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Labudina AA, Meier M, Gimenez G, Tatarakis D, Ketharnathan S, Mackie B, Schilling TF, Antony J, Horsfield JA. Cohesin composition and dosage independently affect early development in zebrafish. Development 2024; 151:dev202593. [PMID: 38975838 DOI: 10.1242/dev.202593] [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: 12/07/2023] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed 'cohesinopathies' are characterized by germline variants of cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear whether mutations in individual cohesin subunits have independent developmental consequences. Here, we show that zebrafish rad21 or stag2b mutants independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2b mutants have narrower notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single-cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2b, but not rad21, mutants. Our results suggest that mutations altering the quantity versus composition of cohesin have independent developmental consequences, with implications for the understanding and management of cohesinopathies.
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Affiliation(s)
- Anastasia A Labudina
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Michael Meier
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - David Tatarakis
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Sarada Ketharnathan
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Bridget Mackie
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
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Lizana L, Schwartz YB. The scales, mechanisms, and dynamics of the genome architecture. SCIENCE ADVANCES 2024; 10:eadm8167. [PMID: 38598632 PMCID: PMC11006219 DOI: 10.1126/sciadv.adm8167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit into the cell nuclei unless massively folded. Such folding must accommodate the need for timely access to selected parts of the genome by transcription factors, RNA polymerases, and DNA replication machinery. Here, we review our current understanding of the genome folding inside the interphase nuclei. We consider the resulting genome architecture at three scales with a particular focus on the intermediate (meso) scale and summarize the insights gained from recent experimental observations and diverse computational models.
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Affiliation(s)
- Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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3
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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4
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl +/- mouse embryos foreshadows the development of syndromic birth defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.558465. [PMID: 37905011 PMCID: PMC10614802 DOI: 10.1101/2023.10.16.558465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl-deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and CdLS. Teaser Gene expression changes during gastrulation of Nipbl-deficient mice shed light on early origins of structural birth defects.
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5
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Tehrani Fateh S, Mohammad Zadeh N, Salehpour S, Hashemi-Gorji F, Omidi A, Sadeghi H, Mirfakhraie R, Moghimi P, Keyvanfar S, Mohammadi Sarvaleh S, Miryounesi M, Ghasemi MR. Comprehensive review and expanding the genetic landscape of Cornelia-de-Lange spectrum: insights from novel mutations and skin biopsy in exome-negative cases. BMC Med Genomics 2024; 17:20. [PMID: 38216990 PMCID: PMC10787426 DOI: 10.1186/s12920-024-01798-7] [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: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Cornelia de Lange Syndrome (CdLS) is a rare genetic disorder characterized by a range of physical, cognitive, and behavioral abnormalities. This study aimed to perform a comprehensive review of the literature on CdLS and investigate two cases of CdLS with distinct phenotypes that underwent WES to aid in their diagnosis. METHODS We conducted a comprehensive review of the literature on CdLS along with performing whole-exome sequencing on two CdLS patients with distinct phenotypes, followed by Sanger sequencing validation and in-silico analysis. RESULTS The first case exhibited a classic CdLS phenotype, but the initial WES analysis of blood-derived DNA failed to identify any mutations in CdLS-related genes. However, a subsequent WES analysis of skin-derived DNA revealed a novel heterozygous mutation in the NIPBL gene (NM_133433.4:c.6534_6535del, p.Met2178Ilefs*8). The second case was presented with a non-classic CdLS phenotype, and WES analysis of blood-derived DNA identified a heterozygous missense variant in the SMC1A gene (NM_006306.4:c.2320G>A, p.Asp774Asn). CONCLUSIONS The study shows the importance of considering mosaicism in classic CdLS cases and the value of WES for identifying genetic defects. These findings contribute to our understanding of CdLS genetics and underscore the need for comprehensive genetic testing to enhance the diagnosis and management of CdLS patients.
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Affiliation(s)
- Sahand Tehrani Fateh
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Nadia Mohammad Zadeh
- School of Medicine, Islamic Azad University Tehran Medical sciences, Tehran, Iran
| | - Shadab Salehpour
- Department of Pediatrics, Clinical Research Development Unit, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ashkan Omidi
- School of Medicine, Islamic Azad University Tehran Medical sciences, Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical sciences, Tehran, Iran
| | - Sepideh Keyvanfar
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Miryounesi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad-Reza Ghasemi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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Sui JY, Eichenfield DZ, Sun BK. The role of enhancers in psoriasis and atopic dermatitis. Br J Dermatol 2023; 190:10-19. [PMID: 37658835 DOI: 10.1093/bjd/ljad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/05/2023]
Abstract
Regulatory elements, particularly enhancers, play a crucial role in disease susceptibility and progression. Enhancers are DNA sequences that activate gene expression and can be affected by epigenetic modifications, interactions with transcription factors (TFs) or changes to the enhancer DNA sequence itself. Altered enhancer activity impacts gene expression and contributes to disease. In this review, we define enhancers and the experimental techniques used to identify and characterize them. We also discuss recent studies that examine how enhancers contribute to atopic dermatitis (AD) and psoriasis. Articles in the PubMed database were identified (from 1 January 2010 to 28 February 2023) that were relevant to enhancer variants, enhancer-associated TFs and enhancer histone modifications in psoriasis or AD. Most enhancers associated with these conditions regulate genes affecting epidermal homeostasis or immune function. These discoveries present potential therapeutic targets to complement existing treatment options for AD and psoriasis.
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Affiliation(s)
- Jennifer Y Sui
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Dawn Z Eichenfield
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
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7
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Chen J, Floyd EN, Dawson DS, Rankin S. Cornelia de Lange Syndrome mutations in SMC1A cause cohesion defects in yeast. Genetics 2023; 225:iyad159. [PMID: 37650609 PMCID: PMC10550314 DOI: 10.1093/genetics/iyad159] [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: 05/20/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a developmental disorder characterized by limb truncations, craniofacial abnormalities, and cognitive delays. CdLS is caused mainly by mutations in genes encoding subunits or regulators of the cohesin complex. Cohesin plays 2 distinct roles in chromosome dynamics as follows: it promotes looping, organization, and compaction of individual chromosomes, and it holds newly replicated sister chromatids together until cell division. CdLS-associated mutations result in altered gene expression likely by affecting chromosome architecture. Whether CdLS mutations cause phenotypes through impact on sister chromatid cohesion is less clear. Here, we show that CdLS-associated mutations introduced into the SMC1A gene of budding yeast had measurable impacts on sister chromatid cohesion, mitotic progression, and DNA damage sensitivity. These data suggest that sister chromatid cohesion-related defects may contribute to phenotypes seen in CdLS affected individuals.
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Affiliation(s)
- Jingrong Chen
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
| | - Erin N Floyd
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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8
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Mfarej MG, Hyland CA, Sanchez AC, Falk MM, Iovine MK, Skibbens RV. Cohesin: an emerging master regulator at the heart of cardiac development. Mol Biol Cell 2023; 34:rs2. [PMID: 36947206 PMCID: PMC10162415 DOI: 10.1091/mbc.e22-12-0557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Cohesins are ATPase complexes that play central roles in cellular processes such as chromosome division, DNA repair, and gene expression. Cohesinopathies arise from mutations in cohesin proteins or cohesin complex regulators and encompass a family of related developmental disorders that present with a range of severe birth defects, affect many different physiological systems, and often lead to embryonic fatality. Treatments for cohesinopathies are limited, in large part due to the lack of understanding of cohesin biology. Thus, characterizing the signaling networks that lie upstream and downstream of cohesin-dependent pathways remains clinically relevant. Here, we highlight alterations in cohesins and cohesin regulators that result in cohesinopathies, with a focus on cardiac defects. In addition, we suggest a novel and more unifying view regarding the mechanisms through which cohesinopathy-based heart defects may arise.
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Affiliation(s)
- Michael G. Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Caitlin A. Hyland
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Annie C. Sanchez
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Matthias M. Falk
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - M. Kathryn Iovine
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
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9
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Lipinski RJ, Krauss RS. Gene-environment interactions in birth defect etiology: Challenges and opportunities. Curr Top Dev Biol 2023; 152:1-30. [PMID: 36707208 PMCID: PMC9942595 DOI: 10.1016/bs.ctdb.2022.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Birth defects are relatively common congenital outcomes that significantly impact affected individuals, their families, and communities. Effective development and deployment of prevention and therapeutic strategies for these conditions requires sufficient understanding of etiology, including underlying genetic and environmental causes. Tremendous progress has been made in defining the genetic basis of familial and syndromic forms of birth defects. However, the majority of birth defect cases are considered nonsyndromic and thought to result from multifactorial gene-environment interactions. While substantial advances have been made in elucidating the genetic landscape of these etiologically complex conditions, significant biological and technical constraints have stymied progress toward a refined knowledge of environmental risk factors. Defining specific gene-environment interactions in birth defect etiology is even more challenging. However, progress has been made, including demonstration of critical proofs of concept and development of new conceptual and technical approaches for resolving complex gene-environment interactions. In this review, we discuss current views of multifactorial birth defect etiology, comparing them with other diseases that also involve gene-environment interactions, including primary immunodeficiency and cancer. We describe how various model systems have illuminated mechanisms of multifactorial etiology and these models' individual strengths and weaknesses. Finally, suggestions for areas of future emphasis are proposed.
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Affiliation(s)
- Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, United States,Corresponding authors: ;
| | - Robert S. Krauss
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Corresponding authors: ;
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10
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Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [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: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
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11
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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12
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Sanchez AC, Thren ED, Iovine MK, Skibbens RV. Esco2 and cohesin regulate CRL4 ubiquitin ligase ddb1 expression and thalidomide teratogenicity. Cell Cycle 2022; 21:501-513. [PMID: 34989322 PMCID: PMC8942496 DOI: 10.1080/15384101.2021.2023304] [Citation(s) in RCA: 2] [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: 04/22/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/03/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) and Roberts syndrome (RBS) are severe developmental maladies that arise from mutation of cohesin (including SMC3, CdLS) and ESCO2 (RBS). Though ESCO2 activates cohesin, CdLS and RBS etiologies are currently considered non-synonymous and for which pharmacological treatments are unavailable. Here, we identify a unifying mechanism that integrates these genetic maladies to pharmacologically-induced teratogenicity via thalidomide. Our results reveal that Esco2 and cohesin co-regulate the transcription of a component of CRL4 ubiquitin ligase through which thalidomide exerts teratogenic effects. These findings are the first to link RBS and CdLS to thalidomide teratogenicity and offer new insights into treatments.
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Affiliation(s)
- Annie C. Sanchez
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Elise D. Thren
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - M. Kathryn Iovine
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
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13
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Pearson E, Nielsen E, Kita S, Groves L, Nelson L, Moss J, Oliver C. Low speech rate but high gesture rate during conversational interaction in people with Cornelia de Lange syndrome. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:601-607. [PMID: 33694205 DOI: 10.1111/jir.12829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/28/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cornelia de Lange syndrsome (CdLS) is a rare genetic syndrome with notable impaired expressive communication characterised by reduced spoken language. We examined gesture use to refine the description of expressive communication impairments in CdLS. METHODS During conversations, we compared gesture use in people with CdLS to peers with Down syndrome (DS) matched for receptive language and adaptive ability, and typically developing (TD) individuals of similar chronological age. RESULTS As anticipated the DS and CdLS groups used fewer words during conversation than TD peers (P < .001). However, the CdLS group used twice the number of gestures per 100 words compared with the DS and TD groups (P = .003). CONCLUSIONS Individuals with CdLS have a significantly higher gesture rate than expected given their level of intellectual disability and chronological age. This result indicates the cause of reduced use of spoken language does not extend to all forms of expressive communication.
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Affiliation(s)
- E Pearson
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- School of Psychology, College of Health and Life Sciences, Aston University, Birmingham, UK
| | - E Nielsen
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - S Kita
- Department of Psychology, University of Warwick, Coventry, UK
| | - L Groves
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - L Nelson
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- Royal Derby Hospital, Derby, UK
| | - J Moss
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- School of Psychology, University of Surrey, Surrey, UK
| | - C Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
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14
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Abstract
PURPOSE OF REVIEW While previous reviews have extended descriptions of the behavioural phenotype of Cornelia de Lange syndrome (CdLS) significantly, potential changes with age across the lifespan have been neglected. Age-related difference in the behavioural phenotype constitutes preliminary evidence of change with age. Documenting and understanding the developmental trajectories of behaviours is informative as it enables identification of risk periods for behavioural challenges and compromised mental health. RECENT FINDINGS Recent cross sectional, longitudinal and mixed design studies report differing presentations of the behavioural phenotype across the lifespan. Of particular interest are autistic characteristics and behaviours consistent with compromised mental health, particularly anxiety and negative affect, which are reported to be more common and severe in older individuals. Preliminary evidence for identified causal pathways with consideration of biological, cognitive and environmental factors are discussed. SUMMARY Older individuals with CdLS appear to be at greater risk of poorer psychological wellbeing than younger peers with significant implications for risk informed preventive and early interventions. Further work is required to document the behavioural phenotype across the lifespan with consideration of multiple factors that may influence the trajectory and extent of negative outcomes.
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15
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El Hamichi S, Kon Graversen V, Gold AS, Berrocal AM, Murray TG. Case Report: Endogenous Candida Endophthalmitis in Cornelia de Lange Syndrome: Atypical Stellate Neuroretinitis. Optom Vis Sci 2021; 98:104-108. [PMID: 33617168 DOI: 10.1097/opx.0000000000001639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
SIGNIFICANCE This study aimed to highlight the association of stellate neuroretinitis occurring secondary to endogenous candidemia. PURPOSE We report an unusual presentation of endogenous Candida endophthalmitis as a stellate neuroretinitis in the setting of Cornelia de Lange syndrome. CASE REPORT A 34-month-old girl with severe Cornelia de Lange syndrome and a history of parenteral nutrition dependence requiring a chronic central venous catheter presented with bilateral endophthalmitis secondary to candidemia. In one eye, the endophthalmitis had the atypical presentation as a stellate neuroretinitis. CONCLUSIONS This case represents a unique association of stellate neuroretinitis secondary to Candida infection in a patient with Cornelia de Lange syndrome.
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Affiliation(s)
| | | | - Aaron S Gold
- Murray Ocular Oncology and Retina, Miami, Florida
| | - Audina M Berrocal
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Timothy G Murray
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
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16
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van Schie JJM, Faramarz A, Balk JA, Stewart GS, Cantelli E, Oostra AB, Rooimans MA, Parish JL, de Almeida Estéves C, Dumic K, Barisic I, Diderich KEM, van Slegtenhorst MA, Mahtab M, Pisani FM, Te Riele H, Ameziane N, Wolthuis RMF, de Lange J. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion. Nat Commun 2020; 11:4287. [PMID: 32855419 PMCID: PMC7452896 DOI: 10.1038/s41467-020-18066-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Warsaw Breakage Syndrome (WABS) is a rare disorder related to cohesinopathies and Fanconi anemia, caused by bi-allelic mutations in DDX11. Here, we report multiple compound heterozygous WABS cases, each displaying destabilized DDX11 protein and residual DDX11 function at the cellular level. Patient-derived cell lines exhibit sensitivity to topoisomerase and PARP inhibitors, defective sister chromatid cohesion and reduced DNA replication fork speed. Deleting DDX11 in RPE1-TERT cells inhibits proliferation and survival in a TP53-dependent manner and causes chromosome breaks and cohesion defects, independent of the expressed pseudogene DDX12p. Importantly, G-quadruplex (G4) stabilizing compounds induce chromosome breaks and cohesion defects which are strongly aggravated by inactivation of DDX11 but not FANCJ. The DNA helicase domain of DDX11 is essential for sister chromatid cohesion and resistance to G4 stabilizers. We propose that DDX11 is a DNA helicase protecting against G4 induced double-stranded breaks and concomitant loss of cohesion, possibly at DNA replication forks.
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Affiliation(s)
- Janne J M van Schie
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Atiq Faramarz
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Jesper A Balk
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Cantelli
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Anneke B Oostra
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Martin A Rooimans
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Hospital Centre Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Ingeborg Barisic
- Children's Hospital Zagreb, Center of Excellence for Reproductive and Regenerative Medicine, Medical School University of Zagreb, Zagreb, Croatia
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Najim Ameziane
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
- Centogene, Am Strande 7, 18055, Rostock, Germany
| | - Rob M F Wolthuis
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| | - Job de Lange
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
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17
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Luppino JM, Park DS, Nguyen SC, Lan Y, Xu Z, Yunker R, Joyce EF. Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes. Nat Genet 2020; 52:840-848. [PMID: 32572210 PMCID: PMC7416539 DOI: 10.1038/s41588-020-0647-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 05/18/2020] [Indexed: 01/10/2023]
Abstract
The human genome can be segmented into topologically associating domains (TADs), which have been proposed to spatially sequester genes and regulatory elements through chromatin looping. Interactions between TADs have also been suggested, presumably because of variable boundary positions across individual cells. However, the nature, extent and consequence of these dynamic boundaries remain unclear. Here, we combine high-resolution imaging with Oligopaint technology to quantify the interaction frequencies across both weak and strong boundaries. We find that chromatin intermingling across population-defined boundaries is widespread but that the extent of permissibility is locus-specific. Cohesin depletion, which abolishes domain formation at the population level, does not induce ectopic interactions but instead reduces interactions across all boundaries tested. In contrast, WAPL or CTCF depletion increases inter-domain contacts in a cohesin-dependent manner. Reduced chromatin intermingling due to cohesin loss affects the topology and transcriptional bursting frequencies of genes near boundaries. We propose that cohesin occasionally bypasses boundaries to promote incorporation of boundary-proximal genes into neighboring domains.
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Affiliation(s)
- Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel S Park
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Son C Nguyen
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhuxuan Xu
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Yunker
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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18
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Singh VP, McKinney S, Gerton JL. Persistent DNA Damage and Senescence in the Placenta Impacts Developmental Outcomes of Embryos. Dev Cell 2020; 54:333-347.e7. [PMID: 32800293 DOI: 10.1016/j.devcel.2020.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cohesin is an evolutionarily conserved chromosome-associated protein complex essential for chromosome segregation, gene expression, and repair of DNA damage. Mutations that affect this complex cause the human developmental disorder Cornelia de Lange syndrome (CdLS), thought to arise from defective embryonic transcription. We establish a significant role for placental defects in the development of CdLS mouse embryos (Nipbl and Hdac8). Placenta is a naturally senescent tissue; we demonstrate that persistent DNA damage potentiates senescence and activates cytokine signaling. Mutant embryo developmental outcomes are significantly improved in the context of a wild-type placenta or by genetically restricting cytokine signaling. Our study highlights that cohesin is required for maintaining ploidy and the repair of spontaneous DNA damage in placental cells, suggesting that genotoxic stress and ensuing placental senescence and cytokine production could represent a broad theme in embryo health and viability.
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Affiliation(s)
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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19
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Luppino JM, Joyce EF. Single cell analysis pushes the boundaries of TAD formation and function. Curr Opin Genet Dev 2020; 61:25-31. [PMID: 32302920 DOI: 10.1016/j.gde.2020.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 11/30/2022]
Abstract
Eukaryotic genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex three-dimensional structures. Fueled by a growing collection of sequencing and imaging-based technologies, studies have uncovered a hierarchy of DNA interactions, from small chromatin loops that connect genes and enhancers to larger topologically associated domains (TADs) and compartments. However, despite the remarkable conservation of these organizational features, we have a very limited understanding of how this organization influences gene expression. This issue is further complicated in the context of single-cell heterogeneity, as has recently been revealed at both the level of gene activation and chromatin topology. Here, we provide a perspective on recent studies that address cell-to-cell variability and the relationship between structural heterogeneity and gene expression. We propose that transcription is regulated by variable 3D structures driven by at least two independent and partially redundant mechanisms. Collectively, this may provide flexibility to transcriptional regulation at the level of individual cells as well as reproducibility across whole tissues.
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Affiliation(s)
- Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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20
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Thanh DC, Ngoc CTB, Nguyen NL, Vu CD, Tung NV, Nguyen HH. De novo NIPBL Mutations in Vietnamese Patients with Cornelia de Lange Syndrome. ACTA ACUST UNITED AC 2020; 56:medicina56020076. [PMID: 32074972 PMCID: PMC7073647 DOI: 10.3390/medicina56020076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) is a rare congenital genetic disease causing abnormal unique facial phenotypes, several defects in organs and body parts, and mental disorder or intellectual disorder traits. Main causes of CdLS have been reported as variants in cohesin complex genes, in which mutations in the NIPBL gene have been estimated to account for up to 80%. Our study included three Vietnamese patients with typical CdLS phenotypes. Whole exome sequencing revealed two known heterozygous mutations c.6697G>A (p.Val2233Met) and c.2602C>T (p.Arg868X), and a novel heterozygous mutation c.4504delG (p.Val1502fsX87) in the NIPBL gene of the three patients. In silico analyses of the identified mutations predicted possible damaging and truncating effects on the NIPBL protein. Inherited analyses in the patients' families showed that all of the mutations are de novo. Our results lead a definitive diagnosis of patients with CdLS and expand the spectrum of mutations in the NIPBL gene. These findings also confirm whole exome sequencing is an efficient tool for genetic screening of CdLS.
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Affiliation(s)
- Duong Chi Thanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Can Thi Bich Ngoc
- Center for Rare Diseases and Newborn Screening, Department of Endocrinology, Metabolism and Genetics, Vietnam National Hospital of Pediatrics, 18/879 La Thanh str., Dong Da, Hanoi 100000, Vietnam; (C.T.B.N.); (C.D.V.)
| | - Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Chi Dung Vu
- Center for Rare Diseases and Newborn Screening, Department of Endocrinology, Metabolism and Genetics, Vietnam National Hospital of Pediatrics, 18/879 La Thanh str., Dong Da, Hanoi 100000, Vietnam; (C.T.B.N.); (C.D.V.)
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Huy Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
- Correspondence: ; Tel.: +84-243-7918012
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21
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Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet 2019; 20:437-455. [DOI: 10.1038/s41576-019-0128-0] [Citation(s) in RCA: 486] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Small SM, Bacher RS. Diphenhydramine-Refractory Antipsychotic-Induced Dystonia in an Adolescent Male With Cornelia de Lange Syndrome. J Pediatr Pharmacol Ther 2019; 24:160-165. [PMID: 31019410 DOI: 10.5863/1551-6776-24.2.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cornelia de Lange Syndrome is a rare genetic disorder that results in distinctive craniofacial deformities, developmental delay, hirsutism, and other physical abnormalities. Case reports suggest some of these patients exhibit sensitivity and paradoxical reactions to certain psychoactive drugs. This report of a 16-year-old male with Cornelia de Lange is the first to describe dystonia from a first-generation antipsychotic that did not respond to conventional treatment with diphenhydramine. The patient initially presented to the Emergency Department for agitation, which progressively worsened after administration of diphenhydramine, olanzapine, and intramuscular haloperidol. The patient returned to the Emergency Department the following day because of altered mental status and lethargy that progressed to periodic lip-smacking movements and contraction of his upper extremities. His symptoms continued despite administration of diphenhydramine and loading doses of 3 antiepileptic drugs. His abnormal labs included an elevated creatine kinase and a prolonged QTc interval on his electrocardiogram. His symptoms were later deemed a probable drug-induced dystonic reaction to haloperidol once seizures were excluded by an unremarkable electroencephalogram. This case supports previous reports suggesting an association between Cornelia de Lange and paradoxical drug reactions, and it is recommended that clinicians strongly weigh the risks of prescribing first-generation antipsychotics for this patient population. These medications should be carefully titrated, with close patient monitoring to prevent adverse drug effects and other iatrogenic complications because antidotes may be rendered ineffective by this condition.
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23
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Tang H, Guo J, Linpeng S, Wu L. Next generation sequencing identified two novel mutations in NIPBL and a frame shift mutation in CREBBP in three Chinese children. Orphanet J Rare Dis 2019; 14:45. [PMID: 30770747 PMCID: PMC6377774 DOI: 10.1186/s13023-019-1022-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 02/04/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) and Rubinstein-Taybi syndrome (RSTS) are both rare congenital multiple malformation disorders caused by genes associated with transcription. They share a number of similar features clinically. In addition, it is difficult to make a molecular diagnosis rapidly and detect the mosaic mutation when only sanger sequencing is taken. This study aims to report three novel mutations in three Chinese children identified by next generation sequencing. RESULTS We describe patient 1 and patient 2 presenting with characteristics of CdLS with mutations in NIPBL and patient 3 with a frame shift mutation in CREBBP who can be diagnosed as RSTS clinically and also have similar symptoms with CdLS to some extent. The splicing site c.4321-1G > A transversion in NIPBL is a mosaic mutation and produces an abnormal transcript bearing the loss of exon 20. The nonsense mutation c.218C > A in NIPBL and the frame shift c.1715delC mutation in CREBBP generate stop codon and yield the premature termination of proteins. CONCLUSIONS In general, we detect three novel heterozygous mutations including a splicing mutation and a nonsense mutation in NIPBL and a frame shift in CREBBP. And several similar features observed in patients indicate the clinical complexity and clinically overlapping of CdLS and RSTS termed "transcriptomopathies", suggest the underlying molecular mechanism and emphasize the utilization of next generation sequencing technologies.
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Affiliation(s)
- Hui Tang
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Jing Guo
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Siyuan Linpeng
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
| | - Lingqian Wu
- Center for Medical Genetics, School of life sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078 People’s Republic of China
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24
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Krawczynska N, Wierzba J, Jasiecki J, Wasag B. Molecular characterization of two novel intronic variants of NIPBL gene detected in unrelated Cornelia de Lange syndrome patients. BMC MEDICAL GENETICS 2019; 20:1. [PMID: 30606125 PMCID: PMC6318863 DOI: 10.1186/s12881-018-0738-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/21/2018] [Indexed: 11/17/2022]
Abstract
Background Cornelia de Lange syndrome (CdLS), a rare, multisystemic disorder, has been linked to genetic alterations in NIPBL, SMC1A, SMC3, HDAC8, and RAD21 genes. Approximately 60% of CdLS patients harbor various NIPBL variants. Genetic changes predicted to affect NIPBL gene splicing represent 15% of all NIPBL genetic abnormalities. Yet, only a few studies have investigated the molecular consequences of such variants. Case presentation This study reports two novel, intronic NIPBL genetic variants in unrelated CdLS patients with the characteristic phenotype. A c.6954 + 3A > C substitution and a c.5862 + 1delG deletion were identified, one of each, in a 6 year-old boy and 39 month-old girl. Further studies confirmed that both variants introduce premature termination codons, resulting in the formation of truncated proteins p.(Ser2255LeufsTer20) and p.(Leu1955Ter), respectively. Conclusion Single nucleotide alterations located within the conserved splice-donor site of intronic regions of the NIPBL gene can give rise to a premature termination of the translation and cause significant changes in the sequence of mRNA transcripts and NIPBL protein structure and function. The latter underline development of Cornelia de Lange syndrome phenotype. Electronic supplementary material The online version of this article (10.1186/s12881-018-0738-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Krawczynska
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland.,Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Jolanta Wierzba
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland.,Department of General Nursery, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Jasiecki
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland. .,Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland.
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25
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Krawczynska N, Wierzba J, Wasag B. Genetic Mosaicism in a Group of Patients With Cornelia de Lange Syndrome. Front Pediatr 2019; 7:203. [PMID: 31157197 PMCID: PMC6530423 DOI: 10.3389/fped.2019.00203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/01/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Cornelia de Lange Syndrome (CdLS) is a heterogeneous disorder. Diverse expression of clinical symptoms can be caused by a variety of pathogenic variants located within the sequence of different genes correlated with the cohesin complex. Methods: Sixty-nine patients with confirmed clinical diagnosis of CdLS were enrolled in the study. Blood and buccal swab samples were collected for molecular studies. Mutational analysis was performed using the Next Generation (deep) Sequencing (NGS) covering 24 genes. In addition, the MLPA technique was applied to detect large rearrangements of NIPBL. Results: MLPA and NGS analysis were performed in 66 (95,7%) and 67 (97,1%) patients, respectively. Large rearrangements of NIPBL were not identified in the studied group. Germline pathogenic variants were detected in 18 (26,1%) patients. Fourteen variants (20,3%) were identified in NIPBL, two (2,9%) in SMC1A, and two (2,9%) in HDAC8. In total, 13 (18,8%) buccal swabs were suitable for deep sequencing. Mosaic variants were found in four (30,8%; 4/13) patients negative for germline alterations. Three mosaic substitutions were detected in NIPBL while one in KMT2A gene. Conclusions: Comprehensive and sensitive molecular techniques allow detecting novel pathogenic variants responsible for the molecular basis of CdLS. In addition, molecular testing of different tissues should be applied since such an approach allows detect mosaic variants specific for a subgroup of CdLS patients. Finally, to test possible pathogenicity of intronic variants, RNA analysis should be conducted.
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Affiliation(s)
- Natalia Krawczynska
- Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland.,Laboratory of Clinical Genetics, University Clinical Centre, Gdańsk, Poland
| | - Jolanta Wierzba
- Department of General Nursery, Medical University of Gdańsk, Gdańsk, Poland
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland.,Laboratory of Clinical Genetics, University Clinical Centre, Gdańsk, Poland
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26
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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27
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Zhao YJ, Ma HW. [NIPBL gene mutations in two children with Cornelia de Lange syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:387-391. [PMID: 29764576 PMCID: PMC7389061 DOI: 10.7499/j.issn.1008-8830.2018.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Both children (one boy and one girl) experienced disease onset in infancy and visited the hospital due to growth retardation. They had unusual facies including thick hair, arched and confluent eyebrows, long and curly eyelashes, short nose, and micrognathia. Patient 1 had congenital heart disease (atrial septal defect and pulmonary stenosis) and special dermatoglyph (a single palmar crease). Patient 2 had cleft palate and moderate-to-severe deafness. Clinical features suggested Cornelia de Lange syndrome in both children. High-throughput sequencing was used to detect the seven known pathogenic genes of Cornelia de Lange syndrome, i.e., the NIPBL, SMC1A, SMC3, HDAC8, RAD21, EP300, and ANKRD11 genes. Sanger sequencing was used to analyze and verify gene mutations. Both patients were found to have novel mutations in the NIPBL gene. One patient had a frameshift mutation in exon 45, c.7834dupA, which caused early termination of translation and produced truncated protein p.R2612fsX20. The other patient had a nonsense mutation, c.505C>T, which caused a premature stop codon and produced truncated protein Q169X. Such mutations were not found in their parents or 50 unrelated healthy individuals.
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Affiliation(s)
- Yun-Jing Zhao
- Department of Developmental Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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28
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Hei M, Gao X, Wu L. Clinical and genetic study of 20 patients from China with Cornelia de Lange syndrome. BMC Pediatr 2018; 18:64. [PMID: 29452578 PMCID: PMC5815176 DOI: 10.1186/s12887-018-1004-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/23/2018] [Indexed: 11/24/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare congenital syndrome with no racial difference. The objective of this study is to report the clinical characteristics and genetic study of 20 CdLS cases from China. Methods This is an observational study. Suspected patients were referred for further confirmation, clinical treatment, and genetic testing under voluntary condition. Demographic data and family history, data of clinical manifestations including facial dysmorphism and developmental delay of each patient were collected. Chromosomal analysis and NIPBL/SMC1A/SMC3 gene mutational analysis were carried out by PCR, reverse transcription PCR direct sequencing in the probands, and SNP array to detect the genome-wide copy number variations. Results Twenty CdLS cases from China were included in this study. Facial dysmorphisms, feeding difficulties, and developmental delay were the major clinical manifestations. Seven patients underwent gene mutation tests. Both the SMC1A and SMC3 gene mutation tests were negative in all. A heterozygous mutation in exon 20 of the NIPBL gene in proband 2, and a heterozygous mutation in intron 38 of the NIPBL gene in proband 3 were found in 1 patient, and RT-PCR revealed a splicing mutation in exon 38, generating both normal transcript and an aberrant alternatively spliced transcript with exon 38 deletion. Conclusions Clinical manifestations of CdLS patients from China are similar to those in the other countries. Heterozygous mutations of NIPBL gene were found.
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Affiliation(s)
- Mingyan Hei
- Department of Pediatrics, the Third Xiangya Hospital of Central South University, Togzipo Road 138, Yuelu District, Changsha, Hunan, 410013, China. .,Neonatal Center, Beijing Children's Hospital of Capital Medical University, Beijing, 100045, China.
| | - Xiangyu Gao
- Department of Pediatrics, Xuzhou Affiliated Hospital of East West University, Xuzhou, Jiangsu, 220018, China
| | - Lingqian Wu
- National Key Laboratory of Medical Genetics of Central South University, Changsha, Hunan, 410008, China
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Avagliano L, Grazioli P, Mariani M, Bulfamante GP, Selicorni A, Massa V. Integrating molecular and structural findings: Wnt as a possible actor in shaping cognitive impairment in Cornelia de Lange syndrome. Orphanet J Rare Dis 2017; 12:174. [PMID: 29162129 PMCID: PMC5696803 DOI: 10.1186/s13023-017-0723-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/10/2017] [Indexed: 11/10/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a choesinopathy: a severe genetic disorder caused by mutations in the cohesin complex genes. The phenotype is characterized by typical facial dysmorphism, growth impairment and multiorgan abnormalities including brain alterations. Wnt pathway is known to play a fundamental role in central nervous system development and it has been shown that Wnt pathway is disrupted in CdLS animal models and patients cells. In this review we investigate the possible link between Wnt pathway disruption and brain abnormalities in Cornelia de Lange Syndrome as such molecular impairment could lead to an abnormal embryonic development resulting in brain abnormalities (i.e. microcephaly, cerebellar hypoplasia, abnormal cortical development) in patients with Cornelia de Lange Syndrome.
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Affiliation(s)
- Laura Avagliano
- Department of Health Sciences, San Paolo Hospital Medical School University of Milan, Via A. di Rudinì, 8, 20142, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, San Paolo Hospital Medical School University of Milan, Via A. di Rudinì, 8, 20142, Milan, Italy
| | | | - Gaetano P Bulfamante
- Department of Health Sciences, San Paolo Hospital Medical School University of Milan, Via A. di Rudinì, 8, 20142, Milan, Italy
| | | | - Valentina Massa
- Department of Health Sciences, San Paolo Hospital Medical School University of Milan, Via A. di Rudinì, 8, 20142, Milan, Italy.
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Banerji R, Skibbens RV, Iovine MK. How many roads lead to cohesinopathies? Dev Dyn 2017; 246:881-888. [PMID: 28422453 DOI: 10.1002/dvdy.24510] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/10/2017] [Accepted: 04/11/2017] [Indexed: 12/16/2023] Open
Abstract
Genetic mapping studies reveal that mutations in cohesion pathways are responsible for multispectrum developmental abnormalities termed cohesinopathies. These include Roberts syndrome (RBS), Cornelia de Lange Syndrome (CdLS), and Warsaw Breakage Syndrome (WABS). The cohesinopathies are characterized by overlapping phenotypes ranging from craniofacial deformities, limb defects, and mental retardation. Though these syndromes share a similar suite of phenotypes and arise due to mutations in a common cohesion pathway, the underlying mechanisms are currently believed to be distinct. Defects in mitotic failure and apoptosis i.e. trans DNA tethering events are believed to be the underlying cause of RBS, whereas the underlying cause of CdLS is largely modeled as occurring through defects in transcriptional processes i.e. cis DNA tethering events. Here, we review recent findings described primarily in zebrafish, paired with additional studies in other model systems, including human patient cells, which challenge the notion that cohesinopathies represent separate syndromes. We highlight numerous studies that illustrate the utility of zebrafish to provide novel insights into the phenotypes, genes affected and the possible mechanisms underlying cohesinopathies. We propose that transcriptional deregulation is the predominant mechanism through which cohesinopathies arise. Developmental Dynamics 246:881-888, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
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Newkirk DA, Chen YY, Chien R, Zeng W, Biesinger J, Flowers E, Kawauchi S, Santos R, Calof AL, Lander AD, Xie X, Yokomori K. The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome. Clin Epigenetics 2017; 9:89. [PMID: 28855971 PMCID: PMC5574093 DOI: 10.1186/s13148-017-0391-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, expression changes of multiple genes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder. However, the effect of NIPBL haploinsufficiency on cohesin binding, and how this relates to the clinical presentation of CdLS, has not been fully investigated. Nipbl haploinsufficiency causes CdLS-like phenotype in mice. We examined genome-wide cohesin binding and its relationship to gene expression using mouse embryonic fibroblasts (MEFs) from Nipbl+/- mice that recapitulate the CdLS phenotype. RESULTS We found a global decrease in cohesin binding, including at CCCTC-binding factor (CTCF) binding sites and repeat regions. Cohesin-bound genes were found to be enriched for histone H3 lysine 4 trimethylation (H3K4me3) at their promoters; were disproportionately downregulated in Nipbl mutant MEFs; and displayed evidence of reduced promoter-enhancer interaction. The results suggest that gene activation is the primary cohesin function sensitive to Nipbl reduction. Over 50% of significantly dysregulated transcripts in mutant MEFs come from cohesin target genes, including genes involved in adipogenesis that have been implicated in contributing to the CdLS phenotype. CONCLUSIONS Decreased cohesin binding at the gene regions is directly linked to disease-specific expression changes. Taken together, our Nipbl haploinsufficiency model allows us to analyze the dosage effect of cohesin loading on CdLS development.
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Affiliation(s)
- Daniel A. Newkirk
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
| | - Yen-Yun Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: ResearchDx Inc., 5 Mason, Irvine, CA 92618 USA
| | - Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: Thermo Fisher Scientific, Inc., 180 Oyster Point Blvd South, San Francisco, CA 94080 USA
| | - Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: Department of Developmental & Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697 USA
| | - Jacob Biesinger
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
- Current address: Verily Life Scienceds, 1600 Amphitheatre Pkwy, Mountain View, CA 94043 USA
| | - Ebony Flowers
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- California State University Long Beach, Long Beach, CA 90840 USA
- Current address: UT Southwestern Medical Center, 5323 Harry Hines Blvd, NA8.124, Dallas, TX 75390 USA
| | - Shimako Kawauchi
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Rosaysela Santos
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Anne L. Calof
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Arthur D. Lander
- Department of Developmental & Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697 USA
| | - Xiaohui Xie
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
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Deardorff MA, Porter NJ, Christianson DW. Structural aspects of HDAC8 mechanism and dysfunction in Cornelia de Lange syndrome spectrum disorders. Protein Sci 2016; 25:1965-1976. [PMID: 27576763 PMCID: PMC5079251 DOI: 10.1002/pro.3030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 11/08/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) encompasses a broad spectrum of phenotypes characterized by distinctive craniofacial abnormalities, limb malformations, growth retardation, and intellectual disability. CdLS spectrum disorders are referred to as cohesinopathies, with ∼70% of patients having a mutation in a gene encoding a core cohesin protein (SMC1A, SMC3, or RAD21) or a cohesin regulatory protein (NIPBL or HDAC8). Notably, the regulatory function of HDAC8 in cohesin biology has only recently been discovered. This Zn2+ -dependent hydrolase catalyzes the deacetylation of SMC3, a necessary step for cohesin recycling during the cell cycle. To date, 23 different missense mutants in the gene encoding HDAC8 have been identified in children with developmental features that overlap those of CdLS. Enzymological, biophysical, and structural studies of CdLS HDAC8 protein mutants have yielded critical insight on compromised catalysis in vitro. Most CdLS HDAC8 mutations trigger structural changes that directly or indirectly impact substrate binding and catalysis. Additionally, several mutations significantly compromise protein thermostability. Intriguingly, catalytic activity in many HDAC8 mutants can be partially or fully restored by an N-acylthiourea activator, suggesting a plausible strategy for the chemical rescue of compromised HDAC8 catalysis in vivo.
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Affiliation(s)
- Matthew A Deardorff
- Division of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, Pennsylvania, 19104.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.
| | - Nicholas J Porter
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323.
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Cereda A, Mariani M, Rebora P, Sajeva A, Ajmone PF, Gervasini C, Russo S, Kullmann G, Valsecchi G, Selicorni A. A new prognostic index of severity of intellectual disabilities in Cornelia de Lange syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:179-89. [PMID: 27148700 DOI: 10.1002/ajmg.c.31494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Cornelia de Lange syndrome is a well-known multiple congenital anomalies/intellectual disability syndrome with genetic heterogeneity and wide clinical variability, regarding the severity of both the intellectual disabilities and the physical features, not completely explained by the genotype-phenotype correlations known to date. The aim of the study was the identification of prognostic features, ascertainable precociously in the patient's life, of a better intellectual outcome and the development of a new prognostic index of severity of intellectual disability in CdLS patients. In 66 italian CdLS patients aged 8 years or more, we evaluated the association of the degree of intellectual disability with various clinical parameters ascertainable before 6 months of life and with the molecular data by the application of cumulative regression logistic model. Based on these results and on the previously known genotype-phenotype correlations, we selected seven parameters to be used in a multivariate cumulative regression logistic model to develop a prognostic index of severity of intellectual disability. The probability of a mild ID increases with the reducing final score less than two, the probability of a severe ID increases with the increasing final score more than three. This prognostic index allows to define, precociously in the life of a baby, the probability of a better or worse intellectual outcome in CdLS patients. © 2016 Wiley Periodicals, Inc.
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Kaur M, Mehta D, Noon SE, Deardorff MA, Zhang Z, Krantz ID. NIPBL expression levels in CdLS probands as a predictor of mutation type and phenotypic severity. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:163-70. [PMID: 27125329 DOI: 10.1002/ajmg.c.31495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare, genetically heterogeneous multisystem developmental disorder with a high degree of variability in its clinical presentation. Approximately 65% of probands harbor mutations in genes that encode core components (SMC1A, SMC3, and RAD21) or regulators (NIPBL, HDAC8) of the cohesin complex, of which mutations in NIPBL are the most common. Cohesin plays a canonical role in sister chromatid cohesion during cell division and non-canonical roles in DNA repair, stem cell maintenance and differentiation, and regulation of gene expression. Disruption of the latter role seems to be the major contributor to the underlying molecular pathogenesis of CdLS. NIPBL is required for loading and unloading the cohesin complex onto chromosomes. The expression levels of NIPBL itself appear to be tightly regulated and highly evolutionarily conserved. Droplet digital PCR was used to quantify NIPBL mRNA expression levels with high precision from a cohort of 37 samples (NIPBL, SMC1A, SMC3, and HDAC8 mutation positive probands and negative control). Probands with severe forms of CdLS or severe mutation types were found to have lower levels of NIPBL in comparison to phenotypically milder patients and controls. Levels of NIPBL also correlated with the presence of mutations in different CdLS-causing genes. The data suggests that NIPBL levels are closely correlated with the severity of CdLS and with specific causative genes and types of mutations. ddPCR may provide a tool to assist in diagnostic approaches to CdLS, for genetic counseling and prognosis, and for monitoring potential therapeutic modalities in the future. © 2016 Wiley Periodicals, Inc.
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Lopez-Burks ME, Santos R, Kawauchi S, Calof AL, Lander AD. Genetic enhancement of limb defects in a mouse model of Cornelia de Lange syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:146-54. [PMID: 27120109 DOI: 10.1002/ajmg.c.31491] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) is characterized by a wide variety of structural and functional abnormalities in almost every organ system of the body. CdLS is now known to be caused by mutations that disrupt the function of the cohesin complex or its regulators, and studies of animal models and cell lines tell us that the effect of these mutations is to produce subtle yet pervasive dysregulation of gene expression. With many hundreds of mostly small gene expression changes occurring in every cell type and tissue, identifying the etiology of any particular birth defect is very challenging. Here we focus on limb abnormalities, which are commonly seen in CdLS. In the limb buds of the Nipbl-haploinsufficient mouse (Nipbl(+/-) mouse), a model for the most common form of CdLS, modest gene expression changes are observed in several candidate pathways whose disruption is known to cause limb abnormalities, yet the limbs of Nipbl(+/-) mice develop relatively normally. We hypothesized that further impairment of candidate pathways might produce limb defects similar to those seen in CdLS, and performed genetic experiments to test this. Focusing on Sonic hedgehog (Shh), Bone morphogenetic protein (Bmp), and Hox gene pathways, we show that decreasing Bmp or Hox function (but not Shh function) enhances polydactyly in Nipbl(+/-) mice, and in some cases produces novel skeletal phenotypes. However, frank limb reductions, as are seen in a subset of individuals with CdLS, do not occur, suggesting that additional signaling and/or gene regulatory pathways are involved in producing such dramatic changes. © 2016 Wiley Periodicals, Inc.
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Kawauchi S, Santos R, Muto A, Lopez-Burks ME, Schilling TF, Lander AD, Calof AL. Using mouse and zebrafish models to understand the etiology of developmental defects in Cornelia de Lange Syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:138-45. [PMID: 27120001 DOI: 10.1002/ajmg.c.31484] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) is a multisystem birth defects disorder that affects every tissue and organ system in the body. Understanding the factors that contribute to the origins, prevalence, and severity of these developmental defects provides the most direct approach for developing screens and potential treatments for individuals with CdLS. Since the majority of cases of CdLS are caused by haploinsufficiency for NIPBL (Nipped-B-like, which encodes a cohesin-associated protein), we have developed mouse and zebrafish models of CdLS by using molecular genetic tools to create Nipbl-deficient mice and zebrafish (Nipbl(+/-) mice, zebrafish nipbl morphants). Studies of these vertebrate animal models have yielded novel insights into the developmental etiology and genes/gene pathways that contribute to CdLS-associated birth defects, particularly defects of the gut, heart, craniofacial structures, nervous system, and limbs. Studies of these mouse and zebrafish CdLS models have helped clarify how deficiency for NIPBL, a protein that associates with cohesin and other transcriptional regulators in the nucleus, affects processes important to the emergence of the structural and physiological birth defects observed in CdLS: NIPBL exerts chromosome position-specific effects on gene expression; it influences long-range interactions between different regulatory elements of genes; and it regulates combinatorial and synergistic actions of genes in developing tissues. Our current understanding is that CdLS should be considered as not only a cohesinopathy, but also a "transcriptomopathy," that is, a disease whose underlying etiology is the global dysregulation of gene expression throughout the organism. © 2016 Wiley Periodicals, Inc.
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Identification and Functional Characterization of Two Intronic NIPBL Mutations in Two Patients with Cornelia de Lange Syndrome. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8742939. [PMID: 26925417 PMCID: PMC4746300 DOI: 10.1155/2016/8742939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/16/2015] [Indexed: 12/03/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare genetically heterogeneous disorder with a high phenotypic variability including mental retardation, developmental delay, and limb malformations. The genetic causes in about 30% of patients with CdLS are still unknown. We report on the functional characterization of two intronic NIPBL mutations in two patients with CdLS that do not affect a conserved splice-donor or acceptor site. Interestingly, mRNA analyses showed aberrantly spliced transcripts missing exon 28 or 37, suggesting the loss of the branch site by the c.5329-15A>G transition and a disruption of the polypyrimidine by the c.6344del(-13)_(-8) deletion. While the loss of exon 28 retains the reading frame of the NIBPL transcript resulting in a shortened protein, the loss of exon 37 shifts the reading frame with the consequence of a premature stop of translation. Subsequent quantitative PCR analysis demonstrated a 30% decrease of the total NIPBL mRNA levels associated with the frameshift transcript. Consistent with our results, this patient shows a more severe phenotype compared to the patient with the aberrant transcript that retains its reading frame. Thus, intronic variants identified by sequencing analysis in CdLS diagnostics should carefully be examined before excluding them as nonrelevant to disease.
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Yuen KC, Xu B, Krantz ID, Gerton JL. NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR. Cell Rep 2015; 14:93-102. [PMID: 26725122 PMCID: PMC4904785 DOI: 10.1016/j.celrep.2015.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/27/2015] [Accepted: 11/23/2015] [Indexed: 12/30/2022] Open
Abstract
NIPBL, a cohesin loader, has been implicated in transcriptional control and genome organization. Mutations in NIPBL, cohesin, and its deacetylase HDAC8 result in Cornelia de Lange syndrome. We report activation of the RNA-sensing kinase PKR in human lymphoblastoid cell lines carrying NIPBL or HDAC8 mutations, but not SMC1A or SMC3 mutations. PKR activation can be triggered by unmodified RNAs. Gene expression profiles in NIPBL-deficient lymphoblastoid cells and mouse embryonic stem cells reveal lower expression of genes involved in RNA processing and modification. NIPBL mutant lymphoblastoid cells show reduced proliferation and protein synthesis with increased apoptosis, all of which are partially reversed by a PKR inhibitor. Non-coding RNAs from an NIPBL mutant line had less m6A modification and activated PKR activity in vitro. This study provides insight into the molecular pathology of Cornelia de Lange syndrome by establishing a relationship between NIPBL and HDAC8 mutations and PKR activation.
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Affiliation(s)
- Kobe C Yuen
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Baoshan Xu
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Ian D Krantz
- Children's Hospital of Philadelphia, Division of Human Genetics, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA; University of Kansas School of Medicine, Department of Biochemistry and Molecular Biology, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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Singh VP, Gerton JL. Cohesin and human disease: lessons from mouse models. Curr Opin Cell Biol 2015; 37:9-17. [PMID: 26343989 DOI: 10.1016/j.ceb.2015.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
Abstract
Cohesin is an evolutionarily conserved large ring-like multi-subunit protein structure that can encircle DNA. Cohesin affects many processes that occur on chromosomes such as segregation, DNA replication, double-strand break repair, condensation, chromosome organization, and gene expression. Mutations in the genes that encode cohesin and its regulators cause human developmental disorders and cancer. Several mouse models have been established with the aim of understanding the cohesin mediated processes that are disrupted in these diseases. Mouse models support the idea that cohesin is essential for cell division, but partial loss of function can alter gene expression, DNA replication and repair, gametogenesis, and nuclear organization.
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Affiliation(s)
- Vijay Pratap Singh
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States; Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, United States.
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Wu Y, Gause M, Xu D, Misulovin Z, Schaaf CA, Mosarla RC, Mannino E, Shannon M, Jones E, Shi M, Chen WF, Katz OL, Sehgal A, Jongens TA, Krantz ID, Dorsett D. Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior. PLoS Genet 2015; 11:e1005655. [PMID: 26544867 PMCID: PMC4636142 DOI: 10.1371/journal.pgen.1005655] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
Individuals with Cornelia de Lange Syndrome (CdLS) display diverse developmental deficits, including slow growth, multiple limb and organ abnormalities, and intellectual disabilities. Severely-affected individuals most often have dominant loss-of-function mutations in the Nipped-B-Like (NIPBL) gene, and milder cases often have missense or in-frame deletion mutations in genes encoding subunits of the cohesin complex. Cohesin mediates sister chromatid cohesion to facilitate accurate chromosome segregation, and NIPBL is required for cohesin to bind to chromosomes. Individuals with CdLS, however, do not display overt cohesion or segregation defects. Rather, studies in human cells and model organisms indicate that modest decreases in NIPBL and cohesin activity alter the transcription of many genes that regulate growth and development. Sister chromatid cohesion factors, including the Nipped-B ortholog of NIPBL, are also critical for gene expression and development in Drosophila melanogaster. Here we describe how a modest reduction in Nipped-B activity alters growth and neurological function in Drosophila. These studies reveal that Nipped-B heterozygous mutant Drosophila show reduced growth, learning, and memory, and altered circadian rhythms. Importantly, the growth deficits are not caused by changes in systemic growth controls, but reductions in cell number and size attributable in part to reduced expression of myc (diminutive) and other growth control genes. The learning, memory and circadian deficits are accompanied by morphological abnormalities in brain structure. These studies confirm that Drosophila Nipped-B mutants provide a useful model for understanding CdLS, and provide new insights into the origins of birth defects. Cornelia de Lange Syndrome (CdLS) alters many aspects of growth and development. CdLS is caused by mutations in genes encoding proteins that ensure that chromosomes are distributed equally when a cell divides. These include genes that encode components of the cohesin complex, and Nipped-B-Like (NIPBL) that puts cohesin onto chromosomes. Individuals with CdLS have only modest reductions in the activities of these genes and do not show changes in chromosome distribution. Instead, they show differences in the expression many genes that control development. Animal models of CdLS will be useful for studies aimed at understanding how development is altered, and testing methods for treating CdLS. We find that Drosophila with one mutant copy of the Nipped-B gene, which is equivalent to the NIPBL gene, show characteristics similar to individuals with CdLS. These include reduced growth, learning, memory, and altered circadian rhythms. These studies thus indicate that Drosophila Nipped-B mutants are a valuable system for investigating the causes of the CdLS birth defects, and developing potential treatments. They also reveal that the slow growth in Drosophila Nipped-B mutants is not caused by disruption of systemic hormonal growth controls, and that the learning and memory deficits may reflect changes in brain structure.
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Affiliation(s)
- Yaning Wu
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Maria Gause
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dongbin Xu
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ziva Misulovin
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Cheri A. Schaaf
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ramya C. Mosarla
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Elizabeth Mannino
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Megan Shannon
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Emily Jones
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Mi Shi
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Wen-Feng Chen
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Olivia L. Katz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Amita Sehgal
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas A. Jongens
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ian D. Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (IDK); (DD)
| | - Dale Dorsett
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail: (IDK); (DD)
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41
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Vietri Rudan M, Hadjur S. Genetic Tailors: CTCF and Cohesin Shape the Genome During Evolution. Trends Genet 2015; 31:651-660. [PMID: 26439501 DOI: 10.1016/j.tig.2015.09.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/11/2015] [Accepted: 09/04/2015] [Indexed: 01/03/2023]
Abstract
Research into chromosome structure and organization is an old field that has seen some fascinating progress in recent years. Modern molecular methods that can describe the shape of chromosomes have begun to revolutionize our understanding of genome organization and the mechanisms that regulate gene activity. A picture is beginning to emerge of chromatin loops representing a widespread organizing principle of the chromatin fiber and the proteins cohesin and CCCTC-binding factor (CTCF) as key players anchoring such chromatin loops. Here we review our current understanding of the features of CTCF- and cohesin-mediated genome organization and how their evolution may have helped to shape genome structure.
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Affiliation(s)
- Matteo Vietri Rudan
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK.
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42
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Decroos C, Christianson NH, Gullett LE, Bowman CM, Christianson KE, Deardorff MA, Christianson DW. Biochemical and structural characterization of HDAC8 mutants associated with Cornelia de Lange syndrome spectrum disorders. Biochemistry 2015; 54:6501-13. [PMID: 26463496 PMCID: PMC4624487 DOI: 10.1021/acs.biochem.5b00881] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/26/2015] [Indexed: 01/06/2023]
Abstract
Cornelia de Lange Syndrome (CdLS) spectrum disorders are characterized by multiple organ system congenital anomalies that result from mutations in genes encoding core cohesin proteins SMC1A, SMC3, and RAD21, or proteins that regulate cohesin function such as NIPBL and HDAC8. HDAC8 is the Zn(2+)-dependent SMC3 deacetylase required for cohesin recycling during the cell cycle, and 17 different HDAC8 mutants have been identified to date in children diagnosed with CdLS. As part of our continuing studies focusing on aberrant HDAC8 function in CdLS, we now report the preparation and biophysical evaluation of five human HDAC8 mutants: P91L, G117E, H180R, D233G, and G304R. Additionally, the double mutants D233G-Y306F and P91L-Y306F were prepared to enable cocrystallization of intact enzyme-substrate complexes. X-ray crystal structures of G117E, P91L-Y306F, and D233G-Y306F HDAC8 mutants reveal that each CdLS mutation causes structural changes that compromise catalysis and/or thermostability. For example, the D233G mutation disrupts the D233-K202-S276 hydrogen bond network, which stabilizes key tertiary structure interactions, thereby significantly compromising thermostability. Molecular dynamics simulations of H180R and G304R HDAC8 mutants suggest that the bulky arginine side chain of each mutant protrudes into the substrate binding site and also causes active site residue Y306 to fluctuate away from the position required for substrate activation and catalysis. Significantly, the catalytic activities of most mutants can be partially or fully rescued by the activator N-(phenylcarbamothioyl)-benzamide, suggesting that HDAC8 activators may serve as possible leads in the therapeutic management of CdLS.
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Affiliation(s)
- Christophe Decroos
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Nicolas H. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Laura E. Gullett
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Christine M. Bowman
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Karen E. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Matthew A. Deardorff
- Division
of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Department
of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
- Radcliffe
Institute for Advanced Study, Harvard University, Cambridge, Massachusetts 02138, United States
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43
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Cavalleri V, Bettini LR, Barboni C, Cereda A, Mariani M, Spinelli M, Gervasini C, Russo S, Biondi A, Jankovic M, Selicorni A. Thrombocytopenia and Cornelia de Lange syndrome: Still an enigma? Am J Med Genet A 2015; 170A:130-4. [PMID: 26437745 DOI: 10.1002/ajmg.a.37390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 08/28/2015] [Indexed: 12/17/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) is a rare genetic disorder caused by mutations in the cohesion complex and its regulators. The syndrome is characterized by multiple organ system abnormalities, pre- and post-natal growth retardation and typical facial features. Thrombocytopenia is a reduction in platelet count to <150 × 10(9) L. It can be caused by congenital or acquired decreased production, increased destruction, or sequestration of platelets. In recent years, several papers reported thrombocytopenia and immune thrombocytopenia in patients affected by CdLS. In 2011, Lambert et al. estimated the risk of idiopathic thrombocytopenia purpura in CdLS patients to be 31-633 times greater than in the general population. We describe the incidence of thrombocytopenia in 127 Italian CdLS patients, identifying patients with transient or persistent thrombocytopenia, but a lower incidence of true idiopathic thrombocytopenic purpura (ITP).
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Affiliation(s)
- Valeria Cavalleri
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Laura R Bettini
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Chiara Barboni
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Anna Cereda
- Department of Pediatrics, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Milena Mariani
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Marco Spinelli
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Cristina Gervasini
- Division of Medical Genetics, San Paolo School of Medicine, University of Milano, Milano, Italy
| | - Silvia Russo
- IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Andrea Biondi
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Momcilo Jankovic
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
| | - Angelo Selicorni
- Department of Pediatrics, Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, San Gerardo Hospital, Milano Bicocca University, Monza, Italy
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44
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Zakari M, Yuen K, Gerton JL. Etiology and pathogenesis of the cohesinopathies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:489-504. [PMID: 25847322 PMCID: PMC6680315 DOI: 10.1002/wdev.190] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 01/12/2023]
Abstract
Cohesin is a chromosome-associated protein complex that plays many important roles in chromosome function. Genetic screens in yeast originally identified cohesin as a key regulator of chromosome segregation. Subsequently, work by various groups has identified cohesin as critical for additional processes such as DNA damage repair, insulator function, gene regulation, and chromosome condensation. Mutations in the genes encoding cohesin and its accessory factors result in a group of developmental and intellectual impairment diseases termed 'cohesinopathies.' How mutations in cohesin genes cause disease is not well understood as precocious chromosome segregation is not a common feature in cells derived from patients with these syndromes. In this review, the latest findings concerning cohesin's function in the organization of chromosome structure and gene regulation are discussed. We propose that the cohesinopathies are caused by changes in gene expression that can negatively impact translation. The similarities and differences between cohesinopathies and ribosomopathies, diseases caused by defects in ribosome biogenesis, are discussed. The contribution of cohesin and its accessory proteins to gene expression programs that support translation suggests that cohesin provides a means of coupling chromosome structure with the translational output of cells.
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Affiliation(s)
- Musinu Zakari
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Universite Pierre et Marie Curie, Paris, France
| | - Kobe Yuen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS, USA
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45
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Mei L, Liang D, Huang Y, Pan Q, Wu L. Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome. Gene 2015; 555:476-80. [DOI: 10.1016/j.gene.2014.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/09/2014] [Accepted: 11/13/2014] [Indexed: 11/25/2022]
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46
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Pavlidis E, Cantalupo G, Bianchi S, Piccolo B, Pisani F. Epileptic features in Cornelia de Lange syndrome: case report and literature review. Brain Dev 2014; 36:837-43. [PMID: 24461912 DOI: 10.1016/j.braindev.2013.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/20/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Cornelia de Lange syndrome is a rare genetic disease, caused by mutations in three known different genes: NIBPL (crom 5p), SMC1A (crom X) and SMC3 (crom 10q), that account for about 65% of cases. This syndrome is characterized by distinctive facial features, psychomotor delay, growth retardation since the prenatal period (second trimester of pregnancy), hands and feet abnormalities, and involvement of other organs/systems. SMC1A and SMC3 mutations are responsible for a mild phenotype of the syndrome. METHODS We report the electroclinical features of epilepsy in a child with a mild Cornelia de Lange syndrome and furthermore we reviewed the descriptions of the epileptic findings available in the literature in patients with such syndrome. RESULTS A large heterogeneity of the epileptic findings in the literature is reported. CONCLUSION The presence of epilepsy could be related to pathophysiological factors independent of those implicated in the characterization of main classical phenotypic features. A more detailed description of the epileptic findings could help clinicians in the diagnosis of this syndrome in those cases lacking of the typical features.
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Affiliation(s)
- Elena Pavlidis
- Child Neuropsychiatry Unit, Department of Neuroscience, University of Parma, Parma, Italy.
| | - Gaetano Cantalupo
- Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Sara Bianchi
- Child Neuropsychiatry Unit, Department of Neuroscience, University of Parma, Parma, Italy
| | - Benedetta Piccolo
- Child Neuropsychiatry Unit, Department of Neuroscience, University of Parma, Parma, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Department of Neuroscience, University of Parma, Parma, Italy
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47
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Muto A, Ikeda S, Lopez-Burks ME, Kikuchi Y, Calof AL, Lander AD, Schilling TF. Nipbl and mediator cooperatively regulate gene expression to control limb development. PLoS Genet 2014; 10:e1004671. [PMID: 25255084 PMCID: PMC4177752 DOI: 10.1371/journal.pgen.1004671] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS), the most common “cohesinopathy”. It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb), knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions. Limb malformations are a striking feature of Cornelia de Lange Syndrome (CdLS), a multi-system birth defects disorder most commonly caused by haploinsufficiency for NIPBL. In addition to its role as a cohesin-loading factor, Nipbl also regulates gene expression, but how partial Nipbl deficiency causes limb defects is unknown. Using zebrafish and mouse models, we show that expression of multiple key regulators of early limb development, including shha, hand2 and hox genes, are sensitive to Nipbl deficiency. Furthermore, we find morphological and gene expression abnormalities similar to those of Nipbl-deficient zebrafish in the limb buds of zebrafish deficient for the Med12 subunit of Mediator—a protein complex that mediates physical interactions between enhancers and promoters—and genetic interaction studies support the view that Mediator and Nipbl act together. Strikingly, depletion of either Nipbl or Med12 leads to characteristic changes in hox gene expression that reflect the locations of genes within their chromosomal clusters, as well as to disruption of large-scale chromosome organization around the hoxda cluster, consistent with impairment of long-range enhancer-promoter interaction. Together, these findings provide insights into both the etiology of limb defects in CdLS, and the mechanisms by which Nipbl and Mediator influence gene expression.
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Affiliation(s)
- Akihiko Muto
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine California
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Shingo Ikeda
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Martha E. Lopez-Burks
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine California
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Anne L. Calof
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, California, United States of America
- * E-mail: (ALC); (ADL)
| | - Arthur D. Lander
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine California
- * E-mail: (ALC); (ADL)
| | - Thomas F. Schilling
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine California
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48
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Decroos C, Bowman CM, Moser JAS, Christianson KE, Deardorff MA, Christianson DW. Compromised structure and function of HDAC8 mutants identified in Cornelia de Lange Syndrome spectrum disorders. ACS Chem Biol 2014; 9:2157-64. [PMID: 25075551 PMCID: PMC4168803 DOI: 10.1021/cb5003762] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Cornelia
de Lange Syndrome (CdLS) is a multiple congenital anomaly
disorder resulting from mutations in genes that encode the core components
of the cohesin complex, SMC1A, SMC3, and RAD21, or two of its regulatory
proteins, NIPBL and HDAC8. HDAC8 is the human SMC3 lysine deacetylase
required for cohesin recycling in the cell cycle. To date, 16 different
missense mutations in HDAC8 have recently been identified in children
diagnosed with CdLS. To understand the molecular effects of these
mutations in causing CdLS and overlapping phenotypes, we have fully
characterized the structure and function of five HDAC8 mutants: C153F,
A188T, I243N, T311M, and H334R. X-ray crystal structures reveal that
each mutation causes local structural changes that compromise catalysis
and/or thermostability. For example, the C153F mutation triggers conformational
changes that block acetate product release channels, resulting in
only 2% residual catalytic activity. In contrast, the H334R mutation
causes structural changes in a polypeptide loop distant from the active
site and results in 91% residual activity, but the thermostability
of this mutant is significantly compromised. Strikingly, the catalytic
activity of these mutants can be partially or fully rescued in vitro by the HDAC8 activator N-(phenylcarbamothioyl)benzamide.
These results suggest that HDAC8 activators might be useful leads
in the search for new therapeutic strategies in managing CdLS.
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Affiliation(s)
- Christophe Decroos
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Christine M. Bowman
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Joe-Ann S. Moser
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Karen E. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Matthew A. Deardorff
- Division
of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 United States
- Department
of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 United States
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
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49
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Abstract
Why certain point mutations in a general transcription factor are associated with specific forms of cancer has been a major question in cancer biology. Enhancers are DNA regulatory elements that are key regulators of tissue-specific gene expression. Recent studies suggest that enhancer malfunction through point mutations in either regulatory elements or factors modulating enhancer-promoter communication could be the cause of tissue-specific cancer development. In this Perspective, we will discuss recent findings in the identification of cancer-related enhancer mutations and the role of Drosophila Trr and its human homologs, the MLL3 and MLL4/COMPASS-like complexes, as enhancer histone H3 lysine 4 (H3K4) monomethyltransferases functioning in enhancer-promoter communication. Recent genome-wide studies in the cataloging of somatic mutations in cancer have identified mutations in intergenic sequences encoding regulatory elements-and in MLL3 and MLL4 in both hematological malignancies and solid tumors. We propose that cancer-associated mutations in MLL3 and MLL4 exert their properties through the malfunction of Trr/MLL3/MLL4-dependent enhancers.
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50
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Cohesin mutations in myeloid malignancies: underlying mechanisms. Exp Hematol Oncol 2014; 3:13. [PMID: 24904756 PMCID: PMC4046106 DOI: 10.1186/2162-3619-3-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 01/09/2023] Open
Abstract
Recently, whole genome sequencing approaches have pinpointed mutations in genes that were previously not associated with cancer. For Acute Myeloid Leukaemia (AML), and other myeloid disorders, these approaches revealed a high prevalence of mutations in genes encoding the chromosome cohesion complex, cohesin. Cohesin mutations represent a novel genetic pathway for AML, but how AML arises from these mutations is unknown. This review will explore the potential mechanisms by which cohesin mutations contribute to AML and other myeloid malignancies.
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