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Zhang B, Zhu Y, Zhang Z, Wu F, Ma X, Sheng W, Dai R, Guo Z, Yan W, Hao L, Huang G, Ma D, Hao B, Ma J. SMC3 contributes to heart development by regulating super-enhancer associated genes. Exp Mol Med 2024:10.1038/s12276-024-01293-0. [PMID: 39085358 DOI: 10.1038/s12276-024-01293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/23/2024] [Accepted: 05/21/2024] [Indexed: 08/02/2024] Open
Abstract
Abnormal cardiac development has been observed in individuals with Cornelia de Lange syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. However, the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed that CdLS patients with SMC3 mutations have high rates of congenital heart disease (CHD). We utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which exhibit varying degrees of outflow tract (OFT) abnormalities, to further explore this relationship. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. By employing single-nucleus RNA sequencing and chromosome conformation capture high-throughput genome-wide translocation sequencing, we revealed that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SEs) and promoters. Notably, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research revealed a novel role for SMC3 in heart development via the regulation of SE-associated genes, suggesting its potential relevance as a CHD-related gene and providing crucial insights into the molecular basis of cardiac development.
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Affiliation(s)
- Bowen Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Yongchang Zhu
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Zhen Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feizhen Wu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Xiaojing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Wei Sheng
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Ranran Dai
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Zhenglong Guo
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Weili Yan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Guoying Huang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Bingtao Hao
- Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- Henan Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, 450000, China.
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
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2
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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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3
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Boukas L, Luperchio TR, Razi A, Hansen KD, Bjornsson HT. Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice. Genome Res 2024; 34:696-710. [PMID: 38702196 PMCID: PMC11216309 DOI: 10.1101/gr.278416.123] [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: 08/17/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically shows phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption-the root of the pathogenesis-is similar in the different disease-relevant cell types. This is possible in principle, because all these cell types are subject to effects from the same causative gene, which has the same kind of function (e.g., methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2 and find that the chromatin accessibility changes in neurons are mostly distinct from changes in B or T cells. This is not because the neuronal accessibility changes occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that regulatory elements disrupted in B/T cells do show chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able to identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators and suggest that blood-derived episignatures, although useful diagnostically, may not be well suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.
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Affiliation(s)
- Leandros Boukas
- Department of Pediatrics, Children's National Hospital, Washington, DC 20010, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
- Landspitali University Hospital, 101 Reykjavík, Iceland
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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. 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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5
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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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6
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Boukas L, Luperchio TR, Razi A, Hansen KD, Bjornsson HT. Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551456. [PMID: 37577516 PMCID: PMC10418197 DOI: 10.1101/2023.08.01.551456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically exhibits phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption - the root of the pathogenesis - is similar in the different disease-relevant cell types. This is possible in principle, since all these cell-types are subject to effects from the same causative gene, that has the same kind of function (e.g. methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2, and find that the chromatin accessibility abnormalities in neurons are mostly distinct from those in B or T cells. This is not because the neuronal abnormalities occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that the regions disrupted in B/T cells do exhibit chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able to identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators, and suggest that blood-derived "episignatures" may not be well-suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.
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Affiliation(s)
- Leandros Boukas
- Department of Pediatrics, Children’s National Hospital
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | | | - Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
| | - Kasper D. Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
- Department of Biomedical Engineering, Johns Hopkins School of Medicine
| | - Hans T. Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine
- Faculty of Medicine, University of Iceland
- Landspitali University Hospital
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7
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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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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Horsfield JA. Full circle: a brief history of cohesin and the regulation of gene expression. FEBS J 2023; 290:1670-1687. [PMID: 35048511 DOI: 10.1111/febs.16362] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
The cohesin complex has a range of crucial functions in the cell. Cohesin is essential for mediating chromatid cohesion during mitosis, for repair of double-strand DNA breaks, and for control of gene transcription. This last function has been the subject of intense research ever since the discovery of cohesin's role in the long-range regulation of the cut gene in Drosophila. Subsequent research showed that the expression of some genes is exquisitely sensitive to cohesin depletion, while others remain relatively unperturbed. Sensitivity to cohesin depletion is also remarkably cell type- and/or condition-specific. The relatively recent discovery that cohesin is integral to forming chromatin loops via loop extrusion should explain much of cohesin's gene regulatory properties, but surprisingly, loop extrusion has failed to identify a 'one size fits all' mechanism for how cohesin controls gene expression. This review will illustrate how early examples of cohesin-dependent gene expression integrate with later work on cohesin's role in genome organization to explain mechanisms by which cohesin regulates gene expression.
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Affiliation(s)
- Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, New Zealand
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10
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Chen Y, Chen Q, Yuan K, Zhu J, Fang Y, Yan Q, Wang C. A Novel de Novo Variant in 5' UTR of the NIPBL Associated with Cornelia de Lange Syndrome. Genes (Basel) 2022; 13:740. [PMID: 35627125 PMCID: PMC9140414 DOI: 10.3390/genes13050740] [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: 02/23/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Cornelia de Lange syndrome (CdLS) is a genetic syndrome characterized by intellectual disability, special facial features, growth retardation, feeding difficulties, and multiple organ system abnormalities. NIPBL variants occur in approximately 80% of CdLS cases. Aims: We report a novel de novo heterozygous pathogenic variant in the NIPBL and its association with CdLS. We also examined the key regulatory sequences of the 5′ untranslated region in NIPBL mRNA. Few studies have reported mutation sites in the 5′ untranslated region (UTR) of the NIPBL that result in CdLS. Methods: The patient’s medical history, clinical manifestations, physical examination, laboratory examination, Griffiths development assessment scale—Chinese version, and cardiac B-ultrasound were examined. Mutation screening was conducted using trio whole exome sequencing (trio-WES) and Sanger sequencing. Quantitative PCR was performed to measure the NIPBL expression in peripheral blood mononuclear cells. A Dual-Luciferase reporter assay was conducted to evaluate the transcription of truncated mutants. Results: The proband showed characteristics of CdLS including thick eyebrows, a concave nasal ridge, long and smooth philtrum, downturned corners of the mouth, intellectual disability, postnatal growth retardation, and a short fifth toe. A novel de novo heterozygous pathogenic variant in the NIPBL (c.-467C > T) was identified. A Dual-Luciferase reporter gene assay showed that SPO1 (-490 bp to -360 bp) and SPO3 (-490 bp to -401 bp) induced the highest activity. Conclusions: We found a novel de novo heterozygous pathogenic variant (c.-467C > T) in the NIPBL resulting in CdLS. Our findings expand the spectrum of pathogenic mutations for CdLS. Our in vitro experiments elucidated important regulatory sequences in the 5′ UTR of the NIPBL.
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Affiliation(s)
- Yonghua Chen
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
| | - Qingqing Chen
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
| | - Ke Yuan
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
| | - Jianfang Zhu
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
| | - Yanlan Fang
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
| | - Qingfeng Yan
- College of Life Science, Zhejiang University, Hangzhou 310027, China;
| | - Chunlin Wang
- Department of Pediatrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (Y.C.); (Q.C.); (K.Y.); (J.Z.); (Y.F.)
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11
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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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12
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Oliver C, Groves L, Hansen BD, Salehi M, Kheradmand S, Carrico CS, Caudill P, Mattingly M, Dorsett D, Chea S, Singh VP, Krantz ID, Huisman S, Deardorff MA, Kline AD. Cornelia de Lange syndrome and the Cohesin complex: Abstracts from the 9th Biennial Scientific and Educational Virtual Symposium 2020. Am J Med Genet A 2021; 188:1005-1014. [PMID: 34877788 DOI: 10.1002/ajmg.a.62591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a spectrum disorder due to variants in genes of the cohesin protein complex. The following abstracts are from the Cornelia de Lange Syndrome Scientific and Educational Symposium held virtually in October 2020. Aspects of behavior, including autistic features, impulsivity, adaptive skills, executive function, and anxiety are described. Applied behavioral analysis is a promising approach for autism, and an N-acetylcysteine trial is proposed. Children below 6 years with CdLS have an increased number of and further travel to medical providers, with insurance type comprising a significant barrier. Speech, language, and feeding abilities fall significantly below expectations for age in CdLS. Augmentative alternative communication can yield potential barriers as well as interesting benefits. Developmentally, studies in animal models further elucidate the mechanisms and roles of cohesin: link with mediator transcriptional complex; facilitation of enhancer-promoter communication; regulation of gene expression; allocation of cells to germ layers; and repair of spontaneous DNA damage in placental cells. Genome and RNA sequencing can help identify the molecular cause in the 20% of individuals with suspected CdLS and negative testing. The phenotypes in individuals with variants in the SMC1A gene are distinct, and that with intractable seizures has been further evaluated. AMA CME credits provided by GBMC, Baltimore, MD. All studies approved by an ethics committee.
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Affiliation(s)
- Chris Oliver
- School of Psychology, University of Birmingham, Birmingham, UK
| | - Laura Groves
- School of Psychology, University of Birmingham, Birmingham, UK
| | | | - Masoud Salehi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shaydah Kheradmand
- Master's in Genetic Counseling Training Program, University of Maryland, Baltimore, Maryland, USA
| | - Cheri S Carrico
- Communication Sciences and Disorders, Elmhurst College, Elmhurst, Illinois, USA
| | - Patti Caudill
- Milton J. Dance, Jr Head & Neck Center, Baltimore, Maryland, USA
| | - Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA
| | - Stephenson Chea
- Department of Developmental and Cell Biology, and the Center for Complex Biological Systems, University of California, Irvine, California, USA
| | | | - Ian D Krantz
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sylvia Huisman
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, and Prinsenstichting, Purmerend, The Netherlands
| | - Matthew A Deardorff
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, Maryland, USA
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13
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Marí-Beffa M, Mesa-Román AB, Duran I. Zebrafish Models for Human Skeletal Disorders. Front Genet 2021; 12:675331. [PMID: 34490030 PMCID: PMC8418114 DOI: 10.3389/fgene.2021.675331] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
In 2019, the Nosology Committee of the International Skeletal Dysplasia Society provided an updated version of the Nosology and Classification of Genetic Skeletal Disorders. This is a reference list of recognized diseases in humans and their causal genes published to help clinician diagnosis and scientific research advances. Complementary to mammalian models, zebrafish has emerged as an interesting species to evaluate chemical treatments against these human skeletal disorders. Due to its versatility and the low cost of experiments, more than 80 models are currently available. In this article, we review the state-of-art of this “aquarium to bedside” approach describing the models according to the list provided by the Nosology Committee. With this, we intend to stimulate research in the appropriate direction to efficiently meet the actual needs of clinicians under the scope of the Nosology Committee.
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Affiliation(s)
- Manuel Marí-Beffa
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain.,Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
| | - Ana B Mesa-Román
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain
| | - Ivan Duran
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain.,Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
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14
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García-Gutiérrez P, García-Domínguez M. BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome. Front Mol Biosci 2021; 8:709232. [PMID: 34386522 PMCID: PMC8353280 DOI: 10.3389/fmolb.2021.709232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental syndrome with complex multisystem phenotypic features. It has been traditionally considered a cohesinopathy together with other phenotypically related diseases because of their association with mutations in subunits of the cohesin complex. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably and, although their precise molecular mechanisms are not well defined yet, the potential pathomechanisms underlying these diverse developmental defects have been theoretically linked to alterations of the cohesin complex function. The cohesin complex plays a critical role in sister chromatid cohesion, but this function is not affected in CdLS. In the last decades, a non-cohesion-related function of this complex on transcriptional regulation has been well established and CdLS pathoetiology has been recently associated to gene expression deregulation. Up to 70% of CdLS cases are linked to mutations in the cohesin-loading factor NIPBL, which has been shown to play a prominent function on chromatin architecture and transcriptional regulation. Therefore, it has been suggested that CdLS can be considered a transcriptomopathy. Actually, CdLS-like phenotypes have been associated to mutations in chromatin-associated proteins, as KMT2A, AFF4, EP300, TAF6, SETD5, SMARCB1, MAU2, ZMYND11, MED13L, PHIP, ARID1B, NAA10, BRD4 or ANKRD11, most of which have no known direct association with cohesin. In the case of BRD4, a critical highly investigated transcriptional coregulator, an interaction with NIPBL has been recently revealed, providing evidence on their cooperation in transcriptional regulation of developmentally important genes. This new finding reinforces the notion of an altered gene expression program during development as the major etiological basis for CdLS. In this review, we intend to integrate the recent available evidence on the molecular mechanisms underlying the clinical manifestations of CdLS, highlighting data that favors a transcription-centered framework, which support the idea that CdLS could be conceptualized as a transcriptomopathy.
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Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
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15
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Gu W, Wang L, Gu R, Ouyang H, Bao B, Zheng L, Xu B. Defects of cohesin loader lead to bone dysplasia associated with transcriptional disturbance. J Cell Physiol 2021; 236:8208-8225. [PMID: 34170011 DOI: 10.1002/jcp.30491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023]
Abstract
Cohesin loader nipped-B-like protein (Nipbl) is increasingly recognized for its important role in development and cancer. Cornelia de Lange Syndrome (CdLS), mostly caused by heterozygous mutations of Nipbl, is an autosomal dominant disease characterized by multiorgan malformations. However, the regulatory role and underlying mechanism of Nipbl in skeletal development remain largely elusive. In this study, we constructed a Nipbl-a Cas9-knockout (KO) zebrafish, which displayed severe retardation of global growth and skeletal development. Deficiency of Nipbl remarkably compromised cell growth and survival, and osteogenic differentiation of mammalian osteoblast precursors. Furthermore, Nipbl depletion impaired the cell cycle process, and caused DNA damage accumulation and cellular senescence. In addition, nucleolar fibrillarin expression, global rRNA biogenesis, and protein translation were defective in the Nipbl-depleted osteoblast precursors. Interestingly, an integrated stress response inhibitor (ISRIB), partially rescued Nipbl depletion-induced cellular defects in proliferation and apoptosis, osteogenesis, and nucleolar function. Simultaneously, we performed transcriptome analysis of Nipbl deficiency on human neural crest cells and mouse embryonic fibroblasts in combination with Nipbl ChIP-Seq. We found that Nipbl deficiency caused thousands of differentially expressed genes including some important genes in bone and cartilage development. In conclusion, Nipbl deficiency compromised skeleton development through impairing osteoblast precursor cell proliferation and survival, and osteogenic differentiation, and also disturbing the expression of some osteogenesis-regulatory genes. Our study elucidated that Nipbl played a pivotal role in skeleton development, and supported the fact that treatment of ISRIB may provide an early intervention strategy to alleviate the bone dysplasia of CdLS.
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Affiliation(s)
- Weihuai Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lihong Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renjie Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huiya Ouyang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baicheng Bao
- Hospital of Stomatology, Orthodontic Department, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, Department of Pediatric Dentistry, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Baoshan Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
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16
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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17
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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18
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Labudina A, Horsfield JA. The three-dimensional genome in zebrafish development. Brief Funct Genomics 2021:elab008. [PMID: 33675363 DOI: 10.1093/bfgp/elab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
In recent years, remarkable progress has been made toward understanding the three-dimensional (3D) organisation of genomes and the influence of genome organisation on gene regulation. Although 3D genome organisation probably plays a crucial role in embryo development, animal studies addressing the developmental roles of chromosome topology are only just starting to emerge. Zebrafish, an important model system for early development, have already contributed important advances in understanding the developmental consequences of perturbation in 3D genome organisation. Zebrafish have been used to determine the effects of mutations in proteins responsible for 3D genome organisation: cohesin and CTCF. In this review, we highlight research to date from zebrafish that has provided insight into how 3D genome organisation contributes to tissue-specific gene regulation and embryo development.
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19
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Bertero A, Rosa-Garrido M. Three-dimensional chromatin organization in cardiac development and disease. J Mol Cell Cardiol 2021; 151:89-105. [PMID: 33242466 PMCID: PMC11056610 DOI: 10.1016/j.yjmcc.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Recent technological advancements in the field of chromatin biology have rewritten the textbook on nuclear organization. We now appreciate that the folding of chromatin in the three-dimensional space (i.e. its 3D "architecture") is non-random, hierarchical, and highly complex. While 3D chromatin structure is partially encoded in the primary sequence and thereby broadly conserved across cell types and states, a substantial portion of the genome seems to be dynamic during development or in disease. Moreover, there is growing evidence that at least some of the 3D structure of chromatin is functionally linked to gene regulation, both being modulated by and impacting on multiple nuclear processes (including DNA replication, transcription, and RNA splicing). In recent years, these new concepts have nourished several investigations about the functional role of 3D chromatin topology dynamics in the heart during development and disease. This review aims to provide a comprehensive overview of our current understanding in this field, and to discuss how this knowledge can inform further research as well as clinical practice.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA.
| | - Manuel Rosa-Garrido
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, 650 Charles Young Dr, Los Angeles, CA 90095, USA.
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20
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Spreafico M, Mangano E, Mazzola M, Consolandi C, Bordoni R, Battaglia C, Bicciato S, Marozzi A, Pistocchi A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. Int J Mol Sci 2020; 21:E9719. [PMID: 33352756 PMCID: PMC7766774 DOI: 10.3390/ijms21249719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.
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Affiliation(s)
- Marco Spreafico
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Eleonora Mangano
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Mara Mazzola
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Roberta Bordoni
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Cristina Battaglia
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio-Emilia, Via G. Campi 287, 41125 Modena, Italy;
| | - Anna Marozzi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Anna Pistocchi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
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21
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Ketharnathan S, Labudina A, Horsfield JA. Cohesin Components Stag1 and Stag2 Differentially Influence Haematopoietic Mesoderm Development in Zebrafish Embryos. Front Cell Dev Biol 2020; 8:617545. [PMID: 33365313 PMCID: PMC7750468 DOI: 10.3389/fcell.2020.617545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Cohesin is a multiprotein complex made up of core subunits Smc1, Smc3, and Rad21, and either Stag1 or Stag2. Normal haematopoietic development relies on crucial functions of cohesin in cell division and regulation of gene expression via three-dimensional chromatin organization. Cohesin subunit STAG2 is frequently mutated in myeloid malignancies, but the individual contributions of Stag variants to haematopoiesis or malignancy are not fully understood. Zebrafish have four Stag paralogues (Stag1a, Stag1b, Stag2a, and Stag2b), allowing detailed genetic dissection of the contribution of Stag1-cohesin and Stag2-cohesin to development. Here we characterize for the first time the expression patterns and functions of zebrafish stag genes during embryogenesis. Using loss-of-function CRISPR-Cas9 zebrafish mutants, we show that stag1a and stag2b contribute to primitive embryonic haematopoiesis. Both stag1a and stag2b mutants present with erythropenia by 24 h post-fertilization. Homozygous loss of either paralogue alters the number of haematopoietic/vascular progenitors in the lateral plate mesoderm. The lateral plate mesoderm zone of scl-positive cells is expanded in stag1a mutants with concomitant loss of kidney progenitors, and the number of spi1-positive cells are increased, consistent with skewing toward primitive myelopoiesis. In contrast, stag2b mutants have reduced haematopoietic/vascular mesoderm and downregulation of primitive erythropoiesis. Our results suggest that Stag1 and Stag2 proteins cooperate to balance the production of primitive haematopoietic/vascular progenitors from mesoderm.
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Affiliation(s)
- Sarada Ketharnathan
- Department of Pathology, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Anastasia Labudina
- Department of Pathology, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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22
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De Koninck M, Lapi E, Badía-Careaga C, Cossío I, Giménez-Llorente D, Rodríguez-Corsino M, Andrada E, Hidalgo A, Manzanares M, Real FX, Losada A. Essential Roles of Cohesin STAG2 in Mouse Embryonic Development and Adult Tissue Homeostasis. Cell Rep 2020; 32:108014. [PMID: 32783938 DOI: 10.1016/j.celrep.2020.108014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 07/17/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin mediates sister chromatid cohesion and 3D genome folding. Two versions of the complex carrying STAG1 or STAG2 coexist in somatic vertebrate cells. STAG2 is commonly mutated in cancer, and germline mutations have been identified in cohesinopathy patients. To better understand the underlying pathogenic mechanisms, we report the consequences of Stag2 ablation in mice. STAG2 is largely dispensable in adults, and its tissue-wide inactivation does not lead to tumors but reduces fitness and affects both hematopoiesis and intestinal homeostasis. STAG2 is also dispensable for murine embryonic fibroblasts in vitro. In contrast, Stag2-null embryos die by mid-gestation and show global developmental delay and defective heart morphogenesis, most prominently in structures derived from secondary heart field progenitors. Both decreased proliferation and altered transcription of tissue-specific genes contribute to these defects. Our results provide compelling evidence on cell- and tissue-specific roles of different cohesin complexes and how their dysfunction contributes to disease.
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Affiliation(s)
- Magali De Koninck
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; CIBERONC, Madrid, Spain
| | | | - Itziar Cossío
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Elena Andrada
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Andrés Hidalgo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, 28049 Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; CIBERONC, Madrid, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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Abstract
Structural Maintenance of Chromosomes (SMCs) are part of a large family of ring complexes that participates in a number of DNA transactions. Among SMCs, SMC1A gene is unique. It encodes a subunit of the cohesin-core complex that tethers sister chromatids together to ensure correct chromosome segregation in both mitosis and meiosis. As a member of the cohesin ring, SMC1A takes part in gene transcription regulation and genome organization; and it participates in the DNA Damage Repair (DDR) pathway, being phosphorylated by Ataxia Telangiectasia Mutated (ATM) and Ataxia Telangiectasia and Rad3 Related (ATR) threonine/serine kinases. It is also a component of the Recombination protein complex (RC-1) involved in DNA repair by recombination. SMC1A pathogenic variants have been described in Cornelia de Lange syndrome (CdLS), a human rare disease, and recently SMC1A variants have been associated with epilepsy or resembling Rett syndrome phenotype. Finally, SMC1A variants have been identified in several human cancers. In this review, our current knowledge of the SMC1A gene has been summarized.
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Affiliation(s)
- Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Pisa, Italy.
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24
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Cucco F, Sarogni P, Rossato S, Alpa M, Patimo A, Latorre A, Magnani C, Puisac B, Ramos FJ, Pié J, Musio A. Pathogenic variants in EP300 and ANKRD11 in patients with phenotypes overlapping Cornelia de Lange syndrome. Am J Med Genet A 2020; 182:1690-1696. [PMID: 32476269 DOI: 10.1002/ajmg.a.61611] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/20/2020] [Accepted: 04/20/2020] [Indexed: 12/22/2022]
Abstract
Cornelia de Lange syndrome (CdLS), Rubinstein-Taybi syndrome (RSTS), and KBG syndrome are three distinct developmental human disorders. Variants in seven genes belonging to the cohesin pathway, NIPBL, SMC1A, SMC3, HDAC8, RAD21, ANKRD11, and BRD4, were identified in about 80% of patients with CdLS, suggesting that additional causative genes remain to be discovered. Two genes, CREBBP and EP300, have been associated with RSTS, whereas KBG results from variants in ANKRD11. By exome sequencing, a genetic cause was elucidated in two patients with clinical diagnosis of CdLS but without variants in known CdLS genes. In particular, genetic variants in EP300 and ANKRD11 were identified in the two patients with CdLS. EP300 and ANKRD11 pathogenic variants caused the reduction of the respective proteins suggesting that their low levels contribute to CdLS-like phenotype. These findings highlight the clinical overlap between CdLS, RSTS, and KBG and support the notion that these rare disorders are linked to abnormal chromatin remodeling, which in turn affects the transcriptional machinery.
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Affiliation(s)
- Francesco Cucco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Patrizia Sarogni
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Sara Rossato
- U.O.C. Pediatria, Ospedale San Bortolo, Vicenza, Italy
| | - Mirella Alpa
- Department of Clinical and Biological Sciences, Center of Research of Immunopathology and Rare Diseases, Coordinating Center of the Network for Rare Diseases of Piedmont and Aosta Valley, Turin, Italy
| | - Alessandra Patimo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Ana Latorre
- Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, Unidad de Genética Clínica y Genómica Funcional, Zaragoza, Spain
| | - Cinzia Magnani
- Neonatology and Neonatal Intensive Care Unit, Maternal and Child Department, University of Parma, Parma, Italy
| | - Beatriz Puisac
- Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, Unidad de Genética Clínica y Genómica Funcional, Zaragoza, Spain
| | - Feliciano J Ramos
- Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, Unidad de Genética Clínica y Genómica Funcional, Zaragoza, Spain
| | - Juan Pié
- Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, Unidad de Genética Clínica y Genómica Funcional, Zaragoza, Spain
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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25
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Sarogni P, Pallotta MM, Musio A. Cornelia de Lange syndrome: from molecular diagnosis to therapeutic approach. J Med Genet 2020; 57:289-295. [PMID: 31704779 PMCID: PMC7231464 DOI: 10.1136/jmedgenet-2019-106277] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/08/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a severe genetic disorder characterised by multisystemic malformations. CdLS is due to pathogenetic variants in NIPBL, SMC1A, SMC3, RAD21 and HDAC8 genes which belong to the cohesin pathway. Cohesin plays a pivotal role in chromatid cohesion, gene expression, and DNA repair. In this review, we will discuss how perturbations in those biological processes contribute to CdLS phenotype and will emphasise the state-of-art of CdLS therapeutic approaches.
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Affiliation(s)
- Patrizia Sarogni
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Maria M Pallotta
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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26
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Holowiecki A, Linstrum K, Ravisankar P, Chetal K, Salomonis N, Waxman JS. Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development 2020; 147:dev185652. [PMID: 32094112 PMCID: PMC7063670 DOI: 10.1242/dev.185652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Vertebrate heart development requires the integration of temporally distinct differentiating progenitors. However, few signals are understood that restrict the size of the later-differentiating outflow tract (OFT). We show that improper specification and proliferation of second heart field (SHF) progenitors in zebrafish lazarus (lzr) mutants, which lack the transcription factor Pbx4, produces enlarged hearts owing to an increase in ventricular and smooth muscle cells. Specifically, Pbx4 initially promotes the partitioning of the SHF into anterior progenitors, which contribute to the OFT, and adjacent endothelial cell progenitors, which contribute to posterior pharyngeal arches. Subsequently, Pbx4 limits SHF progenitor (SHFP) proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed previously unappreciated distinct differentiation states and progenitor subpopulations that normally reside within the SHF and arterial pole of the heart. Specifically, the transcriptional profiles of Pbx4-deficient nkx2.5+ SHFPs are less distinct and display characteristics of normally discrete proliferative progenitor and anterior, differentiated cardiomyocyte populations. Therefore, our data indicate that the generation of proper OFT size and arch arteries requires Pbx-dependent stratification of unique differentiation states to facilitate both homeotic-like transformations and limit progenitor production within the SHF.
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Affiliation(s)
- Andrew Holowiecki
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kelsey Linstrum
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Molecular Genetics Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Padmapriyadarshini Ravisankar
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kashish Chetal
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joshua S Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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27
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Yang Q, Wu F, Mi Y, Wang F, Cai K, Yang X, Zhang R, Liu L, Zhang Y, Wang Y, Wang X, Xu M, Gui Y, Li Q. Aberrant expression of miR-29b-3p influences heart development and cardiomyocyte proliferation by targeting NOTCH2. Cell Prolif 2020; 53:e12764. [PMID: 32077168 PMCID: PMC7106969 DOI: 10.1111/cpr.12764] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/24/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives microRNA‐29 (miR‐29) family have shown different expression patterns in cardiovascular diseases. Our study aims to explore the effect and mechanism of miR‐29 family on cardiac development. Materials and methods A total of 13 patients with congenital heart disease (CHD) and 7 controls were included in our study. Tissues were obtained from the right ventricular outflow tract (RVOT) after surgical resection or autopsy. The next‐generation sequencing was applied to screen the microRNA expression profiles of CHD. Quantitative RT‐PCR and Western blot were employed to measure genes expression. Tg Cmlc2: GFP reporter zebrafish embryos were injected with microRNA (miRNA) to explore its role in cardiac development in vivo. Dual‐luciferase reporter assay was designed to validate the target gene of miRNAs. CCK‐8 and EdU incorporation assays were performed to evaluate cardiomyocyte proliferation. Results Our study showed miR‐29b‐3p expression was significantly increased in the RVOT of the CHD patients. Injection of miR‐29b‐3p into zebrafish embryos induced higher mortality and malformation rates, developmental delay, cardiac malformation and dysfunction. miR‐29b‐3p inhibited cardiomyocyte proliferation, and its inhibitor promoted cardiomyocyte proliferation in vitro and in vivo. Furthermore, we identified that miR‐29b‐3p influenced cardiomyocyte proliferation by targeting NOTCH2, which was down‐regulated in the RVOT of the CHD patients. Conclusion This study reveals that miR‐29b‐3p functions as a novel regulator of cardiac development and inhibits cardiomyocyte proliferation via NOTCH2, which provides novel insights into the aetiology and potential treatment of CHD.
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Affiliation(s)
- Qian Yang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Wu
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yaping Mi
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ke Cai
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaoshan Yang
- Department of Bioscience, Bengbu Medical College, Bengbu, China
| | - Ranran Zhang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lian Liu
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yawen Zhang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Youhua Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Wang
- Cancer Metabolism Laboratory, Cancer Institute, Fudan University, Shanghai, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yonghao Gui
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.,Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
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28
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Piché J, Van Vliet PP, Pucéat M, Andelfinger G. The expanding phenotypes of cohesinopathies: one ring to rule them all! Cell Cycle 2019; 18:2828-2848. [PMID: 31516082 PMCID: PMC6791706 DOI: 10.1080/15384101.2019.1658476] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022] Open
Abstract
Preservation and development of life depend on the adequate segregation of sister chromatids during mitosis and meiosis. This process is ensured by the cohesin multi-subunit complex. Mutations in this complex have been associated with an increasing number of diseases, termed cohesinopathies. The best characterized cohesinopathy is Cornelia de Lange syndrome (CdLS), in which intellectual and growth retardations are the main phenotypic manifestations. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably. Novel roles of the cohesin complex have emerged during the past decades, suggesting that important cell cycle regulators exert important biological effects through non-cohesion-related functions and broadening the potential pathomechanisms involved in cohesinopathies. This review focuses on non-cohesion-related functions of the cohesin complex, gene dosage effect, epigenetic regulation and TGF-β in cohesinopathy context, especially in comparison to Chronic Atrial and Intestinal Dysrhythmia (CAID) syndrome, a very distinct cohesinopathy caused by a homozygous Shugoshin-1 (SGO1) mutation (K23E) and characterized by pacemaker failure in both heart (sick sinus syndrome followed by atrial flutter) and gut (chronic intestinal pseudo-obstruction) with no intellectual or growth delay. We discuss the possible impact of SGO1 alterations in human pathologies and the potential impact of the SGO1 K23E mutation in the sinus node and gut development and functions. We suggest that the human phenotypes observed in CdLS, CAID syndrome and other cohesinopathies can inform future studies into the less well-known non-cohesion-related functions of cohesin complex genes. Abbreviations: AD: Alzheimer Disease; AFF4: AF4/FMR2 Family Member 4; ANKRD11: Ankyrin Repeat Domain 11; APC: Anaphase Promoter Complex; ASD: Atrial Septal Defect; ATRX: ATRX Chromatin Remodeler; ATRX: Alpha Thalassemia X-linked intellectual disability syndrome; BIRC5: Baculoviral IAP Repeat Containing 5; BMP: Bone Morphogenetic Protein; BRD4: Bromodomain Containing 4; BUB1: BUB1 Mitotic Checkpoint Serine/Threonine Kinase; CAID: Chronic Atrial and Intestinal Dysrhythmia; CDK1: Cyclin Dependent Kinase 1; CdLS: Cornelia de Lange Syndrome; CHD: Congenital Heart Disease; CHOPS: Cognitive impairment, coarse facies, Heart defects, Obesity, Pulmonary involvement, Short stature, and skeletal dysplasia; CIPO: Chronic Intestinal Pseudo-Obstruction; c-kit: KIT Proto-Oncogene Receptor Tyrosine Kinase; CoATs: Cohesin Acetyltransferases; CTCF: CCCTC-Binding Factor; DDX11: DEAD/H-Box Helicase 11; ERG: Transcriptional Regulator ERG; ESCO2: Establishment of Sister Chromatid Cohesion N-Acetyltransferase 2; GJC1: Gap Junction Protein Gamma 1; H2A: Histone H2A; H3K4: Histone H3 Lysine 4; H3K9: Histone H3 Lysine 9; HCN4: Hyperpolarization Activated Cyclic Nucleotide Gated Potassium and Sodium Channel 4;p HDAC8: Histone deacetylases 8; HP1: Heterochromatin Protein 1; ICC: Interstitial Cells of Cajal; ICC-MP: Myenteric Plexus Interstitial cells of Cajal; ICC-DMP: Deep Muscular Plexus Interstitial cells of Cajal; If: Pacemaker Funny Current; IP3: Inositol trisphosphate; JNK: C-Jun N-Terminal Kinase; LDS: Loeys-Dietz Syndrome; LOAD: Late-Onset Alzheimer Disease; MAPK: Mitogen-Activated Protein Kinase; MAU: MAU Sister Chromatid Cohesion Factor; MFS: Marfan Syndrome; NIPBL: NIPBL, Cohesin Loading Factor; OCT4: Octamer-Binding Protein 4; P38: P38 MAP Kinase; PDA: Patent Ductus Arteriosus; PDS5: PDS5 Cohesin Associated Factor; P-H3: Phospho Histone H3; PLK1: Polo Like Kinase 1; POPDC1: Popeye Domain Containing 1; POPDC2: Popeye Domain Containing 2; PP2A: Protein Phosphatase 2; RAD21: RAD21 Cohesin Complex Component; RBS: Roberts Syndrome; REC8: REC8 Meiotic Recombination Protein; RNAP2: RNA polymerase II; SAN: Sinoatrial node; SCN5A: Sodium Voltage-Gated Channel Alpha Subunit 5; SEC: Super Elongation Complex; SGO1: Shogoshin-1; SMAD: SMAD Family Member; SMC1A: Structural Maintenance of Chromosomes 1A; SMC3: Structural Maintenance of Chromosomes 3; SNV: Single Nucleotide Variant; SOX2: SRY-Box 2; SOX17: SRY-Box 17; SSS: Sick Sinus Syndrome; STAG2: Cohesin Subunit SA-2; TADs: Topology Associated Domains; TBX: T-box transcription factors; TGF-β: Transforming Growth Factor β; TGFBR: Transforming Growth Factor β receptor; TOF: Tetralogy of Fallot; TREK1: TREK-1 K(+) Channel Subunit; VSD: Ventricular Septal Defect; WABS: Warsaw Breakage Syndrome; WAPL: WAPL Cohesin Release Factor.
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Affiliation(s)
- Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
| | - Patrick Piet Van Vliet
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
| | - Michel Pucéat
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
- INSERM U-1251, MMG,Aix-Marseille University, Marseille, 13885, France
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
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29
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Mazzola M, Deflorian G, Pezzotta A, Ferrari L, Fazio G, Bresciani E, Saitta C, Ferrari L, Fumagalli M, Parma M, Marasca F, Bodega B, Riva P, Cotelli F, Biondi A, Marozzi A, Cazzaniga G, Pistocchi A. NIPBL: a new player in myeloid cell differentiation. Haematologica 2019; 104:1332-1341. [PMID: 30630974 PMCID: PMC6601076 DOI: 10.3324/haematol.2018.200899] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/03/2019] [Indexed: 12/19/2022] Open
Abstract
The nucleophosmin 1 gene (NPM1) is the most frequently mutated gene in acute myeloid leukemia. Notably, NPM1 mutations are always accompanied by additional mutations such as those in cohesin genes RAD21, SMC1A, SMC3, and STAG2 but not in the cohesin regulator, nipped B-like (NIPBL). In this work, we analyzed a cohort of adult patients with acute myeloid leukemia and NPM1 mutation and observed a specific reduction in the expression of NIPBL but not in other cohesin genes. In our zebrafish model, overexpression of the mutated form of NPM1 also induced downregulation of nipblb, the zebrafish ortholog of human NIPBL To investigate the hematopoietic phenotype and the interaction between mutated NPM1 and nipblb, we generated a zebrafish model with nipblb downregulation which showed an increased number of myeloid progenitors. This phenotype was due to hyper-activation of the canonical Wnt pathway: myeloid cells blocked in an undifferentiated state could be rescued when the Wnt pathway was inhibited by dkk1b mRNA injection or indomethacin administration. Our results reveal, for the first time, a role for NIPBL during zebrafish hematopoiesis and suggest that an interplay between NIPBL/NPM1 may regulate myeloid differentiation in zebrafish and humans through the canonical Wnt pathway and that dysregulation of these interactions may drive leukemic transformation.
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MESH Headings
- Adult
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Embryo, Nonmammalian/metabolism
- Embryo, Nonmammalian/pathology
- Gene Expression Regulation, Neoplastic
- Hematopoiesis
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Nuclear Proteins/genetics
- Nucleophosmin
- Phenotype
- Wnt Signaling Pathway
- Zebrafish
- Cohesins
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Affiliation(s)
- Mara Mazzola
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
| | | | - Alex Pezzotta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
| | - Laura Ferrari
- Istituto FIRC di Oncologia Molecolare, IFOM, Milano, Italy
| | - Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica Università di Milano-Bicocca, Centro Maria Letizia Verga, Monza, Italy
| | - Erica Bresciani
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Claudia Saitta
- Centro Ricerca Tettamanti, Clinica Pediatrica Università di Milano-Bicocca, Centro Maria Letizia Verga, Monza, Italy
| | - Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
| | - Monica Fumagalli
- Clinica Ematologica e Centro Trapianti di Midollo Osseo, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Matteo Parma
- Clinica Ematologica e Centro Trapianti di Midollo Osseo, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Federica Marasca
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), Milano, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), Milano, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica Università di Milano-Bicocca, Centro Maria Letizia Verga, Monza, Italy
| | - Anna Marozzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica Università di Milano-Bicocca, Centro Maria Letizia Verga, Monza, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Segrate, Italy
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Cukrov D, Newman TAC, Leask M, Leeke B, Sarogni P, Patimo A, Kline AD, Krantz ID, Horsfield JA, Musio A. Antioxidant treatment ameliorates phenotypic features of SMC1A-mutated Cornelia de Lange syndrome in vitro and in vivo. Hum Mol Genet 2019; 27:3002-3011. [PMID: 29860495 DOI: 10.1093/hmg/ddy203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/30/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease characterized by cognitive impairment, multisystemic alterations and premature aging. Furthermore, CdLS cells display gene expression dysregulation and genomic instability. Here, we demonstrated that treatment with antioxidant drugs, such as ascorbic acid and riboceine, reduced the level of genomic instability and extended the in vitro lifespan of CdLS cell lines. We also found that antioxidant treatment partially rescued the phenotype of a zebrafish model of CdLS. Gene expression profiling showed that antioxidant drugs caused dysregulation of gene transcription; notably, a number of genes coding for the zinc finger (ZNF)-containing Krueppel-associated box (KRAB) protein domain (KRAB-ZNF) were found to be downregulated. Taken together, these data suggest that antioxidant drugs have the potential to ameliorate the developmental phenotype of CdLS.
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Affiliation(s)
- Dubravka Cukrov
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Trent A C Newman
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Megan Leask
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bryony Leeke
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Patrizia Sarogni
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Alessandra Patimo
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag, Auckland, New Zealand
| | - Antonio Musio
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
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Takayama K, Muto A, Kikuchi Y. Leucine/glutamine and v-ATPase/lysosomal acidification via mTORC1 activation are required for position-dependent regeneration. Sci Rep 2018; 8:8278. [PMID: 29844341 PMCID: PMC5974189 DOI: 10.1038/s41598-018-26664-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 05/02/2018] [Indexed: 11/13/2022] Open
Abstract
In animal regeneration, control of position-dependent cell proliferation is crucial for the complete restoration of patterned appendages in terms of both, shape and size. However, detailed mechanisms of this process are largely unknown. In this study, we identified leucine/glutamine and v-ATPase/lysosomal acidification, via mechanistic target of rapamycin complex 1 (mTORC1) activation, as effectors of amputation plane-dependent zebrafish caudal fin regeneration. mTORC1 activation, which functions in cell proliferation, was regulated by lysosomal acidification possibly via v-ATPase activity at 3 h post amputation (hpa). Inhibition of lysosomal acidification resulted in reduced growth factor-related gene expression and suppression of blastema formation at 24 and 48 hpa, respectively. Along the proximal-distal axis, position-dependent lysosomal acidification and mTORC1 activation were observed from 3 hpa. We also report that Slc7a5 (L-type amino acid transporter), whose gene expression is position-dependent, is necessary for mTORC1 activation upstream of lysosomal acidification during fin regeneration. Furthermore, treatment with leucine and glutamine, for both proximal and distal fin stumps, led to an up-regulation in cell proliferation via mTORC1 activation, indicating that leucine/glutamine signaling possesses the ability to change the position-dependent regeneration. Our findings reveal that leucine/glutamine and v-ATPase/lysosomal acidification via mTORC1 activation are required for position-dependent zebrafish fin regeneration.
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Affiliation(s)
- Kazuya Takayama
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Akihiko Muto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.,Hematology Business Development, HU Business Development, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe, 651-2271, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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NIPBL +/- haploinsufficiency reveals a constellation of transcriptome disruptions in the pluripotent and cardiac states. Sci Rep 2018; 8:1056. [PMID: 29348408 PMCID: PMC5773608 DOI: 10.1038/s41598-018-19173-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex disorder with multiple structural and developmental defects caused by mutations in structural and regulatory proteins involved in the cohesin complex. NIPBL, a cohesin regulatory protein, has been identified as a critical protein responsible for the orchestration of transcriptomic regulatory networks necessary for embryonic development. Mutations in NIPBL are responsible for the majority of cases of CdLS. Through RNA-sequencing of human induced pluripotent stem cells and in vitro-derived cardiomyocytes, we identified hundreds of mRNAs, pseudogenes, and non-coding RNAs with altered expression in NIPBL+/− patient-derived cells. We demonstrate that NIPBL haploinsufficiency leads to upregulation of gene sets identified in functions related to nucleosome, chromatin assembly, RNA modification and downregulation of Wnt signaling, cholesterol biosynthesis and vesicular transport in iPSC and cardiomyocytes. Mutations in NIPBL result in the dysregulation of many genes responsible for normal heart development likely resulting in the variety of structural cardiac defects observed in the CdLS population.
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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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Rohban S, Cerutti A, Morelli MJ, d'Adda di Fagagna F, Campaner S. The cohesin complex prevents Myc-induced replication stress. Cell Death Dis 2017; 8:e2956. [PMID: 28749464 PMCID: PMC5550886 DOI: 10.1038/cddis.2017.345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022]
Abstract
The cohesin complex is mutated in cancer and in a number of rare syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells rescued Myc-dependent transcription and promoted S-phase entry but failed to sustain S-phase progression due to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc-dependent transcription but essential to prevent Myc-induced replicative stress. This suggests the presence of a feed-forward regulatory loop where cohesins by regulating Myc level control S-phase entry and prevent replicative stress.
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Affiliation(s)
- Sara Rohban
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Aurora Cerutti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
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37
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Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. Genetics 2017; 207:139-151. [PMID: 28679547 DOI: 10.1534/genetics.117.202291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS.
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38
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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Deniz E, Jonas S, Hooper M, N. Griffin J, Choma MA, Khokha MK. Analysis of Craniocardiac Malformations in Xenopus using Optical Coherence Tomography. Sci Rep 2017; 7:42506. [PMID: 28195132 PMCID: PMC5307353 DOI: 10.1038/srep42506] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
Birth defects affect 3% of children in the United States. Among the birth defects, congenital heart disease and craniofacial malformations are major causes of mortality and morbidity. Unfortunately, the genetic mechanisms underlying craniocardiac malformations remain largely uncharacterized. To address this, human genomic studies are identifying sequence variations in patients, resulting in numerous candidate genes. However, the molecular mechanisms of pathogenesis for most candidate genes are unknown. Therefore, there is a need for functional analyses in rapid and efficient animal models of human disease. Here, we coupled the frog Xenopus tropicalis with Optical Coherence Tomography (OCT) to create a fast and efficient system for testing craniocardiac candidate genes. OCT can image cross-sections of microscopic structures in vivo at resolutions approaching histology. Here, we identify optimal OCT imaging planes to visualize and quantitate Xenopus heart and facial structures establishing normative data. Next we evaluate known human congenital heart diseases: cardiomyopathy and heterotaxy. Finally, we examine craniofacial defects by a known human teratogen, cyclopamine. We recapitulate human phenotypes readily and quantify the functional and structural defects. Using this approach, we can quickly test human craniocardiac candidate genes for phenocopy as a critical first step towards understanding disease mechanisms of the candidate genes.
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Affiliation(s)
- Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
| | - Stephan Jonas
- Department of Medical Informatics, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Michael Hooper
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
| | - John N. Griffin
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
| | - Michael A. Choma
- Department of Radiology and Biomedical Imaging, Department of Pediatrics, Yale University, 333 Cedar, Street New Haven, CT 06510, USA
- Department of Biomedical Engineering and Applied Physics, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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40
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Abstract
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor.This chapter summarizes our current knowledge on kollerin function and the recent studies on the genomic localization of Scc2, highlighting and critically discussing controversial data.
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Affiliation(s)
- Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Faculty Building, Room Ee1020, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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41
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Grant MG, Patterson VL, Grimes DT, Burdine RD. Modeling Syndromic Congenital Heart Defects in Zebrafish. Curr Top Dev Biol 2017; 124:1-40. [DOI: 10.1016/bs.ctdb.2016.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Abstract
The cohesin protein complex regulates multiple cellular events including sister chromatid cohesion and gene expression. Several distinct human diseases called cohesinopathies have been associated with genetic mutations in cohesin subunit genes or genes encoding regulators of cohesin function. Studies in different model systems, from yeast to mouse have provided insights into the molecular mechanisms of action of cohesin/cohesin regulators and their implications in the pathogenesis of cohesinopathies. The zebrafish has unique advantages for embryonic analyses and quantitative gene knockdown with morpholinos during the first few days of development, in contrast to knockouts of cohesin regulators in flies or mammals, which are either lethal as homozygotes or dramatically compensated for in heterozygotes. This has been particularly informative for Rad21, where a role in gene expression was first shown in zebrafish, and Nipbl, where the fish work revealed tissue-specific functions in heart, gut, and limbs, and long-range enhancer-promoter interactions that control Hox gene expression in vivo. Here we discuss the utility of the zebrafish in studying the developmental and pathogenic roles of cohesin.
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Affiliation(s)
- Akihiko Muto
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
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43
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Hagen EM, Sicko RJ, Kay DM, Rigler SL, Dimopoulos A, Ahmad S, Doleman MH, Fan R, Romitti PA, Browne ML, Caggana M, Brody LC, Shaw GM, Jelliffe-Pawlowski LL, Mills JL. Copy-number variant analysis of classic heterotaxy highlights the importance of body patterning pathways. Hum Genet 2016; 135:1355-1364. [PMID: 27637763 PMCID: PMC5065782 DOI: 10.1007/s00439-016-1727-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 09/04/2016] [Indexed: 01/08/2023]
Abstract
Classic heterotaxy consists of congenital heart defects with abnormally positioned thoracic and abdominal organs. We aimed to uncover novel, genomic copy-number variants (CNVs) in classic heterotaxy cases. A microarray containing 2.5 million single-nucleotide polymorphisms (SNPs) was used to genotype 69 infants (cases) with classic heterotaxy identified from California live births from 1998 to 2009. CNVs were identified using the PennCNV software. We identified 56 rare CNVs encompassing genes in the NODAL (NIPBL, TBX6), BMP (PPP4C), and WNT (FZD3) signaling pathways, not previously linked to classic heterotaxy. We also identified a CNV involving FGF12, a gene previously noted in a classic heterotaxy case. CNVs involving RBFOX1 and near MIR302F were detected in multiple cases. Our findings illustrate the importance of body patterning pathways for cardiac development and left/right axes determination. FGF12, RBFOX1, and MIR302F could be important in human heterotaxy, because they were noted in multiple cases. Further investigation into genes involved in the NODAL, BMP, and WNT body patterning pathways and into the dosage effects of FGF12, RBFOX1, and MIR302F is warranted.
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Affiliation(s)
- Erin M Hagen
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Boulevard, Bethesda, MD, 20892, USA
| | - Robert J Sicko
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12201-2002, USA
| | - Denise M Kay
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12201-2002, USA
| | - Shannon L Rigler
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Boulevard, Bethesda, MD, 20892, USA
| | - Aggeliki Dimopoulos
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Boulevard, Bethesda, MD, 20892, USA
| | - Shabbir Ahmad
- California Birth Defects Monitoring Program, California Department of Public Health, 1615 Capitol Avenue, MS 8304, Sacramento, CA, 95899-7420, USA
| | - Margaret H Doleman
- California Birth Defects Monitoring Program, California Department of Public Health, 1615 Capitol Avenue, MS 8304, Sacramento, CA, 95899-7420, USA
| | - Ruzong Fan
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Boulevard, Bethesda, MD, 20892, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N. Riverside Drive, S416 CPHB, Iowa City, IA, 52242, USA
| | - Marilyn L Browne
- Congenital Malformations Registry, New York State Department of Health, Empire State Plaza-Corning Tower, Albany, NY, 12237, USA
- University at Albany School of Public Health, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12201-2002, USA
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 50, 50 South Drive, MSC 8004, Bethesda, MD, 20892, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Medical Office Building, 1265 Welch Road Room X159, Stanford, CA, 94305, USA
| | - Laura L Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, 550 16th Street, San Francisco, CA, 94158, USA
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Boulevard, Bethesda, MD, 20892, USA.
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Santos R, Kawauchi S, Jacobs RE, Lopez-Burks ME, Choi H, Wikenheiser J, Hallgrimsson B, Jamniczky HA, Fraser SE, Lander AD, Calof AL. Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects. PLoS Biol 2016; 14:e2000197. [PMID: 27606604 PMCID: PMC5016002 DOI: 10.1371/journal.pbio.2000197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/05/2016] [Indexed: 12/16/2022] Open
Abstract
Elucidating the causes of congenital heart defects is made difficult by the complex morphogenesis of the mammalian heart, which takes place early in development, involves contributions from multiple germ layers, and is controlled by many genes. Here, we use a conditional/invertible genetic strategy to identify the cell lineage(s) responsible for the development of heart defects in a Nipbl-deficient mouse model of Cornelia de Lange Syndrome, in which global yet subtle transcriptional dysregulation leads to development of atrial septal defects (ASDs) at high frequency. Using an approach that allows for recombinase-mediated creation or rescue of Nipbl deficiency in different lineages, we uncover complex interactions between the cardiac mesoderm, endoderm, and the rest of the embryo, whereby the risk conferred by genetic abnormality in any one lineage is modified, in a surprisingly non-additive way, by the status of others. We argue that these results are best understood in the context of a model in which the risk of heart defects is associated with the adequacy of early progenitor cell populations relative to the sizes of the structures they must eventually form.
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Affiliation(s)
- Rosaysela Santos
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America.,Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Shimako Kawauchi
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America.,Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Russell E Jacobs
- Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, California, United States of America
| | - Martha E Lopez-Burks
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America.,Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Hojae Choi
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Jamie Wikenheiser
- Department of Anatomy and Neurobiology, University of California, Irvine, California, United States of America
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada
| | - Scott E Fraser
- Departments of Biology and Bioengineering, University of Southern California, Los Angeles, California, United States of America
| | - Arthur D Lander
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America.,Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, California, United States of America
| | - Anne L Calof
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America.,Center for Complex Biological Systems, University of California, Irvine, California, United States of America.,Department of Anatomy and Neurobiology, University of California, Irvine, California, United States of America
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45
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Gelb BD. The Hole and the Whole: Lessons from Manipulation of Nipbl Deficiency. PLoS Biol 2016; 14:e2000494. [PMID: 27606622 PMCID: PMC5015829 DOI: 10.1371/journal.pbio.2000494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Congenital heart defects (CHDs) affect 2%–3% of newborns and remain challenging clinically. There is an ongoing project to elucidate the causes of CHDs, focusing primarily on genetics as dictated by the epidemiology. In a paper published in this issue, Santos and colleagues describe studies of Cornelia de Lange syndrome-associated secundum atrial septal defects (ASDs) caused by NIPBL mutations, undertaken with a targeted trapping allele in mice. They show that Nipbl haploinsufficiency in either of two cell populations was sufficient to engender ASDs but that expression solely in either one of those populations was sufficient to rescue them. This work provides novel insights into incomplete penetrance and oligogenic effects underlying CHDs.
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Affiliation(s)
- Bruce D. Gelb
- The Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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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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Watrin E, Kaiser FJ, Wendt KS. Gene regulation and chromatin organization: relevance of cohesin mutations to human disease. Curr Opin Genet Dev 2016; 37:59-66. [PMID: 26821365 DOI: 10.1016/j.gde.2015.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/16/2015] [Accepted: 12/19/2015] [Indexed: 10/22/2022]
Abstract
Consistent with the diverse roles of the cohesin complex in chromosome biology, mutations in genes encoding cohesin and its regulators are found in different types of cancer and in developmental disorders such as Cornelia de Lange Syndrome. It is so far considered that the defects caused by these mutations result from altered function of cohesin in regulating gene expression during development. Chromatin conformation analyses have established the importance of cohesin for the architecture of developmental gene clusters and in vivo studies in mouse and zebrafish demonstrated how cohesin defects lead to gene misregulation and to malformations similar to the related human syndromes. Here we present our current knowledge on cohesin's involvement in gene expression, highlighting molecular and mechanistic consequences of pathogenic mutations in the Cornelia de Lange syndrome.
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Affiliation(s)
- Erwan Watrin
- Centre National de la Recherche Scientifique, UMR 6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes 1, SFR BIOSIT, Rennes, France
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
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Fazio G, Gaston-Massuet C, Bettini LR, Graziola F, Scagliotti V, Cereda A, Ferrari L, Mazzola M, Cazzaniga G, Giordano A, Cotelli F, Bellipanni G, Biondi A, Selicorni A, Pistocchi A, Massa V. CyclinD1 Down-Regulation and Increased Apoptosis Are Common Features of Cohesinopathies. J Cell Physiol 2016. [PMID: 26206533 DOI: 10.1002/jcp.25106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic variants within components of the cohesin complex (NIPBL, SMC1A, SMC3, RAD21, PDS5, ESCO2, HDAC8) are believed to be responsible for a spectrum of human syndromes known as "cohesinopathies" that includes Cornelia de Lange Syndrome (CdLS). CdLS is a multiple malformation syndrome affecting almost any organ and causing severe developmental delay. Cohesinopathies seem to be caused by dysregulation of specific developmental pathways downstream of mutations in cohesin components. However, it is still unclear how mutations in different components of the cohesin complex affect the output of gene regulation. In this study, zebrafish embryos and SMC1A-mutated patient-derived fibroblasts were used to analyze abnormalities induced by SMC1A loss of function. We show that the knockdown of smc1a in zebrafish impairs neural development, increases apoptosis, and specifically down-regulates Ccnd1 levels. The same down-regulation of cohesin targets is observed in SMC1A-mutated patient fibroblasts. Previously, we have demonstrated that haploinsufficiency of NIPBL produces similar effects in zebrafish and in patients fibroblasts indicating a possible common feature for neurological defects and mental retardation in cohesinopathies. Interestingly, expression analysis of Smc1a and Nipbl in developing mouse embryos reveals a specific pattern in the hindbrain, suggesting a role for cohesins in neural development in vertebrates.
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Affiliation(s)
- Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Carles Gaston-Massuet
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Laura Rachele Bettini
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Federica Graziola
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK.,Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Valeria Scagliotti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Anna Cereda
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Mara Mazzola
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy.,Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Angelo Selicorni
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy.,Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
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50
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Xu B, Gogol M, Gaudenz K, Gerton JL. Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. BMC Genomics 2016; 17:25. [PMID: 26729373 PMCID: PMC4700579 DOI: 10.1186/s12864-015-2354-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/21/2015] [Indexed: 12/25/2022] Open
Abstract
Background Roberts syndrome (RBS) is a human developmental disorder caused by mutations in the cohesin acetyltransferase ESCO2. We previously reported that mTORC1 signaling was depressed and overall translation was reduced in RBS cells and zebrafish models for RBS. Treatment of RBS cells and zebrafish RBS models with L-leucine partially rescued mTOR function and protein synthesis, correlating with increased cell division and improved development. Results In this study, we use RBS cells to model mTORC1 repression and analyze transcription and translation with ribosome profiling to determine gene-level effects of L-leucine. L-leucine treatment partially rescued translational efficiency of ribosomal subunits, translation initiation factors, snoRNA production, and mitochondrial function in RBS cells, consistent with these processes being mTORC1 controlled. In contrast, other genes are differentially expressed independent of L-leucine treatment, including imprinted genes such as H19 and GTL2, miRNAs regulated by GTL2, HOX genes, and genes in nucleolar associated domains. Conclusions Our study distinguishes between gene expression changes in RBS cells that are TOR dependent and those that are independent. Some of the TOR independent gene expression changes likely reflect the architectural role of cohesin in chromatin looping and gene expression. This study reveals the dramatic rescue effects of L-leucine stimulation of mTORC1 in RBS cells and supports that normal gene expression and translation requires ESCO2 function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2354-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Baoshan Xu
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.
| | - Karin Gaudenz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA. .,Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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