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Abstract
Somatic or acquired mutations are postzygotic genetic variations that can occur within any tissue. These mutations accumulate during aging and have classically been linked to malignant processes. Tremendous advancements over the past years have led to a deeper understanding of the role of somatic mutations in benign and malignant age-related diseases. Here, we review the somatic mutations that accumulate in the blood and their connection to disease states, with a particular focus on inflammatory diseases and myelodysplastic syndrome. We include a definition of clonal hematopoiesis (CH) and an overview of the origins and implications of these mutations. In addition, we emphasize somatic disorders with overlapping inflammation and hematologic disease beyond CH, including paroxysmal nocturnal hemoglobinuria and aplastic anemia, focusing on VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome. Finally, we provide a practical view of the implications of somatic mutations in clinical hematology, pathology, and beyond.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, New York, USA
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA;
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, Maryland, USA
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2
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Abstract
INTRODUCTION VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a recently described, late-onset, acquired autoinflammatory disorder caused by mutations in the UBA1 gene. The various clinical manifestations of VEXAS broadly divided into inflammatory or haematological. VEXAS defines a new disease category - the hematoinflammatory disorders triggered by somatic mutations restricted to blood but causing systemic inflammation with multi-organ involvement and associated with aberrant bone marrow status. VEXAS causes significant morbidity and reduced life expectancy, but the optimum standard of care remains undefined. AREAS COVERED This review describes the discovery of VEXAS, relevant genetic causes and immunopathology of the disease. A detailed account of its various clinical manifestations and disease mimics is provided. Current treatment and management options are discussed. EXPERT OPINION New rare variants in UBA1 and VEXAS-like UBA1 negative cases are reported. Consensus diagnostic criteria might be required to define VEXAS and its related disorders. Investigation of sporadic, VEXAS-like cases will require the application of deep sequencing using DNA obtained from various cellular or tissue locations. Prospective studies are needed to define the optimal supportive and treatment options for patients with varying disease severity and prognosis. VEXAS-specific hematopoietic stem cell transplant selection criteria also require development.
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Affiliation(s)
- Adam Al-Hakim
- Department of Clinical Immunology and Allergy, Leeds Teaching Hospitals, NHS Trust, Leeds, UK
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, Leeds Teaching Hospitals, NHS Trust, Leeds, UK.,Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), School of Medicine, University of Leeds, Leeds, UK.,National Institute for Health Research (NIHR) Leeds Biomedical Research Centre, School of Medicine, University of Leeds, Leeds, UK
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3
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Vitale A, Caggiano V, Bimonte A, Caroni F, Tosi GM, Fabbiani A, Renieri A, Bocchia M, Frediani B, Fabiani C, Cantarini L. VEXAS syndrome: a new paradigm for adult-onset monogenic autoinflammatory diseases. Intern Emerg Med 2023; 18:711-722. [PMID: 36662445 PMCID: PMC10082120 DOI: 10.1007/s11739-023-03193-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/02/2023] [Indexed: 01/21/2023]
Abstract
VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is a recently described pathological entity. It is an acquired monogenic autoinflammatory disease caused by somatic mutations of the UBA1 gene in blood cells precursors; the gene encodes one of the two E1 enzyme isoforms that initiates ubiquitylation in cell's cytoplasm. VEXAS syndrome leads to systemic inflammation, with all organs and tissues potentially involved. The clinical picture may be extremely heterogenous, mimicking different other systemic rheumatologic entities coexisting with haematological disorders, especially myelodysplastic syndrome. This new disease represents a very intriguing clinical condition in several respects: it accounts for the paradigm of adult-onset monogenic autoinflammatory diseases determined by a genetic mosaicism resulting in the development of a challenging multiorgan inflammatory condition. Moreover, VEXAS syndrome is perhaps not an exceptionally rare condition and represents an example of a systemic genetic autoinflammatory disease drawing its origin in bone marrow disorders. VEXAS syndrome should be strongly considered in each adult patient with an unexplained systemic inflammatory condition, especially when recurrent fevers, neutrophilic dermatosis, relapsing polychondritis, ocular inflammation and other systemic inflammatory symptoms accompanying myelodysplastic syndrome or other haematological disorders. The syndrome deserves a multidisciplinary approach to reach the diagnosis and ensure the best management of a potentially very challenging condition. To quickly describe the clinical course, long-term outcomes, and the optimal management of this new syndrome it is essential to join forces internationally. To this end, the international AutoInflammatory Disease Alliance (AIDA) registry dedicated to VEXAS syndrome has been developed and is already active.
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Affiliation(s)
- Antonio Vitale
- Research Center of Systemic Autoinflammatory Diseases and Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, Policlinico "Le Scotte", Viale Bracci 1, 53100, Siena, Italy
| | - Valeria Caggiano
- Research Center of Systemic Autoinflammatory Diseases and Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, Policlinico "Le Scotte", Viale Bracci 1, 53100, Siena, Italy
| | - Antonio Bimonte
- Research Center of Systemic Autoinflammatory Diseases and Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, Policlinico "Le Scotte", Viale Bracci 1, 53100, Siena, Italy
| | - Federico Caroni
- Hematology, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena, Italy
| | - Gian Marco Tosi
- Ophthalmology Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Alessandra Fabbiani
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Monica Bocchia
- Hematology, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena, Italy
| | - Bruno Frediani
- Research Center of Systemic Autoinflammatory Diseases and Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, Policlinico "Le Scotte", Viale Bracci 1, 53100, Siena, Italy
| | - Claudia Fabiani
- Ophthalmology Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Luca Cantarini
- Research Center of Systemic Autoinflammatory Diseases and Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, Policlinico "Le Scotte", Viale Bracci 1, 53100, Siena, Italy.
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4
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Rasch MNB, Szabados F, Jensen JMB, Nielsen KO, Hauge EM, Troldborg A. Patients with VEXAS diagnosed in a Danish tertiary rheumatology setting have highly elevated inflammatory markers, macrocytic anaemia and negative autoimmune biomarkers. RMD Open 2022. [PMCID: PMC9462080 DOI: 10.1136/rmdopen-2022-002492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) is an autoinflammatory condition with overlapping features of rheumatology and haematology caused by somatic mutations in the UBA1 gene. Patients present with highly variable symptoms and their path towards diagnosis are often complicated and characterised by extensive examinations. It is, therefore, pivotal that clinicians become familiar with the clinical presentation of VEXAS to advance identification of patients with the disease. Objectives We aimed to (1) characterise patients diagnosed with VEXAS in a tertiary rheumatology referral centre, (2) identify common rheumatological biomarkers that may distinguish VEXAS from other rheumatic diseases and (3) suggest which clinical findings should motivate genetic testing for VEXAS. Methods Patients were identified and diagnosed at the department of Rheumatology, Aarhus University Hospital (AUH), Denmark. Blood samples were examined for VEXAS-associated UBA1 variants by Sanger sequencing at the department of Clinical Immunology, AUH. Clinical and biochemical data were retrieved from the hospital electronic patient chart. Results Eleven male patients with clinical suspicion of VEXAS underwent sequencing. Five of these carried known VEXAS-associated variants. Median age at diagnosis was 84 (75–87) years. All patients had significantly elevated inflammatory markers with a median C-reactive protein (CRP) of 297 (196–386) mg/L and macrocytic anaemia. None of the patients presented common biomarkers for autoimmunity. Conclusion Danish patients with VEXAS syndrome are men with persistent inflammation, constitutional symptoms and heterogeneous clinical presentations. Shared features for all patients in this study were highly elevated inflammatory markers, macrocytic anaemia and negative autoimmune biomarkers.
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Affiliation(s)
| | - Fruzsina Szabados
- Rheumatology, Sygehus Vendsyssel i Hjørring, Hjorring, Nordjylland, Denmark
| | - Jens Magnus Bernth Jensen
- Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Ellen-Margrethe Hauge
- Rheumatology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne Troldborg
- Rheumatology, Aarhus University Hospital, Aarhus, Denmark
- Biomedicine, Aarhus University, Aarhus, Denmark
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5
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Poulter J, Morgan A, Cargo C, Savic S. A High-Throughput Amplicon Screen for Somatic UBA1 Variants in Cytopenic and Giant Cell Arteritis Cohorts. J Clin Immunol 2022; 42:947-951. [PMID: 35366150 DOI: 10.1007/s10875-022-01258-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Affiliation(s)
- James Poulter
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | | | - Ann Morgan
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK.,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, Leeds, UK
| | - Catherine Cargo
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, St James's University Hospital, Leeds, UK
| | - Sinisa Savic
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, Leeds, UK. .,Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.
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6
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A master autoantigen-ome links alternative splicing, female predilection, and COVID-19 to autoimmune diseases. J Transl Autoimmun 2022; 5:100147. [PMID: 35237749 PMCID: PMC8872718 DOI: 10.1016/j.jtauto.2022.100147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/27/2022] Open
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare adverse effects of the currently available mRNA and viral vector-based COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine BCMB Graduate Program in Biomedical Sciences, New York, NY, USA
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7
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Patel N, Dulau-Florea A, Calvo KR. Characteristic bone marrow findings in patients with UBA1 somatic mutations and VEXAS syndrome. Semin Hematol 2021; 58:204-211. [PMID: 34802541 DOI: 10.1053/j.seminhematol.2021.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/16/2021] [Accepted: 10/20/2021] [Indexed: 11/11/2022]
Abstract
VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a newly characterized syndrome with underlying somatic UBA1 mutations in myeloid cells linking hematologic disease with autoinflammatory rheumatologic disorders. Hematologic abnormalities, particularly peripheral blood cytopenia(s) may prompt bone marrow evaluation in patients with known or unrecognized VEXAS syndrome. This review highlights key findings and diagnostic considerations encountered during bone marrow examination in patients with this disorder. Frequently reported hematologic changes include macrocytic anemia, cytoplasmic vacuoles in myeloid and erythroid precursors, marrow hypercellularity, and varying degrees of dysplasia. Myelodysplastic syndrome and plasma cell neoplasms have been diagnosed in patients with VEXAS syndrome. Macrophage activation syndrome and/or hemophagocytic lymphohistiocytosis and monoclonal B-cell lymphocytosis have also been reported. The bone marrow is a target organ in VEXAS syndrome. Heightened awareness of the bone marrow features and hematologic complications may aid in identifying individuals with VEXAS who may benefit from increased disease surveillance or alternative therapeutic strategies.
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Affiliation(s)
- Nisha Patel
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Alina Dulau-Florea
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD.
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8
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases. bioRxiv 2021:2021.07.30.454526. [PMID: 34373855 PMCID: PMC8351778 DOI: 10.1101/2021.07.30.454526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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10
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Abstract
RBM10 is a nuclear RNA-binding protein (RBP) that regulates the alternative splicing of primary transcripts. Recently, research on RBM10 has become increasingly active owing to its clinical importance, as indicated by studies on RBM0 mutations that cause TARP syndrome, an X-linked congenital pleiotropic developmental anomaly, and various cancers such as lung adenocarcinoma in adults. Herein, the molecular biology of RBM10 and its significance in medicine are reviewed, focusing on the gene and protein structures of RBM10, its cell biology, molecular functions and regulation, relationship with the paralogous protein RBM5, and the mutations of RBM10 and their associated diseases. Finally, the challenges in future studies of RBM10 are discussed in the concluding remarks.
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Affiliation(s)
- Akira Inoue
- Department of Otolaryngology, Osaka City University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan.
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Liu J, Wang K, Li B, Yang X. A novel Xp11.22-22.33 deletion suggesting a possible mechanism of congenital cervical spinal muscular atrophy. Mol Genet Genomic Med 2021; 9:e1606. [PMID: 33513289 PMCID: PMC8104167 DOI: 10.1002/mgg3.1606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Congenital cervical spinal muscular atrophy (CCSMA) is a rare, nonprogressive, neurogenic disorder characterized by symmetric arthrogryposis and motor deficits mainly confined to upper extremities. Since its first proposal by Darwish et al. 39 years ago, only few cases have ever been reported. Vascular insult to the anterior horn of cervical spinal cord during fetal development was speculated to be the cause, however, the exact pathogenesis is still not well understood. METHODS In this study, whole-exome sequencing (WES) and copy number variation (CNV) analysis were conducted on a definitive CCSMA patient, confirmed by the clinical manifestations and other supplementary examinations. RESULTS On physical examination, the patient was mainly characterized by symmetric, congenital, nonprogressive contractures, hypotonia, and muscle weakness mainly confined to the upper limbs, which were further supported by MRI and electromyography. Neuromuscular biopsy of the deltoid muscle demonstrated the type 1 myofiber predominance without any infiltration of inflammatory cells. The WES and CNV analysis unveiled a de novo Xp11.22-22.33 deletion. On further examination of the genes contained within this segment, we recognize UBA1 gene as the most likely pathogenic gene. Ubiquitin-like modifier activating enzyme 1 is encoded by UBA1 gene (MIM 314370) located in Xp11.3 and is a critical protein that plays a vital role in ubiquitin-proteasome system and autophagy. It is well documented that UBA1 gene mutation causes X-linked infantile spinal muscular atrophy (XL-SMA), which manifests phenotypes of arthrogryposis, hypotonia, and myopathic face. Type 2 XL-SMA, which follows a nonprogressive and nonlethal course is very similar to the presentations of CCSMA. CONCLUSION The phenotypic similarities between this CCSMA case and XL-SMA prompt us to hypothesize a possible connection between UBA1 gene deficit and the pathogenesis of CCSMA. Our study is the first to demonstrate that CCSMA might have a genetic etiology, thus, expanding our insights into the underlying cause of CCSMA.
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Affiliation(s)
- Jingwei Liu
- Department of Pediatric Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Kelai Wang
- Department of Pediatric Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Baomin Li
- Department of Pediatric, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiaofan Yang
- Department of Pediatric, Qilu Hospital of Shandong University, Jinan, Shandong, China.,Department of Genetics, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China
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12
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Lambrou GI, Adamaki M, Hatziagapiou K, Vlahopoulos S. Gene Expression and Resistance to Glucocorticoid-Induced Apoptosis in Acute Lymphoblastic Leukemia: A Brief Review and Update. Curr Drug Res Rev 2021; 12:131-149. [PMID: 32077838 DOI: 10.2174/2589977512666200220122650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/29/2019] [Accepted: 01/23/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND Resistance to glucocorticoid (GC)-induced apoptosis in Acute Lymphoblastic Leukemia (ALL), is considered one of the major prognostic factors for the disease. Prednisolone is a corticosteroid and one of the most important agents in the treatment of acute lymphoblastic leukemia. The mechanics of GC resistance are largely unknown and intense ongoing research focuses on this topic. AIM The aim of the present study is to review some aspects of GC resistance in ALL, and in particular of Prednisolone, with emphasis on previous and present knowledge on gene expression and signaling pathways playing a role in the phenomenon. METHODS An electronic literature search was conducted by the authors from 1994 to June 2019. Original articles and systematic reviews selected, and the titles and abstracts of papers screened to determine whether they met the eligibility criteria, and full texts of the selected articles were retrieved. RESULTS Identification of gene targets responsible for glucocorticoid resistance may allow discovery of drugs, which in combination with glucocorticoids may increase the effectiveness of anti-leukemia therapies. The inherent plasticity of clinically evolving cancer justifies approaches to characterize and prevent undesirable activation of early oncogenic pathways. CONCLUSION Study of the pattern of intracellular signal pathway activation by anticancer drugs can lead to development of efficient treatment strategies by reducing detrimental secondary effects.
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Affiliation(s)
- George I Lambrou
- First Department of Pediatrics, National and Kapodistrian University of Athens, Choremeio Research Laboratory, Athens, Greece
| | - Maria Adamaki
- First Department of Pediatrics, National and Kapodistrian University of Athens, Choremeio Research Laboratory, Athens, Greece
| | - Kyriaki Hatziagapiou
- First Department of Pediatrics, National and Kapodistrian University of Athens, Choremeio Research Laboratory, Athens, Greece
| | - Spiros Vlahopoulos
- First Department of Pediatrics, National and Kapodistrian University of Athens, Choremeio Research Laboratory, Athens, Greece
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13
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Singh NN, Hoffman S, Reddi PP, Singh RN. Spinal muscular atrophy: Broad disease spectrum and sex-specific phenotypes. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166063. [PMID: 33412266 DOI: 10.1016/j.bbadis.2020.166063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% of cases of SMA result from deletions of or mutations in the Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. The spectrum of SMA is broad, ranging from prenatal death to infant mortality to survival into adulthood. All tissues, including brain, spinal cord, bone, skeletal muscle, heart, lung, liver, pancreas, gastrointestinal tract, kidney, spleen, ovary and testis, are directly and/or indirectly affected in SMA. Accumulating evidence on impaired mitochondrial biogenesis and defects in X chromosome-linked modifying factors, coupled with the sexual dimorphic nature of many tissues, point to sex-specific vulnerabilities in SMA. Here we review the role of sex in the pathogenesis of SMA.
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14
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Kraus TFJ, Haider M, Spanner J, Steinmaurer M, Dietinger V, Kretzschmar HA. Altered Long Noncoding RNA Expression Precedes the Course of Parkinson’s Disease—a Preliminary Report. Mol Neurobiol 2016; 54:2869-2877. [DOI: 10.1007/s12035-016-9854-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/11/2016] [Indexed: 02/06/2023]
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15
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Hunter JM, Kiefer J, Balak CD, Jooma S, Ahearn ME, Hall JG, Baumbach-Reardon L. Review of X-linked syndromes with arthrogryposis or early contractures-aid to diagnosis and pathway identification. Am J Med Genet A 2015; 167A:931-73. [DOI: 10.1002/ajmg.a.36934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/05/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Jesse M. Hunter
- Integrated Functional Cancer Genomics; Translational Genomics Research Institute; Phoenix Arizona
| | - Jeff Kiefer
- Knowledge Mining; Translational Genomics Research Institute; Phoenix Arizona
| | - Christopher D. Balak
- Integrated Functional Cancer Genomics; Translational Genomics Research Institute; Phoenix Arizona
| | - Sonya Jooma
- Integrated Functional Cancer Genomics; Translational Genomics Research Institute; Phoenix Arizona
| | - Mary Ellen Ahearn
- Integrated Functional Cancer Genomics; Translational Genomics Research Institute; Phoenix Arizona
| | - Judith G. Hall
- Departments of Medical Genetics and Pediatrics; University of British Columbia and BC Children's Hospital Vancouver; British Columbia Canada
| | - Lisa Baumbach-Reardon
- Integrated Functional Cancer Genomics; Translational Genomics Research Institute; Phoenix Arizona
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16
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Abstract
In humans over 15% of X-linked genes have been shown to ‘escape’ from X-chromosome inactivation (XCI): they continue to be expressed to some extent from the inactive X chromosome. Mono-allelic expression is anticipated within a cell for genes subject to XCI, but random XCI usually results in expression of both alleles in a cell population. Using a study of allelic expression from cultured lymphoblasts and fibroblasts, many of which showed substantial skewing of XCI, we recently reported that the expression of genes lies on a contiunuum between those that are subject to inactivation, and those that escape. We now review allelic expression studies from mouse, and discuss the variability in escape seen in both humans and mice in genic expression levels, between X chromosomes and between tissues. We also discuss current knowledge of the heterochromatic features, DNA elements and three-dimensional topology of the inactive X that contribute to the balance of expression from the otherwise inactive X chromosome.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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17
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Cotton AM, Lam L, Affleck JG, Wilson IM, Peñaherrera MS, McFadden DE, Kobor MS, Lam WL, Robinson WP, Brown CJ. Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum Genet 2011; 130:187-201. [PMID: 21597963 PMCID: PMC3132437 DOI: 10.1007/s00439-011-1007-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/06/2011] [Indexed: 12/04/2022]
Abstract
X-chromosome inactivation (XCI) results in the differential marking of the active and inactive X with epigenetic modifications including DNA methylation. Consistent with the previous studies showing that CpG island-containing promoters of genes subject to XCI are approximately 50% methylated in females and unmethylated in males while genes which escape XCI are unmethylated in both sexes; our chromosome-wide (Methylated DNA ImmunoPrecipitation) and promoter-targeted methylation analyses (Illumina Infinium HumanMethylation27 array) showed the largest methylation difference (D = 0.12, p < 2.2 E-16) between male and female blood at X-linked CpG islands promoters. We used the methylation differences between males and females to predict XCI statuses in blood and found that 81% had the same XCI status as previously determined using expression data. Most genes (83%) showed the same XCI status across tissues (blood, fetal: muscle, kidney and nerual); however, the methylation of a subset of genes predicted different XCI statuses in different tissues. Using previously published expression data the effect of transcription on gene-body methylation was investigated and while X-linked introns of highly expressed genes were more methylated than the introns of lowly expressed genes, exonic methylation did not differ based on expression level. We conclude that the XCI status predicted using methylation of X-linked promoters with CpG islands was usually the same as determined by expression analysis and that 12% of X-linked genes examined show tissue-specific XCI whereby a gene has a different XCI status in at least one of the four tissues examined.
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Affiliation(s)
- Allison M. Cotton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Molecular Epigenetics Group, Life Sciences Institute, Vancouver, BC Canada
| | - Lucia Lam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Child and Family Research Institute, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC Canada
| | - Joslynn G. Affleck
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Molecular Epigenetics Group, Life Sciences Institute, Vancouver, BC Canada
| | - Ian M. Wilson
- British Columbia Cancer Research Centre, Vancouver, BC Canada
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Maria S. Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Child and Family Research Institute, Vancouver, BC Canada
| | | | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Child and Family Research Institute, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC Canada
| | - Wan L. Lam
- British Columbia Cancer Research Centre, Vancouver, BC Canada
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Child and Family Research Institute, Vancouver, BC Canada
| | - Carolyn J. Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
- Molecular Epigenetics Group, Life Sciences Institute, Vancouver, BC Canada
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18
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Dementyeva EV, Shevchenko AI, Anopriyenko OV, Mazurok NA, Elisaphenko EA, Nesterova TB, Brockdorff N, Zakian SM. Difference between random and imprinted X inactivation in common voles. Chromosoma 2010; 119:541-52. [PMID: 20473512 DOI: 10.1007/s00412-010-0277-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/15/2010] [Accepted: 04/26/2010] [Indexed: 11/24/2022]
Abstract
During early development in female mammals, most genes on one of the two X-chromosomes undergo transcriptional silencing. In the extraembryonic lineages of some eutherian species, imprinted X-inactivation of the paternal X-chromosome occurs. In the cells of the embryo proper, the choice of the future inactive X-chromosome is random. We mapped several genes on the X-chromosomes of five common vole species and compared their expression and methylation patterns in somatic and extraembryonic tissues, where random and imprinted X-inactivation occurs, respectively. In extraembryonic tissues, more genes were expressed on the inactive X-chromosome than in somatic tissues. We also found that the methylation status of the X-linked genes was always in accordance with their expression pattern in somatic, but not in extraembryonic tissues. The data provide new evidence that imprinted X-inactivation is less complete and/or stable than the random form and DNA methylation contributes less to its maintenance.
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Affiliation(s)
- Elena V Dementyeva
- Russian Academy of Sciences, Siberian Department, Institute of Cytology and Genetics, ac. Lavrentyev Avenue 10, Novosibirsk, Russia
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19
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Goto Y, Kimura H. Inactive X chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene. Nucleic Acids Res 2010; 37:7416-28. [PMID: 19843608 PMCID: PMC2794193 DOI: 10.1093/nar/gkp860] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In mammals, the dosage compensation of sex chromosomes between males and females is achieved by transcriptional inactivation of one of the two X chromosomes in females. However, a number of genes escape X-inactivation in humans. It remains poorly understood how the transcriptional activity of these ‘escape genes’ is maintained despite the chromosome-wide heterochromatin formation. To address this question, we analyzed a putative chromatin boundary between the inactivated RBM10 and an escape gene, UBA1/UBE1. Chromatin immunoprecipitation revealed that trimethylated histone H3 lysine 9 and H4 lysine 20 were enriched in the last exon through the proximal downstream region of RBM10, but were remarkably diminished at ∼2 kb upstream of the UBA1 transcription start site. Whereas RNA polymerase II was not loaded onto the intergenic region, CTCF (CCCTC binding factor) was enriched around the boundary, where some CpG sites were hypomethylated specifically on inactive X. These findings suggest that local DNA hypomethylation and CTCF binding are involved in the formation of a chromatin boundary, which protects the UBA1 escape gene against the chromosome-wide transcriptional silencing.
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Affiliation(s)
- Yuji Goto
- Nuclear Function and Dynamics Unit, Horizontal Medical Research Organization, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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20
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Illingworth R, Kerr A, Desousa D, Jørgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008;6:e22. [PMID: 18232738 PMCID: PMC2214817 DOI: 10.1371/journal.pbio.0060022] [Citation(s) in RCA: 455] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/13/2007] [Indexed: 12/13/2022] Open
Abstract
CpG islands (CGIs) are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%–8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues. The human genome contains about 22,000 genes, each encoding one of the proteins required for human life. A particular cell type (e.g., blood, skin, etc.) expresses a specific subset of protein genes and silences the remainder. To shed light on the mechanisms that cause genes to be activated or shut down, we studied DNA sequences called “CpG islands” (CGIs). These sequences are found at over half of all human genes and can exist in either the active or silent state depending on the presence or absence of methyl groups on the DNA. We devised a method for purifying all CGIs and showed that, unexpectedly, only half occur at the beginning of genes near the promoter, the rest occurring within or between genes. Notably, methylation of CGIs causes stable gene silencing. We tested 17,000 CGIs in four human tissues and found that 6%–8% were methylated in each. Genes whose protein products play an essential role during embryonic development were preferentially methylated, suggesting that gene expression during development could be regulated by CGI methylation. CpG island methylation, an epigenetic phenomenon usually associated with abnormality in disease, is little characterised in the context of "normal" human cells. Here we highlight tissue-specific CpG Island methylation, which frequently associates with developmental genes.
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21
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Johnston CM, Lovell FL, Leongamornlert DA, Stranger BE, Dermitzakis ET, Ross MT. Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet 2008; 4:e9. [PMID: 18208332 DOI: 10.1371/journal.pgen.0040009] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 12/04/2007] [Indexed: 11/19/2022] Open
Abstract
X chromosome inactivation in female mammals results in dosage compensation of X-linked gene products between the sexes. In humans there is evidence that a substantial proportion of genes escape from silencing. We have carried out a large-scale analysis of gene expression in lymphoblastoid cell lines from four human populations to determine the extent to which escape from X chromosome inactivation disrupts dosage compensation. We conclude that dosage compensation is virtually complete. Overall expression from the X chromosome is only slightly higher in females and can largely be accounted for by elevated female expression of approximately 5% of X-linked genes. We suggest that the potential contribution of escape from X chromosome inactivation to phenotypic differences between the sexes is more limited than previously believed.
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22
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Karnani N, Taylor C, Malhotra A, Dutta A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 2007; 17:865-76. [PMID: 17568004 PMCID: PMC1891345 DOI: 10.1101/gr.5427007] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In eukaryotes, accurate control of replication time is required for the efficient completion of S phase and maintenance of genome stability. We present a high-resolution genome-tiling array-based profile of replication timing for approximately 1% of the human genome studied by The ENCODE Project Consortium. Twenty percent of the investigated segments replicate asynchronously (pan-S). These areas are rich in genes and CpG islands, features they share with early-replicating loci. Interphase FISH showed that pan-S replication is a consequence of interallelic variation in replication time and is not an artifact derived from a specific cell cycle synchronization method or from aneuploidy. The interallelic variation in replication time is likely due to interallelic variation in chromatin environment, because while the early- or late-replicating areas were exclusively enriched in activating or repressing histone modifications, respectively, the pan-S areas had both types of histone modification. The replication profile of the chromosomes identified contiguous chromosomal segments of hundreds of kilobases separated by smaller segments where the replication time underwent an acute transition. Close examination of one such segment demonstrated that the delay of replication time was accompanied by a decrease in level of gene expression and appearance of repressive chromatin marks, suggesting that the transition segments are boundary elements separating chromosomal domains with different chromatin environments.
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Affiliation(s)
- Neerja Karnani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Christopher Taylor
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Department of Computer Science, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Ankit Malhotra
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Department of Computer Science, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Corresponding author.E-mail ; fax (434) 924-5069
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23
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Shevchenko AI, Pavlova SV, Dementyeva EV, Golubeva DV, Zakian SM. Chromatin modifications during X-chromosome inactivation in female mammals. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406090080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Lopes AM, Ross N, Close J, Dagnall A, Amorim A, Crow TJ. Inactivation status of PCDH11X: sexual dimorphisms in gene expression levels in brain. Hum Genet 2006; 119:267-75. [PMID: 16425037 DOI: 10.1007/s00439-006-0134-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 11/23/2005] [Indexed: 10/25/2022]
Abstract
Genes escaping X-inactivation are predicted to contribute to differences in gene dosage between the sexes and are the prime candidates for being involved in the phenotype observed in individuals with X chromosome aneuploidies. Of particular interest is ProtocadherinX (PCDH11X or PCDHX), a recently described gene expressed in brain. In humans, PCDH11X has a homologue on the Y chromosome and is predicted to escape from X-inactivation. Employing bisulphite sequencing analysis we found absence of CpG island methylation on both the active and the inactive X chromosomes, providing a strong indication that PCDH11X escapes inactivation in humans. Furthermore, a sexual dimorphism in levels of expression in brain tissue was observed by quantitative real-time PCR, with females presenting an up to 2-fold excess in the abundance of PCDH11X transcripts. We relate these findings to sexually dimorphic traits in the human brain. Interestingly, PCDH11X/Y gene pair is unique to Homo sapiens, since the X-linked gene was transposed to the Y chromosome after the human-chimpanzee lineages split. Although no differences in promoter methylation were found between humans and chimpanzees, evidence of an upregulation of PCDH11X in humans deserves further investigation.
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Affiliation(s)
- Alexandra M Lopes
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, R. Dr Roberto Frias, S/N, 4200-465, Porto, Portugal.
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25
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Okamoto I, Arnaud D, Le Baccon P, Otte AP, Disteche CM, Avner P, Heard E. Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature 2005; 438:369-73. [PMID: 16227973 DOI: 10.1038/nature04155] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 08/22/2005] [Indexed: 11/09/2022]
Abstract
In mammals, one of the two X chromosomes is inactivated in females to enable dosage compensation for X-linked gene products. In rodents and marsupials, only the X chromosome of paternal origin (Xp) is silenced during early embryogenesis. This could be due to a carry-over effect of the X chromosome's passage through the male germ line, where it becomes transiently silenced together with the Y chromosome, during meiotic sex chromosome inactivation (MSCI). Here we show that Xist (X inactive specific transcript) transgenes, located on autosomes, do not undergo MSCI in the male germ line of mice and yet can induce imprinted cis-inactivation when paternally inherited, with identical kinetics to the Xp chromosome. This suggests that MSCI is not necessary for imprinted X-chromosome inactivation in mice. We also show that the Xp is transcribed, like autosomes, at zygotic gene activation rather than being 'pre-inactivated'. We propose that expression of the paternal Xist gene at zygotic gene activation is sufficient to trigger cis-inactivation of the X chromosome, or of an autosome carrying a Xist transgene.
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Affiliation(s)
- Ikuhiro Okamoto
- CNRS UMR218, Curie Institute, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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26
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Craig IW, Mill J, Craig GM, Loat C, Schalkwyk LC. Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes. Eur J Hum Genet 2004; 12:639-46. [PMID: 15114374 DOI: 10.1038/sj.ejhg.5201212] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Dosage compensation in mammalian females is achieved by the random inactivation of one X chromosome early in development; however, inactivation is not complete. In addition to a majority of pseudoautosomal loci, there are genes that are expressed from both the active and the inactive X chromosomes, and which are interspersed among other genes subject to regular dosage compensation. The patterns of X-linked gene expression in different tissues are of great significance for interpreting their impact on sex differences in development. We have examined the suitability and sensitivity of a microarray approach for determining the inactivation status of X-linked genes. Biotinylated cRNA from six female and six male lymphocyte samples were hybridised to Affymetrix HG-U133A microarrays. A total of 36 X-linked targets detected significantly higher levels of female transcripts, suggesting that these corresponded to sequences from loci that escaped, at least partly, from inactivation. These included genes for which previous experimental evidence, or circumstantial evidence, existed for their escape, and some novel candidates. Six of the targets were represented by more than one probe set, which gave independent support for the conclusions reached.
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Affiliation(s)
- Ian W Craig
- SGDP Centre, Institute of Psychiatry, Box PO 82, Denmark Hill, London SE5, UK.
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27
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Tsuchiya KD, Greally JM, Yi Y, Noel KP, Truong JP, Disteche CM. Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse. Genome Res 2004; 14:1275-84. [PMID: 15197169 PMCID: PMC442142 DOI: 10.1101/gr.2575904] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome.
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Affiliation(s)
- Karen D Tsuchiya
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.
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28
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Abstract
In mammals, dosage compensation ensures equal X-chromosome expression between males (XY) and females (XX) by transcriptionally silencing one X chromosome in XX embryos. In the prevailing view, the XX zygote inherits two active X chromosomes, one each from the mother and father, and X inactivation does not occur until after implantation. Here, we report evidence to the contrary in mice. We find that one X chromosome is already silent at zygotic gene activation (2-cell stage). This X chromosome is paternal in origin and exhibits a gradient of silencing. Genes close to the X-inactivation centre show the greatest degree of inactivation, whereas more distal genes show variable inactivation and can partially escape silencing. After implantation, imprinted silencing in extraembryonic tissues becomes globalized and more complete on a gene-by-gene basis. These results argue that the XX embryo is in fact dosage compensated at conception along much of the X chromosome. We propose that imprinted X inactivation results from inheritance of a pre-inactivated X chromosome from the paternal germ line.
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Affiliation(s)
- Khanh D Huynh
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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29
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Percec I, Thorvaldsen JL, Plenge RM, Krapp CJ, Nadeau JH, Willard HF, Bartolomei MS. An N-ethyl-N-nitrosourea mutagenesis screen for epigenetic mutations in the mouse. Genetics 2003; 164:1481-94. [PMID: 12930754 PMCID: PMC1462673 DOI: 10.1093/genetics/164.4.1481] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mammalian epigenetic phenomena of X inactivation and genomic imprinting are incompletely understood. X inactivation equalizes X-linked expression between males and females by silencing genes on one X chromosome during female embryogenesis. Genomic imprinting functionally distinguishes the parental genomes, resulting in parent-specific monoallelic expression of particular genes. N-ethyl-N-nitrosourea (ENU) mutagenesis was used in the mouse to screen for mutations in novel factors involved in X inactivation. Previously, we reported mutant pedigrees identified through this screen that segregate aberrant X-inactivation phenotypes and we mapped the mutation in one pedigree to chromosome 15. We now have mapped two additional mutations to the distal chromosome 5 and the proximal chromosome 10 in a second pedigree and show that each of the mutations is sufficient to induce the mutant phenotype. We further show that the roles of these factors are specific to embryonic X inactivation as neither genomic imprinting of multiple genes nor imprinted X inactivation is perturbed. Finally, we used mice bearing selected X-linked alleles that regulate X chromosome choice to demonstrate that the phenotypes of all three mutations are consistent with models in which the mutations have affected molecules involved specifically in the choice or the initiation of X inactivation.
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Affiliation(s)
- Ivona Percec
- Howard Hughes Medical Institute, and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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30
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Abstract
Dosage compensation in mammals is achieved by the transcriptional inactivation of one X chromosome in female cells. From the time X chromosome inactivation was initially described, it was clear that several mechanisms must be precisely integrated to achieve correct regulation of this complex process. X-inactivation appears to be triggered upon differentiation, suggesting its regulation by developmental cues. Whereas any number of X chromosomes greater than one is silenced, only one X chromosome remains active. Silencing on the inactive X chromosome coincides with the acquisition of a multitude of chromatin modifications, resulting in the formation of extraordinarily stable facultative heterochromatin that is faithfully propagated through subsequent cell divisions. The integration of all these processes requires a region of the X chromosome known as the X-inactivation center, which contains the Xist gene and its cis-regulatory elements. Xist encodes an RNA molecule that plays critical roles in the choice of which X chromosome remains active, and in the initial spread and establishment of silencing on the inactive X chromosome. We are now on the threshold of discovering the factors that regulate and interact with Xist to control X-inactivation, and closer to an understanding of the molecular mechanisms that underlie this complex process.
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Affiliation(s)
- Kathrin Plath
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143, USA.
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31
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Abstract
Tsix controls X-chromosome inactivation (XCI) by blocking the accumulation of Xist RNA on the future active X chromosome. Deleting Tsix on one X chromosome (X(Delta)X) skews XCI toward the mutated X chromosome in the female soma. Here I have generated homozygous Tsix-null mice (X(Delta)X(Delta)) to test how deleting the second allele affects the choice of XCI. Homozygosity leads to extremely low fertility and reveals two previously unknown non-mendelian patterns of inheritance. First, the sex ratio is skewed against female births so that one daughter is born for every two to three sons. Second, the pattern of XCI unexpectedly returns to random in surviving X(Delta)X(Delta) mice. Thus, with respect to choice, mutation of Tsix yields a phenotypic abnormality in heterozygotes but not homozygotes. To reconcile the paradox of female loss with apparent reversion to random choice, I propose that deleting both Tsix alleles results in chaotic choice and that randomness in X(Delta)X(Delta) survivors reflects a fortuitous selection of distinct X chromosomes as active and inactive.
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Affiliation(s)
- Jeannie T Lee
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
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32
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Abstract
X chromosome inactivation is the silencing mechanism eutherian mammals use to equalize the expression of X-linked genes between males and females early in embryonic development. In the mouse, genetic control of inactivation requires elements within the X inactivation center (Xic) on the X chromosome that influence the choice of which X chromosome is to be inactivated in individual cells. It has long been posited that unidentified autosomal factors are essential to the process. We have used chemical mutagenesis in the mouse to identify specific factors involved in X inactivation and report two genetically distinct autosomal mutations with dominant effects on X chromosome choice early in embryogenesis.
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Affiliation(s)
- Ivona Percec
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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33
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Abstract
DNA methylation, a covalent modification of the genome, is emerging as an important player in the regulation of gene expression. This review discusses the different components of the DNA methylation machinery responsible for replicating the DNA methylation pattern. Recent data have changed our basic understanding of the DNA methylation machinery. A number of DNA methyltransferases (DNMT) have been identified and a demethylase has recently been reported. Because the DNA methylation pattern is critical for gene expression programs, the cell possesses a number of mechanisms to coordinate DNA replication and methylation. DNMT1 levels are regulated with the cell cycle and are induced upon entry into the S phase of the cell cycle. DNMT1 also regulates expression of cell-cycle proteins by its other regulatory functions and not through its DNA methylation activity. Once the mechanisms that coordinate DNMT1 and the cell cycle are disrupted, DNMT1 exerts an oncogenic activity. Tumor suppressor genes are frequently methylated in cancer but the mechanisms responsible are unclear. Overexpression of DNMT1 is probably not responsible for the aberrant methylation of tumor suppressor genes. Unraveling how the different components of the DNA methylation machinery interact to replicate the DNA methylation pattern, and how they are disrupted in cancer, is critical for understanding the molecular mechanisms of cancer.
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Affiliation(s)
- M Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada.
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34
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Abstract
We developed a selective antibody to a synthetic peptide corresponding to an N-terminal sequence of the PCTAIRE-1 protein. In rodent brain extracts it recognized only the protein doublet characteristic of PCTAIRE-1, and this signal is completely abolished by preincubation of the antibody with the immunopeptide. Immunolabeling experiments done with this PCTAIRE-1-specific antibody reveal that the protein is widely distributed in the rodent brain as are the mRNAs visualized using an antisense riboprobe corresponding to the entire PCTAIRE-1 open reading frame. Two types of PCTAIRE-1 protein localizations were observed: first a diffuse labeling of almost all brain regions, particularly intense in the molecular layer of the cerebellum and the mossy fiber region of the hippocampus, and second a spot-like localization in the nuclei of large neurons such as cerebellar Purkinje cells and pyramidal cells of the hippocampus. Colocalization with the B23 protein allows one to identify these compartments as nucleoli. Our results suggest a nucleolar function of PCTAIRE-1 in large neurons and a role in regions containing important granule cell projections.
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Affiliation(s)
- F Le Bouffant
- CNRS UPR 2212, Institut Alfred Fessard, Gif-sur-Yvette, France
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Raskind WH, Niakan KK, Wolff J, Matsushita M, Vaughan T, Stamatoyannopoulos G, Watanabe C, Rios J, Ochs HD. Mapping of a syndrome of X-linked thrombocytopenia with thalassemia to band Xp11-12: further evidence of genetic heterogeneity of X-linked thrombocytopenia. Blood 2000; 95:2262-8. [DOI: 10.1182/blood.v95.7.2262] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
X-linked thrombocytopenia with thalassemia (XLTT; Online Mendelian Inheritance in Man [OMIM] accession number 314050) is a rare disorder characterized by thrombocytopenia, platelet dysfunction, splenomegaly, reticulocytosis, and unbalanced hemoglobin chain synthesis. In a 4-generation family, the gene responsible for XLTT was mapped to the X chromosome, short arm, bands 11-12 (band Xp11-12). The maximum lod score possible in this family, 2.39, was obtained for markers DXS8054 and DXS1003, at a recombination fraction of 0. Recombination events observed for XLTT and markers DXS8080 and DXS8023 or DXS991 define a critical region that is less than or equal to 7.65 KcM and contains the gene responsible for the Wiskott-Aldrich syndrome (WAS; OMIM accession number 301000) and its allelic variant X-linked thrombocytopenia (XLT; OMIM accession number 313900). Manifestations of WAS include thrombocytopenia, eczema, and immunodeficiency. In WAS/XLT the platelets are usually small, and bleeding is proportional to the degree of thrombocytopenia. In contrast, in XLTT the platelet morphology is normal, and the bleeding time is disproportionately prolonged. In this study no alteration in the WAS gene was detected by Northern blot or Western blot analysis, flow cytometry, or complimentary DNA dideoxynucleotide fingerprinting or sequencing. As has been reported for WAS and some cases of XLT, almost total inactivation of the XLTTgene-bearing X chromosome was observed in granulocytes and peripheral blood mononuclear cells from 1 asymptomatic obligate carrier. The XLTT carrier previously found to have an elevated :β hemoglobin chain ratio had a skewed, but not clonal, X-inactivation pattern favoring activity of the abnormal allele. Clinical differences and results of the mutation analyses make it very unlikely that XLTT is another allelic variant of WAS/XLT and strongly suggest that X-linked thrombocytopenia mapping to band Xp11-12 is a genetically heterogeneous disorder.
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Raskind WH, Niakan KK, Wolff J, Matsushita M, Vaughan T, Stamatoyannopoulos G, Watanabe C, Rios J, Ochs HD. Mapping of a syndrome of X-linked thrombocytopenia with thalassemia to band Xp11-12: further evidence of genetic heterogeneity of X-linked thrombocytopenia. Blood 2000; 95:2262-2268. [DOI: 10.1182/blood.v95.7.2262.007k32_2262_2268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
X-linked thrombocytopenia with thalassemia (XLTT; Online Mendelian Inheritance in Man [OMIM] accession number 314050) is a rare disorder characterized by thrombocytopenia, platelet dysfunction, splenomegaly, reticulocytosis, and unbalanced hemoglobin chain synthesis. In a 4-generation family, the gene responsible for XLTT was mapped to the X chromosome, short arm, bands 11-12 (band Xp11-12). The maximum lod score possible in this family, 2.39, was obtained for markers DXS8054 and DXS1003, at a recombination fraction of 0. Recombination events observed for XLTT and markers DXS8080 and DXS8023 or DXS991 define a critical region that is less than or equal to 7.65 KcM and contains the gene responsible for the Wiskott-Aldrich syndrome (WAS; OMIM accession number 301000) and its allelic variant X-linked thrombocytopenia (XLT; OMIM accession number 313900). Manifestations of WAS include thrombocytopenia, eczema, and immunodeficiency. In WAS/XLT the platelets are usually small, and bleeding is proportional to the degree of thrombocytopenia. In contrast, in XLTT the platelet morphology is normal, and the bleeding time is disproportionately prolonged. In this study no alteration in the WAS gene was detected by Northern blot or Western blot analysis, flow cytometry, or complimentary DNA dideoxynucleotide fingerprinting or sequencing. As has been reported for WAS and some cases of XLT, almost total inactivation of the XLTTgene-bearing X chromosome was observed in granulocytes and peripheral blood mononuclear cells from 1 asymptomatic obligate carrier. The XLTT carrier previously found to have an elevated :β hemoglobin chain ratio had a skewed, but not clonal, X-inactivation pattern favoring activity of the abnormal allele. Clinical differences and results of the mutation analyses make it very unlikely that XLTT is another allelic variant of WAS/XLT and strongly suggest that X-linked thrombocytopenia mapping to band Xp11-12 is a genetically heterogeneous disorder.
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Affiliation(s)
- M J Mitchell
- Inserm U.491, Faculté de médecine, Marseille, France
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Abstract
In females, most genes on the X chromosome are generally assumed to be transcriptionally silenced on the inactive X as a result of X inactivation. However, particularly in humans, an increasing number of genes are known to "escape" X inactivation and are expressed from both the active (Xa) and inactive (Xi) X chromosomes; such genes reflect different molecular and epigenetic responses to X inactivation and are candidates for phenotypes associated with X aneuploidy. To identify genes that escape X inactivation and to generate a first-generation X-inactivation profile of the X, we have evaluated the expression of 224 X-linked genes and expressed sequence tags by reverse-transcription-PCR analysis of a panel of multiple independent mouse/human somatic cell hybrids containing a normal human Xi but no Xa. The resulting survey yields an initial X-inactivation profile that is estimated to represent approximately 10% of all X-linked transcripts. Of the 224 transcripts tested here, 34 (three of which are pseudoautosomal) were expressed in as many as nine Xi hybrids and thus appear to escape inactivation. The genes that escape inactivation are distributed nonrandomly along the X; 31 of 34 such transcripts map to Xp, implying that the two arms of the X are epigenetically and/or evolutionarily distinct and suggesting that genetic imbalance of Xp may be more severe clinically than imbalance of Xq. A complete X-inactivation profile will provide information relevant to clinical genetics and genetic counseling and should yield insight into the genomic and epigenetic organization of the X chromosome.
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Affiliation(s)
- L Carrel
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4955, USA
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Takada S, Kamiya M, Arima T, Kagebayashi H, Shibata H, Muramatsu M, Chapman VM, Wake N, Hayashizaki Y, Takagi N. Detection and cloning of an X-linked locus associated with a NotI site that is not methylated on mouse inactivated X chromosome by the RLGS-M method. Genomics 1999; 61:92-100. [PMID: 10512684 DOI: 10.1006/geno.1999.5944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In looking for genes that escape X chromosome inactivation, we scanned the methylation status of genomic DNA from XX, X0, and XY mice using the method of restriction landmark genomic scanning using methylation-sensitive endonuclease. We detected and cloned a candidate locus and identified the Orf1 gene. Orf1 has sequence similarities to the B2 repetitive element and human CXORF4 (formerly called EXLM1), which escapes X inactivation. The B2 element spans the 3' terminus of the ORF and the 3' UTR of Orf1. The Orf1 gene encompasses 18.5 kb of genomic DNA including 11 exons and 10 introns. Taking advantage of genomic polymorphisms present between MSM and C3H/He, we showed that murine Orf1 is mapped to the proximal region of the X chromosome. Despite the unmethylation of the NotI site, Orf1 is subject to X inactivation.
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Affiliation(s)
- S Takada
- Graduate School of Environmental Earth Science, Hokkaido University, North 10 West 5 Kita-ku, Sapporo, 060-0810, Japan
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40
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Hurvitz JR, Suwairi WM, Van Hul W, El-Shanti H, Superti-Furga A, Roudier J, Holderbaum D, Pauli RM, Herd JK, Van Hul EV, Rezai-Delui H, Legius E, Le Merrer M, Al-Alami J, Bahabri SA, Warman ML. Mutations in the CCN gene family member WISP3 cause progressive pseudorheumatoid dysplasia. Nat Genet 1999; 23:94-8. [PMID: 10471507 DOI: 10.1038/12699] [Citation(s) in RCA: 208] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the CCN (for CTGF, cyr61/cef10, nov) gene family encode cysteine-rich secreted proteins with roles in cell growth and differentiation. Cell-specific and tissue-specific differences in the expression and function of different CCN family members suggest they have non-redundant roles. Using a positional-candidate approach, we found that mutations in the CCN family member WISP3 are associated with the autosomal recessive skeletal disorder progressive pseudorheumatoid dysplasia (PPD; MIM 208230). PPD is an autosomal recessive disorder that may be initially misdiagnosed as juvenile rheumatoid arthritis. Its population incidence has been estimated at 1 per million in the United Kingdom, but it is likely to be higher in the Middle East and Gulf States. Affected individuals are asymptomatic in early childhood. Signs and symptoms of disease typically develop between three and eight years of age. Clinically and radiographically, patients experience continued cartilage loss and destructive bone changes as they age, in several instances necessitating joint replacement surgery by the third decade of life. Extraskeletal manifestations have not been reported in PPD. Cartilage appears to be the primary affected tissue, and in one patient, a biopsy of the iliac crest revealed abnormal nests of chondrocytes and loss of normal cell columnar organization in growth zones. We have identified nine different WISP3 mutations in unrelated, affected individuals, indicating that the gene is essential for normal post-natal skeletal growth and cartilage homeostasis.
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Affiliation(s)
- J R Hurvitz
- Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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41
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Abstract
DNA methylation patterns are a critical component of the epigenetic machinery that controls the expression of genetic programs in vertebrates. DNA methyltransferase gene (dnmt1) encodes the enzyme catalyzing the methylation of DNA during replication. We tested the hypothesis that the expression of dnmt1 is regulated with the developmental state of neuronal cells. We show that DNA methyltransferase (Dnmt1) activity is sharply reduced 4 days after induction of differentiation of PC12 cells with NGF. Similarly, the adult brain expresses reduced levels of Dnmt1 activity. We propose that the level of Dnmt1 is downregulated to adjust the activity of the DNA methyltransferase to a different role in mature post-mitotic neurons. Both the abundance of dnmt1 mRNA as well as the Dnmt1 polypeptide are downregulated. Downregulation of dnmt1 parallels other indicators of withdrawal from the cell cycle such as induction of p21, and downregulation of the S phase maker PCNA (proliferating cell nuclear antigen). The temporal pattern of downregulation of dnmt1 in nerve growth factor (NGF)-induced PC12 cells is different from myotube differentiation where downregulation of DNA methyltransferase and demethylation is an early event and was proposed to play a causal role in differentiation. We propose that NGF differentiation of PC12 cells represents a different paradigm of involvement of DNA methylation in terminal differentiation.
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Affiliation(s)
- J Deng
- Department of Pharmacology and Therapeutics, McGill University, 3655 Drummond Street, Montreal, PQ, Canada
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Brown AL, Kay GF. Bex1, a gene with increased expression in parthenogenetic embryos, is a member of a novel gene family on the mouse X chromosome. Hum Mol Genet 1999; 8:611-9. [PMID: 10072429 DOI: 10.1093/hmg/8.4.611] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Parthenogenetic and normal blastocysts were compared using differential display analysis as a means to identify new imprinted genes. A single gene was identified with increased expression in parthenogenetic blastocysts, suggesting it might be an imprinted gene expressed from the maternally inherited allele. The gene, named Bex1 (brainexpressedX-linked gene), maps near Plp on the mouse X chromosome and to Xq22 in humans. Database homology searches revealed two additional uncharacterized cDNAs similar to Bex1 that were named Bex2 and Bex3. Allele-specific expression analysis of Bex1 using F1 blastocysts indicated an excess of transcript expressed from the maternally inherited allele compared with the paternally inherited allele. This excess level of transcript derived from the maternally inherited allele may be due to imprinted X inactivation of the paternally inherited allele in the extraembryonic lineages of female embryos rather than a result of genomic imprinting.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Chromosome Mapping
- DNA Primers
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Dosage Compensation, Genetic
- Embryo, Mammalian/metabolism
- Embryonic and Fetal Development
- Female
- Gene Expression Regulation, Developmental
- Genes/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Molecular Sequence Data
- Muridae
- Nerve Tissue Proteins/genetics
- Parthenogenesis
- RNA/genetics
- RNA/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- X Chromosome/genetics
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Affiliation(s)
- A L Brown
- QCF Transgenic Laboratory, Joint Experimental Oncology Program, The Queensland Institute of Medical Research and The University of Queensland, PO Royal Brisbane Hospital, Queensland 4029, Australia
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43
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Abstract
Prior to entry into meiosis, XX germ cells in the fetal ovary undergo X chromosome reactivation. The signal for reactivation is thought to emanate from the genital ridge, but it is unclear whether it is specific to the developing ovary. To determine whether the signals are present in the developing testis as well as the ovary, we examined the expression of X-linked genes in germ cells from XXY male mice. To facilitate this analysis, we generated XXY and XX fetuses carrying X chromosomes that were differentially marked and subject to nonrandom inactivation. This pattern of nonrandom inactivation was maintained in somatic cells but, in XX as well as XXY fetuses, both parental alleles were expressed in germ cell-enriched cell populations. Because testis differentiation is temporally and morphologically normal in the XXY testis and because all germ cells embark upon a male pathway of development, these results provide compelling evidence that X chromosome reactivation in fetal germ cells is independent of the somatic events of sexual differentiation. Proper X chromosome dosage is essential for the normal fertility of male mammals, and abnormalities in germ cell development are apparent in the XXY testis within several days of X reactivation. Studies of exceptional germ cells that survive in the postnatal XXY testis demonstrated that surviving germ cells are exclusively XY and result from rare nondisjunctional events that give rise to clones of XY cells.
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Affiliation(s)
- K Mroz
- Department of Genetics and Center for Human Genetics, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, 44106-4955, USA
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44
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Abstract
A 2Mb contig was constructed of yeast artificial chromosomes (YACs) and P1 artificial chromosomes (PACs), extending from DXS6849 to a new marker EC7034R, 1Mb distal to UBE1, within the p11.3 region of the human X chromosome. This contig, which has on average four-fold cloned coverage, was assembled using 37 markers, including 13 new sequence tagged sites (STSs) developed from YAC and PAC end-fragments, for an average inter-marker distance of 55kb. The inferred marker order predicted from SEGMAP analysis, STS content and cell hybrid data is Xpter-EC7034R-EC8058R-FB20E11-DXS7804-D XS8308-(DXS1264, DXS1055)-DXS1003-UBE1-(UHX), PCTK1)-DXS1364-DXS1266-DXS337-SYN1-DXS6 849-cen. One (TC)n dinucleotide sequence from an end-clone was identified and found to be polymorphic (48% heterozygosity). The contig is merged with published physical maps both in the distal and in the centromeric direction of Xp, and provides reagents to aid in the DNA sequencing and the finding of genes in this region of the human genome.
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Affiliation(s)
- K L Stoddart
- Department of Medical Genetics, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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45
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Ottolenghi C, Vekemans M. Genetic divergence between mouse and humans: a useful direction for gene pathway analysis. Teratology 1998; 58:82-7. [PMID: 9802187 DOI: 10.1002/(sici)1096-9926(199809/10)58:3/4<82::aid-tera3>3.0.co;2-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Preliminary results in comparative genetics have revealed a growing list of differences between mice and humans (Strachan et al. [1997]: Nat. Genet. 16:126-132). However, it is increasingly apparent that some of these differences are not accompanied by changes in function. Such differences are nevertheless useful because they represent a sort of genetic experiment that provides evidence helpful in deducing how the genetic circuits work. This article draws attention to some recent results. First, we briefly report on representative examples of genetic differences between rodents and humans, suggesting, as expected, that such divergence is abundant and diverse at all levels of gene regulation. Second, on the basis of a more detailed analysis bearing on four examples, we emphasize that the study of genetic differences associated with little or no functional divergence is likely to be a profitable direction for future analysis of genetic pathways. Finally, we suggest that apparently nonfunctional genetic divergence may underlie different susceptibilities to disease. A detailed knowledge of human-mouse genetic divergence will provide an indispensable framework for extrapolating the molecular effects of mutations and teratogens from mice to humans in studies of abnormal development.
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Affiliation(s)
- C Ottolenghi
- Department of Genetics, Hôpital Necker Enfants-Malades, Université Paris V, France
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46
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Miller AP, Willard HF. Chromosomal basis of X chromosome inactivation: identification of a multigene domain in Xp11.21-p11.22 that escapes X inactivation. Proc Natl Acad Sci U S A 1998; 95:8709-14. [PMID: 9671743 PMCID: PMC21141 DOI: 10.1073/pnas.95.15.8709] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of genes have been identified that escape mammalian X chromosome inactivation and are expressed from both active and inactive X chromosomes. The basis for escape from inactivation is unknown and, a priori, could be a result of local factors that act in a gene-specific manner or of chromosomal control elements that act regionally. Models invoking the latter predict that such genes should be clustered in specific domains on the X chromosome, rather than distributed at random along the length of the X. To distinguish between these possibilities, we have constructed a transcription map composed of at least 23 distinct expressed sequences in an approximately 5.5-megabase region on the human X chromosome spanning Xp11.21-p11.22. The inactivation status of these transcribed sequences has been determined in a somatic cell hybrid system and correlated with the position of the genes on the physical map. Although the majority of transcribed sequences in this region are subject to X inactivation, eight expressed sequences (representing at least six different genes) escape inactivation, and all are localized to within a region of less than 370 kb. Genes located both distal and proximal to this cluster are subject to inactivation, thereby defining a unique multigene domain on the proximal short arm that is transcriptionally active on the inactive X chromosome.
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Affiliation(s)
- A P Miller
- Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
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White WM, Willard HF, Van Dyke DL, Wolff DJ. The spreading of X inactivation into autosomal material of an x;autosome translocation: evidence for a difference between autosomal and X-chromosomal DNA. Am J Hum Genet 1998; 63:20-8. [PMID: 9634520 PMCID: PMC1377243 DOI: 10.1086/301922] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
X inactivation involves initiation, propagation, and maintenance of genetic inactivation. Studies of replication timing in X;autosome translocations have suggested that X inactivation may spread into adjacent autosomal DNA. To examine the inactivation of autosomal material at the molecular level, we assessed the transcriptional activity of X-linked and autosomal loci spanning an inactive translocation in a phenotypically normal female with a karyotype of 46,X,der(X)t(X;4)(q22;q24). Since 4q duplications usually manifest dysmorphic features and severe growth and mental retardation, the normal phenotype of this individual suggested the spreading of X inactivation throughout the autosomal material. Consistent with this model, reverse transcription-PCR analysis of 20 transcribed sequences spanning 4q24-qter revealed that three known genes and 11 expressed sequence tags (ESTs) were not expressed in a somatic-cell hybrid that carries the translocation chromosome. However, three ESTs and three known genes were expressed from the t(X;4) chromosome and thus "escaped" X inactivation. This direct assay of expression demonstrated that the spreading of inactivation from the adjoining X chromosome was incomplete and noncontiguous. These findings are broadly consistent with the existence of genes known to escape inactivation on normal inactive X chromosomes. However, the fact that a high proportion (30%) of tested autosomal genes escaped inactivation may indicate that autosomal material lacks X chromosome-specific features that are associated with the spreading and/or maintenance of inactivation.
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Affiliation(s)
- W M White
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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48
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Abstract
We determined the genomic structure of the gene encoding human DNA methyltransferase (DNA MTase). Six overlapping human genomic DNA clones which include all of the known cDNA sequence were isolated. Analysis of these clones demonstrates that the human DNA MTase gene consists of at least 40 exons and 39 introns spanning a distance of 60 kilobases. Elucidation of the chromosomal organization of the human DNA MTase gene provides the template for future structure-function analysis of the properties of mammalian DNA MTase.
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Affiliation(s)
- S Ramchandani
- Department of Pharmacology and Therapeutics, McGill University, Montreal, PQ, Canada
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49
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Abstract
The inactive X chromosome differs from the active X in a number of ways; some of these, such as allocyclic replication and altered histone acetylation, are associated with all types of epigenetic silencing, whereas others, such as DNA methylation, are of more restricted use. These features are acquired progressively by the inactive X after onset of initiation. Initiation of X-inactivation is controlled by the X-inactivation center (Xic) and influenced by the X chromosome controlling element (Xce), which causes primary nonrandom X-inactivation. Other examples of nonrandom X-inactivation are also presented in this review. The definition of a major role for Xist, a noncoding RNA, in X-inactivation has enabled investigation of the mechanism leading to establishment of the heterochromatinized X-chromosome and also of the interactions between X-inactivation and imprinting as well as between X-inactivation and developmental processes in the early embryo.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, URA CNRS 1968, Institut Pasteur, Paris, France.
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50
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Meguro M, Mitsuya K, Sui H, Shigenami K, Kugoh H, Nakao M, Oshimura M. Evidence for uniparental, paternal expression of the human GABAA receptor subunit genes, using microcell-mediated chromosome transfer. Hum Mol Genet 1997; 6:2127-33. [PMID: 9328477 DOI: 10.1093/hmg/6.12.2127] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have constructed mouse A9 hybrids containing a single normal human chromosome 15, via microcell-mediated chromosome transfer. Cytogenetic and DNA-polymorphic analyses identified mouse A9 hybrids that contained either a paternal or maternal human chromosome 15. Paternal specific expression of the known imprinted genes SNRPN (small nuclear ribonucleoprotein-associated polypeptide N gene) and IPW (imprinted gene in the Prader-Willi syndrome region) was maintained in the A9 hybrids. Using this system, we first demonstrated that human GABAAreceptor subunit genes, GABRB3 , GABRA5 and GABRG3 , were expressed exclusively from the paternal allele and that E6-AP (E6-associated protein or UBE3A ) was biallelically expressed. Moreover, the 5' portion of the GABRB3 gene was found to be hypermethylated on the paternal allele. Our data imply that GABAAreceptor subunit genes are imprinted and are possible candidates for Prader-Willi syndrome, and that this human monochromosomal hybrid system enables the efficient analysis of imprinted loci.
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Affiliation(s)
- M Meguro
- Department of Molecular and Cell Genetics, School of Life Sciences, Faculty of Medicine, Tottori University, Nishimachi 86, Yonago, Tottori 683, Japan
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