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Ferrer P, Upadhyay S, Cai JJ, Clement TM. Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582797. [PMID: 38464253 PMCID: PMC10925299 DOI: 10.1101/2024.02.29.582797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
A mechanistic role for nuclear function of testis-specific actin related proteins (ARPs) is proposed here through contributions of ARP subunit swapping in canonical chromatin regulatory complexes. This is significant to our understanding of both mechanisms controlling regulation of spermiogenesis, and the expanding functional roles of the ARPs in cell biology. Among these roles, actins and ARPs are pivotal not only in cytoskeletal regulation, but also in intranuclear chromatin organization, influencing gene regulation and nucleosome remodeling. This study focuses on two testis-specific ARPs, ACTL7A and ACTL7B, exploring their intranuclear activities and broader implications utilizing combined in vivo, in vitro, and in silico approaches. ACTL7A and ACTL7B, previously associated with structural roles, are hypothesized here to serve in chromatin regulation during germline development. This study confirms the intranuclear presence of ACTL7B in spermatocytes and round spermatids, revealing a potential role in intranuclear processes, and identifies a putative nuclear localization sequence conserved across mammalian ACTL7B, indicating a potentially unique mode of nuclear transport which differs from conventional actin. Ablation of ACTL7B leads to varied transcriptional changes reported here. Additionally, in the absence of ACTL7A or ACTL7B there is a loss of intranuclear localization of HDAC1 and HDAC3, which are known regulators of epigenetic associated acetylation changes that in turn regulate gene expression. Thus, these HDACs are implicated as contributors to the aberrant gene expression observed in the KO mouse testis transcriptomic analysis. Furthermore, this study employed and confirmed the accuracy of in silico models to predict ARP interactions with Helicase-SANT-associated (HSA) domains, uncovering putative roles for testis-specific ARPs in nucleosome remodeling complexes. In these models, ACTL7A and ACTL7B were found capable of binding to INO80 and SWI/SNF nucleosome remodeler family members in a manner akin to nuclear actin and ACTL6A. These models thus implicate germline-specific ARP subunit swapping within chromatin regulatory complexes as a potential regulatory mechanism for chromatin and associated molecular machinery adaptations in nuclear reorganizations required during spermiogenesis. These results hold implications for male fertility and epigenetic programing in the male-germline that warrant significant future investigation. In summary, this study reveals that ACTL7A and ACTL7B play intranuclear gene regulation roles in male gametogenesis, adding to the multifaceted roles identified also spanning structural, acrosomal, and flagellar stability. ACTL7A and ACTL7B unique nuclear transport, impact on HDAC nuclear associations, impact on transcriptional processes, and proposed mechanism for involvement in nucleosome remodeling complexes supported by AI facilitated in silico modeling contribute to a more comprehensive understanding of the indispensable functions of ARPs broadly in cell biology, and specifically in male fertility.
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Affiliation(s)
- Pierre Ferrer
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - James J Cai
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Tracy M Clement
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
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Hernández-Oliveras A, Zarain-Herzberg A. The role of Ca 2+-signaling in the regulation of epigenetic mechanisms. Cell Calcium 2024; 117:102836. [PMID: 37988873 DOI: 10.1016/j.ceca.2023.102836] [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: 07/04/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Epigenetic mechanisms regulate multiple cell functions like gene expression and chromatin conformation and stability, and its misregulation could lead to several diseases including cancer. Epigenetic drugs are currently under investigation in a broad range of diseases, but the cellular processes involved in regulating epigenetic mechanisms are not fully understood. Calcium (Ca2+) signaling regulates several cellular mechanisms such as proliferation, gene expression, and metabolism, among others. Moreover, Ca2+ signaling is also involved in diseases such as neurological disorders, cardiac, and cancer. Evidence indicates that Ca2+ signaling and epigenetics are involved in the same cellular functions, which suggests a possible interplay between both mechanisms. Ca2+-activated transcription factors regulate the recruitment of chromatin remodeling complexes into their target genes, and Ca2+-sensing proteins modulate their activity and intracellular localization. Thus, Ca2+ signaling is an important regulator of epigenetic mechanisms. Moreover, Ca2+ signaling activates epigenetic mechanisms that in turn regulate genes involved in Ca2+ signaling, suggesting possible feedback between both mechanisms. The understanding of how epigenetics are regulated could lead to developing better therapeutical approaches.
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Affiliation(s)
- Andrés Hernández-Oliveras
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Angel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.
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Increase of c-FOS promoter transcriptional activity by the dual leucine zipper kinase. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:1223-1233. [PMID: 36700987 DOI: 10.1007/s00210-023-02401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
The dual leucine zipper kinase (DLK) and the ubiquitously expressed transcription factor c-FOS have important roles in beta-cell proliferation and function. Some studies in neuronal cells suggest that DLK can influence c-FOS expression. Given that c-FOS is mainly regulated at the transcriptional level, the effect of DLK on c-FOS promoter activity was investigated in the beta-cell line HIT. The methods used in this study are the following: Luciferase reporter gene assays, immunoblot analysis, CRISPR-Cas9-mediated genome editing, and real-time quantitative PCR. In the beta-cell line HIT, overexpressed DLK increased c-FOS promoter activity twofold. Using 5'-,3'-promoter deletions, the promoter regions from - 348 to - 339 base pairs (bp) and from a - 284 to - 53 bp conferred basal activity, whereas the promoter region from - 711 to - 348 bp and from - 53 to + 48 bp mediated DLK responsiveness. Mutation of the cAMP response element within the promoter prevented the stimulatory effect of DLK. Treatment of HIT cells with KCl and the adenylate cyclase activator forskolin increased c-FOS promoter transcriptional activity ninefold. Since the transcriptional activity of those promoter fragments activated by KCl and forskolin was decreased by DLK, DLK might interfere with KCl/forskolin-induced signaling. In a newly generated, genome-edited HIT cell line lacking catalytically active DLK, c-Fos mRNA levels were reduced by 80% compared to the wild-type cell line. DLK increased c-FOS promoter activity but decreased stimulated transcriptional activity, suggesting that DLK fine-tunes c-FOS promoter-dependent gene transcription. Moreover, at least in HIT cells, DLK is required for FOS mRNA expression.
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Singh G, Lucas K, Keller A, Martin R, Behrman A, Vissarionov S, Gerasimenko YP. Transcutaneous Spinal Stimulation From Adults to Children: A Review. Top Spinal Cord Inj Rehabil 2022; 29:16-32. [PMID: 36819932 PMCID: PMC9936896 DOI: 10.46292/sci21-00084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuromodulation via spinal stimulation is a promising therapy that can augment the neuromuscular capacity for voluntary movements, standing, stepping, and posture in individuals with spinal cord injury (SCI). The spinal locomotor-related neuronal network known as a central pattern generator (CPG) can generate a stepping-like motor output in the absence of movement-related afferent signals from the limbs. Using epidural stimulation (EP) in conjunction with activity-based locomotor training (ABLT), the neural circuits can be neuromodulated to facilitate the recovery of locomotor functions in persons with SCI. Recently, transcutaneous spinal stimulation (scTS) has been developed as a noninvasive alternative to EP. Early studies of scTS at thoracolumbar, coccygeal, and cervical regions have demonstrated its effectiveness in producing voluntary leg movements, posture control, and independent standing and improving upper extremity function in adults with chronic SCI. In pediatric studies, the technology of spinal neuromodulation is not yet widespread. There are a limited number of publications reporting on the use of scTS in children and adolescents with either cerebral palsy, spina bifida, or SCI.
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Affiliation(s)
- Goutam Singh
- Kosair Charities School of Physical Therapy, Spalding University, Louisville, Kentucky
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky
| | - Kathryn Lucas
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky
| | - Anastasia Keller
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Rebecca Martin
- International Center for Spinal Cord Injury, Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, Maryland
- Department of Physical Medicine and Rehabilitation, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrea Behrman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky
| | - Sergey Vissarionov
- Turner Scientific Research Institute for Children's Orthopedics, St. Petersburg, Russia
| | - Yury P Gerasimenko
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky
- Department of Physiology, University of Louisville, Louisville, Kentucky
- Pavlov Institute of Physiology Russian Academy of Sciences, St. Petersburg, Russia
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Yadav Y, Dey CS. Ser/Thr phosphatases: One of the key regulators of insulin signaling. Rev Endocr Metab Disord 2022; 23:905-917. [PMID: 35697962 DOI: 10.1007/s11154-022-09727-8] [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] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
Protein phosphorylation is an important post-translational modification that regulates several cellular processes including insulin signaling. The evidences so far have already portrayed the importance of balanced actions of kinases and phosphatases in regulating the insulin signaling cascade. Therefore, elucidating the role of both kinases and phosphatases are equally important. Unfortunately, the role of phosphatases is less studied as compared to kinases. Since brain responds to insulin and insulin signaling is reported to be crucial for many neuronal processes, it is important to understand the role of neuronal insulin signaling regulators. Ser/Thr phosphatases seem to play significant roles in regulating neuronal insulin signaling. Therefore, in this review, we discussed the involvement of Ser/Thr phosphatases in regulating insulin signaling and insulin resistance in neuronal system at the backdrop of the same phosphatases in peripheral insulin sensitive tissues.
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Affiliation(s)
- Yamini Yadav
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Chinmoy Sankar Dey
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, 110016, India.
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SWI/SNF chromatin remodeler complex within the reward pathway is required for behavioral adaptations to stress. Nat Commun 2022; 13:1807. [PMID: 35379786 PMCID: PMC8980038 DOI: 10.1038/s41467-022-29380-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/22/2022] [Indexed: 01/01/2023] Open
Abstract
Enduring behavioral changes upon stress exposure involve changes in gene expression sustained by epigenetic modifications in brain circuits, including the mesocorticolimbic pathway. Brahma (BRM) and Brahma Related Gene 1 (BRG1) are ATPase subunits of the SWI/SNF complexes involved in chromatin remodeling, a process essential to enduring plastic changes in gene expression. Here, we show that in mice, social defeat induces changes in BRG1 nuclear distribution. The inactivation of the Brg1/Smarca4 gene within dopamine-innervated regions or the constitutive inactivation of the Brm/Smarca2 gene leads to resilience to repeated social defeat and decreases the behavioral responses to cocaine without impacting midbrain dopamine neurons activity. Within striatal medium spiny neurons, Brg1 gene inactivation reduces the expression of stress- and cocaine-induced immediate early genes, increases levels of heterochromatin and at a global scale decreases chromatin accessibility. Altogether these data demonstrate the pivotal function of SWI/SNF complexes in behavioral and transcriptional adaptations to salient environmental challenges. Repeated exposure to social stressors in rodents results in behavioural changes. Here the authors show that behavioural adaptations to stress are associated with nuclear organization changes through SWI/SNF chromatin remodeler in specific neuronal populations of the mesolimbic system.
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Abstract
In mammalian cells, genomic DNA is packaged with histone proteins and condensed into chromatin. To gain access to the DNA, chromatin remodelling is required that is enhanced through histone post-translational modifications, which subsequently stimulate processes including DNA repair and transcription. Histone acetylation is one of the most well understood modifications and is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). These enzymes play critical roles in normal cellular functioning, and the dysregulation of HDAC expression in particular has been linked with the development of a number of different cancer types. Conversely, tumour cell killing following radiotherapy is triggered through DNA damage and HDACs can help co-ordinate the cellular DNA damage response which promotes radioresistance. Consequently, HDAC inhibitors have been investigated as potential radiosensitizers in vitro and in vivo to improve the efficacy or radiotherapy in specific tumour types. In this review, we provide an up-to-date summary of HDACs and their cellular functions, including in DNA damage repair. We also review evidence demonstrating that HDAC inhibitors can effectively enhance tumour radiosensitisation, and which therefore show potential for translation into the clinic for cancer patient benefit.
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Grabowska A, Sas-Nowosielska H, Wojtas B, Holm-Kaczmarek D, Januszewicz E, Yushkevich Y, Czaban I, Trzaskoma P, Krawczyk K, Gielniewski B, Martin-Gonzalez A, Filipkowski RK, Olszynski KH, Bernas T, Szczepankiewicz AA, Sliwinska MA, Kanhema T, Bramham CR, Bokota G, Plewczynski D, Wilczynski GM, Magalska A. Activation-induced chromatin reorganization in neurons depends on HDAC1 activity. Cell Rep 2022; 38:110352. [PMID: 35172152 DOI: 10.1016/j.celrep.2022.110352] [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: 02/09/2021] [Revised: 11/09/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Spatial chromatin organization is crucial for transcriptional regulation and might be particularly important in neurons since they dramatically change their transcriptome in response to external stimuli. We show that stimulation of neurons causes condensation of large chromatin domains. This phenomenon can be observed in vitro in cultured rat hippocampal neurons as well as in vivo in the amygdala and hippocampal neurons. Activity-induced chromatin condensation is an active, rapid, energy-dependent, and reversible process. It involves calcium-dependent pathways but is independent of active transcription. It is accompanied by the redistribution of posttranslational histone modifications and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that the histone deacetylase HDAC1 is the key regulator of this process. Our results suggest that HDAC1-dependent chromatin reorganization constitutes an important level of transcriptional regulation in neurons.
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Affiliation(s)
- Agnieszka Grabowska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Hanna Sas-Nowosielska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dagmara Holm-Kaczmarek
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Elzbieta Januszewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Yana Yushkevich
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Pawel Trzaskoma
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ana Martin-Gonzalez
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, San Juan de Alicante, 03550 Alicante, Spain
| | - Robert Kuba Filipkowski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Krzysztof Hubert Olszynski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Tytus Bernas
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Department of Anatomy and Neurology, VCU School of Medicine, Richmond, VA 23284, USA
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Malgorzata Alicja Sliwinska
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Grzegorz Bokota
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Adriana Magalska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland.
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Rowland ME, Jajarmi JM, Osborne TSM, Ciernia AV. Insights Into the Emerging Role of Baf53b in Autism Spectrum Disorder. Front Mol Neurosci 2022; 15:805158. [PMID: 35185468 PMCID: PMC8852769 DOI: 10.3389/fnmol.2022.805158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Accurate and precise regulation of gene expression is necessary to ensure proper brain development and plasticity across the lifespan. As an ATP-dependent chromatin-remodeling complex, the BAF (Brg1 Associated Factor) complex can alter histone-DNA interactions, facilitating dynamic changes in gene expression by controlling DNA accessibility to the transcriptional machinery. Mutations in 12 of the potential 29 subunit genes that compose the BAF nucleosome remodeling complex have been identified in several developmental disorders including Autism spectrum disorders (ASD) and intellectual disability. A novel, neuronal version of BAF (nBAF) has emerged as promising candidate in the development of ASD as its expression is tied to neuron differentiation and it’s hypothesized to coordinate expression of synaptic genes across brain development. Recently, mutations in BAF53B, one of the neuron specific subunits of the nBAF complex, have been identified in patients with ASD and Developmental and epileptic encephalopathy-76 (DEE76), indicating BAF53B is essential for proper brain development. Recent work in cultured neurons derived from patients with BAF53B mutations suggests links between loss of nBAF function and neuronal dendritic spine formation. Deletion of one or both copies of mouse Baf53b disrupts dendritic spine development, alters actin dynamics and results in fewer synapses in vitro. In the mouse, heterozygous loss of Baf53b severely impacts synaptic plasticity and long-term memory that is reversible with reintroduction of Baf53b or manipulations of the synaptic plasticity machinery. Furthermore, surviving Baf53b-null mice display ASD-related behaviors, including social impairments and repetitive behaviors. This review summarizes the emerging evidence linking deleterious variants of BAF53B identified in human neurodevelopmental disorders to abnormal transcriptional regulation that produces aberrant synapse development and behavior.
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Azieva AM, Sheynov AA, Kirillova DA, Tatarskiy EV, Georgieva SG, Soshnikova NV. PHF10, a Subunit of the PBAF Chromatin Remodeling Complex, Changes Its Localization and Interacts with c-FOS during the Initiation of Long-Term Potentiation in Neuronal Culture. Mol Biol 2021. [DOI: 10.1134/s0026893321050034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kumar S. SWI/SNF (BAF) complexes: From framework to a functional role in endothelial mechanotransduction. CURRENT TOPICS IN MEMBRANES 2021; 87:171-198. [PMID: 34696885 DOI: 10.1016/bs.ctm.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Endothelial cells (ECs) are constantly subjected to an array of mechanical cues, especially shear stress, due to their luminal placement in the blood vessels. Blood flow can regulate various aspects of endothelial biology and pathophysiology by regulating the endothelial processes at the transcriptomic, proteomic, miRNomic, metabolomics, and epigenomic levels. ECs sense, respond, and adapt to altered blood flow patterns and shear profiles by specialized mechanisms of mechanosensing and mechanotransduction, resulting in qualitative and quantitative differences in their gene expression. Chromatin-regulatory proteins can regulate transcriptional activation by modifying the organization of nucleosomes at promoters, enhancers, silencers, insulators, and locus control regions. Recent research efforts have illustrated that SWI/SNF (SWItch/Sucrose Non-Fermentable) or BRG1/BRM-associated factor (BAF) complex regulates DNA accessibility and chromatin structure. Since the discovery, the gene-regulatory mechanisms of the BAF complex associated with chromatin remodeling have been intensively studied to investigate its role in diverse disease phenotypes. Thus far, it is evident that (1) the SWI/SNF complex broadly regulates the activity of transcriptional enhancers to control lineage-specific differentiation and (2) mutations in the BAF complex proteins lead to developmental disorders and cancers. It is unclear if blood flow can modulate the activity of SWI/SNF complex to regulate EC differentiation and reprogramming. This review emphasizes the integrative role of SWI/SNF complex from a structural and functional standpoint with a special reference to cardiovascular diseases (CVDs). The review also highlights how regulation of this complex by blood flow can lead to the discovery of new therapeutic interventions for the treatment of endothelial dysfunction in vascular diseases.
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Affiliation(s)
- Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Institute of Technology, Atlanta, GA, United States.
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Lv F, Shao T, Xue Y, Miao X, Guo Y, Wang Y, Xu Y. Dual Regulation of Tank Binding Kinase 1 by BRG1 in Hepatocytes Contributes to Reactive Oxygen Species Production. Front Cell Dev Biol 2021; 9:745985. [PMID: 34660604 PMCID: PMC8517266 DOI: 10.3389/fcell.2021.745985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/15/2021] [Indexed: 01/14/2023] Open
Abstract
Excessive accumulation of reactive oxygen species (ROS) is considered a major culprit for the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We have previously shown that deletion of Brahma related gene 1 (BRG1) mitigated NAFLD in mice in part by attenuating ROS production in hepatocyte. Here we report that BRG1 deletion led to simultaneous down-regulation in expression and phosphorylation of tank binding kinase 1 (TBK1) in vivo and in vitro. On the one hand, BRG1 interacted with AP-1 to bind to the TBK1 promoter and directly activated TBK1 transcription in hepatocytes. On the other hand, BRG1 interacted with Sp1 to activate the transcription of c-SRC, a tyrosine kinase essential for TBK1 phosphorylation. Over-expression of c-SRC and TBK1 corrected the deficiency in ROS production in BRG1-null hepatocytes whereas depletion of TBK1 or c-SRC attenuated ROS production. In conclusion, our data suggest that dual regulation of TBK1 activity, at the transcription level and the post-transcriptional level, by BRG1 may constitute an important mechanism underlying excessive ROS production in hepatocytes.
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Affiliation(s)
- Fangqiao Lv
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Tinghui Shao
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yujia Xue
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiulian Miao
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yan Guo
- College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yutong Wang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,College of Life Sciences and Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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15
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Shi F, He Y, Chen Y, Yin X, Sha X, Wang Y. Comparative Analysis of Multiple Neurodegenerative Diseases Based on Advanced Epigenetic Aging Brain. Front Genet 2021; 12:657636. [PMID: 34093653 PMCID: PMC8173158 DOI: 10.3389/fgene.2021.657636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Neurodegenerative Diseases (NDs) are age-dependent and include Alzheimer’s disease (AD), Parkinson’s disease (PD), progressive supranuclear palsy (PSP), frontotemporal dementia (FTD), and so on. There have been numerous studies showing that accelerated aging is closely related (even the driver of) ND, thus promoting imbalances in cellular homeostasis. However, the mechanisms of how different ND types are related/triggered by advanced aging are still unclear. Therefore, there is an urgent need to explore the potential markers/mechanisms of different ND types based on aging acceleration at a system level. Methods: AD, PD, PSP, FTD, and aging markers were identified by supervised machine learning methods. The aging acceleration differential networks were constructed based on the aging score. Both the enrichment analysis and sensitivity analysis were carried out to investigate both common and specific mechanisms among different ND types in the context of aging acceleration. Results: The extracellular fluid, cellular metabolisms, and inflammatory response were identified as the common driving factors of cellular homeostasis imbalances during the accelerated aging process. In addition, Ca ion imbalance, abnormal protein depositions, DNA damage, and cytoplasmic DNA in macrophages were also revealed to be special mechanisms that further promote AD, PD, PSP, and FTD, respectively. Conclusion: The accelerated epigenetic aging mechanisms of different ND types were integrated and compared through our computational pipeline.
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Affiliation(s)
- Feitong Shi
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yudan He
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Xinman Yin
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Fundamental Sciences, China Medical University, Shenyang, China.,Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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16
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Du A, Li L, Jiao Z, Zhu G, Peng T, Li H. Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes. Histochem Cell Biol 2021; 155:491-502. [PMID: 33398438 PMCID: PMC8062385 DOI: 10.1007/s00418-020-01942-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 11/27/2022]
Abstract
Calcium-responsive transactivator (CREST), a nuclear protein highly expressed in postmitotic neurons, is involved in the regulation of cell cycle, differentiation and dendritic development of neuronal cells. Its mRNA has been detected in the testis of adult rat, whilst its protein expression and distribution pattern in the testis remain to be elucidated. In this study, we examined the distribution of CREST in the adult testes of both rats and human as well as the expression pattern of CREST in the testes of postnatal developing rats. In the adult testes of both human and rats, immunohistochemical analysis revealed that CREST was selectively distributed in the mature Sertoli cells but not in the spermatogenic cells. In the testes of postnatal developmental rats, CREST was expressed not only in Sertoli cells but also in the gonocytes and spermatogenic cells at the initial stage of spermatogenic cell differentiation. CREST immunoreactivity continued to increase in Sertoli cells during differentiation, reaching its peak in adulthood. However, CREST immunostaining intensity dramatically decreased as the spermatogenic cells differentiate, disappearing in the post-differentiation stage. Furthermore, Brg1 and p300, two CREST-interacting proteins ubiquitously expressed in the body, are found to be colocalized with CREST in the spermatogenic epithelial cells including Sertoli cells. The unique expression pattern of CREST in developing testis suggests that CREST might play regulatory roles in the differentiation of spermatogenic epithelial cells. The Sertoli cell-specific expression of CREST in the adulthood hints that CREST might be a novel biomarker for the mature Sertoli cells.
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Affiliation(s)
- Ana Du
- Department of Histology and Embryology, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhaoshuang Jiao
- Department of Histology and Embryology, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gaochun Zhu
- Department of Anatomy, School of Basic Medicine, Nanchang University, Nanchang, 330006, China
| | - Ting Peng
- Department of Histology and Embryology, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - He Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, 442000, China.
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17
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Smolen P, Wood MA, Baxter DA, Byrne JH. Modeling suggests combined-drug treatments for disorders impairing synaptic plasticity via shared signaling pathways. J Comput Neurosci 2020; 49:37-56. [PMID: 33175283 DOI: 10.1007/s10827-020-00771-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 08/27/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
Genetic disorders such as Rubinstein-Taybi syndrome (RTS) and Coffin-Lowry syndrome (CLS) cause lifelong cognitive disability, including deficits in learning and memory. Can pharmacological therapies be suggested that improve learning and memory in these disorders? To address this question, we simulated drug effects within a computational model describing induction of late long-term potentiation (L-LTP). Biochemical pathways impaired in these and other disorders converge on a common target, histone acetylation by acetyltransferases such as CREB binding protein (CBP), which facilitates gene induction necessary for L-LTP. We focused on four drug classes: tropomyosin receptor kinase B (TrkB) agonists, cAMP phosphodiesterase inhibitors, histone deacetylase inhibitors, and ampakines. Simulations suggested each drug type alone may rescue deficits in L-LTP. A potential disadvantage, however, was the necessity of simulating strong drug effects (high doses), which could produce adverse side effects. Thus, we investigated the effects of six drug pairs among the four classes described above. These combination treatments normalized impaired L-LTP with substantially smaller individual drug 'doses'. In addition three of these combinations, a TrkB agonist paired with an ampakine and a cAMP phosphodiesterase inhibitor paired with a TrkB agonist or an ampakine, exhibited strong synergism in L-LTP rescue. Therefore, we suggest these drug combinations are promising candidates for further empirical studies in animal models of genetic disorders that impair histone acetylation, L-LTP, and learning.
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Affiliation(s)
- Paul Smolen
- Department of Neurobiology and Anatomy, W.M. Keck Center for the Neurobiology of Learning and Memory, McGovern Medical School of the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
| | - Douglas A Baxter
- Department of Neurobiology and Anatomy, W.M. Keck Center for the Neurobiology of Learning and Memory, McGovern Medical School of the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - John H Byrne
- Department of Neurobiology and Anatomy, W.M. Keck Center for the Neurobiology of Learning and Memory, McGovern Medical School of the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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18
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Hogan MK, Hamilton GF, Horner PJ. Neural Stimulation and Molecular Mechanisms of Plasticity and Regeneration: A Review. Front Cell Neurosci 2020; 14:271. [PMID: 33173465 PMCID: PMC7591397 DOI: 10.3389/fncel.2020.00271] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/31/2020] [Indexed: 12/23/2022] Open
Abstract
Neural stimulation modulates the depolarization of neurons, thereby triggering activity-associated mechanisms of neuronal plasticity. Activity-associated mechanisms in turn play a major role in post-mitotic structure and function of adult neurons. Our understanding of the interactions between neuronal behavior, patterns of neural activity, and the surrounding environment is evolving at a rapid pace. Brain derived neurotrophic factor is a critical mediator of activity-associated plasticity, while multiple immediate early genes mediate plasticity of neurons following bouts of neural activity. New research has uncovered genetic mechanisms that govern the expression of DNA following changes in neural activity patterns, including RNAPII pause-release and activity-associated double stranded breaks. Discovery of novel mechanisms governing activity-associated plasticity of neurons hints at a layered and complex molecular control of neuronal response to depolarization. Importantly, patterns of depolarization in neurons are shown to be important mediators of genetic expression patterns and molecular responses. More research is needed to fully uncover the molecular response of different types of neurons-to-activity patterns; however, known responses might be leveraged to facilitate recovery after neural damage. Physical rehabilitation through passive or active exercise modulates neurotrophic factor expression in the brain and spinal cord and can initiate cortical plasticity commensurate with functional recovery. Rehabilitation likely relies on activity-associated mechanisms; however, it may be limited in its application. Electrical and magnetic stimulation direct specific activity patterns not accessible through passive or active exercise and work synergistically to improve standing, walking, and forelimb use after injury. Here, we review emerging concepts in the molecular mechanisms of activity-derived plasticity in order to highlight opportunities that could add value to therapeutic protocols for promoting recovery of function after trauma, disease, or age-related functional decline.
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Affiliation(s)
- Matthew K Hogan
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, United States
| | - Gillian F Hamilton
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, United States
| | - Philip J Horner
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, United States
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19
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López AJ, Hecking JK, White AO. The Emerging Role of ATP-Dependent Chromatin Remodeling in Memory and Substance Use Disorders. Int J Mol Sci 2020; 21:E6816. [PMID: 32957495 PMCID: PMC7555352 DOI: 10.3390/ijms21186816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Long-term memory formation requires coordinated regulation of gene expression and persistent changes in cell function. For decades, research has implicated histone modifications in regulating chromatin compaction necessary for experience-dependent changes to gene expression and cell function during memory formation. Recent evidence suggests that another epigenetic mechanism, ATP-dependent chromatin remodeling, works in concert with the histone-modifying enzymes to produce large-scale changes to chromatin structure. This review examines how histone-modifying enzymes and chromatin remodelers restructure chromatin to facilitate memory formation. We highlight the emerging evidence implicating ATP-dependent chromatin remodeling as an essential mechanism that mediates activity-dependent gene expression, plasticity, and cell function in developing and adult brains. Finally, we discuss how studies that target chromatin remodelers have expanded our understanding of the role that these complexes play in substance use disorders.
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Affiliation(s)
- Alberto J. López
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Julia K. Hecking
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
| | - André O. White
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
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20
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Yu L, Shi Y, Zou Q, Wang S, Zheng L, Gao L. Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model. Int J Mol Sci 2020; 21:E5014. [PMID: 32708644 PMCID: PMC7404256 DOI: 10.3390/ijms21145014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/01/2023] Open
Abstract
Some drugs can be used to treat multiple diseases, suggesting potential patterns in drug treatment. Determination of drug treatment patterns can improve our understanding of the mechanisms of drug action, enabling drug repurposing. A drug can be associated with a multilayer tissue-specific protein-protein interaction (TSPPI) network for the diseases it is used to treat. Proteins usually interact with other proteins to achieve functions that cause diseases. Hence, studying drug treatment patterns is similar to studying common module structures in multilayer TSPPI networks. Therefore, we propose a network-based model to study the treatment patterns of drugs. The method was designated SDTP (studying drug treatment pattern) and was based on drug effects and a multilayer network model. To demonstrate the application of the SDTP method, we focused on analysis of trichostatin A (TSA) in leukemia, breast cancer, and prostate cancer. We constructed a TSPPI multilayer network and obtained candidate drug-target modules from the network. Gene ontology analysis provided insights into the significance of the drug-target modules and co-expression networks. Finally, two modules were obtained as potential treatment patterns for TSA. Through analysis of the significance, composition, and functions of the selected drug-target modules, we validated the feasibility and rationality of our proposed SDTP method for identifying drug treatment patterns. In summary, our novel approach used a multilayer network model to overcome the shortcomings of single-layer networks and combined the network with information on drug activity. Based on the discovered drug treatment patterns, we can predict the potential diseases that the drug can treat. That is, if a disease-related protein module has a similar structure, then the drug is likely to be a potential drug for the treatment of the disease.
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Affiliation(s)
- Liang Yu
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Y.S.); (L.G.)
| | - Yayong Shi
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Y.S.); (L.G.)
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology, Chengdu 650004, China;
| | - Shuhang Wang
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA;
| | - Liping Zheng
- School of Computer Science and Technology, Liaocheng University, Liaocheng 252000, China;
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Y.S.); (L.G.)
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21
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Wenderski W, Wang L, Krokhotin A, Walsh JJ, Li H, Shoji H, Ghosh S, George RD, Miller EL, Elias L, Gillespie MA, Son EY, Staahl BT, Baek ST, Stanley V, Moncada C, Shipony Z, Linker SB, Marchetto MCN, Gage FH, Chen D, Sultan T, Zaki MS, Ranish JA, Miyakawa T, Luo L, Malenka RC, Crabtree GR, Gleeson JG. Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism. Proc Natl Acad Sci U S A 2020; 117:10055-10066. [PMID: 32312822 PMCID: PMC7211998 DOI: 10.1073/pnas.1908238117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Synaptic activity in neurons leads to the rapid activation of genes involved in mammalian behavior. ATP-dependent chromatin remodelers such as the BAF complex contribute to these responses and are generally thought to activate transcription. However, the mechanisms keeping such "early activation" genes silent have been a mystery. In the course of investigating Mendelian recessive autism, we identified six families with segregating loss-of-function mutations in the neuronal BAF (nBAF) subunit ACTL6B (originally named BAF53b). Accordingly, ACTL6B was the most significantly mutated gene in the Simons Recessive Autism Cohort. At least 14 subunits of the nBAF complex are mutated in autism, collectively making it a major contributor to autism spectrum disorder (ASD). Patient mutations destabilized ACTL6B protein in neurons and rerouted dendrites to the wrong glomerulus in the fly olfactory system. Humans and mice lacking ACTL6B showed corpus callosum hypoplasia, indicating a conserved role for ACTL6B in facilitating neural connectivity. Actl6b knockout mice on two genetic backgrounds exhibited ASD-related behaviors, including social and memory impairments, repetitive behaviors, and hyperactivity. Surprisingly, mutation of Actl6b relieved repression of early response genes including AP1 transcription factors (Fos, Fosl2, Fosb, and Junb), increased chromatin accessibility at AP1 binding sites, and transcriptional changes in late response genes associated with early response transcription factor activity. ACTL6B loss is thus an important cause of recessive ASD, with impaired neuron-specific chromatin repression indicated as a potential mechanism.
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Affiliation(s)
- Wendy Wenderski
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Lu Wang
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Andrey Krokhotin
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Jessica J Walsh
- Nancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305
| | - Hongjie Li
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
- Department of Biology, Stanford University, Palo Alto, CA 94305
| | - Hirotaka Shoji
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan
| | - Shereen Ghosh
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Renee D George
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Erik L Miller
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Laura Elias
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | | | - Esther Y Son
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Brett T Staahl
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Seung Tae Baek
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Valentina Stanley
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Cynthia Moncada
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Zohar Shipony
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Maria C N Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Dillon Chen
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health, Children Hospital Lahore, 54000 Lahore, Pakistan
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, 12311 Cairo, Egypt
| | | | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan
| | - Liqun Luo
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
- Department of Biology, Stanford University, Palo Alto, CA 94305
| | - Robert C Malenka
- Nancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305
| | - Gerald R Crabtree
- Department of Pathology, Stanford Medical School, Palo Alto, CA 94305;
- Department of Genetics, Stanford Medical School, Palo Alto, CA 94305
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305
| | - Joseph G Gleeson
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92037;
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037
- Rady Children's Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037
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22
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Roy J, Cyert MS. Identifying New Substrates and Functions for an Old Enzyme: Calcineurin. Cold Spring Harb Perspect Biol 2020; 12:a035436. [PMID: 31308145 PMCID: PMC7050593 DOI: 10.1101/cshperspect.a035436] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biological processes are dynamically regulated by signaling networks composed of protein kinases and phosphatases. Calcineurin, or PP3, is a conserved phosphoserine/phosphothreonine-specific protein phosphatase and member of the PPP family of phosphatases. Calcineurin is unique, however, in its activation by Ca2+ and calmodulin. This ubiquitously expressed phosphatase controls Ca2+-dependent processes in all human tissues, but is best known for driving the adaptive immune response by dephosphorylating the nuclear factor of the activated T-cells (NFAT) family of transcription factors. Therefore, calcineurin inhibitors, FK506 (tacrolimus), and cyclosporin A serve as immunosuppressants. We describe some of the adverse effects associated with calcineurin inhibitors that result from inhibition of calcineurin in nonimmune tissues, illustrating the many functions of this enzyme that have yet to be elucidated. In fact, calcineurin has essential roles beyond the immune system, from yeast to humans, but since its discovery more than 30 years ago, only a small number of direct calcineurin substrates have been shown (∼75 proteins). This is because of limitations in current methods for identification of phosphatase substrates. Here we discuss recent insights into mechanisms of calcineurin activation and substrate recognition that have been critical in the development of novel approaches for identifying its targets systematically. Rather than comprehensively reviewing known functions of calcineurin, we highlight new approaches to substrate identification for this critical regulator that may reveal molecular mechanisms underlying toxicities caused by calcineurin inhibitor-based immunosuppression.
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Affiliation(s)
- Jagoree Roy
- Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, California 94305-5020
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23
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Heavner WE, Smith SEP. Resolving the Synaptic versus Developmental Dichotomy of Autism Risk Genes. Trends Neurosci 2020; 43:227-241. [PMID: 32209454 DOI: 10.1016/j.tins.2020.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 12/28/2022]
Abstract
Genes that are mutated in Autism Spectrum Disorders (ASD) can be classified broadly as either synaptic or developmental. But what if this is a false distinction? A recent spate of publications has provided evidence for developmental mechanisms that rely on neural activity for proper cortical development. Conversely, a growing body of evidence indicates a role for developmental mechanisms, particularly chromatin remodeling, during learning or in response to neural activity. Here, we review these recent publications and propose a model in which genes that confer ASD risk operate in signal transduction networks critical for both cortical development and synaptic homeostasis.
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Affiliation(s)
- Whitney E Heavner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
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The deubiquitinase USP6 affects memory and synaptic plasticity through modulating NMDA receptor stability. PLoS Biol 2019; 17:e3000525. [PMID: 31841517 PMCID: PMC6913916 DOI: 10.1371/journal.pbio.3000525] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022] Open
Abstract
Ubiquitin-specific protease (USP) 6 is a hominoid deubiquitinating enzyme previously implicated in intellectual disability and autism spectrum disorder. Although these findings link USP6 to higher brain function, potential roles for USP6 in cognition have not been investigated. Here, we report that USP6 is highly expressed in induced human neurons and that neuron-specific expression of USP6 enhances learning and memory in a transgenic mouse model. Similarly, USP6 expression regulates N-methyl-D-aspartate-type glutamate receptor (NMDAR)-dependent long-term potentiation and long-term depression in USP6 transgenic mouse hippocampi. Proteomic characterization of transgenic USP6 mouse cortex reveals attenuated NMDAR ubiquitination, with concomitant elevation in NMDAR expression, stability, and cell surface distribution with USP6 overexpression. USP6 positively modulates GluN1 expression in transfected cells, and USP6 down-regulation impedes focal GluN1 distribution at postsynaptic densities and impairs synaptic function in neurons derived from human embryonic stem cells. Together, these results indicate that USP6 enhances NMDAR stability to promote synaptic function and cognition. This study identifies the hominoid-specific USP6 as a novel deubiquitinase of NMDA receptors, and shows that neuronal expression of human USP6 transgene enhances cognitive and synaptic function in mice, suggesting a potential role of USP6 in the evolution of human intelligence.
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25
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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26
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Hong Q, Liu J, Lin Z, Zhuang D, Xu W, Xu Z, Lai M, Zhu H, Zhou W, Liu H. Histone 3 lysine 9 acetylation of BRG1 in the medial prefrontal cortex is associated with heroin self‑administration in rats. Mol Med Rep 2019; 21:405-412. [PMID: 31939625 DOI: 10.3892/mmr.2019.10845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 09/20/2019] [Indexed: 11/06/2022] Open
Abstract
Heroin addiction is a chronic relapsing brain disorder with negative social consequences. Histone acetylation serves a role in drug‑induced behavior and neuroplasticity impairment. Brahma/SWI2‑related gene‑1 (BRG1) participates in cerebellar development, embryogenesis and transcriptional regulation of neuronal genes concurrent with histone modifications. However, little is known about the relationship between histone H3 lysine 9 acetylation (H3K9ac) and BRG1 in response to heroin. The present study aimed to assess the contribution of histone 3 lysine 9 acetylation of BRG1 to heroin self‑administration. The present study established a Sprague‑Dawley rat model of heroin self‑administration under a fixed‑ratio‑1 paradigm. Chromatin immunoprecipitation followed by reverse transcription‑quantitative PCR (RT‑qPCR) was used to detect the accumulation of H3K9ac on BRG1 in the medial prefrontal cortex (mPFC) and nucleus accumbens (NAc) following heroin self‑administration. The relative expression levels of BRG1 were analyzed by RT‑qPCR. H3K9ac at the promoter region of BRG1 was significantly elevated (P=0.002), and the expression of BRG1 in the mPFC increased 1.47‑fold in the heroin self‑administration group compared with the control group. No significant difference in H3K9ac at the BRG1 locus was observed in the NAc (P=0.323), with the expression of BRG1 decreasing 1.38‑fold in the heroin self‑administering rats compared with the control group. H3K9ac is associated with transcriptional activation, and the increased BRG1 expression suggested an essential and novel role for BRG1 and its H3K9ac‑mediated regulation in the mPFC after heroin self‑administration; and this may function through epigenetically modulating the activation of neuroplasticity‑associated genes. This association may provide a novel therapeutic target for the treatment of heroin addiction.
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Affiliation(s)
- Qingxiao Hong
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Jing Liu
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Zi Lin
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Dingding Zhuang
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Wenjin Xu
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Zemin Xu
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Miaojun Lai
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Huaqiang Zhu
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Wenhua Zhou
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
| | - Huifen Liu
- Laboratory of Behavioral Neuroscience, Ningbo Addiction Research and Treatment Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315010, P.R. China
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27
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Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-Oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu MY, Owen-Hughes T, Ettmayer P, Pearson M, McConnell DB, Ciulli A. BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat Chem Biol 2019; 15:672-680. [PMID: 31178587 PMCID: PMC6600871 DOI: 10.1038/s41589-019-0294-6] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/16/2019] [Indexed: 12/22/2022]
Abstract
Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here we develop PROTAC degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization towards ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced antiproliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets and pave the way towards new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.
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Affiliation(s)
- William Farnaby
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Michael J Roy
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - David Zollman
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | | | | | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Nicola Wiechens
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Meng-Ying Wu
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.
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28
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Cheng C, Yang K, Wu X, Zhang Y, Shan S, Gitler A, Ghosh A, Qiu Z. Loss of CREST leads to neuroinflammatory responses and ALS-like motor defects in mice. Transl Neurodegener 2019; 8:13. [PMID: 30976389 PMCID: PMC6444434 DOI: 10.1186/s40035-019-0152-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/18/2019] [Indexed: 12/25/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a late onset neurodegenerative disease with fast progression. ALS has heavy genetic components in which a series of genetic mutations have been identified. In 2013, Mutations of the CREST gene (also known as SS18L1), which functions as a calcium-regulated transcriptional activator, were found in sporadic ALS patients. However, the pathogenic causality and mechanisms of ALS-associated mutations of CREST remain to be determined. Methods In this study, we constructed CREST knockout and Q394X knock-in mice with CRISPR/Cas9 system. Using biochemical and imaging tools, we illustrated core pathological phenotypes in CREST mutant mice and claimed the possible pathogenic mechanisms. Furthermore, we also observed locomotion defects in CREST mutant mice with behavioural tests. Results We demonstrate that ALS-related CREST-Q388X mutation exhibits loss-of-function effects. Importantly, the microglial activation was prevalent in CREST haploinsufficiency mice and Q394X mice mimicking the human CREST Q388X mutation. Furthermore, we showed that both CREST haploinsufficiency and Q394X mice displayed deficits in motor coordination. Finally, we identified the critical role of CREST-BRG1 complex in repressing the expression of immune-related cytokines including Ccl2 and Cxcl10 in neurons, via histone deacetylation, providing the molecular mechanisms underlying inflammatory responses within mice lack of CREST. Conclusion Our findings indicate that elevated inflammatory responses in a subset of ALS may be caused by neuron-derived factors, suggesting potential therapeutic methods through inflammation pathways.
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Affiliation(s)
- Cheng Cheng
- 1Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Kan Yang
- 1Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Xinwei Wu
- 2Xiangya Hospital, Central South University, Changsha, 410008 China
| | - Yuefang Zhang
- 1Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Shifang Shan
- 1Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Aaron Gitler
- 3Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Anirvan Ghosh
- 4Research and Early Development, Biogen, Cambridge, MA 02142 USA
| | - Zilong Qiu
- 1Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
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Sharma N, Pollina EA, Nagy MA, Yap EL, DiBiase FA, Hrvatin S, Hu L, Lin C, Greenberg ME. ARNT2 Tunes Activity-Dependent Gene Expression through NCoR2-Mediated Repression and NPAS4-Mediated Activation. Neuron 2019; 102:390-406.e9. [PMID: 30846309 DOI: 10.1016/j.neuron.2019.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/20/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Abstract
Neuronal activity-dependent transcription is tuned to ensure precise gene induction during periods of heightened synaptic activity, allowing for appropriate responses of activated neurons within neural circuits. The consequences of aberrant induction of activity-dependent genes on neuronal physiology are not yet clear. Here, we demonstrate that, in the absence of synaptic excitation, the basic-helix-loop-helix (bHLH)-PAS family transcription factor ARNT2 recruits the NCoR2 co-repressor complex to suppress neuronal activity-dependent regulatory elements and maintain low basal levels of inducible genes. This restricts inhibition of excitatory neurons, maintaining them in a state that is receptive to future sensory stimuli. By contrast, in response to heightened neuronal activity, ARNT2 recruits the neuronal-specific bHLH-PAS factor NPAS4 to activity-dependent regulatory elements to induce transcription and thereby increase somatic inhibitory input. Thus, the interplay of bHLH-PAS complexes at activity-dependent regulatory elements maintains temporal control of activity-dependent gene expression and scales somatic inhibition with circuit activity.
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Affiliation(s)
- Nikhil Sharma
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Florence A DiBiase
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sinisa Hrvatin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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30
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Alaghband Y, Kramár E, Kwapis JL, Kim ES, Hemstedt TJ, López AJ, White AO, Al-Kachak A, Aimiuwu OV, Bodinayake KK, Oparaugo NC, Han J, Lattal KM, Wood MA. CREST in the Nucleus Accumbens Core Regulates Cocaine Conditioned Place Preference, Cocaine-Seeking Behavior, and Synaptic Plasticity. J Neurosci 2018; 38:9514-9526. [PMID: 30228227 PMCID: PMC6209848 DOI: 10.1523/jneurosci.2911-17.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
Epigenetic mechanisms result in persistent changes at the cellular level that can lead to long-lasting behavioral adaptations. Nucleosome remodeling is a major epigenetic mechanism that has not been well explored with regards to drug-seeking behaviors. Nucleosome remodeling is performed by multi-subunit complexes that interact with DNA or chromatin structure and possess an ATP-dependent enzyme to disrupt nucleosome-DNA contacts and ultimately regulate gene expression. Calcium responsive transactivator (CREST) is a transcriptional activator that interacts with enzymes involved in both histone acetylation and nucleosome remodeling. Here, we examined the effects of knocking down CREST in the nucleus accumbens (NAc) core on drug-seeking behavior and synaptic plasticity in male mice as well as drug-seeking in male rats. Knocking down CREST in the NAc core results in impaired cocaine-induced conditioned place preference (CPP) as well as theta-induced long-term potentiation in the NAc core. Further, similar to the CPP findings, using a self-administration procedure, we found that CREST knockdown in the NAc core of male rats had no effect on instrumental responding for cocaine itself on a first-order schedule, but did significantly attenuate responding on a second-order chain schedule, in which responding has a weaker association with cocaine. Together, these results suggest that CREST in the NAc core is required for cocaine-induced CPP, synaptic plasticity, as well as cocaine-seeking behavior.SIGNIFICANCE STATEMENT This study demonstrates a key role for the role of Calcium responsive transactivator (CREST), a transcriptional activator, in the nucleus accumbens (NAc) core with regard to cocaine-induced conditioned place preference (CPP), self-administration (SA), and synaptic plasticity. CREST is a unique transcriptional regulator that can recruit enzymes from two different major epigenetic mechanisms: histone acetylation and nucleosome remodeling. In this study we also found that the level of potentiation in the NAc core correlated with whether or not animals formed a CPP. Together the results indicate that CREST is a key downstream regulator of cocaine action in the NAc.
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Affiliation(s)
- Yasaman Alaghband
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Irvine Center for Addiction Neuroscience
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Enikö Kramár
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Janine L Kwapis
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, California 92697
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Earnest S Kim
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon 97239
| | - Thekla J Hemstedt
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Alberto J López
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Irvine Center for Addiction Neuroscience
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - André O White
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Irvine Center for Addiction Neuroscience
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Amni Al-Kachak
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Osasumwen V Aimiuwu
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Kasuni K Bodinayake
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Nicole C Oparaugo
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - Joseph Han
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
| | - K Matthew Lattal
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon 97239
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory,
- Irvine Center for Addiction Neuroscience
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, California 92697
- Center for the Neurobiology of Learning and Memory, Irvine, California, 92697, and
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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Tibshirani M, Zhao B, Gentil BJ, Minotti S, Marques C, Keith J, Rogaeva E, Zinman L, Rouaux C, Robertson J, Durham HD. Dysregulation of chromatin remodelling complexes in amyotrophic lateral sclerosis. Hum Mol Genet 2018; 26:4142-4152. [PMID: 28973294 DOI: 10.1093/hmg/ddx301] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis is a fatal neurodegenerative disease with paralysis resulting from dysfunction and loss of motor neurons. A common neuropathological finding is attrition of motor neuron dendrites, which make central connections vital to motor control. The chromatin remodelling complex, neuronal Brahma-related gene 1 (Brg1)-associated factor complex (nBAF), is critical for neuronal differentiation, dendritic extension and synaptic function. We have identified loss of the crucial nBAF subunits Brg1, Brg1-associated factor 53b and calcium responsive transactivator in cultured motor neurons expressing FUS or TAR-DNA Binding Protein 43 (TDP-43) mutants linked to familial ALS. When plasmids encoding wild-type or mutant human FUS or TDP-43 were expressed in motor neurons of dissociated spinal cord cultures prepared from E13 mice, mutant proteins in particular accumulated in the cytoplasm. Immunolabelling of nBAF subunits was reduced in proportion to loss of nuclear FUS or TDP-43 and depletion of Brg1 was associated with nuclear retention of Brg1 mRNA. Dendritic attrition (loss of intermediate and terminal dendritic branches) occurred in motor neurons expressing mutant, but not wild-type, FUS or TDP-43. This attrition was delayed by ectopic over-expression of Brg1 and was reproduced by inhibiting Brg1 activity either through genetic manipulation or treatment with the chemical inhibitor, (E)-1-(2-Hydroxyphenyl)-3-((1R, 4R)-5-(pyridin-2-yl)-2, 5-diazabicyclo[2.2.1]heptan-2-yl)prop-2-en-1-one, demonstrating the importance of Brg1 to maintenance of dendritic architecture. Loss of nBAF subunits was also documented in spinal motor neurons in autopsy tissue from familial amyotrophic sclerosis (chromosome 9 open reading frame 72 with G4C2 nucleotide expansion) and from sporadic cases with no identified mutation, pointing to dysfunction of nBAF chromatin remodelling in multiple forms of ALS.
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Affiliation(s)
- Michael Tibshirani
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Beibei Zhao
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Benoit J Gentil
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Sandra Minotti
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Christine Marques
- Inserm U1118, Faculté de Médecine, Université de Strasbourg, 67 085 Strasbourg Cedex, France
| | - Julia Keith
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Lorne Zinman
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Caroline Rouaux
- Inserm U1118, Faculté de Médecine, Université de Strasbourg, 67 085 Strasbourg Cedex, France
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada.,Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Heather D Durham
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
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Shu G, Kramár EA, López AJ, Huynh G, Wood MA, Kwapis JL. Deleting HDAC3 rescues long-term memory impairments induced by disruption of the neuron-specific chromatin remodeling subunit BAF53b. ACTA ACUST UNITED AC 2018; 25:109-114. [PMID: 29449454 PMCID: PMC5817283 DOI: 10.1101/lm.046920.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022]
Abstract
Multiple epigenetic mechanisms, including histone acetylation and nucleosome remodeling, are known to be involved in long-term memory formation. Enhancing histone acetylation by deleting histone deacetylases, like HDAC3, typically enhances long-term memory formation. In contrast, disrupting nucleosome remodeling by blocking the neuron-specific chromatin remodeling subunit BAF53b impairs long-term memory. Here, we show that deleting HDAC3 can ameliorate the impairments in both long-term memory and synaptic plasticity caused by BAF53b mutation. This suggests a dynamic interplay exists between histone acetylation/deacetylation and nucleosome remodeling mechanisms in the regulation of memory formation.
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Affiliation(s)
- Guanhua Shu
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
| | - Enikö A Kramár
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
| | - Alberto J López
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
| | - Grace Huynh
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
| | - Janine L Kwapis
- Department of Neurobiology and Behavior, University of California, Irvine, California, 92697, USA.,Center for Neurobiology of Learning and Memory, Irvine, California, 92697, USA
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Poston RG, Dunn CJ, Sarkar P, Saha RN. Persistent 6-OH-BDE-47 exposure impairs functional neuronal maturation and alters expression of neurodevelopmentally-relevant chromatin remodelers. ENVIRONMENTAL EPIGENETICS 2018; 4:dvx020. [PMID: 29765770 PMCID: PMC5941167 DOI: 10.1093/eep/dvx020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 06/08/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are a pervasive class of brominated flame retardants that are present in the environment at particularly high levels, especially in the United States. Their environmental stability, propensity for bioaccumulation, and known potential for neurotoxicity has evoked interest regarding their effects on the developing nervous system. Exposure to PBDEs has been strongly associated with neurodevelopmental disorders. However, the details of their mechanistic roles in such disorders are incompletely understood. Here, we report the effects of one of the most prevalent congeners, BDE-47, and its hydroxylated metabolites on the maturation and function of embryonic rat cortical neurons. Prolonged exposure to 6OH-BDE-47 produces the strongest effects amongst the parent BDE-47 congener and its tested hydroxylated metabolites. These effects include: i) disruption of transcriptional responses to neuronal activity, ii) dysregulation of multiple genes associated with neurodevelopmental disorders, and intriguingly, iii) altered expression of several subunits of the developmentally-relevant BAF (Brg1-associated factors) chromatin remodeling complex, including the key subunit BAF170. Taken together, our data indicate that persistent exposure to 6OH-BDE-47 may interfere with neurodevelopmental chromatin remodeling mechanisms and gene transcription programs, which in turn are likely to interfere with downstream processes such as synapse development and overall functional maturity of neurons. Results from this study have identified a novel aspect of 6OH-BDE-47 toxicity and open new avenues to explore the effects of a ubiquitous environmental toxin on epigenetic regulation of neuronal maturation and function.
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Affiliation(s)
- Robert G Poston
- Molecular Cell Biology Unit, School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA 95343, USA
| | - Carissa J Dunn
- Molecular Cell Biology Unit, School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA 95343, USA
| | - Pushpita Sarkar
- Molecular Cell Biology Unit, School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA 95343, USA
| | - Ramendra N Saha
- Molecular Cell Biology Unit, School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA 95343, USA
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35
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Madabhushi R, Kim TK. Emerging themes in neuronal activity-dependent gene expression. Mol Cell Neurosci 2017; 87:27-34. [PMID: 29254824 DOI: 10.1016/j.mcn.2017.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022] Open
Abstract
In this review, we attempt to discuss emerging themes in the regulation of neuronal activity-regulated genes, focusing primarily on an important subset of immediate-early genes. We first discuss earlier studies that have illuminated the role of cis-acting elements within the promoters of immediate-early genes, the corresponding transcription factors that bind these elements, and the roles of major activity-regulated signaling pathways. However, our emphasis is on new studies that have revealed an important role for epigenetic and topological mechanisms, including enhancer-promoter interactions, enhancer RNAs (eRNAs), and activity-induced DNA breaks, that have emerged as important factors that govern the temporal dynamics of activity-induced gene transcription.
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Affiliation(s)
- Ram Madabhushi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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36
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Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y. Wnt11 regulates cardiac chamber development and disease during perinatal maturation. JCI Insight 2017; 2:94904. [PMID: 28878122 PMCID: PMC5621892 DOI: 10.1172/jci.insight.94904] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022] Open
Abstract
Ventricular chamber growth and development during perinatal circulatory transition is critical for functional adaptation of the heart. However, the chamber-specific programs of neonatal heart growth are poorly understood. We used integrated systems genomic and functional biology analyses of the perinatal chamber specific transcriptome and we identified Wnt11 as a prominent regulator of chamber-specific proliferation. Importantly, downregulation of Wnt11 expression was associated with cyanotic congenital heart defect (CHD) phenotypes and correlated with O2 saturation levels in hypoxemic infants with Tetralogy of Fallot (TOF). Perinatal hypoxia treatment in mice suppressed Wnt11 expression and induced myocyte proliferation more robustly in the right ventricle, modulating Rb1 protein activity. Wnt11 inactivation was sufficient to induce myocyte proliferation in perinatal mouse hearts and reduced Rb1 protein and phosphorylation in neonatal cardiomyocytes. Finally, downregulated Wnt11 in hypoxemic TOF infantile hearts was associated with Rb1 suppression and induction of proliferation markers. This study revealed a previously uncharacterized function of Wnt11-mediated signaling as an important player in programming the chamber-specific growth of the neonatal heart. This function influences the chamber-specific development and pathogenesis in response to hypoxia and cyanotic CHDs. Defining the underlying regulatory mechanism may yield chamber-specific therapies for infants born with CHDs.
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Affiliation(s)
- Marlin Touma
- The Children’s Discovery and Innovation Institute (CDI), Department of Pediatrics
- Cardiovascular Research Laboratory
| | - Xuedong Kang
- The Children’s Discovery and Innovation Institute (CDI), Department of Pediatrics
- Cardiovascular Research Laboratory
| | | | - Yan Zhao
- The Children’s Discovery and Innovation Institute (CDI), Department of Pediatrics
- Cardiovascular Research Laboratory
| | | | | | | | | | | | | | - Yibin Wang
- Cardiovascular Research Laboratory
- Department of Anesthesiology, Physiology and Medicine, University of California, Los Angeles, California, USA
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37
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Lim ET, Uddin M, De Rubeis S, Chan Y, Kamumbu AS, Zhang X, D'Gama A, Kim SN, Hill RS, Goldberg AP, Poultney C, Minshew NJ, Kushima I, Aleksic B, Ozaki N, Parellada M, Arango C, Penzol MJ, Carracedo A, Kolevzon A, Hultman CM, Weiss LA, Fromer M, Chiocchetti AG, Freitag CM, Church GM, Scherer SW, Buxbaum JD, Walsh CA. Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Nat Neurosci 2017; 20:1217-1224. [PMID: 28714951 PMCID: PMC5672813 DOI: 10.1038/nn.4598] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/20/2017] [Indexed: 12/17/2022]
Abstract
We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10-6), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5.4 × 10-3). Two genes (KLF16 and MSANTD2) were significantly enriched for PZMs genome-wide, and other PZMs involved genes (SCN2A, HNRNPU and SMARCA4) whose mutation is known to cause ASD or other neurodevelopmental disorders. PZMs constitute a significant proportion of de novo mutations and contribute importantly to ASD risk.
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Affiliation(s)
- Elaine T. Lim
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, College of Medicine, Dubai, UAE
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Yingleong Chan
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Anne S. Kamumbu
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Xiaochang Zhang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Alissa D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Sonia N. Kim
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Robert Sean Hill
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Arthur P. Goldberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Christopher Poultney
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Nancy J. Minshew
- Department of Psychiatry, Center For Excellence in Autism Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Mara Parellada
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid 28007, Spain
| | - Celso Arango
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid 28007, Spain
| | - Maria J. Penzol
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, Madrid 28007, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado-Plataforma de Recursos Biomoleculares y Bioinformaticos-Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela 15782, Spain
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica-SERGAS, Santiago de Compostela 15782, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lauren A. Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Menachem Fromer
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Andreas G. Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt am Main 60528, Germany
| | - Christine M. Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt am Main 60528, Germany
| | | | - George M. Church
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
- Departments of Genetics, Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
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38
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Sokpor G, Xie Y, Rosenbusch J, Tuoc T. Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders. Front Mol Neurosci 2017; 10:243. [PMID: 28824374 PMCID: PMC5540894 DOI: 10.3389/fnmol.2017.00243] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.
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Affiliation(s)
- Godwin Sokpor
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Yuanbin Xie
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Joachim Rosenbusch
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Tran Tuoc
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the BrainGoettingen, Germany
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39
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Evans MD, Tufo C, Dumitrescu AS, Grubb MS. Myosin II activity is required for structural plasticity at the axon initial segment. Eur J Neurosci 2017; 46:1751-1757. [PMID: 28452088 PMCID: PMC5573965 DOI: 10.1111/ejn.13597] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/29/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
In neurons, axons possess a molecularly defined and highly organised proximal region – the axon initial segment (AIS) – that is a key regulator of both electrical excitability and cellular polarity. Despite existing as a large, dense structure with specialised cytoskeletal architecture, the AIS is surprisingly plastic, with sustained alterations in neuronal activity bringing about significant alterations to its position, length or molecular composition. However, although the upstream activity‐dependent signalling pathways that lead to such plasticity have begun to be elucidated, the downstream mechanisms that produce structural changes at the AIS are completely unknown. Here, we use dissociated cultures of rat hippocampus to show that two forms of AIS plasticity in dentate granule cells – long‐term relocation, and more rapid shortening – are completely blocked by treatment with blebbistatin, a potent and selective myosin II ATPase inhibitor. These data establish a link between myosin II and AIS function, and suggest that myosin II's primary role at the structure may be to effect activity‐dependent morphological alterations.
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Affiliation(s)
- Mark D Evans
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Candida Tufo
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Adna S Dumitrescu
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Matthew S Grubb
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.,FENS-Kavli Network of Excellence, Europe-wide
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40
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Chen LF, Zhou AS, West AE. Transcribing the connectome: roles for transcription factors and chromatin regulators in activity-dependent synapse development. J Neurophysiol 2017; 118:755-770. [PMID: 28490640 DOI: 10.1152/jn.00067.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
The wiring of synaptic connections in the developing mammalian brain is shaped by both intrinsic and extrinsic signals. One point where these regulatory pathways converge is via the sensory experience-dependent regulation of new gene transcription. Recent studies have elucidated a number of molecular mechanisms that allow nuclear transcription factors and chromatin regulatory proteins to encode aspects of specificity in experience-dependent synapse development. Here we review the evidence for the transcriptional mechanisms that sculpt activity-dependent aspects of synaptic connectivity during postnatal development and discuss how disruption of these processes is associated with aberrant brain development in autism and intellectual disability.
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Affiliation(s)
- Liang-Fu Chen
- Department of Neurobiology, Duke University, Durham, North Carolina
| | - Allen S Zhou
- Department of Neurobiology, Duke University, Durham, North Carolina
| | - Anne E West
- Department of Neurobiology, Duke University, Durham, North Carolina
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41
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Souslova T, Mirédin K, Millar AM, Albert PR. Recruitment by the Repressor Freud-1 of Histone Deacetylase-Brg1 Chromatin Remodeling Complexes to Strengthen HTR1A Gene Repression. Mol Neurobiol 2016; 54:8263-8277. [PMID: 27914010 DOI: 10.1007/s12035-016-0306-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022]
Abstract
Five-prime repressor element under dual repression binding protein-1 (Freud-1)/CC2D1A is genetically linked to intellectual disability and implicated in neuronal development. Freud-1 represses the serotonin-1A (5-HT1A) receptor gene HTR1A by histone deacetylase (HDAC)-dependent or HDAC-independent mechanisms in 5-HT1A-negative (e.g., HEK-293) or 5-HT1A-expressing cells (SK-N-SH), respectively. To identify the underlying mechanisms, Freud-1-associated proteins were affinity-purified from HEK-293 nuclear extracts and members of the Brg1/SMARCCA chromatin remodeling and Sin3A-HDAC corepressor complexes were identified. Pull-down assays using recombinant proteins showed that Freud-1 interacts directly with the Brg1 carboxyl-terminal domain; interaction with Brg1 required the carboxyl-terminal of Freud-1. Freud-1 complexes in HEK-293 and SK-N-SH cells differed, with low levels of BAF170/SMARCC2 and BAF57/SMARCE1 in HEK-293 cells and low-undetectable BAF155/SMARCC1, Sin3A, and HDAC1/2 in SK-N-SH cells. Similarly, by quantitative chromatin immunoprecipitation, Brg1-BAF170/57 and Sin3A-HDAC complexes were observed at the HTR1A promoter in HEK-293 cells, whereas in SK-N-SH cells, Sin3A-HDAC proteins were not detected. Quantifying 5-HT1A receptor mRNA levels in cells treated with siRNA to Freud-1, Brg1, or both RNAs addressed the functional role of the Freud-1-Brg1 complex. In HEK-293 cells, 5-HT1A receptor mRNA levels were increased only when both Freud-1 and Brg1 were depleted, but in SK-N-SH cells, depletion of either protein upregulated 5-HT1A receptor RNA. Thus, recruitment by Freud-1 of Brg1, BAF155, and Sin3A-HDAC complexes appears to strengthen repression of the HTR1A gene to prevent its expression inappropriate cell types, while recruitment of the Brg1-BAF170/57 complex is permissive to 5-HT1A receptor expression. Alterations in Freud-1-Brg1 interactions in mutants associated with intellectual disability could impair gene repression leading to altered neuronal development.
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Affiliation(s)
- Tatiana Souslova
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Kim Mirédin
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Anne M Millar
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Paul R Albert
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
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42
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Bano D, Jewell SA, Nicotera P. Calcium signaling then and now, via Stockholm. Biochem Biophys Res Commun 2016; 482:384-387. [PMID: 27908727 DOI: 10.1016/j.bbrc.2016.11.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 11/27/2016] [Indexed: 11/19/2022]
Affiliation(s)
- Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sarah A Jewell
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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43
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Kulkarni M, Trifunović D, Schubert T, Euler T, Paquet-Durand F. Calcium dynamics change in degenerating cone photoreceptors. Hum Mol Genet 2016; 25:3729-3740. [PMID: 27402880 DOI: 10.1093/hmg/ddw219] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/24/2016] [Accepted: 06/25/2016] [Indexed: 11/14/2022] Open
Abstract
Cone photoreceptors (cones) are essential for high-resolution daylight vision and colour perception. Loss of cones in hereditary retinal diseases has a dramatic impact on human vision. The mechanisms underlying cone death are poorly understood, and consequently, there are no treatments available. Previous studies suggest a central role for calcium (Ca2+) homeostasis deficits in photoreceptor degeneration; however, direct evidence for this is scarce and physiological measurements of Ca2+ in degenerating mammalian cones are lacking.Here, we took advantage of the transgenic HR2.1:TN-XL mouse line that expresses a genetically encoded Ca2+ biosensor exclusively in cones. We cross-bred this line with mouse models for primary ("cone photoreceptor function loss-1", cpfl1) and secondary ("retinal degeneration-1", rd1) cone degeneration, respectively, and assessed resting Ca2+ levels and light-evoked Ca2+ responses in cones using two-photon imaging. We found that Ca2+ dynamics were altered in cpfl1 cones, showing higher noise and variable Ca2+ levels, with significantly wider distribution than for wild-type and rd1 cones. Unexpectedly, up to 21% of cpfl1 cones still displayed light-evoked Ca2+ responses, which were larger and slower than wild-type responses. In contrast, genetically intact rd1 cones were characterized by lower noise and complete lack of visual function.Our study demonstrates alterations in cone Ca2+ dynamics in both primary and secondary cone degeneration. Our results are consistent with the view that higher (fluctuating) cone Ca2+ levels are involved in photoreceptor cell death in primary (cpfl1) but not in secondary (rd1) cone degeneration. These findings may guide the future development of therapies targeting photoreceptor Ca2+ homeostasis.
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Affiliation(s)
- Manoj Kulkarni
- Institute for Ophthalmic Research.,Werner Reichardt Centre for Integrative Neuroscience.,Graduate School of Cellular & Molecular Neuroscience
| | | | - Timm Schubert
- Institute for Ophthalmic Research.,Werner Reichardt Centre for Integrative Neuroscience
| | - Thomas Euler
- Institute for Ophthalmic Research (F.P-D.) (T.E.).,Werner Reichardt Centre for Integrative Neuroscience.,Bernstein Centre for Computational Neuroscience, University of Tübingen, Tübingen, Germany
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44
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Gopal S, Couchman J, Pocock R. Redefining the role of syndecans in C. elegans biology. WORM 2016; 5:e1142042. [PMID: 27073736 DOI: 10.1080/21624054.2016.1142042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/08/2016] [Indexed: 12/21/2022]
Abstract
Cytosolic calcium is an important factor during fertilization, development and differentiation. Hence, the control of cytosolic calcium levels has been studied extensively for several decades. Numerous calcium channels have been identified and their mechanism of action elucidated. However, the mode of calcium channel regulation remains elusive. Here we discuss our recent findings regarding the role of syndecans in the regulation of cytosolic calcium levels. Syndecans are transmembrane proteoglycans present in both vertebrates and invertebrates that interact with extracellular ligands resulting in the activation of several downstream signaling pathways. We identified a previously unappreciated role of syndecans in cytosolic calcium regulation in mammals that is conserved in C. elegans. We concluded that calcium regulation is the basic, evolutionarily conserved role for syndecans, which enables them to be integral for multiple cellular functions.
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Affiliation(s)
- Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University , Melbourne, Victoria, Australia
| | - John Couchman
- Department of Biomedical Sciences, University of Copenhagen , Copenhagen, Denmark
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University , Melbourne, Victoria, Australia
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45
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Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME. Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron 2015; 89:100-12. [PMID: 26711116 DOI: 10.1016/j.neuron.2015.11.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/27/2015] [Accepted: 11/12/2015] [Indexed: 12/22/2022]
Abstract
Although mechanisms underlying early steps in cerebellar development are known, evidence is lacking on genetic and epigenetic changes during the establishment of the synaptic circuitry. Using metagene analysis, we report pivotal changes in multiple reactomes of epigenetic pathway genes in cerebellar granule cells (GCs) during circuit formation. During this stage, Tet genes are upregulated and vitamin C activation of Tet enzymes increases the levels of 5-hydroxymethylcytosine (5hmC) at exon start sites of upregulated genes, notably axon guidance genes and ion channel genes. Knockdown of Tet1 and Tet3 by RNAi in ex vivo cerebellar slice cultures inhibits dendritic arborization of developing GCs, a critical step in circuit formation. These findings demonstrate a role for Tet genes and chromatin remodeling genes in the formation of cerebellar circuitry.
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Affiliation(s)
- Xiaodong Zhu
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - David Girardo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Keisha John
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Marian Mellén
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jill P Mesirov
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA.
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Autism-Associated Chromatin Regulator Brg1/SmarcA4 Is Required for Synapse Development and Myocyte Enhancer Factor 2-Mediated Synapse Remodeling. Mol Cell Biol 2015; 36:70-83. [PMID: 26459759 DOI: 10.1128/mcb.00534-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/05/2015] [Indexed: 11/20/2022] Open
Abstract
Synapse development requires normal neuronal activities and the precise expression of synapse-related genes. Dysregulation of synaptic genes results in neurological diseases such as autism spectrum disorders (ASD). Mutations in genes encoding chromatin-remodeling factor Brg1/SmarcA4 and its associated proteins are the genetic causes of several developmental diseases with neurological defects and autistic symptoms. Recent large-scale genomic studies predicted Brg1/SmarcA4 as one of the key nodes of the ASD gene network. We report that Brg1 deletion in early postnatal hippocampal neurons led to reduced dendritic spine density and maturation and impaired synapse activities. In developing mice, neuronal Brg1 deletion caused severe neurological defects. Gene expression analyses indicated that Brg1 regulates a significant number of genes known to be involved in synapse function and implicated in ASD. We found that Brg1 is required for dendritic spine/synapse elimination mediated by the ASD-associated transcription factor myocyte enhancer factor 2 (MEF2) and that Brg1 regulates the activity-induced expression of a specific subset of genes that overlap significantly with the targets of MEF2. Our analyses showed that Brg1 interacts with MEF2 and that MEF2 is required for Brg1 recruitment to target genes in response to neuron activation. Thus, Brg1 plays important roles in both synapse development/maturation and MEF2-mediated synapse remodeling. Our study reveals specific functions of the epigenetic regulator Brg1 in synapse development and provides insights into its role in neurological diseases such as ASD.
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Choi KY, Yoo M, Han JH. Toward understanding the role of the neuron-specific BAF chromatin remodeling complex in memory formation. Exp Mol Med 2015; 47:e155. [PMID: 25838002 DOI: 10.1038/emm.2014.129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
The long-term storage of memory requires the finely tuned coordination of intracellular signaling with the transcriptional, translational and epigenetic regulations of gene expression. Among the epigenetic mechanisms, however, we know relatively little about the involvement of chromatin remodeling-dependent control of gene expression in cognitive brain functions, compared with our knowledge of other such mechanisms (for example, histone modifications and DNA methylation). A few recent studies have implicated the Brm/Brg-associated factor (BAF) chromatin-remodeling complex, a mammalian homolog of the yeast Swi/Snf complex, in neuronal structural/functional plasticity and memory formation. The BAF complex was previously known to have a critical role in neurodevelopment, but these recent findings indicate that it also contributes to both cognitive functions in the adult brain and human mental disorders characterized by intellectual disability. In this review, we provide a brief overview of the BAF complexes, introduce recent research findings that link their functions to memory formation, and speculate on the yet-unknown molecular mechanisms that may be relevant to these processes.
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Affiliation(s)
- Kwang-Yeon Choi
- Department of Biological Sciences, KAIST Institute for the BioCentury (KIB), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Miran Yoo
- Department of Biological Sciences, KAIST Institute for the BioCentury (KIB), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jin-Hee Han
- Department of Biological Sciences, KAIST Institute for the BioCentury (KIB), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
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Fukuchi M, Nakashima F, Tabuchi A, Shimotori M, Tatsumi S, Okuno H, Bito H, Tsuda M. Class I histone deacetylase-mediated repression of the proximal promoter of the activity-regulated cytoskeleton-associated protein gene regulates its response to brain-derived neurotrophic factor. J Biol Chem 2015; 290:6825-36. [PMID: 25623071 DOI: 10.1074/jbc.m114.617258] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We examined the transcriptional regulation of the activity-regulated cytoskeleton-associated protein gene (Arc), focusing on BDNF-induced Arc expression in cultured rat cortical cells. Although the synaptic activity-responsive element (SARE), located -7 kbp upstream of the Arc transcription start site, responded to NMDA, BDNF, or FGF2, the proximal region of the promoter (Arc/-1679) was activated by BDNF or FGF2, but not by NMDA, suggesting the presence of at least two distinct Arc promoter regions, distal and proximal, that respond to extracellular stimuli. Specificity protein 4 (SP4) and early growth response 1 (EGR1) controlled Arc/-1679 transcriptional activity via the region encompassing -169 to -37 of the Arc promoter. We found that trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor, significantly enhanced the inductive effects of BDNF or FGF2, but not those of NMDA on Arc expression. Inhibitors of class I/IIb HDACs, SAHA, and class I HDACs, MS-275, but not of class II HDACs, MC1568, enhanced BDNF-induced Arc expression. The enhancing effect of TSA was mediated by the region from -1027 to -1000 bp, to which serum response factor (SRF) and HDAC1 bound. The binding of HDAC1 to this region was reduced by TSA. Thus, Arc expression was suppressed by class I HDAC-mediated mechanisms via chromatin modification of the proximal promoter whereas the inhibition of HDAC allowed Arc expression to be markedly enhanced in response to BDNF or FGF2. These results contribute to our understanding of the physiological role of Arc expression in neuronal functions such as memory consolidation.
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Affiliation(s)
- Mamoru Fukuchi
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Fukumi Nakashima
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Akiko Tabuchi
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Masataka Shimotori
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Saori Tatsumi
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Hiroyuki Okuno
- the Department of Neurochemistry, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Haruhiko Bito
- the Department of Neurochemistry, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaaki Tsuda
- From the Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
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Couthouis J, Raphael AR, Daneshjou R, Gitler AD. Targeted exon capture and sequencing in sporadic amyotrophic lateral sclerosis. PLoS Genet 2014; 10:e1004704. [PMID: 25299611 PMCID: PMC4191946 DOI: 10.1371/journal.pgen.1004704] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/25/2014] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive degeneration of motor neurons, ultimately leading to paralysis and death. Approximately 10% of ALS cases are familial, with the remaining 90% of cases being sporadic. Genetic studies in familial cases of ALS have been extremely informative in determining the causative mutations behind ALS, especially as the same mutations identified in familial ALS can also cause sporadic disease. However, the cause of ALS in approximately 30% of familial cases and in the majority of sporadic cases remains unknown. Sporadic ALS cases represent an underutilized resource for genetic information about ALS; therefore, we undertook a targeted sequencing approach of 169 known and candidate ALS disease genes in 242 sporadic ALS cases and 129 matched controls to try to identify novel variants linked to ALS. We found a significant enrichment in novel and rare variants in cases versus controls, indicating that we are likely identifying disease associated mutations. This study highlights the utility of next generation sequencing techniques combined with functional studies and rare variant analysis tools to provide insight into the genetic etiology of a heterogeneous sporadic disease. Amyotrophic lateral sclerosis (ALS), also known as Charcot disease or Lou Gehrig's disease, is one of the most common neuromuscular diseases worldwide. This disease is characterized by a progressive degeneration of motor neurons, leading to patient death within a few years after onset. Despite the fact that most ALS cases are sporadic, most of the ALS genetic studies have focused on familial forms, leading to the genetic determination of cause for 70% of cases of familial ALS but for only 10% of sporadic ALS cases. This, coupled with the dearth of families available for study, suggests that researchers should begin tapping into the relatively untouched reservoir of available sporadic samples to identify novel genetic causes of sporadic ALS. Here we take advantage of high-throughput target sequencing techniques to test four different hypotheses about the genetic causes of ALS in sporadic ALS and uncover new candidate genes and pathways implicated in ALS.
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Affiliation(s)
- Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alya R. Raphael
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Roxana Daneshjou
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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Abstract
Dendritic arborization is one of the key determinants of precise circuits for information processing in neurons. Unraveling the molecular mechanisms underlying dendrite morphogenesis is critical to understanding the establishment of neuronal connections. Here, using gain- and loss-of-function approaches, we defined the chromodomain protein and transcription corepressor chromodomain Y-like (CDYL) protein as a negative regulator of dendrite morphogenesis in rat/mouse hippocampal neurons both in vitro and in vivo. Overexpressing CDYL decreased, whereas knocking it down increased, the dendritic complexity of the primary cultured rat neurons. High-throughput DNA microarray screening identified a number of CDYL downstream target genes, including the brain-derived neurotrophic factor (BDNF). Knock-down of CDYL in neuronal cells led to increased expression of BDNF, which is primarily responsible for CDYL's effects on dendrite patterns. Mechanistically, CDYL interacts with EZH2, the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), directly and recruits the H3K27 methyltransferase activity to the promoter region of the BDNF gene. In doing so, CDYL and EZH2 coordinately restrict dendrite morphogenesis in an interdependent manner. Finally, we found that neural activity increased dendritic complexity through degradation of CDYL protein to unleash its inhibition on BDNF. These results link, for the first time, the epigenetic regulators CDYL and EZH2 to dendrite morphogenesis and might shed new light on our understanding of the regulation of the neurodevelopment.
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