1
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Sharma S, Houfani AA, Foster LJ. Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity. J Biomed Sci 2024; 31:52. [PMID: 38745221 PMCID: PMC11092263 DOI: 10.1186/s12929-024-01038-1] [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: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Recent advances in uncovering the mysteries of the human genome suggest that long non-coding RNAs (lncRNAs) are important regulatory components. Although lncRNAs are known to affect gene transcription, their mechanisms and biological implications are still unclear. Experimental research has shown that lncRNA synthesis, subcellular localization, and interactions with macromolecules like DNA, other RNAs, or proteins can all have an impact on gene expression in various biological processes. In this review, we highlight and discuss the major mechanisms through which lncRNAs function as master regulators of the human genome. Specifically, the objective of our review is to examine how lncRNAs regulate different processes like cell division, cell cycle, and immune responses, and unravel their roles in maintaining genomic architecture and integrity.
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Affiliation(s)
- Siddhant Sharma
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada.
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2
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Xie J, Chen S, Bopassa JC, Banerjee S. Drosophila tubulin polymerization promoting protein mutants reveal pathological correlates relevant to human Parkinson's disease. Sci Rep 2021; 11:13614. [PMID: 34193896 PMCID: PMC8245532 DOI: 10.1038/s41598-021-92738-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder with no known cure. PD is characterized by locomotion deficits, nigrostriatal dopaminergic neuronal loss, mitochondrial dysfunctions and formation of α-Synuclein aggregates. A well-conserved and less understood family of Tubulin Polymerization Promoting Proteins (TPPP) is also implicated in PD and related disorders, where TPPP exists in pathological aggregates in neurons in patient brains. However, there are no in vivo studies on mammalian TPPP to understand the genetics and neuropathology linking TPPP aggregation or neurotoxicity to PD. Recently, we discovered the only Drosophila homolog of human TPPP named Ringmaker (Ringer). Here, we report that adult ringer mutants display progressive locomotor disabilities, reduced lifespan and neurodegeneration. Importantly, our findings reveal that Ringer is associated with mitochondria and ringer mutants have mitochondrial structural damage and dysfunctions. Adult ringer mutants also display progressive loss of dopaminergic neurons. Together, these phenotypes of ringer mutants recapitulate some of the salient features of human PD patients, thus allowing us to utilize ringer mutants as a fly model relevant to PD, and further explore its genetic and molecular underpinnings to gain insights into the role of human TPPP in PD.
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Affiliation(s)
- Jing Xie
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Shuting Chen
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Jean C Bopassa
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Swati Banerjee
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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3
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Orosz F. Truncated TPPP - An Endopterygota-specific protein. Heliyon 2021; 7:e07135. [PMID: 34136696 PMCID: PMC8180608 DOI: 10.1016/j.heliyon.2021.e07135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/18/2021] [Accepted: 05/19/2021] [Indexed: 11/26/2022] Open
Abstract
TPPP proteins exhibiting microtubule stabilizing function constitute a eukaryotic protein superfamily, characterized by the presence of the p25alpha domain of various lengths. Vertebrate species possess three TPPP paralogs; all of them possess a full-length p25alpha domain of 160-170 amino acids and are encoded by three exons. Species of Endopterygota (Holometabola) have, besides a full-size TPPP ortholog, a protein with a truncated p25alpha domain as well, where the last coding exon, responsible for microtubule binding, is missing. It is not the result of an alternative splicing but is coded by another gene. In Drosophila melanogaster, they are named as CG45057 (long-type) and CG6709 (truncated). The truncated protein has been found in the Endopterygota orders Diptera, Coleoptera, Hymenoptera, Lepidoptera and Raphidioptera. In Lepidoptera, in several superfamilies (Gelechioidea, Bombycoidea, Noctuoidea, Pyraloidea) two paralogs of the truncated TPPP occur. Truncated orthologs (CG6709) were not found in other insects or in arthropods and are absent in any other organism, as well, while the long-type TPPPs (CG45057 orthologs) occur commonly in all animals. Thus it seems that CG6709 orthologs occur only in insects undergoing on metamorphosis.
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Affiliation(s)
- Ferenc Orosz
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
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4
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Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F. A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division. Nat Commun 2020; 11:1851. [PMID: 32296040 PMCID: PMC7160116 DOI: 10.1038/s41467-020-14978-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/09/2020] [Indexed: 01/21/2023] Open
Abstract
Genome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. With a high-content RNAi imaging screen targeting more than 2,000 human lncRNAs, we identify numerous lncRNAs involved in key steps of cell division such as chromosome segregation, mitotic duration and cytokinesis. Here, we provide evidence that the chromatin-associated lncRNA, linc00899, leads to robust mitotic delay upon its depletion in multiple cell types. We perform transcriptome analysis of linc00899-depleted cells and identify the neuronal microtubule-binding protein, TPPP/p25, as a target of linc00899. We further show that linc00899 binds TPPP/p25 and suppresses its transcription. In cells depleted of linc00899, upregulation of TPPP/p25 alters microtubule dynamics and delays mitosis. Overall, our comprehensive screen uncovers several lncRNAs involved in genome stability and reveals a lncRNA that controls microtubule behaviour with functional implications beyond cell division.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Genentech, Inc., South San Francisco, CA, USA
| | - Patrice Mascalchi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- DRVision Technologies, Bordeaux, France
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Jasmin Mangei
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexis R Barr
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC London Institute of Medical Sciences (LMS), Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Vicky Bousgouni
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Chris Bakal
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
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5
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Oláh J, Lehotzky A, Szunyogh S, Szénási T, Orosz F, Ovádi J. Microtubule-Associated Proteins with Regulatory Functions by Day and Pathological Potency at Night. Cells 2020; 9:E357. [PMID: 32033023 PMCID: PMC7072251 DOI: 10.3390/cells9020357] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 12/23/2022] Open
Abstract
The sensing, integrating, and coordinating features of the eukaryotic cells are achieved by the complex ultrastructural arrays and multifarious functions of the cytoskeleton, including the microtubule network. Microtubules play crucial roles achieved by their decoration with proteins/enzymes as well as by posttranslational modifications. This review focuses on the Tubulin Polymerization Promoting Protein (TPPP/p25), a new microtubule associated protein, on its "regulatory functions by day and pathological functions at night". Physiologically, the moonlighting TPPP/p25 modulates the dynamics and stability of the microtubule network by bundling microtubules and enhancing the tubulin acetylation due to the inhibition of tubulin deacetylases. The optimal endogenous TPPP/p25 level is crucial for its physiological functions, to the differentiation of oligodendrocytes, which are the major constituents of the myelin sheath. Pathologically, TPPP/p25 forms toxic oligomers/aggregates with α-synuclein in neurons and oligodendrocytes in Parkinson's disease and Multiple System Atrophy, respectively; and their complex is a potential therapeutic drug target. TPPP/p25-derived microtubule hyperacetylation counteracts uncontrolled cell division. All these issues reveal the anti-mitotic and α-synuclein aggregation-promoting potency of TPPP/p25, consistent with the finding that Parkinson's disease patients have reduced risk for certain cancers.
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Affiliation(s)
| | | | | | | | | | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary; (J.O.); (A.L.); (S.S.); (T.S.); (F.O.)
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6
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Vargas EJM, Matamoros AJ, Qiu J, Jan CH, Wang Q, Gorczyca D, Han TW, Weissman JS, Jan YN, Banerjee S, Song Y. The microtubule regulator ringer functions downstream from the RNA repair/splicing pathway to promote axon regeneration. Genes Dev 2020; 34:194-208. [PMID: 31919191 PMCID: PMC7000917 DOI: 10.1101/gad.331330.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]
Abstract
In this study, Vargas et al. set out to elucidate the downstream effectors of the Rtca-mediated RNA repair/splicing pathway. Using genome-wide transcriptome analysis, the authors demonstrate that the microtubule-associated protein (MAP) tubulin polymerization-promoting protein (TPPP) ringer functions downstream from and is suppressed by Rtca via Xbp1-dependent transcription. Ringer cell-autonomously promotes axon regeneration in the peripheral and central nervous system. Promoting axon regeneration in the central and peripheral nervous system is of clinical importance in neural injury and neurodegenerative diseases. Both pro- and antiregeneration factors are being identified. We previously reported that the Rtca mediated RNA repair/splicing pathway restricts axon regeneration by inhibiting the nonconventional splicing of Xbp1 mRNA under cellular stress. However, the downstream effectors remain unknown. Here, through transcriptome profiling, we show that the tubulin polymerization-promoting protein (TPPP) ringmaker/ringer is dramatically increased in Rtca-deficient Drosophila sensory neurons, which is dependent on Xbp1. Ringer is expressed in sensory neurons before and after injury, and is cell-autonomously required for axon regeneration. While loss of ringer abolishes the regeneration enhancement in Rtca mutants, its overexpression is sufficient to promote regeneration both in the peripheral and central nervous system. Ringer maintains microtubule stability/dynamics with the microtubule-associated protein futsch/MAP1B, which is also required for axon regeneration. Furthermore, ringer lies downstream from and is negatively regulated by the microtubule-associated deacetylase HDAC6, which functions as a regeneration inhibitor. Taken together, our findings suggest that ringer acts as a hub for microtubule regulators that relays cellular status information, such as cellular stress, to the integrity of microtubules in order to instruct neuroregeneration.
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Affiliation(s)
- Ernest J Monahan Vargas
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew J Matamoros
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jingyun Qiu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Calvin H Jan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David Gorczyca
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Tina W Han
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Swati Banerjee
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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7
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Shi Q, Lin YQ, Saliba A, Xie J, Neely GG, Banerjee S. Tubulin Polymerization Promoting Protein, Ringmaker, and MAP1B Homolog Futsch Coordinate Microtubule Organization and Synaptic Growth. Front Cell Neurosci 2019; 13:192. [PMID: 31156389 PMCID: PMC6529516 DOI: 10.3389/fncel.2019.00192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Drosophila Ringmaker (Ringer) is homologous to the human Tubulin Polymerization Promoting Proteins (TPPPs) that are implicated in the stabilization and bundling of microtubules (MTs) that are particularly important for neurons and are also implicated in synaptic organization and plasticity. No in vivo functional data exist that have addressed the role of TPPP in synapse organization in any system. Here, we present the phenotypic and functional characterization of ringer mutants during Drosophila larval neuromuscular junction (NMJ) synaptic development. ringer mutants show reduced synaptic growth and transmission and display phenotypic similarities and genetic interactions with the Drosophila homolog of vertebrate Microtubule Associated Protein (MAP)1B, futsch. Immunohistochemical and biochemical analyses show that individual and combined loss of Ringer and Futsch cause a significant reduction in MT loops at the NMJs and reduced acetylated-tubulin levels. Presynaptic over-expression of Ringer and Futsch causes elevated levels of acetylated-tubulin and significant increase in NMJ MT loops. These results indicate that Ringer and Futsch regulate synaptic MT organization in addition to synaptic growth. Together our findings may inform studies on the close mammalian homolog, TPPP, and provide insights into the role of MTs and associated proteins in synapse growth and organization.
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Affiliation(s)
- Qian Shi
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health, San Antonio, TX, United States
| | - Yong Qi Lin
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Afaf Saliba
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health, San Antonio, TX, United States
| | - Jing Xie
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health, San Antonio, TX, United States
- Xiangya School of Medicine, Central South University, Changsha, China
| | - G. Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Swati Banerjee
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health, San Antonio, TX, United States
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8
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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