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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 PMCID: PMC11361640 DOI: 10.1242/dev.202891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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2
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Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
The intricate landscape of cellular processes governing gene transcription, chromatin organization, and genome stability is a fascinating field of study. A key player in maintaining this delicate equilibrium is the cohesin complex, a molecular machine with multifaceted roles. This review presents an in-depth exploration of these intricate connections and their significant impact on various human diseases.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
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3
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Gruca-Stryjak K, Doda-Nowak E, Dzierla J, Wróbel K, Szymankiewicz-Bręborowicz M, Mazela J. Advancing the Clinical and Molecular Understanding of Cornelia de Lange Syndrome: A Multidisciplinary Pediatric Case Series and Review of the Literature. J Clin Med 2024; 13:2423. [PMID: 38673696 PMCID: PMC11050916 DOI: 10.3390/jcm13082423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex genetic disorder with distinct facial features, growth limitations, and limb anomalies. Its broad clinical spectrum presents significant challenges in pediatric diagnosis and management. Due to cohesin complex mutations, the disorder's variable presentation requires extensive research to refine care and improve outcomes. This article provides a case series review of pediatric CdLS patients alongside a comprehensive literature review, exploring clinical variability and the relationship between genotypic changes and phenotypic outcomes. It also discusses the evolution of diagnostic and therapeutic techniques, emphasizing innovations in genetic testing, including detecting mosaicism and novel genetic variations. The aim is to synthesize case studies with current research to advance our understanding of CdLS and the effectiveness of management strategies in pediatric healthcare. This work highlights the need for an integrated, evidence-based approach to diagnosis and treatment. It aims to fill existing research gaps and advocate for holistic care protocols and tailored treatment plans for CdLS patients, ultimately improving their quality of life.
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Affiliation(s)
- Karolina Gruca-Stryjak
- Department of Perinatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
- Department of Obstetrics and Gynecology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland
- Centers for Medical Genetics Diagnostyka GENESIS, 60-406 Poznan, Poland
| | - Emilia Doda-Nowak
- Faculty of Medicine, University of Medical Sciences, 61-701 Poznan, Poland (J.D.)
| | - Julia Dzierla
- Faculty of Medicine, University of Medical Sciences, 61-701 Poznan, Poland (J.D.)
| | - Karolina Wróbel
- Department of Neonatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
| | | | - Jan Mazela
- Department of Neonatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
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4
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Boulet F, Odelin G, Harrington A, Moore-Morris T. Nipbl Haploinsufficiency Leads to Delayed Outflow Tract Septation and Aortic Valve Thickening. Int J Mol Sci 2023; 24:15564. [PMID: 37958548 PMCID: PMC10648932 DOI: 10.3390/ijms242115564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Cornelia de Lange Syndrome (CdLS) patients, who frequently carry a mutation in NIPBL, present an increased incidence of outflow tract (OFT)-related congenital heart defects (CHDs). Nipbl+/- mice recapitulate a number of phenotypic traits of CdLS patients, including a small body size and cardiac defects, but no study has specifically focused on the valves. Here, we show that adult Nipbl+/- mice present aortic valve thickening, a condition that has been associated with stenosis. During development, we observed that OFT septation and neural crest cell condensation was delayed in Nipbl+/- embryos. However, we did not observe defects in the deployment of the main lineages contributing to the semilunar valves. Indeed, endocardial endothelial-to-mesenchymal transition (EndMT), analysed via outflow tract explants, and neural crest migration, analysed via genetic lineage tracing, did not significantly differ in Nipbl+/- mice and their wild-type littermates. Our study provides the first direct evidence for valve formation defects in Nipbl+/- mice and points to specific developmental defects as an origin for valve disease in patients.
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Affiliation(s)
- Fanny Boulet
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34094 Montpellier, France
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Gaelle Odelin
- Aix Marseille University, INSERM, MMG, 13005 Marseille, France
| | - Alenca Harrington
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34094 Montpellier, France
| | - Thomas Moore-Morris
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34094 Montpellier, France
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5
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Alonso-Gil D, Losada A. NIPBL and cohesin: new take on a classic tale. Trends Cell Biol 2023; 33:860-871. [PMID: 37062615 DOI: 10.1016/j.tcb.2023.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
Cohesin folds the genome in dynamic chromatin loops and holds the sister chromatids together. NIPBLScc2 is currently considered the cohesin loader, a role that may need reevaluation. NIPBL activates the cohesin ATPase, which is required for topological entrapment of sister DNAs and to fuel DNA loop extrusion, but is not required for chromatin association. Mechanistic dissection of these processes suggests that both NIPBL and the cohesin STAG subunit bind DNA. NIPBL also regulates conformational switches of the complex. Interactions of NIPBL with chromatin factors, including remodelers, replication proteins, and the transcriptional machinery, affect cohesin loading and distribution. Here, we discuss recent research addressing how NIPBL modulates cohesin activities and how its mutation causes a developmental disorder, Cornelia de Lange Syndrome (CdLS).
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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Kean CM, Tracy CJ, Mitra A, Rahat B, Van Winkle MT, Gebert CM, Noeker JA, Calof AL, Lander AD, Kassis JA, Pfeifer K. Decreasing Wapl dosage partially corrects embryonic growth and brain transcriptome phenotypes in Nipbl+/- embryos. SCIENCE ADVANCES 2022; 8:eadd4136. [PMID: 36449618 DOI: 10.1101/2022.05.31.493745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cohesin rings interact with DNA and modulate the expression of thousands of genes. NIPBL loads cohesin onto chromosomes, and WAPL takes it off. Haploinsufficiency for NIPBL causes a developmental disorder, Cornelia de Lange syndrome (CdLS), that is modeled by Nipbl+/- mice. Mutations in WAPL have not been shown to cause disease or gene expression changes in mammals. Here, we show dysregulation of >1000 genes in WaplΔ/+ embryonic mouse brain. The patterns of dysregulation are highly similar in Wapl and Nipbl heterozygotes, suggesting that Wapl mutations may also cause human disease. Since WAPL and NIPBL have opposite effects on cohesin's association with DNA, we asked whether decreasing Wapl dosage could correct phenotypes seen in Nipbl+/- mice. Gene expression and embryonic growth are partially corrected, but perinatal lethality is not. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.
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Affiliation(s)
- Connor M Kean
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J Tracy
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Apratim Mitra
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Beenish Rahat
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Matthew T Van Winkle
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Claudia M Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jacob A Noeker
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anne L Calof
- Department of Anatomy and Neurobiology, University of California School of Medicine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Judith A Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Kean CM, Tracy CJ, Mitra A, Rahat B, Van Winkle MT, Gebert CM, Noeker JA, Calof AL, Lander AD, Kassis JA, Pfeifer K. Decreasing Wapl dosage partially corrects embryonic growth and brain transcriptome phenotypes in Nipbl+/- embryos. SCIENCE ADVANCES 2022; 8:eadd4136. [PMID: 36449618 PMCID: PMC9710879 DOI: 10.1126/sciadv.add4136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Cohesin rings interact with DNA and modulate the expression of thousands of genes. NIPBL loads cohesin onto chromosomes, and WAPL takes it off. Haploinsufficiency for NIPBL causes a developmental disorder, Cornelia de Lange syndrome (CdLS), that is modeled by Nipbl+/- mice. Mutations in WAPL have not been shown to cause disease or gene expression changes in mammals. Here, we show dysregulation of >1000 genes in WaplΔ/+ embryonic mouse brain. The patterns of dysregulation are highly similar in Wapl and Nipbl heterozygotes, suggesting that Wapl mutations may also cause human disease. Since WAPL and NIPBL have opposite effects on cohesin's association with DNA, we asked whether decreasing Wapl dosage could correct phenotypes seen in Nipbl+/- mice. Gene expression and embryonic growth are partially corrected, but perinatal lethality is not. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.
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Affiliation(s)
- Connor M. Kean
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J. Tracy
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Apratim Mitra
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Beenish Rahat
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Matthew T. Van Winkle
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Claudia M. Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jacob A. Noeker
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anne L. Calof
- Department of Anatomy and Neurobiology, University of California School of Medicine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Judith A. Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Umbach A, Maule G, Kheir E, Cutarelli A, Foglia M, Guarrera L, Fava LL, Conti L, Garattini E, Terao M, Cereseto A. Generation of corrected hiPSC clones from a Cornelia de Lange Syndrome (CdLS) patient through CRISPR-Cas-based technology. Stem Cell Res Ther 2022; 13:440. [PMID: 36056433 PMCID: PMC9438151 DOI: 10.1186/s13287-022-03135-0] [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: 04/07/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare multisystem genetic disorder which is caused by genetic defects involving the Nipped-B-like protein (NIPBL) gene in the majority of clinical cases (60–70%). Currently, there are no specific cures available for CdLS and clinical management is needed for life. Disease models are highly needed to find a cure. Among therapeutic possibilities are genome editing strategies based on CRISPR-Cas technology. Methods A comparative analysis was performed to test the most recent CRISPR-Cas technologies comprising base- and prime-editors which introduce modifications without DNA cleavages and compared with sequence substitution approaches through homology directed repair (HDR) induced by Cas9 nuclease activity. The HDR method that was found more efficient was applied to repair a CdLS-causing mutation in the NIPBL gene. Human-induced pluripotent stem cells (hiPSCs) derived from a CdLS patient carrying the c.5483G > A mutation in the NIPBL were modified through HDR to generate isogenic corrected clones. Results This study reports an efficient method to repair the NIPBL gene through HDR mediated by CRISPR-Cas and induced with a compound (NU7441) inhibiting non-homologous end joining (NHEJ) repair. This sequence repair method allowed the generation of isogenic wild-type hiPSCs clones with regular karyotype and preserved pluripotency. Conclusions CdLS cellular models were generated which will facilitate the investigation of the disease molecular determinants and the identification of therapeutic targets. In particular, the hiPSC-based cellular models offer the paramount advantage to study the tissue differentiation stages which are altered in the CdLS clinical development. Importantly, the hiPSCs that were generated are isogenic thus providing the most controlled experimental set up between wild-type and mutated conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03135-0.
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Affiliation(s)
- Alessandro Umbach
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Giulia Maule
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Eyemen Kheir
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | | | - Marika Foglia
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca L Fava
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Cereseto
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy.
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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Pileggi S, La Vecchia M, Colombo EA, Fontana L, Colapietro P, Rovina D, Morotti A, Tabano S, Porta G, Alcalay M, Gervasini C, Miozzo M, Sirchia SM. Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/ IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines. Biomolecules 2021; 11:1622. [PMID: 34827619 PMCID: PMC8615450 DOI: 10.3390/biom11111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Elisa Adele Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Annamaria Morotti
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giovanni Porta
- Centro di Medicina Genomica, Department of Medicine and Surgery, Università degli Studi dell’Insubria, 21100 Varese, Italy;
| | - Myriam Alcalay
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
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11
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García-Gutiérrez P, García-Domínguez M. BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome. Front Mol Biosci 2021; 8:709232. [PMID: 34386522 PMCID: PMC8353280 DOI: 10.3389/fmolb.2021.709232] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental syndrome with complex multisystem phenotypic features. It has been traditionally considered a cohesinopathy together with other phenotypically related diseases because of their association with mutations in subunits of the cohesin complex. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably and, although their precise molecular mechanisms are not well defined yet, the potential pathomechanisms underlying these diverse developmental defects have been theoretically linked to alterations of the cohesin complex function. The cohesin complex plays a critical role in sister chromatid cohesion, but this function is not affected in CdLS. In the last decades, a non-cohesion-related function of this complex on transcriptional regulation has been well established and CdLS pathoetiology has been recently associated to gene expression deregulation. Up to 70% of CdLS cases are linked to mutations in the cohesin-loading factor NIPBL, which has been shown to play a prominent function on chromatin architecture and transcriptional regulation. Therefore, it has been suggested that CdLS can be considered a transcriptomopathy. Actually, CdLS-like phenotypes have been associated to mutations in chromatin-associated proteins, as KMT2A, AFF4, EP300, TAF6, SETD5, SMARCB1, MAU2, ZMYND11, MED13L, PHIP, ARID1B, NAA10, BRD4 or ANKRD11, most of which have no known direct association with cohesin. In the case of BRD4, a critical highly investigated transcriptional coregulator, an interaction with NIPBL has been recently revealed, providing evidence on their cooperation in transcriptional regulation of developmentally important genes. This new finding reinforces the notion of an altered gene expression program during development as the major etiological basis for CdLS. In this review, we intend to integrate the recent available evidence on the molecular mechanisms underlying the clinical manifestations of CdLS, highlighting data that favors a transcription-centered framework, which support the idea that CdLS could be conceptualized as a transcriptomopathy.
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Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
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12
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Selicorni A, Mariani M, Lettieri A, Massa V. Cornelia de Lange Syndrome: From a Disease to a Broader Spectrum. Genes (Basel) 2021; 12:1075. [PMID: 34356091 PMCID: PMC8307173 DOI: 10.3390/genes12071075] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a genetic disease that exemplifies the evolution of knowledge in the field of rare genetic disorders. Originally described as a unique pattern of major and minor anomalies, over time this syndrome has been shown to be characterized by a significant variability of clinical expression. By increasing the number of patients described, knowledge of the natural history of the condition has been enriched with the demonstration of the relative frequency of various potential comorbidities. Since 2006, the discovery of CdLS's molecular basis has shown an equally vast genetic heterogeneity linked to the presence of variants in genes encoding for the cohesin complex pathway. The most recent clinical-genetic data led to the classification of the "original syndrome" into a "clinical spectrum" that foresees the presence of classic patients, of non-classic forms, and of conditions that show a modest phenotypic overlapping with the original disease. Finally, the knowledge of the molecular basis of the disease has allowed the development of basic research projects that could lay the foundations for the development of possible innovative pharmacological treatments.
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Affiliation(s)
- Angelo Selicorni
- Mariani Foundation Center for Fragile Child, Pediatric Unit ASST Lariana, 22100 Como, Italy;
| | - Milena Mariani
- Mariani Foundation Center for Fragile Child, Pediatric Unit ASST Lariana, 22100 Como, Italy;
| | - Antonella Lettieri
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (A.L.); (V.M.)
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (A.L.); (V.M.)
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy
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13
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Gu W, Wang L, Gu R, Ouyang H, Bao B, Zheng L, Xu B. Defects of cohesin loader lead to bone dysplasia associated with transcriptional disturbance. J Cell Physiol 2021; 236:8208-8225. [PMID: 34170011 DOI: 10.1002/jcp.30491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023]
Abstract
Cohesin loader nipped-B-like protein (Nipbl) is increasingly recognized for its important role in development and cancer. Cornelia de Lange Syndrome (CdLS), mostly caused by heterozygous mutations of Nipbl, is an autosomal dominant disease characterized by multiorgan malformations. However, the regulatory role and underlying mechanism of Nipbl in skeletal development remain largely elusive. In this study, we constructed a Nipbl-a Cas9-knockout (KO) zebrafish, which displayed severe retardation of global growth and skeletal development. Deficiency of Nipbl remarkably compromised cell growth and survival, and osteogenic differentiation of mammalian osteoblast precursors. Furthermore, Nipbl depletion impaired the cell cycle process, and caused DNA damage accumulation and cellular senescence. In addition, nucleolar fibrillarin expression, global rRNA biogenesis, and protein translation were defective in the Nipbl-depleted osteoblast precursors. Interestingly, an integrated stress response inhibitor (ISRIB), partially rescued Nipbl depletion-induced cellular defects in proliferation and apoptosis, osteogenesis, and nucleolar function. Simultaneously, we performed transcriptome analysis of Nipbl deficiency on human neural crest cells and mouse embryonic fibroblasts in combination with Nipbl ChIP-Seq. We found that Nipbl deficiency caused thousands of differentially expressed genes including some important genes in bone and cartilage development. In conclusion, Nipbl deficiency compromised skeleton development through impairing osteoblast precursor cell proliferation and survival, and osteogenic differentiation, and also disturbing the expression of some osteogenesis-regulatory genes. Our study elucidated that Nipbl played a pivotal role in skeleton development, and supported the fact that treatment of ISRIB may provide an early intervention strategy to alleviate the bone dysplasia of CdLS.
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Affiliation(s)
- Weihuai Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lihong Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renjie Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huiya Ouyang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baicheng Bao
- Hospital of Stomatology, Orthodontic Department, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, Department of Pediatric Dentistry, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Baoshan Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
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14
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Weiss FD, Calderon L, Wang YF, Georgieva R, Guo Y, Cvetesic N, Kaur M, Dharmalingam G, Krantz ID, Lenhard B, Fisher AG, Merkenschlager M. Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin. Nat Commun 2021; 12:2919. [PMID: 34006846 PMCID: PMC8131595 DOI: 10.1038/s41467-021-23141-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet unexplained feature of CdLS. We characterize the transcriptional profile of cortical neurons from CdLS patients and find deregulation of hundreds of genes enriched for neuronal functions related to synaptic transmission, signalling processes, learning and behaviour. Inducible proteolytic cleavage of cohesin disrupts 3D genome organization and transcriptional control in post-mitotic cortical mouse neurons, demonstrating that cohesin is continuously required for neuronal gene expression. The genes affected by acute depletion of cohesin belong to similar gene ontology classes and show significant numerical overlap with genes deregulated in CdLS. Interestingly, reconstitution of cohesin function largely rescues altered gene expression, including the expression of genes deregulated in CdLS.
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Affiliation(s)
- Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Lesly Calderon
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Radina Georgieva
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nevena Cvetesic
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Maninder Kaur
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ian D Krantz
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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15
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George RM, Firulli AB. Epigenetics and Heart Development. Front Cell Dev Biol 2021; 9:637996. [PMID: 34026751 PMCID: PMC8136428 DOI: 10.3389/fcell.2021.637996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/26/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenetic control of gene expression during cardiac development and disease has been a topic of intense research in recent years. Advances in experimental methods to study DNA accessibility, transcription factor occupancy, and chromatin conformation capture technologies have helped identify regions of chromatin structure that play a role in regulating access of transcription factors to the promoter elements of genes, thereby modulating expression. These chromatin structures facilitate enhancer contacts across large genomic distances and function to insulate genes from cis-regulatory elements that lie outside the boundaries for the gene of interest. Changes in transcription factor occupancy due to changes in chromatin accessibility have been implicated in congenital heart disease. However, the factors controlling this process and their role in changing gene expression during development or disease remain unclear. In this review, we focus on recent advances in the understanding of epigenetic factors controlling cardiac morphogenesis and their role in diseases.
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Affiliation(s)
- Rajani M George
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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16
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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17
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Spreafico M, Mangano E, Mazzola M, Consolandi C, Bordoni R, Battaglia C, Bicciato S, Marozzi A, Pistocchi A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. Int J Mol Sci 2020; 21:E9719. [PMID: 33352756 PMCID: PMC7766774 DOI: 10.3390/ijms21249719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.
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Affiliation(s)
- Marco Spreafico
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Eleonora Mangano
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Mara Mazzola
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Roberta Bordoni
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Cristina Battaglia
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio-Emilia, Via G. Campi 287, 41125 Modena, Italy;
| | - Anna Marozzi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Anna Pistocchi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
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18
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Chin CV, Antony J, Ketharnathan S, Labudina A, Gimenez G, Parsons KM, He J, George AJ, Pallotta MM, Musio A, Braithwaite A, Guilford P, Hannan RD, Horsfield JA. Cohesin mutations are synthetic lethal with stimulation of WNT signaling. eLife 2020; 9:e61405. [PMID: 33284104 PMCID: PMC7746233 DOI: 10.7554/elife.61405] [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: 07/24/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding subunits of the cohesin complex are common in several cancers, but may also expose druggable vulnerabilities. We generated isogenic MCF10A cell lines with deletion mutations of genes encoding cohesin subunits SMC3, RAD21, and STAG2 and screened for synthetic lethality with 3009 FDA-approved compounds. The screen identified several compounds that interfere with transcription, DNA damage repair and the cell cycle. Unexpectedly, one of the top 'hits' was a GSK3 inhibitor, an agonist of Wnt signaling. We show that sensitivity to GSK3 inhibition is likely due to stabilization of β-catenin in cohesin-mutant cells, and that Wnt-responsive gene expression is highly sensitized in STAG2-mutant CMK leukemia cells. Moreover, Wnt activity is enhanced in zebrafish mutant for cohesin subunits stag2b and rad21. Our results suggest that cohesin mutations could progress oncogenesis by enhancing Wnt signaling, and that targeting the Wnt pathway may represent a novel therapeutic strategy for cohesin-mutant cancers.
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Affiliation(s)
- Chue Vin Chin
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Jisha Antony
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Sarada Ketharnathan
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Anastasia Labudina
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Gregory Gimenez
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Kate M Parsons
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Jinshu He
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Amee J George
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Maria Michela Pallotta
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antony Braithwaite
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
| | - Parry Guilford
- Department of Biochemistry, University of OtagoDunedinNew Zealand
| | - Ross D Hannan
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
- Department of Biochemistry and Molecular Biology, University of MelbourneParkvilleAustralia
- Sir Peter MacCallum Department of Oncology, University of MelbourneParkvilleAustralia
- School of Biomedical Sciences, University of QueenslandSt LuciaAustralia
| | - Julia A Horsfield
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
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19
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Transcriptome Analysis of iPSC-Derived Neurons from Rubinstein-Taybi Patients Reveals Deficits in Neuronal Differentiation. Mol Neurobiol 2020; 57:3685-3701. [PMID: 32562237 PMCID: PMC7399686 DOI: 10.1007/s12035-020-01983-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare multisystem developmental disorder with moderate to severe intellectual disability caused by heterozygous mutations of either CREBBP or EP300 genes encoding CBP/p300 chromatin regulators. We explored the gene programs and processes underlying the morphological and functional alterations shown by iPSC-derived neurons modeling RSTS to bridge the molecular changes resulting from defective CBP/p300 to cognitive impairment. By global transcriptome analysis, we compared the differentially expressed genes (DEGs) marking the transition from iPSC-derived neural progenitors to cortical neurons (iNeurons) of five RSTS patients carrying private CREBBP/EP300 mutations and manifesting differently graded neurocognitive signs with those of four healthy controls. Our data shows a defective and altered neuroprogenitor to neuron transcriptional program in the cells from RSTS patients. First, transcriptional regulation is weaker in RSTS as less genes than in controls are modulated, including genes of key processes of mature functional neurons, such as those for voltage-gated channels and neurotransmitters and their receptors. Second, regulation is subverted as genes acting at pre-terminal stages of neural differentiation in cell polarity and adhesive functions (members of the cadherin family) and axon extension/guidance (members of the semaphorins and SLIT receptors families) are improperly upregulated. Impairment or delay of RSTS neuronal differentiation program is also evidenced by decreased modulation of the overall number of neural differentiation markers, significantly impacting the initial and final stages of the differentiation cascade. Last, extensive downregulation of genes for RNA/DNA metabolic processes confirms that RSTS is a global transcription disorder, consistent with a syndrome driven by chromatin dysregulation. Interestingly, the morphological and functional alterations we have previously appointed as biomarkers of RSTS iNeurons provide functional support to the herein designed transcriptome profile pointing to key dysregulated neuronal genes as main contributors to patients’ cognitive deficit. The impact of RSTS transcriptome may go beyond RSTS as comparison of dysregulated genes across modeled neurodevelopmental disorders could unveil convergent genes of cognitive impairment.
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20
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Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, van Staveren T, van IJcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Rep 2020; 31:107647. [PMID: 32433956 DOI: 10.1016/j.celrep.2020.107647] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022] Open
Abstract
The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations in NIPBL account for most cases of the rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report a MAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus. Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable for normal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fatal outcome of an out-of-frame single nucleotide duplication in NIPBL, engineered in two different cell lines, alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interact with MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protective against out-of-frame mutations that is potentially relevant for other genetic conditions.
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Affiliation(s)
- Ilaria Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Farah Diab
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Sara Ruiz Gil
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | | | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Riccardo Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Rutger W W Brouwer
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Valerie Dupé
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Juliane Eckhold
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Feliciano Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Wilfred F J van IJcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany.
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands.
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Piché J, Van Vliet PP, Pucéat M, Andelfinger G. The expanding phenotypes of cohesinopathies: one ring to rule them all! Cell Cycle 2019; 18:2828-2848. [PMID: 31516082 PMCID: PMC6791706 DOI: 10.1080/15384101.2019.1658476] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022] Open
Abstract
Preservation and development of life depend on the adequate segregation of sister chromatids during mitosis and meiosis. This process is ensured by the cohesin multi-subunit complex. Mutations in this complex have been associated with an increasing number of diseases, termed cohesinopathies. The best characterized cohesinopathy is Cornelia de Lange syndrome (CdLS), in which intellectual and growth retardations are the main phenotypic manifestations. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably. Novel roles of the cohesin complex have emerged during the past decades, suggesting that important cell cycle regulators exert important biological effects through non-cohesion-related functions and broadening the potential pathomechanisms involved in cohesinopathies. This review focuses on non-cohesion-related functions of the cohesin complex, gene dosage effect, epigenetic regulation and TGF-β in cohesinopathy context, especially in comparison to Chronic Atrial and Intestinal Dysrhythmia (CAID) syndrome, a very distinct cohesinopathy caused by a homozygous Shugoshin-1 (SGO1) mutation (K23E) and characterized by pacemaker failure in both heart (sick sinus syndrome followed by atrial flutter) and gut (chronic intestinal pseudo-obstruction) with no intellectual or growth delay. We discuss the possible impact of SGO1 alterations in human pathologies and the potential impact of the SGO1 K23E mutation in the sinus node and gut development and functions. We suggest that the human phenotypes observed in CdLS, CAID syndrome and other cohesinopathies can inform future studies into the less well-known non-cohesion-related functions of cohesin complex genes. Abbreviations: AD: Alzheimer Disease; AFF4: AF4/FMR2 Family Member 4; ANKRD11: Ankyrin Repeat Domain 11; APC: Anaphase Promoter Complex; ASD: Atrial Septal Defect; ATRX: ATRX Chromatin Remodeler; ATRX: Alpha Thalassemia X-linked intellectual disability syndrome; BIRC5: Baculoviral IAP Repeat Containing 5; BMP: Bone Morphogenetic Protein; BRD4: Bromodomain Containing 4; BUB1: BUB1 Mitotic Checkpoint Serine/Threonine Kinase; CAID: Chronic Atrial and Intestinal Dysrhythmia; CDK1: Cyclin Dependent Kinase 1; CdLS: Cornelia de Lange Syndrome; CHD: Congenital Heart Disease; CHOPS: Cognitive impairment, coarse facies, Heart defects, Obesity, Pulmonary involvement, Short stature, and skeletal dysplasia; CIPO: Chronic Intestinal Pseudo-Obstruction; c-kit: KIT Proto-Oncogene Receptor Tyrosine Kinase; CoATs: Cohesin Acetyltransferases; CTCF: CCCTC-Binding Factor; DDX11: DEAD/H-Box Helicase 11; ERG: Transcriptional Regulator ERG; ESCO2: Establishment of Sister Chromatid Cohesion N-Acetyltransferase 2; GJC1: Gap Junction Protein Gamma 1; H2A: Histone H2A; H3K4: Histone H3 Lysine 4; H3K9: Histone H3 Lysine 9; HCN4: Hyperpolarization Activated Cyclic Nucleotide Gated Potassium and Sodium Channel 4;p HDAC8: Histone deacetylases 8; HP1: Heterochromatin Protein 1; ICC: Interstitial Cells of Cajal; ICC-MP: Myenteric Plexus Interstitial cells of Cajal; ICC-DMP: Deep Muscular Plexus Interstitial cells of Cajal; If: Pacemaker Funny Current; IP3: Inositol trisphosphate; JNK: C-Jun N-Terminal Kinase; LDS: Loeys-Dietz Syndrome; LOAD: Late-Onset Alzheimer Disease; MAPK: Mitogen-Activated Protein Kinase; MAU: MAU Sister Chromatid Cohesion Factor; MFS: Marfan Syndrome; NIPBL: NIPBL, Cohesin Loading Factor; OCT4: Octamer-Binding Protein 4; P38: P38 MAP Kinase; PDA: Patent Ductus Arteriosus; PDS5: PDS5 Cohesin Associated Factor; P-H3: Phospho Histone H3; PLK1: Polo Like Kinase 1; POPDC1: Popeye Domain Containing 1; POPDC2: Popeye Domain Containing 2; PP2A: Protein Phosphatase 2; RAD21: RAD21 Cohesin Complex Component; RBS: Roberts Syndrome; REC8: REC8 Meiotic Recombination Protein; RNAP2: RNA polymerase II; SAN: Sinoatrial node; SCN5A: Sodium Voltage-Gated Channel Alpha Subunit 5; SEC: Super Elongation Complex; SGO1: Shogoshin-1; SMAD: SMAD Family Member; SMC1A: Structural Maintenance of Chromosomes 1A; SMC3: Structural Maintenance of Chromosomes 3; SNV: Single Nucleotide Variant; SOX2: SRY-Box 2; SOX17: SRY-Box 17; SSS: Sick Sinus Syndrome; STAG2: Cohesin Subunit SA-2; TADs: Topology Associated Domains; TBX: T-box transcription factors; TGF-β: Transforming Growth Factor β; TGFBR: Transforming Growth Factor β receptor; TOF: Tetralogy of Fallot; TREK1: TREK-1 K(+) Channel Subunit; VSD: Ventricular Septal Defect; WABS: Warsaw Breakage Syndrome; WAPL: WAPL Cohesin Release Factor.
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Affiliation(s)
- Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
| | - Patrick Piet Van Vliet
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
| | - Michel Pucéat
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
- INSERM U-1251, MMG,Aix-Marseille University, Marseille, 13885, France
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
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Comparative AAV-eGFP Transgene Expression Using Vector Serotypes 1-9, 7m8, and 8b in Human Pluripotent Stem Cells, RPEs, and Human and Rat Cortical Neurons. Stem Cells Int 2019; 2019:7281912. [PMID: 30800164 PMCID: PMC6360060 DOI: 10.1155/2019/7281912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 01/03/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV), produced from a nonpathogenic parvovirus, has become an increasing popular vector for gene therapy applications in human clinical trials. However, transduction and transgene expression of rAAVs can differ across in vitro and ex vivo cellular transduction strategies. This study compared 11 rAAV serotypes, carrying one reporter transgene cassette containing a cytomegalovirus immediate-early enhancer (eCMV) and chicken beta actin (CBA) promoter driving the expression of an enhanced green-fluorescent protein (eGFP) gene, which was transduced into four different cell types: human iPSC, iPSC-derived RPE, iPSC-derived cortical, and dissociated embryonic day 18 rat cortical neurons. Each cell type was exposed to three multiplicity of infections (MOI: 1E4, 1E5, and 1E6 vg/cell). After 24, 48, 72, and 96 h posttransduction, GFP-expressing cells were examined and compared across dosage, time, and cell type. Retinal pigmented epithelium showed highest AAV-eGFP expression and iPSC cortical the lowest. At an MOI of 1E6 vg/cell, all serotypes show measurable levels of AAV-eGFP expression; moreover, AAV7m8 and AAV6 perform best across MOI and cell type. We conclude that serotype tropism is not only capsid dependent but also cell type plays a significant role in transgene expression dynamics.
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Moore-Morris T, van Vliet PP, Andelfinger G, Puceat M. Role of Epigenetics in Cardiac Development and Congenital Diseases. Physiol Rev 2019; 98:2453-2475. [PMID: 30156497 DOI: 10.1152/physrev.00048.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.
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Affiliation(s)
- Thomas Moore-Morris
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Patrick Piet van Vliet
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Gregor Andelfinger
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Michel Puceat
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
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