
MAP2 is a critical cytoskeletal regulator in neurons. The phosphorylation of MAP2 (MAP2-P) is well known to regulate core functions of MAP2, including microtubule (MT)/actin binding and facilitation of tubulin polymerization. However, site-specific studies of MAP2-P function in regions outside of the MT-binding domain (MTBD) are lacking. We previously identified a set of MAP2 phosphopeptides which are differentially expressed and predominantly increased in the cortex of individuals with schizophrenia relative to nonpsychiatric comparison subjects. The phosphopeptides originated not from the MTBD, but from the flanking proline-rich and C-terminal domains of MAP2. We sought to understand the contribution of MAP2-P at these sites on MAP2 function. To this end, we isolated a series of phosphomimetic MAP2C constructs and subjected them to cell-free tubulin polymerization, MT-binding, actin-binding, and actin polymerization assays. A subset of MAP2-P events significantly impaired these functions, with the two domains displaying different patterns of MAP2 regulation: proline-rich domain mutants T293E and T300E impaired MT assembly and actin-binding affinity but did not affect MT-binding, while C-terminal domain mutants S426E and S439D impaired all three functions. S443D also impaired MT assembly with minimal effects on MT- or actin-binding. Using heterologous cells, we also found that S426E but not T293E had a lower capability for process formation than the wild-type protein. These findings demonstrate the functional utility of MAP2-P in the proline-rich and C-terminal domains and point to distinct, domain-dependent regulations of MAP2 function, which can go on to affect cellular morphology.
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Affiliation(s)
- R A DeGiosio
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - P G Needham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - O A Andrews
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - H Tristan
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - M J Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - J L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - C Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Bárez-López S, Gadd GJ, Pauža AG, Murphy D, Greenwood MP. Isoflurane Rapidly Modifies Synaptic and Cytoskeletal Phosphoproteomes of the Supraoptic Nucleus of the Hypothalamus and the Cortex. Neuroendocrinology 2023; 113:1008-1023. [PMID: 37271138 DOI: 10.1159/000531352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Despite the widespread use of general anaesthetics, the mechanisms mediating their effects are still not understood. Although suppressed in most parts of the brain, neuronal activity, as measured by FOS activation, is increased in the hypothalamic supraoptic nucleus (SON) by numerous general anaesthetics, and evidence points to this brain region being involved in the induction of general anaesthesia (GA) and natural sleep. Posttranslational modifications of proteins, including changes in phosphorylation, enable fast modulation of protein function which could be underlying the rapid effects of GA. In order to identify potential phosphorylation events in the brain-mediating GA effects, we have explored the phosphoproteome responses in the rat SON and compared these to cingulate cortex (CC) which displays no FOS activation in response to general anaesthetics. METHODS Adult Sprague-Dawley rats were treated with isoflurane for 15 min. Proteins from the CC and SON were extracted and processed for nano-LC mass spectrometry (LC-MS/MS). Phosphoproteomic determinations were performed by LC-MS/MS. RESULTS We found many changes in the phosphoproteomes of both the CC and SON in response to 15 min of isoflurane exposure. Pathway analysis indicated that proteins undergoing phosphorylation adaptations are involved in cytoskeleton remodelling and synaptic signalling events. Importantly, changes in protein phosphorylation appeared to be brain region specific suggesting that differential phosphorylation adaptations might underlie the different neuronal activity responses to GA between the CC and SON. CONCLUSION In summary, these data suggest that rapid posttranslational modifications in proteins involved in cytoskeleton remodelling and synaptic signalling events might mediate the central mechanisms mediating GA.
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Affiliation(s)
- Soledad Bárez-López
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - George J Gadd
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
| | - Audrys G Pauža
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
- Translational Cardio-Respiratory Research Group, Department of Physiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
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Ninomiya T, Noritake A, Tatsumoto S, Go Y, Isoda M. Cognitive genomics of learning delay and low level of social performance monitoring in macaque. Sci Rep 2022; 12:16539. [PMID: 36192455 PMCID: PMC9529886 DOI: 10.1038/s41598-022-20948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Cognitive skills and the underlying neural architecture are under the influence of genetics. Cognitive genomics research explores the triadic relationship between genes, brain, and cognition, with its major strategy being genotype-driven. Here we show that an inverse strategy is feasible to identify novel candidate genes for particular neuro-cognitive phenotypes in macaques. Two monkeys, originally involved in separate psychological studies, exhibited learning delay and low levels of social performance monitoring. In one monkey, mirror neurons were fewer compared to controls and mu suppression was absent in the frontal cortex. The other monkey showed heightened visual responsiveness in both frontal cortex and dopamine-rich midbrain, with a lack of inter-areal synchronization. Exome analyses revealed that the two monkeys were most likely cousins and shared variants in MAP2, APOC1, and potentially HTR2C. This phenotype-driven strategy in cognitive genomics provides a useful means to clarify the genetic basis of phenotypic variation and develop macaque models of neuropsychiatric disorders.
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Affiliation(s)
- Taihei Ninomiya
- Division of Behavioral Development, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan.,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Japan
| | - Atsushi Noritake
- Division of Behavioral Development, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan.,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Yasuhiro Go
- Division of Behavioral Development, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan.,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Japan.,Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Masaki Isoda
- Division of Behavioral Development, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan. .,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Japan.
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12
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DeGiosio RA, Grubisha MJ, MacDonald ML, McKinney BC, Camacho CJ, Sweet RA. More than a marker: potential pathogenic functions of MAP2. Front Mol Neurosci 2022; 15:974890. [PMID: 36187353 PMCID: PMC9525131 DOI: 10.3389/fnmol.2022.974890] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/29/2022] [Indexed: 12/27/2022] Open
Abstract
Microtubule-associated protein 2 (MAP2) is the predominant cytoskeletal regulator within neuronal dendrites, abundant and specific enough to serve as a robust somatodendritic marker. It influences microtubule dynamics and microtubule/actin interactions to control neurite outgrowth and synaptic functions, similarly to the closely related MAP Tau. Though pathology of Tau has been well appreciated in the context of neurodegenerative disorders, the consequences of pathologically dysregulated MAP2 have been little explored, despite alterations in its immunoreactivity, expression, splicing and/or stability being observed in a variety of neurodegenerative and neuropsychiatric disorders including Huntington’s disease, prion disease, schizophrenia, autism, major depression and bipolar disorder. Here we review the understood structure and functions of MAP2, including in neurite outgrowth, synaptic plasticity, and regulation of protein folding/transport. We also describe known and potential mechanisms by which MAP2 can be regulated via post-translational modification. Then, we assess existing evidence of its dysregulation in various brain disorders, including from immunohistochemical and (phospho) proteomic data. We propose pathways by which MAP2 pathology could contribute to endophenotypes which characterize these disorders, giving rise to the concept of a “MAP2opathy”—a series of disorders characterized by alterations in MAP2 function.
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Affiliation(s)
- Rebecca A. DeGiosio
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brandon C. McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Robert A. Sweet
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13
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Specific phosphorylation of microtubule-associated protein 2c by extracellular signal-regulated kinase reduces interactions at its Pro-rich regions. J Biol Chem 2022; 298:102384. [PMID: 35987383 PMCID: PMC9520037 DOI: 10.1016/j.jbc.2022.102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022] Open
Abstract
Microtubule-associated protein 2 (MAP2) is an important neuronal target of extracellular signal-regulated kinase 2 (ERK2) involved in Raf signaling pathways, but mechanistic details of MAP2 phosphorylation are unclear. Here, we used NMR spectroscopy to quantitatively describe the kinetics of phosphorylation of individual serines and threonines in the embryonic MAP2 variant MAP2c. We carried out real-time monitoring of phosphorylation to discover major phosphorylation sites that were not identified in previous studies relying on specific antibodies. Our comparison with phosphorylation of MAP2c by a model cyclin-dependent kinase CDK2 and with phosphorylation of the MAP2c homolog Tau revealed differences in phosphorylation profiles that explain specificity of regulation of biological functions of MAP2c and Tau. To probe the molecular basis of the regulatory effect of ERK2, we investigated the interactions of phosphorylated and unphosphorylated MAP2c by NMR with single-residue resolution. As ERK2 phosphorylates mostly outside the regions binding microtubules, we studied the binding of proteins other than tubulin, namely regulatory subunit RIIα of cAMP-dependent protein kinase (PKA), adaptor protein Grb2, Src homology domain 3 of tyrosine kinases Fyn and Abl, and ERK2 itself. We found ERK2 phosphorylation interfered mostly with binding to proline-rich regions of MAP2c. Furthermore, our NMR experiments in SH-SY5Y neuroblastoma cell lysates showed that the kinetics of dephosphorylation are compatible with in-cell NMR studies and that residues targeted by ERK2 and PKA are efficiently phosphorylated in the cell lysates. Taken together, our results provide a deeper characterization of MAP2c phosphorylation and its effects on interactions with other proteins.
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14
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Ahangari M, Everest E, Nguyen TH, Verrelli BC, Webb BT, Bacanu SA, Tahir Turanli E, Riley BP. Genome-wide analysis of schizophrenia and multiple sclerosis identifies shared genomic loci with mixed direction of effects. Brain Behav Immun 2022; 104:183-190. [PMID: 35714915 DOI: 10.1016/j.bbi.2022.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Common genetic variants identified in genome-wide association studies (GWAS) show varying degrees of genetic pleiotropy across complex human disorders. Clinical studies of schizophrenia (SCZ) suggest that in addition to neuropsychiatric symptoms, patients with SCZ also show variable immune dysregulation. Epidemiological studies of multiple sclerosis (MS), an autoimmune, neurodegenerative disorder of the central nervous system, suggest that in addition to the manifestation of neuroinflammatory complications, patients with MS may also show co-occurring neuropsychiatric symptoms with disease progression. In this study, we analyzed the largest available GWAS datasets for SCZ (N = 161,405) and MS (N = 41,505) using Gaussian causal mixture modeling (MiXeR) and conditional/conjunctional false discovery rate (condFDR) frameworks to explore and quantify the shared genetic architecture of these two complex disorders at common variant level. Despite detecting only a negligible genetic correlation (rG = 0.057), we observe polygenic overlap between SCZ and MS, and a substantial genetic enrichment in SCZ conditional on associations with MS, and vice versa. By leveraging this cross-disorder enrichment, we identified 36 loci jointly associated with SCZ and MS at conjunctional FDR < 0.05 with mixed direction of effects. Follow-up functional analysis of the shared loci implicates candidate genes and biological processes involved in immune response and B-cell receptor signaling pathways. In conclusion, this study demonstrates the presence of polygenic overlap between SCZ and MS in the absence of a genetic correlation and provides new insights into the shared genetic architecture of these two disorders at the common variant level.
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Affiliation(s)
- Mohammad Ahangari
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Integrative Life Sciences PhD Program, Virginia Commonwealth University, Richmond, VA, USA.
| | - Elif Everest
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Tan-Hoang Nguyen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Bradley T Webb
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Eda Tahir Turanli
- Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Acibadem University, Istanbul, Turkey
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA; Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
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15
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Karpov D, Golimbet V. Cellular and supracellular models in the study of molecular mechanisms associated with schizophrenia. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:46-50. [DOI: 10.17116/jnevro202212211146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Smith BJ, Carregari VC. Post-Translational Modifications During Brain Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:29-38. [DOI: 10.1007/978-3-031-05460-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Grubisha MJ, Sweet RA, MacDonald ML. Investigating Post-translational Modifications in Neuropsychiatric Disease: The Next Frontier in Human Post-mortem Brain Research. Front Mol Neurosci 2021; 14:689495. [PMID: 34335181 PMCID: PMC8322442 DOI: 10.3389/fnmol.2021.689495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Gene expression and translation have been extensively studied in human post-mortem brain tissue from subjects with psychiatric disease. Post-translational modifications (PTMs) have received less attention despite their implication by unbiased genetic studies and importance in regulating neuronal and circuit function. Here we review the rationale for studying PTMs in psychiatric disease, recent findings in human post-mortem tissue, the required controls for these types of studies, and highlight the emerging mass spectrometry approaches transforming this research direction.
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Affiliation(s)
- Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, United States
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18
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Proteomic Analysis Unveils Expressional Changes in Cytoskeleton- and Synaptic Plasticity-Associated Proteins in Rat Brain Six Months after Withdrawal from Morphine. Life (Basel) 2021; 11:life11070683. [PMID: 34357055 PMCID: PMC8304287 DOI: 10.3390/life11070683] [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: 05/28/2021] [Revised: 06/28/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022] Open
Abstract
Drug withdrawal is associated with abstinence symptoms including deficits in cognitive functions that may persist even after prolonged discontinuation of drug intake. Cognitive deficits are, at least partially, caused by alterations in synaptic plasticity but the precise molecular mechanisms have not yet been fully identified. In the present study, changes in proteomic and phosphoproteomic profiles of selected brain regions (cortex, hippocampus, striatum, and cerebellum) from rats abstaining for six months after cessation of chronic treatment with morphine were determined by label-free quantitative (LFQ) proteomic analysis. Interestingly, prolonged morphine withdrawal was found to be associated especially with alterations in protein phosphorylation and to a lesser extent in protein expression. Gene ontology (GO) term analysis revealed enrichment in biological processes related to synaptic plasticity, cytoskeleton organization, and GTPase activity. More specifically, significant changes were observed in proteins localized in synaptic vesicles (e.g., synapsin-1, SV2a, Rab3a), in the active zone of the presynaptic nerve terminal (e.g., Bassoon, Piccolo, Rims1), and in the postsynaptic density (e.g., cadherin 13, catenins, Arhgap35, Shank3, Arhgef7). Other differentially phosphorylated proteins were associated with microtubule dynamics (microtubule-associated proteins, Tppp, collapsin response mediator proteins) and the actin–spectrin network (e.g., spectrins, adducins, band 4.1-like protein 1). Taken together, a six-month morphine withdrawal was manifested by significant alterations in the phosphorylation of synaptic proteins. The altered phosphorylation patterns modulating the function of synaptic proteins may contribute to long-term neuroadaptations induced by drug use and withdrawal.
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