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Tu J, Wan C, Zhang F, Cao L, Law PWN, Tian Y, Lu G, Rennert OM, Chan W, Cheung H. Genetic correction of Werner syndrome gene reveals impaired pro-angiogenic function and HGF insufficiency in mesenchymal stem cells. Aging Cell 2020; 19:e13116. [PMID: 32320127 PMCID: PMC7253065 DOI: 10.1111/acel.13116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/02/2019] [Revised: 12/30/2019] [Accepted: 01/26/2020] [Indexed: 12/21/2022] Open
Abstract
WRN mutation causes a premature aging disease called Werner syndrome (WS). However, the mechanism by which WRN loss leads to progeroid features evident with impaired tissue repair and regeneration remains unclear. To determine this mechanism, we performed gene editing in reprogrammed induced pluripotent stem cells (iPSCs) derived from WS fibroblasts. Gene correction restored the expression of WRN. WRN+/+ mesenchymal stem cells (MSCs) exhibited improved pro‐angiogenesis. An analysis of paracrine factors revealed that hepatocyte growth factor (HGF) was downregulated in WRN−/− MSCs. HGF insufficiency resulted in poor angiogenesis and cutaneous wound healing. Furthermore, HGF was partially regulated by PI3K/AKT signaling, which was desensitized in WRN−/− MSCs. Consistently, the inhibition of the PI3K/AKT pathway in WRN+/+ MSC resulted in reduced angiogenesis and poor wound healing. Our findings indicate that the impairment in the pro‐angiogenic function of WS‐MSCs is due to HGF insufficiency and PI3K/AKT dysregulation, suggesting trophic disruption between stromal and epithelial cells as a mechanism for WS pathogenesis.
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Affiliation(s)
- Jiajie Tu
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- Institute of Clinical Pharmacology Key Laboratory of Anti‐Inflammatory and Immune Medicine Ministry of Education Anhui Collaborative Innovation Center of Anti‐Inflammatory and Immune Medicine Anhui Medical University Hefei China
- CUHK‐SDU Joint Laboratory on Reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Hong Kong SAR China
| | - Chao Wan
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- School of Biomedical Sciences Core Laboratory Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China
- Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Fengjie Zhang
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Lianbao Cao
- CUHK‐SDU Joint Laboratory on Reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Hong Kong SAR China
| | - Patrick Wai Nok Law
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
| | - Yuyao Tian
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
| | - Gang Lu
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- CUHK‐SDU Joint Laboratory on Reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Hong Kong SAR China
| | - Owen M. Rennert
- Division of Intramural Research Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD USA
| | - Wai‐Yee Chan
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- CUHK‐SDU Joint Laboratory on Reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Hong Kong SAR China
- Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Hoi‐Hung Cheung
- School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong SAR China
- CUHK‐SDU Joint Laboratory on Reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Hong Kong SAR China
- School of Biomedical Sciences Core Laboratory Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China
- Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
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Ziats CA, Rennert OM, Ziats MN. Toward a Pathway-Driven Clinical-Molecular Framework for Classifying Autism Spectrum Disorders. Pediatr Neurol 2019; 98:46-52. [PMID: 31272785 DOI: 10.1016/j.pediatrneurol.2019.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/08/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND The current classification system of neurodevelopmental disorders is based on clinical criteria; however, this method alone fails to incorporate what is now known about genomic similarities and differences between closely related clinical neurodevelopmental disorders. Here we present an alternative clinical molecular classification system of neurodevelopmental disorders based on shared molecular and cellular pathways, using syndromes with autistic features as examples. METHODS Using the Online Mendelian Inheritance in Man database, we identified 83 syndromes that had "autism" as a feature of disease, which in combination were associated with 69 autism disease-causing genes. Using annotation terms generated from the DAVID annotation tool, we grouped each gene and its associated autism syndrome into three biological pathways: ion transport, cellular synaptic function, and transcriptional regulation. RESULTS The majority of the autism syndromes we analyzed (54 of 83) enriched for processes related to transcriptional regulation and were associated with more non-neurologic symptoms and co-morbid psychiatric disease when compared with the other two pathways studied. Disorders with disrupted cellular synaptic function had significantly more motor-related symptoms when compared with the other groups of disorders. CONCLUSION Our pathway-based classification system identified unique clinical characteristics within each group that may help guide clinical diagnosis, prognosis, and treatment. These results suggest that shifting current clinical classification of autism disorders toward molecularly driven, pathway-related diagnostic groups such as this may more precisely guide clinical decision making and may be informative for future clinical trial and drug development approaches.
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Affiliation(s)
- Catherine A Ziats
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - Owen M Rennert
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Mark N Ziats
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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Ziats CA, Grosvenor LP, Sarasua SM, Thurm AE, Swedo SE, Mahfouz A, Rennert OM, Ziats MN. Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment. PLoS One 2019; 14:e0213921. [PMID: 30875393 PMCID: PMC6420160 DOI: 10.1371/journal.pone.0213921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/04/2019] [Indexed: 12/02/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is a neurodevelopmental disorder characterized by varying degrees of intellectual disability, severely delayed language development and specific facial features, and is caused by a deletion within chromosome 22q13.3. SHANK3, which is located at the terminal end of this region, has been repeatedly implicated in other neurodevelopmental disorders and deletion of this gene specifically is thought to cause much of the neurologic symptoms characteristic of PMS. However, it is still unclear to what extent SHANK3 deletions contribute to the PMS phenotype, and what other genes nearby are causal to the neurologic disease. In an effort to better understand the functional landscape of the PMS region during normal neurodevelopment, we assessed RNA-sequencing (RNA-seq) expression data collected from post-mortem brain tissue from developmentally normal subjects over the course of prenatal to adolescent age and analyzed expression changes of 65 genes on 22q13. We found that the majority of genes within this region were expressed in the brain, with ATNX10, MLC1, MAPK8IP2, and SULT4A1 having the highest overall expression. Analysis of the temporal profiles of the highest expressed genes revealed a trend towards peak expression during the early post-natal period, followed by a drop in expression later in development. Spatial analysis revealed significant region specific differences in the expression of SHANK3, MAPK8IP2, and SULT4A1. Region specific expression over time revealed a consistently unique gene expression profile within the cerebellum, providing evidence for a distinct developmental program within this region. Exon-specific expression of SHANK3 showed higher expression within exons contributing to known brain specific functional isoforms. Overall, we provide an updated roadmap of the PMS region, implicating several genes and time periods as important during neurodevelopment, with the hope that this information can help us better understand the phenotypic heterogeneity of PMS.
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Affiliation(s)
- Catherine A. Ziats
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Luke P. Grosvenor
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
- Simons Foundation Autism Research Initiative, New York, New York, United States of America
| | - Sara M. Sarasua
- School of Nursing, Clemson University, Clemson, South Carolina, United States of America
| | - Audrey E. Thurm
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan E. Swedo
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Owen M. Rennert
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark N. Ziats
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, United States of America
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Abstract
Barakat syndrome also known as HDR syndrome (Online Mendelian Inheritance in Man [OMIM] 146255), was first described by Barakat et al. in . It is a rare genetic disorder characterized by the triad of hypoparathyroidism "H," sensorineural deafness "D," and renal disease "R." The defect is caused by deletions in chromosome 10p14 or mutations in the GATA3 gene. Although the syndrome has been phenotypically defined by this triad the literature identifies cases with different components with, or without GATA3 defects making the definition of the syndrome confusing. We analyzed 180 cases and attempted to define the phenotype of the syndrome and suggest guidelines for diagnosis. We suggest that the diagnosis could be confirmed in patients who have all three components, and in those who have two components with a positive family history. GATA3 testing is optional to establish the diagnosis in these patients. The syndrome should be considered in patients with isolated "D" where other causes of "D" have been excluded and those with isolated "R," especially if there is family history of any of these components. In these instances, confirmatory GATA3 testing is indicated to confirm the diagnosis. In patients with nonsurgical "H," where "D" and "R" have been conclusively ruled out GATA3 studies are not needed as none of these patients were shown to be GATA3 haploinsufficient. Only 64.4% of patients in our review had "HDR." Some findings might have not been recognized or may could have appeared later in life, but it is evident that this syndrome is genotypically heterogeneous.
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Affiliation(s)
| | - Margarita Raygada
- Georgetown University Medical Center, Washington, DC
- Section on Endocrinology & Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Owen M Rennert
- Section on Endocrinology & Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC
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Affiliation(s)
- Owen M Rennert
- National Institute of Child Health and Human Development, NIH, Bestheda, MD, United States
| | - Mark N Ziats
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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Liu X, Campanac E, Cheung HH, Ziats MN, Canterel-Thouennon L, Raygada M, Baxendale V, Pang ALY, Yang L, Swedo S, Thurm A, Lee TL, Fung KP, Chan WY, Hoffman DA, Rennert OM. Idiopathic Autism: Cellular and Molecular Phenotypes in Pluripotent Stem Cell-Derived Neurons. Mol Neurobiol 2016; 54:4507-4523. [PMID: 27356918 DOI: 10.1007/s12035-016-9961-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/07/2016] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorder is a complex neurodevelopmental disorder whose pathophysiology remains elusive as a consequence of the unavailability for study of patient brain neurons; this deficit may potentially be circumvented by neural differentiation of induced pluripotent stem cells. Rare syndromes with single gene mutations and autistic symptoms have significantly advanced the molecular and cellular understanding of autism spectrum disorders; however, in aggregate, they only represent a fraction of all cases of autism. In an effort to define the cellular and molecular phenotypes in human neurons of non-syndromic autism, we generated induced pluripotent stem cells (iPSCs) from three male autism spectrum disorder patients who had no identifiable clinical syndromes, and their unaffected male siblings and subsequently differentiated these patient-specific stem cells into electrophysiologically active neurons. iPSC-derived neurons from these autistic patients displayed decreases in the frequency and kinetics of spontaneous excitatory postsynaptic currents relative to controls, as well as significant decreases in Na+ and inactivating K+ voltage-gated currents. Moreover, whole-genome microarray analysis of gene expression identified 161 unique genes that were significantly differentially expressed in autistic patient iPSC-derived neurons (>twofold, FDR < 0.05). These genes were significantly enriched for processes related to synaptic transmission, such as neuroactive ligand-receptor signaling and extracellular matrix interactions, and were enriched for genes previously associated with autism spectrum disorder. Our data demonstrate aberrant voltage-gated currents and underlying molecular changes related to synaptic function in iPSC-derived neurons from individuals with idiopathic autism as compared to unaffected siblings controls.
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Affiliation(s)
- Xiaozhuo Liu
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Emilie Campanac
- Molecular Neurophysiology and Biophysics Section, Program in Development Neuroscience, NICHD, NIH, 35 Convent Drive, MSC 4995, Porter Neuroscience Research Center Building 35, Room 3C-905, Bethesda, MD, 20892-4995, USA
| | - Hoi-Hung Cheung
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
- CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark N Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
- Baylor College of Medicine, Houston, TX, 77030, USA
- University at Cambridge, Cambridge, CB3 9AN, UK
| | - Lucile Canterel-Thouennon
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
| | - Margarita Raygada
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
| | - Vanessa Baxendale
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
| | - Alan Lap-Yin Pang
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
| | - Lu Yang
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA
| | - Susan Swedo
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, 20892, USA
| | - Audrey Thurm
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, 20892, USA
| | - Tin-Lap Lee
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok-Pui Fung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai-Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Dax A Hoffman
- Molecular Neurophysiology and Biophysics Section, Program in Development Neuroscience, NICHD, NIH, 35 Convent Drive, MSC 4995, Porter Neuroscience Research Center Building 35, Room 3C-905, Bethesda, MD, 20892-4995, USA.
| | - Owen M Rennert
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 10 Center Drive, MSC 1255, Building 10, Room 1C-250, Bethesda, MD, 20892-1255, USA.
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Abstract
The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome.
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Affiliation(s)
- Mark N. Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeshire, UK
- Medical Scientist Training Program, Baylor College of MedicineHouston, TX, USA
| | - Owen M. Rennert
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Edmonson CA, Ziats MN, Rennert OM. A Non-inflammatory Role for Microglia in Autism Spectrum Disorders. Front Neurol 2016; 7:9. [PMID: 26869989 PMCID: PMC4734207 DOI: 10.3389/fneur.2016.00009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/19/2016] [Indexed: 12/25/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social interaction, difficulties with language, and repetitive/restricted behaviors. The etiology of ASD is still largely unclear, but immune dysfunction and abnormalities in synaptogenesis have repeatedly been implicated as contributing to the disease phenotype. However, an understanding of how and if these two processes are related has not firmly been established. As non-inflammatory roles of microglia become increasingly recognized as critical to normal neurodevelopment, it is important to consider how dysfunction in these processes might explain the seemingly disparate findings of immune dysfunction and aberrant synaptogenesis seen in ASD. In this review, we highlight research demonstrating the importance of microglia to the development of normal neural networks, review recent studies demonstrating abnormal microglia in autism, and discuss how the relationship between these processes may contribute to the development of autism and other neurodevelopmental disorders at the cellular level.
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Affiliation(s)
- Catherine A Edmonson
- University of Florida College of Medicine, Gainesville, FL, USA; National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mark N Ziats
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Owen M Rennert
- National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, MD , USA
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9
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Ziats MN, Grosvenor LP, Rennert OM. Functional genomics of human brain development and implications for autism spectrum disorders. Transl Psychiatry 2015; 5:e665. [PMID: 26506051 PMCID: PMC4930130 DOI: 10.1038/tp.2015.153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/03/2015] [Accepted: 09/06/2015] [Indexed: 12/13/2022] Open
Abstract
Transcription of the inherited DNA sequence into copies of messenger RNA is the most fundamental process by which the genome functions to guide development. Encoded sequence information, inherited epigenetic marks and environmental influences all converge at the level of mRNA gene expression to allow for cell-type-specific, tissue-specific, spatial and temporal patterns of expression. Thus, the transcriptome represents a complex interplay between inherited genomic structure, dynamic experiential demands and external signals. This property makes transcriptome studies uniquely positioned to provide insight into complex genetic-epigenetic-environmental processes such as human brain development, and disorders with non-Mendelian genetic etiologies such as autism spectrum disorders. In this review, we describe recent studies exploring the unique functional genomics profile of the human brain during neurodevelopment. We then highlight two emerging areas of research with great potential to increase our understanding of functional neurogenomics-non-coding RNA expression and gene interaction networks. Finally, we review previous functional genomics studies of autism spectrum disorder in this context, and discuss how investigations at the level of functional genomics are beginning to identify convergent molecular mechanisms underlying this genetically heterogeneous disorder.
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Affiliation(s)
- M N Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA,University of Cambridge, Robinson College, Cambridgeshire, UK,Baylor College of Medicine MSTP, One Baylor Plaza, Houston, TX, USA,Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C08, Bethesda, MD 20814, USA. E-mail:
| | - L P Grosvenor
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - O M Rennert
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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10
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Mahfouz A, Ziats MN, Rennert OM, Lelieveldt BPF, Reinders MJT. Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome. J Mol Neurosci 2015; 57:580-94. [PMID: 26399424 PMCID: PMC4644211 DOI: 10.1007/s12031-015-0641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 02/26/2014] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental syndrome known to have a significant but complex genetic etiology. Hundreds of diverse genes have been implicated in ASD; yet understanding how many genes, each with disparate function, can all be linked to a single clinical phenotype remains unclear. We hypothesized that understanding functional relationships between autism candidate genes during normal human brain development may provide convergent mechanistic insight into the genetic heterogeneity of ASD. We analyzed the co-expression relationships of 455 genes previously implicated in autism using the BrainSpan human transcriptome database, across 16 anatomical brain regions spanning prenatal life through adulthood. We discovered modules of ASD candidate genes with biologically relevant temporal co-expression dynamics, which were enriched for functional ontologies related to synaptogenesis, apoptosis, and GABA-ergic neurons. Furthermore, we also constructed co-expression networks from the entire transcriptome and found that ASD candidate genes were enriched in modules related to mitochondrial function, protein translation, and ubiquitination. Hub genes central to these ASD-enriched modules were further identified, and their functions supported these ontological findings. Overall, our multi-dimensional co-expression analysis of ASD candidate genes in the normal developing human brain suggests the heterogeneous set of ASD candidates share transcriptional networks related to synapse formation and elimination, protein turnover, and mitochondrial function.
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Affiliation(s)
- Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands. .,Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Mark N Ziats
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,University of Cambridge, Cambridge, UK.,Baylor College of Medicine, Houston, TX, USA
| | - Owen M Rennert
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Boudewijn P F Lelieveldt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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Abstract
The etiology of autism spectrum disorders (ASDs) is complex and largely unclear. Among various lines of inquiry, many have suggested convergence onto disruptions in both neural circuitry and immune regulation/glial cell function pathways. However, the interpretation of the relationship between these two putative mechanisms has largely focused on the role of exogenous factors and insults, such as maternal infection, in activating immune pathways that in turn result in neural network abnormalities. Yet, given recent insights into our understanding of human neurodevelopment, and in particular the critical role of glia and the immune system in normal brain development, it is important to consider these putative pathological processes in their appropriate normal neurodevelopmental context. In this review, we explore the hypothesis that the autistic brain cellular phenotype likely represents intrinsic abnormalities of glial/immune processes constitutively operant in normal brain development that result in the observed neural network dysfunction. We review recent studies demonstrating the intercalated role of neural circuit development, the immune system, and glial cells in the normal developing brain, and integrate them with studies demonstrating pathological alterations in these processes in autism. By discussing known abnormalities in the autistic brain in the context of normal brain development, we explore the hypothesis that the glial/immune component of ASD may instead be related to intrinsic exaggerated/abnormal constitutive neurodevelopmental processes such as network pruning. Moreover, this hypothesis may be relevant to other neurodevelopmental disorders that share genetic, pathologic, and clinical features with autism.
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Affiliation(s)
- Mark N Ziats
- National Institute of Child Health and Human Development, NIH Bethesda, MD, USA ; Medical Scientist Training Program, Baylor College of Medicine Houston, TX, USA
| | - Catherine Edmonson
- National Institute of Child Health and Human Development, NIH Bethesda, MD, USA ; College of Medicine, University of Florida Gainesville, FL, USA
| | - Owen M Rennert
- National Institute of Child Health and Human Development, NIH Bethesda, MD, USA
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12
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Tu J, Ng SH, Luk ACS, Liao J, Jiang X, Feng B, Lun Mak KK, Rennert OM, Chan WY, Lee TL. MicroRNA-29b/Tet1 regulatory axis epigenetically modulates mesendoderm differentiation in mouse embryonic stem cells. Nucleic Acids Res 2015; 43:7805-22. [PMID: 26130713 PMCID: PMC4652748 DOI: 10.1093/nar/gkv653] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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] [Received: 03/20/2015] [Accepted: 06/13/2015] [Indexed: 12/03/2022] Open
Abstract
Ten eleven translocation (Tet) family-mediated DNA oxidation on 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) represents a novel epigenetic modification that regulates dynamic gene expression during embryonic stem cells (ESCs) differentiation. Through the role of Tet on 5hmC regulation in stem cell development is relatively defined, how the Tet family is regulated and impacts on ESCs lineage development remains elusive. In this study, we show non-coding RNA regulation on Tet family may contribute to epigenetic regulation during ESCs differentiation, which is suggested by microRNA-29b (miR-29b) binding sites on the Tet1 3′ untranslated region (3′ UTR). We demonstrate miR-29b increases sharply after embyoid body (EB) formation, which causes Tet1 repression and reduction of cellular 5hmC level during ESCs differentiation. Importantly, we show this miR-29b/Tet1 regulatory axis promotes the mesendoderm lineage formation both in vitro and in vivo by inducing the Nodal signaling pathway and repressing the key target of the active demethylation pathway, Tdg. Taken together, our findings underscore the contribution of small non-coding RNA mediated regulation on DNA demethylation dynamics and the differential expressions of key mesendoderm regulators during ESCs lineage specification. MiR-29b could potentially be applied to enrich production of mesoderm and endoderm derivatives and be further differentiated into desired organ-specific cells.
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Affiliation(s)
- Jiajie Tu
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Shuk Han Ng
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Alfred Chun Shui Luk
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jinyue Liao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xiaohua Jiang
- Stem Cell and Regeneration Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Bo Feng
- Stem Cell and Regeneration Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kingston King Lun Mak
- Stem Cell and Regeneration Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Owen M Rennert
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Wai-Yee Chan
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Tin-Lap Lee
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Luk ACS, Gao H, Xiao S, Liao J, Wang D, Tu J, Rennert OM, Chan WY, Lee TL. GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. Database (Oxford) 2015; 2015:bav044. [PMID: 25982314 PMCID: PMC4433719 DOI: 10.1093/database/bav044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/15/2015] [Indexed: 12/16/2022]
Abstract
Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs. GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis. Database URL: http://germlncrna.cbiit.cuhk.edu.hk/
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Affiliation(s)
- Alfred Chun-Shui Luk
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Huayan Gao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sizhe Xiao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jinyue Liao
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Daxi Wang
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jiajie Tu
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Owen M Rennert
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Wai-Yee Chan
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and T
| | - Tin-Lap Lee
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and T
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Luk ACS, Chan WY, Rennert OM, Lee TL. Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies. Reproduction 2014; 147:R131-41. [PMID: 24713396 DOI: 10.1530/rep-13-0594] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spermatogenesis is a complex developmental process in which undifferentiated spermatogonia are differentiated into spermatocytes and spermatids through two rounds of meiotic division and finally giving rise to mature spermatozoa (sperm). These processes involve many testis- or male germ cell-specific gene products that undergo strict developmental regulations. As a result, identifying critical, regulatory genes controlling spermatogenesis provide the clues not only to the regulatory mechanism of spermatogenesis at the molecular level, but also to the identification of candidate genes for infertility or contraceptives development. Despite the biological importance in male germ cell development, the underlying mechanisms of stage-specific gene regulation and cellular transition during spermatogenesis remain largely elusive. Previous genomic studies on transcriptome profiling were largely limited to protein-coding genes. Importantly, protein-coding genes only account for a small percentage of transcriptome; the majority are noncoding transcripts that do not translate into proteins. Although small noncoding RNAs (ncRNAs) such as microRNAs, siRNAs, and Piwi-interacting RNAs are extensively investigated in male germ cell development, the role of long ncRNAs (lncRNAs), commonly defined as ncRNAs longer than 200 bp, is relatively unexplored. Herein, we summarize recent transcriptome studies on spermatogenesis and show examples that a subset of noncoding transcript population, known as lncRNAs, constitutes a novel regulatory target in spermatogenesis.
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Affiliation(s)
- Alfred Chun-Shui Luk
- School of Biomedical Sciences, Room 622A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Pang ALY, Title AC, Rennert OM. Modulation of microRNA expression in human lung cancer cells by the G9a histone methyltransferase inhibitor BIX01294. Oncol Lett 2014; 7:1819-1825. [PMID: 24932239 PMCID: PMC4049738 DOI: 10.3892/ol.2014.2034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 09/03/2013] [Accepted: 03/14/2014] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression of their target genes at the post-transcriptional level. In cancer cells, miRNAs, depending on the biological functions of their target genes, may have a tumor-promoting or -suppressing effect. Treatment of cancer cells with inhibitors of DNA methylation and/or histone deacetylation modulates the expression level of miRNAs, which provides evidence for epigenetic regulation of miRNA expression. The consequences of inhibition of histone methyltransferase on miRNA expression, however, have not been thoroughly investigated. The present study examined the expression pattern of miRNAs in the non-small cell lung cancer cell line, H1299 with or without treatment of BIX01294, a potent chemical inhibitor of G9a methyltransferase that catalyzes the mono-and di-methylation of the lysine 9 residue of histone H3. By coupling microarray analysis with quantitative real-time polymerase chain reaction analysis, two miRNAs were identified that showed consistent downregulation following BIX01294 treatment. The results indicate that histone H3 methylation regulates miRNA expression in lung cancer cells, which may provide additional insight for future chemical treatment of lung cancer.
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Affiliation(s)
- Alan Lap-Yin Pang
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4429, USA
| | - Alexandra C Title
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4429, USA
| | - Owen M Rennert
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4429, USA
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Cheung HH, Liu X, Canterel-Thouennon L, Li L, Edmonson C, Rennert OM. Telomerase protects werner syndrome lineage-specific stem cells from premature aging. Stem Cell Reports 2014; 2:534-46. [PMID: 24749076 PMCID: PMC3986587 DOI: 10.1016/j.stemcr.2014.02.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [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] [Received: 08/21/2013] [Revised: 02/20/2014] [Accepted: 02/20/2014] [Indexed: 12/12/2022] Open
Abstract
Werner syndrome (WS) patients exhibit premature aging predominantly in mesenchyme-derived tissues, but not in neural lineages, a consequence of telomere dysfunction and accelerated senescence. The cause of this lineage-specific aging remains unknown. Here, we document that reprogramming of WS fibroblasts to pluripotency elongated telomere length and prevented telomere dysfunction. To obtain mechanistic insight into the origin of tissue-specific aging, we differentiated iPSCs to mesenchymal stem cells (MSCs) and neural stem/progenitor cells (NPCs). We observed recurrence of premature senescence associated with accelerated telomere attrition and defective synthesis of the lagging strand telomeres in MSCs, but not in NPCs. We postulate this “aging” discrepancy is regulated by telomerase. Expression of hTERT or p53 knockdown ameliorated the accelerated aging phenotypein MSC, whereas inhibition of telomerase sensitized NPCs to DNA damage. Our findings unveil a role for telomerase in the protection of accelerated aging in a specific lineage of stem cells. Prevention of premature senescence with corrected telomeres in reprogrammed WS iPSCs Recurrence of premature senescence and telomere dysfunction in WS iPSC-derived MSCs Rescue of premature senescence in WS MSCs by hTERT overexpression or p53 depletion Telomerase protects and prevents NPCs from DNA damage
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Affiliation(s)
- Hoi-Hung Cheung
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA ; School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, N.T., 852 Hong Kong S.A.R
| | - Xiaozhuo Liu
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA ; School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, N.T., 852 Hong Kong S.A.R
| | - Lucile Canterel-Thouennon
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lu Li
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, N.T., 852 Hong Kong S.A.R
| | - Catherine Edmonson
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Owen M Rennert
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
The recent revolution of genomics techniques has allowed the detection of various sequence features and biological variations on whole-genome scale. However, these high-resolution data present significant challenges for experimental biologists to understand and analyze. The conventional way is to use genome browsers to locate and visualize regions of interest. But it lacks user-friendly data mining functionality. Here we present a protocol that allows rapid annotation of genomic coordinate data by using TileMapper. Interesting biological annotations from large-scale genomic data, such as transcriptome analysis, chromatin immunoprecipitation on chip, or methyl-DNA immunoprecipitation (MeDIP) studies generated from the tiling microarrays and other platforms, could be analyzed without requiring computational skills. The outputs are saved in tabulated format, which permit flexible and simple processing in spreadsheet software, or to be exported to other pipelines for subsequent analysis.
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Affiliation(s)
- Hoi-Hung Cheung
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Edmonson C, Ziats MN, Rennert OM. Altered glial marker expression in autistic post-mortem prefrontal cortex and cerebellum. Mol Autism 2014; 5:3. [PMID: 24410870 PMCID: PMC3914711 DOI: 10.1186/2040-2392-5-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [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] [Received: 09/14/2013] [Accepted: 12/23/2013] [Indexed: 01/29/2023] Open
Abstract
Background The cellular mechanism(s) underlying autism spectrum disorders (ASDs) are not completely understood, but ASDs are thought to ultimately result from disrupted synaptogenesis. However, studies have also shown that glial cell numbers and function are abnormal in post-mortem brain tissue from autistic patients. Direct assessment of glial cells in post-mortem human brain tissue is technically challenging, limiting glial research in human ASD studies. Therefore, we attempted to determine if glial cell-type specific markers may be altered in autistic brain tissue in a manner that is consistent with known cellular findings, such that they could serve as a proxy for glial cell numbers and/or activation patterns. Methods We assessed the relative expression of five glial-specific markers and two neuron-specific markers via qRT-PCR. We studied tissue samples from the prefrontal cortex (PFC) and cerebellum of nine post-mortem autistic brain samples and nine neurologically-normal controls. Relative fold-change in gene expression was determined using the ΔΔCt method normalized to housekeeping gene β-actin, with a two-tailed Student’s t-test P <0.05 between groups considered as significant. Results Both astrocyte- and microglial-specific markers were significantly more highly expressed in autistic PFC as compared to matched controls, while in the cerebellum only astrocyte markers were elevated in autistic samples. In contrast, neuron-specific markers showed significantly lower expression in both the PFC and cerebellum of autistic patients as compared to controls. Conclusions These results are in line with previous findings showing increased glial cell numbers and up-regulation of glial cell gene expression in autistic post-mortem brain tissue, particularly in the PFC, as well as decreased number of neurons in both the PFC and cerebellum of autistic patients. The concordance of these results with cell-level studies in post-mortem autistic brain tissue suggests that expression of glial cell-type specific markers may serve as a useful alternative to traditional cellular characterization methods, especially when appropriately-preserved post-mortem tissue is lacking. Additionally, these results demonstrate abnormal glial-specific gene expression in autistic brains, supporting previous studies that have observed altered glial cell numbers or activation patterns in ASDs. Future work should directly assess the correlation between cell-type specific marker levels and cell number and activation patterns.
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Affiliation(s)
- Catherine Edmonson
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C078, Bethesda, MD 20814, USA.,University of Florida College of Medicine, 1600 SW Archer Rd, Gainesville, FL 32603, USA
| | - Mark N Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C078, Bethesda, MD 20814, USA.,University of Cambridge, Robinson College, Grange Rd, Cambridgeshire CB3 9AN, UK.,Baylor College of Medicine MSTP, One Baylor Plaza, Houston, TX 77030, USA
| | - Owen M Rennert
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C078, Bethesda, MD 20814, USA
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Ziats MN, Rennert OM. Sex-biased gene expression in the developing brain: implications for autism spectrum disorders. Mol Autism 2013; 4:10. [PMID: 23651621 PMCID: PMC3653724 DOI: 10.1186/2040-2392-4-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 04/16/2013] [Indexed: 12/03/2022] Open
Abstract
Autism spectrum disorders affect significantly more males than females. Understanding sex differences in normal human brain development may provide insight into the mechanism(s) underlying this disparity; however, studies of sex differences in brain development at the genomic level are lacking. Here, we report a re-analysis of sex-specific gene expression from a recent large transcriptomic study of normal human brain development, to determine whether sex-biased genes relate to specific mechanistic processes. We discovered that male-biased genes are enriched for the processes of extracellular matrix formation/glycoproteins, immune response, chromatin, and cell cytoskeleton. We highlight that these pathways have been repeatedly implicated in autism and demonstrate that autism candidate genes are also enriched for these pathways. We propose that the overlap of these male-specific brain transcriptional modules with the same pathways in autism spectrum disorders may partially explain the increased incidence of autism in males.
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Affiliation(s)
- Mark N Ziats
- National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C08, Bethesda, MD 20814, USA.
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21
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Pang AL, Title AC, Rennert OM. Expression of the mouse
Lin28a
gene is epigenetically regulated by histone modification. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.550.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Han JC, Thurm A, Golden Williams C, Joseph LA, Zein WM, Brooks BP, Butman JA, Brady SM, Fuhr SR, Hicks MD, Huey AE, Hanish AE, Danley KM, Raygada MJ, Rennert OM, Martinowich K, Sharp SJ, Tsao JW, Swedo SE. Association of brain-derived neurotrophic factor (BDNF) haploinsufficiency with lower adaptive behaviour and reduced cognitive functioning in WAGR/11p13 deletion syndrome. Cortex 2013; 49:2700-10. [PMID: 23517654 DOI: 10.1016/j.cortex.2013.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 12/23/2022]
Abstract
In animal studies, brain-derived neurotrophic factor (BDNF) is an important regulator of central nervous system development and synaptic plasticity. WAGR (Wilms tumour, Aniridia, Genitourinary anomalies, and mental Retardation) syndrome is caused by 11p13 deletions of variable size near the BDNF locus and can serve as a model for studying human BDNF haploinsufficiency (+/-). We hypothesized that BDNF+/- would be associated with more severe cognitive impairment in subjects with WAGR syndrome. Twenty-eight subjects with WAGR syndrome (6-28 years), 12 subjects with isolated aniridia due to PAX6 mutations/microdeletions (7-54 years), and 20 healthy controls (4-32 years) received neurocognitive assessments. Deletion boundaries for the subjects in the WAGR group were determined by high-resolution oligonucleotide array comparative genomic hybridization. Within the WAGR group, BDNF+/- subjects (n = 15), compared with BDNF intact (+/+) subjects (n = 13), had lower adaptive behaviour (p = .02), reduced cognitive functioning (p = .04), higher levels of reported historical (p = .02) and current (p = .02) social impairment, and higher percentage meeting cut-off score for autism (p = .047) on Autism Diagnostic Interview-Revised. These differences remained nominally significant after adjusting for visual acuity. Using diagnostic measures and clinical judgement, 3 subjects (2 BDNF+/- and 1 BDNF+/+) in the WAGR group (10.7%) were classified with autism spectrum disorder. A comparison group of visually impaired subjects with isolated aniridia had cognitive functioning comparable to that of healthy controls. In summary, among subjects with WAGR syndrome, BDNF+/- subjects had a mean Vineland Adaptive Behaviour Compose score that was 14-points lower and a mean intelligence quotient (IQ) that was 20-points lower than BDNF+/+ subjects. Our findings support the hypothesis that BDNF plays an important role in human neurocognitive development.
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Affiliation(s)
- Joan C Han
- Unit on Metabolism and Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD, USA; Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, NICHD, National Institutes of Health, Bethesda, MD, USA.
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23
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Huen NY, Pang ALY, Tucker JA, Lee TL, Vergati M, Jochems C, Intrivici C, Cereda V, Chan WY, Rennert OM, Madan RA, Gulley JL, Schlom J, Tsang KY. Up-regulation of proliferative and migratory genes in regulatory T cells from patients with metastatic castration-resistant prostate cancer. Int J Cancer 2013; 133:373-82. [PMID: 23319273 DOI: 10.1002/ijc.28026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 12/17/2012] [Indexed: 12/21/2022]
Abstract
A higher frequency of regulatory T cells (Tregs) has been observed in peripheral blood mononuclear cells (PBMC) of patients with different types of solid tumors and hematological malignancies as compared to healthy donors. In prostate cancer patients, Tregs in PBMC have been shown to have increased suppressive function. Tumor-induced biological changes in Tregs may enable tumor cells to escape immunosurveillance. We performed genome-wide expression analyses comparing the expression levels of more than 38,500 genes in Tregs with similar suppressive activity, isolated from the peripheral blood of healthy donors and patients with metastatic castration-resistant prostate cancer (mCRPC). The differentially expressed genes in mCRPC Tregs are involved in cell cycle processes, cellular growth and proliferation, immune responses, hematological system development and function and the interleukin-2 (IL-2) and transforming growth factor-β (TGF-β) pathways. Studies revealed that the levels of expression of genes responsible for T-cell proliferation (C-FOS, C-JUN and DUSP1) and cellular migration (RGS1) were greater in Tregs from mCRPC patients as compared to values observed in healthy donors. Increased RGS1 expression in Tregs from mCRPC patients suggests a decrease in these Tregs' migratory ability. In addition, the higher frequency of CD4(+) CD25(high) CD127(-) Tregs in the peripheral blood of mCRPC patients may be the result of an increase in Treg proliferation capacity. Results also suggest that the alterations observed in gene expression profiles of Tregs in mCRPC patients may be part of the mechanism of tumor escape from host immune surveillance.
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Affiliation(s)
- Ngar-Yee Huen
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Pang ALY, Taylor HC, Johnson W, Alexander S, Chen Y, Su YA, Li X, Ravindranath N, Dym M, Rennert OM, Chan WY. Identification of Differentially Expressed Genes in Mouse Spermatogenesis. ACTA ACUST UNITED AC 2013; 24:899-911. [PMID: 14581517 DOI: 10.1002/j.1939-4640.2003.tb03142.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 11/11/2022]
Abstract
Complementary DNA microarray and quantitative polymerase chain reaction were used as tools for discovering genes that are differentially expressed in the mouse under normal physiological conditions at distinctive stages of male germ cell development, that is, type A spermatogonia, pachytene spermatocytes, and round spermatids. By using this strategy, we identified a set of genes exhibiting differential expression patterns in spermatogenesis, suggesting that specific functions of the encoded products occurred during the developmental process. Among them were several genes previously not known to be active in testis, which signified undiscovered functional roles of these genes during spermatogenesis. Many of the genes identified were not previously characterized. This study highlights new targets for manipulation to unravel the molecular mechanism of spermatogenesis.
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Affiliation(s)
- Alan L Y Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, USA
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25
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Boucheron-Houston C, Canterel-Thouennon L, Lee TL, Baxendale V, Nagrani S, Chan WY, Rennert OM. Long-term vitamin A deficiency induces alteration of adult mouse spermatogenesis and spermatogonial differentiation: direct effect on spermatogonial gene expression and indirect effects via somatic cells. J Nutr Biochem 2012; 24:1123-35. [PMID: 23253600 DOI: 10.1016/j.jnutbio.2012.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 08/03/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
The objective of this study was to further understand the genetic mechanisms of vitamin A deficiency (VAD) induced arrest of spermatogonial stem-cell differentiation. Vitamin A and its derivatives (the retinoids) participate in many physiological processes including vision, cellular differentiation and reproduction. VAD affects spermatogenesis, the subject of our present study. Spermatogenesis is a highly regulated process of differentiation and complex morphologic alterations that leads to the formation of sperm in the seminiferous epithelium. VAD causes early cessation of spermatogenesis, characterized by degeneration of meiotic germ cells, leading to seminiferous tubules containing mostly type A spermatogonia and Sertoli cells. These observations led us to the hypothesis that VAD affects not only germ cells but also somatic cells. To investigate the effects of VAD on spermatogenesis in mice we used adult Balb/C mice fed with Control or VAD diet for an extended period of time (6-28 weeks). We first observed the chronology, then the extent of the effects of VAD on the testes. Using microarray analysis of isolated pure populations of spermatogonia, Leydig and Sertoli cells from control and VAD 18- and 25-week mice, we examined the effects of VAD on gene expression and identified target genes involved in the arrest of spermatogonial differentiation and spermatogenesis. Our results provide a more precise definition of the chronology and magnitude of the consequences of VAD on mouse testes than the previously available literature and highlight direct and indirect (via somatic cells) effects of VAD on germ cell differentiation.
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Affiliation(s)
- Catherine Boucheron-Houston
- Laboratory of Clinical Genomics, Section on Developmental Genomics, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4429, USA
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26
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Abstract
The autism spectrum disorders (ASD) have a significant hereditary component, but the implicated genetic loci are heterogeneous and complex. Consequently, there is a gap in understanding how diverse genomic aberrations all result in one clinical ASD phenotype. Gene expression studies from autism brain tissue have demonstrated that aberrantly expressed protein-coding genes may converge onto common molecular pathways, potentially reconciling the strong heritability and shared clinical phenotypes with the genomic heterogeneity of the disorder. However, the regulation of gene expression is extremely complex and governed by many mechanisms, including noncoding RNAs. Yet no study in ASD brain tissue has assessed for changes in regulatory long noncoding RNAs (lncRNAs), which represent a large proportion of the human transcriptome, and actively modulate mRNA expression. To assess if aberrant expression of lncRNAs may play a role in the molecular pathogenesis of ASD, we profiled over 33,000 annotated lncRNAs and 30,000 mRNA transcripts from postmortem brain tissue of autistic and control prefrontal cortex and cerebellum by microarray. We detected over 200 differentially expressed lncRNAs in ASD, which were enriched for genomic regions containing genes related to neurodevelopment and psychiatric disease. Additionally, comparison of differences in expression of mRNAs between prefrontal cortex and cerebellum within individual donors showed ASD brains had more transcriptional homogeneity. Moreover, this was also true of the lncRNA transcriptome. Our results suggest that further investigation of lncRNA expression in autistic brain may further elucidate the molecular pathogenesis of this disorder.
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Affiliation(s)
- Mark N Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA.
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27
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Lee TL, Raitano JM, Rennert OM, Chan SW, Chan WY. Accessing the genomic effects of naked nanoceria in murine neuronal cells. Nanomedicine 2012; 8:599-608. [PMID: 21889474 PMCID: PMC3245889 DOI: 10.1016/j.nano.2011.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 08/08/2011] [Accepted: 08/15/2011] [Indexed: 11/16/2022]
Abstract
Cerium oxide nanoparticles (nanoceria) are engineered nanoparticles whose versatility is due to their unique redox properties. We and others have demonstrated that naked nanoceria can act as antioxidants to protect cells against oxidative damage. Although the redox properties may be beneficial, the genome-wide effects of nanoceria on gene transcription and associated biological processes remain elusive. Here we applied a functional genomic approach to examine the genome-wide effects of nanoceria on global gene transcription and cellular functions in mouse neuronal cells. Importantly, we demonstrated that nanoceria induced chemical- and size-specific changes in the murine neuronal cell transcriptome. The nanoceria contributed more than 83% of the population of uniquely altered genes and were associated with a unique spectrum of genes related to neurological disease, cell cycle control, and growth. These observations suggest that an in-depth assessment of potential health effects of naked nanoceria and other naked nanoparticles is both necessary and imminent. FROM THE CLINICAL EDITOR Cerium oxide nanoparticles are important antioxidants, with potential applications in neurodegenerative conditions. This team of investigators demonstrated the genomic effects of nanoceria, showing that it induced chemical- and size-specific changes in the murine neuronal cell transcriptome.
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Affiliation(s)
- Tin-Lap Lee
- Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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28
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Abstract
Apoptosis is essential for embryogenesis, organ metamorphosis, and tissue homeostasis. In embryonic stem cells, self-renewal is balanced with proliferative potential, inhibition of differentiation, and prevention of senescence and apoptosis. Growing evidence supports the role of apoptosis in self-renewal, differentiation of pluripotent stem cells, and dedifferentiation (reprogramming) of somatic cells. In this paper we discuss the multiple roles of apoptosis in embryonic stem cells (ESCs) and reprogramming of differentiated cells to pluripotency. The role of caspases and p53 as key effectors in controlling the generation of iPSC is emphasized. Remarkably, the complication of apoptosis arising during reprogramming may provide insights into technical improvements for derivation of iPSC from senescent cells as a tool for modeling aging-related diseases.
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Affiliation(s)
- Hoi-Hung Cheung
- Section on Clinical and Developmental Genomics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaozhuo Liu
- Section on Clinical and Developmental Genomics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Owen M. Rennert
- Section on Clinical and Developmental Genomics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Abstract
DNA methylation is an important epigenetic modification that regulates development and plays a role in the pathophysiology of many diseases. It is dynamically changed during germline development. Methylated DNA immunoprecipitation (MeDIP) is an efficient, cost-effective method for locus-specific and genome-wide analysis. Methylated DNA fragments are enriched by a 5-methylcytidine-recognizing antibody, therefore allowing the analysis of both CpG and non-CpG methylation. The enriched DNA fragments can be amplified and hybridized to tiling arrays covering CpG islands, promoters, or the entire genome. Comparison of different methylomes permits the discovery of differentially methylated regions that might be important in disease- or tissue-specific expression. Here, we describe an established MeDIP protocol and tiling array hybridization method for profiling methylation of testicular germ cells.
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Affiliation(s)
- Hoi-Hung Cheung
- Section on Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA.
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30
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Lee TL, Raygada MJ, Rennert OM. Integrative gene network analysis provides novel regulatory relationships, genetic contributions and susceptible targets in autism spectrum disorders. Gene 2012; 496:88-96. [PMID: 22306264 PMCID: PMC3303594 DOI: 10.1016/j.gene.2012.01.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 01/11/2012] [Accepted: 01/17/2012] [Indexed: 01/23/2023]
Abstract
Autism spectrum disorders (ASDs) are a group of diseases exhibiting impairment in social drive, communication/language skills and stereotyped behaviors. Though an increased number of candidate genes and molecular interactions have been identified by various approaches, the pathogenesis remains elusive. Based on clinical observations, data from accessible GWAS and expression datasets we identified ASDs gene candidates. Integrative gene network and a novel CNV-centric Node Network (CNN) analysis method highlighted ASDs-associated key elements and biological processes. Functional analysis identified neurological functions including synaptic cholinergic receptor (CHRNA) families, dopamine receptor (DRD2), and correlations between social behavior and oxytocin related pathways. CNN analysis of genome-wide genetic and expression data identified inheritance-related clusters related to PTEN/TSC1/FMR1 and mTor/PI3K regulation. Integrative analysis identified potential regulators of networks, specifically TNF and beta-estradiol, suggesting a potential central role in ASDs. Our data provide information on potential disease mechanisms, and key regulators that may generate novel postulations, and diagnostic molecular biomarkers.
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Affiliation(s)
- Tin-Lap Lee
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Abstract
In the past decade, the advent of microarray technologies has allowed functional genomic studies of male germ cell development, resulting in the identification of genes governing various processes. A major limitation with conventional gene expression microarray is that results obtained are biased due to gene probe design. The gene probes for expression microarrays are usually represented by a small number of probes located at the 3' end of a transcript. Tiling microarrays eliminate such issue by interrogating the genome in an unbiased fashion through probes tiled across the entire genome. These arrays provide higher genomic resolution and allow the identification of novel transcripts. To reveal the complexity of the genomic landscape of developing male germ cells, we applied tiling microarray to evaluate the transcriptome in spermatogonial cells. Over 50% of all known mouse genes are expressed during testicular development. More than 47% of the transcripts are uncharacterized. The results suggested that the transcription machinery in spermaotogonial cells is more complex than previously envisioned.
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Affiliation(s)
- Tin-Lap Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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32
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Abstract
Emerging evidence from these studies suggested that the male germ cell transcriptome is more complex than previously envisioned. In addition to protein-coding genes, the transcriptome also encodes a significant number of nonprotein-coding transcripts. These noncoding (nc) RNAs appear to be involved in a variety of cellular activities, ranging from simple housekeeping to complex regulatory functions. A class of ncRNAs known as long ncRNAs (lncRNAs) were recently shown to be expressed in a developmentally regulated manner during brain and embryonic stem cell development. This protocol aims to predict and identify potential lncRNA candidates using Serial Analysis of Gene Expression (SAGE) data. We also illustrate how to validate the potential lncRNAs by expression analyses using real-time PCR and Northern Blot. Potential lncRNA candidates in male germ cells are identified using our previously established male germ cell SAGE database (GermSAGE).
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Affiliation(s)
- Tin-Lap Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Pang ALY, Clark J, Chan WY, Rennert OM. Expression of human NAA11 (ARD1B) gene is tissue-specific and is regulated by DNA methylation. Epigenetics 2011; 6:1391-9. [PMID: 22048246 DOI: 10.4161/epi.6.11.18125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
NAA10 gene encodes the catalytic subunit of N(alpha)-acetyltransferase NatA that catalyzes the acetylation of the N-termini of many eukaryotic proteins. A homologous gene called NAA11 is also present in mammalian cells. hNaa10p and hNaa11p are reported to be co-expressed in human cell cultures. In mouse tissues, however, Naa11 transcripts can only be detected in gonadal tissues whereas Naa10 transcripts are present in various tissues. We re-examined the expression of NAA11 in human cell lines and expanded the test to normal as well as cancerous human tissues. Surprisingly, we did not detect the expression of NAA11 in human cell lines that previously were reported to express it. Similar to its mouse ortholog, NAA10 displayed widespread expression in human tissues. NAA11 transcripts, however, were only detected in testicular and placental tissues. The lack of NAA11 expression was also demonstrated in eight different types of human cancerous tissues. By methylation-specific polymerase chain reaction and bisulfite sequencing, we found that the absence of NAA11 expression correlated with hypermethylation of the CpG island located at the proximal promoter of NAA11 gene. We also found that the cloned NAA11 gene promoter fragment was active when introduced into non NAA11-expressing human cells and its promoter activity was lost upon in vitro DNA methylation. Taken together, our results indicate NAA11 expression is tissue-specific and is epigenetically regulated by DNA methylation.
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Affiliation(s)
- Alan L Y Pang
- Section on Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Institutes of Health, Bethesda, MD, USA.
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LEE TIN, Xiao A, Chan W, Rennert OM. Identification of novel long non‐coding RNA candidates in male germ cell development. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.924.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- TIN‐LAP LEE
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
- School of Biomedical ScienceThe Chinese University of Hong KongShatinHong Kong
| | - Amy Xiao
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
| | - Wai‐Yee Chan
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
- School of Biomedical ScienceThe Chinese University of Hong KongShatinHong Kong
| | - Owen M Rennert
- Laboratory of Clinical and Developmental GenomicsNICHD, Nattional Institutes of HealthBethesdaMD
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Nagrani SR, Levens ED, Baxendale V, Boucheron C, Chan WY, Rennert OM. Methylation patterns of Brahma during spermatogenesis and oogenesis: potential implications. Fertil Steril 2010; 95:382-4. [PMID: 20719309 DOI: 10.1016/j.fertnstert.2010.05.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/22/2010] [Accepted: 05/24/2010] [Indexed: 11/25/2022]
Abstract
To compare methylation profiles and expression levels of Brahma at different stages of spermatogenesis, and to identify the methylation pattern during oogenesis, we analyzed gene expression and methylation patterns in murine germ cells at various developmental stages. The methylation levels of CpG islands within Brahma increased during spermatogenesis and decreased during oogenesis. This change in methylation pattern correlates with the change in expression of Brahma during spermatogenesis. As the degree of methylation increases, the expression decreases. The change in methylation is opposite during oogenesis, which suggests opposite expression levels.
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Affiliation(s)
- Sohan R Nagrani
- Laboratory of Clinical and Developmental Genomics, Program in Reproductive and Adult Endocrinology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20814, USA.
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36
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Saito M, Kumamoto K, Horikawa I, Robles AI, Furusato B, Okamura S, Goto A, Yamashita T, Nagashima M, Lee TL, Baxendale V, Rennert OM, Takenoshita S, Yokota J, Sesterhenn IA, Trivers GE, Hussain P, Harris CC. Abstract 4890: ING2, a p53- and chromatin-interacting protein, is essential to mammalian spermatogenesis: Implications in male infertility in humans. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
ING2 (inhibitor of growth family, member 2) plays pivotal roles in the regulation of cellular senescence, apoptosis, DNA damage repair, gene transcription and chromatin modification. Our previous in vitro studies on cellular senescence suggested that ING2 functionally interplays with the p53 tumor suppressor protein in two different manners: endogenous ING2 inhibits senescence and the transcriptional repression of ING2 by p53 abrogates this inhibition; and overexpressed ING2 enhances p53 acetylation and stability to induce senescence. ING2, as a subunit of the mSin3A-HDAC1 (histone deacetylase 1) complex, specifically binds to tri-methylated lysine 4 of histone H3 (H3K4me3) via its plant homeodomain (PHD) finger and regulates gene expression through chromatin modifications in response to DNA damage. This study investigates the in vivo developmental and physiological functions of ING2. Abundant expression of ING2 in mouse and human testes and its decreased expression associated with male infertility and defective spermatogenesis in humans suggested an essential role of ING2 in spermatogenesis, which is a process tightly regulated by chromatin modifications. Consistently, male mice deficient for Ing2 were infertile. Their testes had degeneration of seminiferous tubules, which became more severe with age, and showed enhanced p53-dependent and -independent apoptosis. Spermatogenesis arrest at meiotic phase in Ing2−/− testes was due to impaired HDAC1 accumulation and deregulated chromatin acetylation. This study establishes ING2 as a novel mammalian regulator of spermatogenesis, suggests that an HDAC1/ING2/H3K4me3-regulated, stage-specific coordination of chromatin modifications is essential to normal spermatogenesis, and provides a model system to study idiopathic and iatrogenic infertility in men, including those who had cancer chemotherapy and radiotherapy. Spontaneous tumor incidence and spectrum were similar in wild-type and Ing2-deficient mice.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4890.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tin-Lap Lee
- 3National Institute of Child Health and Human Development, Bethesda, MD
| | - Vanessa Baxendale
- 3National Institute of Child Health and Human Development, Bethesda, MD
| | - Owen M. Rennert
- 3National Institute of Child Health and Human Development, Bethesda, MD
| | | | - Jun Yokota
- 5National Cancer Center Research Institute, Tokyo, Japan
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Abstract
DNA methylation plays an important role in regulating normal development and carcinogenesis. Current understanding of the biological roles of DNA methylation is limited to its role in the regulation of gene transcription, genomic imprinting, genomic stability, and X chromosome inactivation. In the past 2 decades, a large number of changes have been identified in cancer epigenomes when compared with normals. These alterations fall into two main categories, namely, hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin, respectively. Aberrant methylation of genes controlling the cell cycle, proliferation, apoptosis, metastasis, drug resistance, and intracellular signaling has been identified in multiple cancer types. Recent advancements in whole-genome analysis of methylome have yielded numerous differentially methylated regions, the functions of which are largely unknown. With the development of high resolution tiling microarrays and high throughput DNA sequencing, more cancer methylomes will be profiled, facilitating the identification of new candidate genes or ncRNAs that are related to oncogenesis, new prognostic markers, and the discovery of new target genes for cancer therapy.
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Affiliation(s)
- Hoi-Hung Cheung
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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Raygada M, Arthur DC, Wayne AS, Rennert OM, Toretsky JA, Stratakis CA. Juvenile xanthogranuloma in a child with previously unsuspected neurofibromatosis type 1 and juvenile myelomonocytic leukemia. Pediatr Blood Cancer 2010; 54:173-5. [PMID: 19785027 PMCID: PMC2783853 DOI: 10.1002/pbc.22297] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [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] [Indexed: 11/10/2022]
Abstract
The association of neurofibromatosis 1 (NF1), juvenile xanthogranulomas (JXG), and juvenile myelomonocytic leukemia (JMML) has been previously reported. We describe herein this triad in a Caucasian male infant with a pathogenic mutation in the NF1 gene (neurofibromin). The clinical course from initial presentation to final diagnosis is detailed; the physical features and hematologic characteristics are discussed. The patient underwent bone marrow transplantation and is currently in remission. Children with concurrent cutaneous café-au-lait and JXG lesions should be evaluated and monitored closely for the possible development of JMML.
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Affiliation(s)
- Margarita Raygada
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Section on Developmental Genetics, Bethesda, MD 20892-1831, USA.
| | - Diane C. Arthur
- National Cancer Institute, Laboratory of Pathology, Building 10 - Room 2A33, 10 Center Dr, Bethesda, MD 20892-1500
| | - Alan S. Wayne
- National Cancer Institute, Pediatric Oncology Branch, 10-CRC - Hatfield Clinical Research Center, 1-3750, 10 Center Dr, Bethesda, MD
| | - Owen M. Rennert
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Section on Developmental Genetics, 10 Center Dr MSC 1831Room # 10N256, Bethesda, MD 20892-1831, Voice Mail: 301-451-8822, FAX: 301-480-7557
| | - Jeffrey A. Toretsky
- Departments of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Rd, Room W311, Washington, DC 20007
| | - Constantine A. Stratakis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Section of Endocrinology and Genetics, 10-CRC Hatfield Clinical Research Center, Room #1–3330, 10 Center Dr MSC 1103, Bethesda, MD 20892
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Lee TL, Chan WY, Rennert OM. Assessing the safety of nanomaterials by genomic approach could be another alternative. ACS Nano 2009; 3:3830-3831. [PMID: 20025301 DOI: 10.1021/nn901155z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Lee TL, Li Y, Cheung HH, Claus J, Singh S, Sastry C, Rennert OM, Lau YFC, Chan WY. GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development. Bioinformatics 2009; 26:585-6. [PMID: 20028690 DOI: 10.1093/bioinformatics/btp695] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Serial analysis of gene expression (SAGE) provides an alternative, with additional advantages, to microarray gene expression studies. GonadSAGE is the first publicly available web-based SAGE database on male gonad development that covers six male mouse embryonic gonad stages, including E10.5, E11.5, E12.5, E13.5, E15.5 and E17.5. The sequence coverage of each SAGE library is beyond 150K, 'which is the most extensive sequence-based male gonadal transcriptome to date'. An interactive web interface with customizable parameters is provided for analyzing male gonad transcriptome information. Furthermore, the data can be visualized and analyzed with the other genomic features in the UCSC genome browser. It represents an integrated platform that leads to a better understanding of male gonad development, and allows discovery of related novel targets and regulatory pathways.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Nwosu BU, Raygada M, Tsilou ET, Rennert OM, Stratakis CA. Rieger's Anomaly and Other Ocular Abnormalities in Association with Osteogenesis Imperfecta and aCOL1A1Mutation. Ophthalmic Genet 2009; 26:135-8. [PMID: 16272059 DOI: 10.1080/13816810500228993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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: 10/25/2022]
Abstract
A patient with osteogenesis imperfecta (OI) and some features of Ehlers-Danlos syndrome had Rieger's anomaly and other associated ocular abnormalities. He carried a COL1A1 mutation (c.3313delA) that has only rarely been seen in OI. The association of ocular anterior chamber abnormalities with OI has not been reported previously, while OI with Ehlers-Danlos syndrome features has only been described in some kindreds. The patient had serious complications as a result of his ocular anomalies. We speculate that the course of his disease and, perhaps, its co-existence with OI could be exacerbated by his collagen type-I defect, although no causality can be established by this report of a single case.
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Affiliation(s)
- Benjamin U Nwosu
- Pediatric Endocrinology Inter-Institute Training Program, Developmental Endocrinology Branch, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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Lee TL, Li Y, Alba D, Vong QP, Wu SM, Baxendale V, Rennert OM, Lau YFC, Chan WY. Developmental staging of male murine embryonic gonad by SAGE analysis. J Genet Genomics 2009; 36:215-27. [PMID: 19376482 DOI: 10.1016/s1673-8527(08)60109-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Revised: 03/18/2009] [Accepted: 03/19/2009] [Indexed: 12/31/2022]
Abstract
Despite the identification of key genes such as Sry integral to embryonic gonadal development, the genomic classification and identification of chromosomal activation of this process is still poorly understood. To better understand the genetic regulation of gonadal development, we performed Serial Analysis of Gene Expression (SAGE) to profile the genes and novel transcripts, and an average of 152,000 tags from male embryonic gonads at E10.5 (embryonic day 10.5), E11.5, E12.5, E13.5, E15.5 and E17.5 were analyzed. A total of 275,583 non-singleton tags that do not map to any annotated sequence were identified in the six gonad libraries, and 47,255 tags were mapped to 24,975 annotated sequences, among which 987 sequences were uncharacterized. Utilizing an unsupervised pattern identification technique, we established molecular staging of male gonadal development. Rather than providing a static descriptive analysis, we developed algorithms to cluster the SAGE data and assign SAGE tags to a corresponding chromosomal position; these data are displayed in chromosome graphic format. A prominent increase in global genomic activity from E10.5 to E17.5 was observed. Important chromosomal regions related to the developmental processes were identified and validated based on established mouse models with developmental disorders. These regions may represent markers for early diagnosis for disorders of male gonad development as well as potential treatment targets.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Su DM, Zhang Q, Wang X, He P, Zhu YJ, Zhao J, Rennert OM, Su YA. Two types of human malignant melanoma cell lines revealed by expression patterns of mitochondrial and survival-apoptosis genes: implications for malignant melanoma therapy. Mol Cancer Ther 2009; 8:1292-304. [PMID: 19383853 DOI: 10.1158/1535-7163.mct-08-1030] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Human malignant melanoma has poor prognosis because of resistance to apoptosis and therapy. We describe identification of the expression profile of 1,037 mitochondria-focused genes and 84 survival-apoptosis genes in 21 malignant melanoma cell lines and 3 normal melanocyte controls using recently developed hMitChip3 cDNA microarrays. Unsupervised hierarchical clustering analysis of 1,037 informative genes, and 84 survival-apoptosis genes, classified these malignant melanoma cell lines into type A (n = 12) and type B (n = 9). Three hundred fifty-five of 1,037 (34.2%) genes displayed significant (P ≤ 0.030; false discovery rate ≤ 3.68%) differences (± ≥ 2.0-fold) in average expression, with 197 genes higher and 158 genes lower in type A than in type B. Of 84 genes with known survival-apoptosis functions, 38 (45.2%) displayed the significant (P < 0.001; false discovery rate < 0.15%) difference. Antiapoptotic (BCL2, BCL2A1, PPARD, and RAF1), antioxidant (MT3, PRDX5, PRDX3, GPX4, GLRX2, and GSR), and proapoptotic (BAD, BNIP1, APAF1, BNIP3L, CASP7, CYCS, CASP1, and VDAC1) genes expressed at higher levels in type A than in type B, whereas the different set of antiapoptotic (PSEN1, PPP2CA, API5, PPP2R1B, PPP2R1A, and FIS1), antioxidant (HSPD1, GSS, SOD1, ATOX1, and CAT), and proapoptotic (ENDOG, BAK1, CASP2, CASP4, PDCD5, HTRA2, SEPT4, TNFSF10, and PRODH) genes expressed at lower levels in type A than in type B. Microarray data were validated by quantitative reverse transcription-PCR. These results showed the presence of two types of malignant melanoma, each with a specific set of dysregulated survival-apoptosis genes, which may prove useful for development of new molecular targets for therapeutic intervention and novel diagnostic biomarkers for treatment and prognosis of malignant melanoma.
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Affiliation(s)
- David M Su
- 1Department of Biochemistry and Molecular Biology and the Catherine Birch McCormick Genomics Center, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia 20037, USA
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Abstract
Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% - 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alan Lap-Yin Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Owen M. Rennert
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Wai-Yee Chan
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Department of Pediatrics, Georgetown University College of Medicine, Washington, DC
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Pang ALY, Peacock S, Johnson W, Bear DH, Rennert OM, Chan WY. Cloning, characterization, and expression analysis of the novel acetyltransferase retrogene Ard1b in the mouse. Biol Reprod 2009; 81:302-9. [PMID: 19246321 DOI: 10.1095/biolreprod.108.073221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
N-alpha-terminal acetylation is a modification process that occurs cotranslationally on most eukaryotic proteins. The major enzyme responsible for this process, N-alpha-terminal acetyltransferase, is composed of the catalytic subunit ARD1A and the auxiliary subunit NAT1. We cloned, characterized, and studied the expression pattern of Ard1b (also known as Ard2), a novel homolog of the mouse Ard1a. Comparison of the genomic structures suggests that the autosomal Ard1b is a retroposed copy of the X-linked Ard1a. Expression analyses demonstrated a testis predominance of Ard1b. A reciprocal expression pattern between Ard1a and Ard1b is also observed during spermatogenesis, suggesting that Ard1b is expressed to compensate for the loss of Ard1a starting from meiosis. Both ARD1A and ARD1B can interact with NAT1 to constitute a functional N-alpha-terminal acetyltransferase in vitro. The expression of ARD1B protein can be detected in mouse testes but is delayed until the first appearance of round spermatids. In a cell culture model, the inclusion of the long 3' untranslated region of Ard1b leads to reduction of luciferase reporter activity, which implicates its role in translational repression of Ard1b during spermatogenesis. Our results suggest that ARD1B may have an important role in the later course of the spermatogenic process.
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Affiliation(s)
- Alan Lap-Yin Pang
- Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Zhang Q, Wu J, Nguyen A, Wang BD, He P, Laurent GS, Rennert OM, Su YA. Molecular mechanism underlying differential apoptosis between human melanoma cell lines UACC903 and UACC903(+6) revealed by mitochondria-focused cDNA microarrays. Apoptosis 2008; 13:993-1004. [PMID: 18563568 PMCID: PMC2470374 DOI: 10.1007/s10495-008-0231-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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: 11/28/2022]
Abstract
Human malignant melanoma cell line UACC903 is resistant to apoptosis while chromosome 6-mediated suppressed cell line UACC903(+6) is sensitive. Here, we describe identification of differential molecular pathways underlying this difference. Using our recently developed mitochondria-focused cDNA microarrays, we identified 154 differentially expressed genes including proapoptotic (BAK1 [6p21.3], BCAP31, BNIP1, CASP3, CASP6, FAS, FDX1, FDXR, TNFSF10 and VDAC1) and antiapoptotic (BCL2L1, CLN3 and MCL1) genes. Expression of these pro- and anti-apoptotic genes was higher in UACC903(+6) than in UACC903 before UV treatment and was altered after UV treatment. qRT-PCR and Western blots validated microarray results. Our bioinformatic analysis mapped these genes to differential molecular pathways that predict resistance and sensitivity of UACC903 and UACC903(+6) to apoptosis respectively. The pathways were functionally confirmed by the FAS ligand-induced cell death and by siRNA knockdown of BAK1 protein. These results demonstrated the differential molecular pathways underlying survival and apoptosis of UACC903 and UACC903(+6) cell lines.
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Affiliation(s)
- Qiuyang Zhang
- Department of Biochemistry and Molecular Biology and the Catherine Birch McCormick Genomics Center, The George Washington University School of Medicine and Health Sciences, Ross Hall, Room 555, 2300 I Street NW, Washington, DC 20037, USA
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Han JC, Liu QR, Jones M, Levinn RL, Menzie CM, Jefferson-George KS, Adler-Wailes DC, Sanford EL, Lacbawan FL, Uhl GR, Rennert OM, Yanovski JA. Brain-derived neurotrophic factor and obesity in the WAGR syndrome. N Engl J Med 2008; 359:918-27. [PMID: 18753648 PMCID: PMC2553704 DOI: 10.1056/nejmoa0801119] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Brain-derived neurotrophic factor (BDNF) has been found to be important in energy homeostasis in animal models, but little is known about its role in energy balance in humans. Heterozygous, variably sized, contiguous gene deletions causing haploinsufficiency of the WT1 and PAX6 genes on chromosome 11p13, approximately 4 Mb centromeric to BDNF (11p14.1), result in the Wilms' tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR) syndrome. Hyperphagia and obesity were observed in a subgroup of patients with the WAGR syndrome. We hypothesized that the subphenotype of obesity in the WAGR syndrome is attributable to deletions that induce haploinsufficiency of BDNF. METHODS We studied the relationship between genotype and body-mass index (BMI) in 33 patients with the WAGR syndrome who were recruited through the International WAGR Syndrome Association. The extent of each deletion was determined with the use of oligonucleotide comparative genomic hybridization. RESULTS Deletions of chromosome 11p in the patients studied ranged from 1.0 to 26.5 Mb; 58% of the patients had heterozygous BDNF deletions. These patients had significantly higher BMI z scores throughout childhood than did patients with intact BDNF (mean [+/-SD] z score at 8 to 10 years of age, 2.08+/-0.45 in patients with heterozygous BDNF deletions vs. 0.88+/-1.28 in patients without BDNF deletions; P=0.03). By 10 years of age, 100% of the patients with heterozygous BDNF deletions (95% confidence interval [CI], 77 to 100) were obese (BMI > or = 95th percentile for age and sex) as compared with 20% of persons without BDNF deletions (95% CI, 3 to 56; P<0.001). The critical region for childhood-onset obesity in the WAGR syndrome was located within 80 kb of exon 1 of BDNF. Serum BDNF concentrations were approximately 50% lower among the patients with heterozygous BDNF deletions (P=0.001). CONCLUSIONS Among persons with the WAGR syndrome, BDNF haploinsufficiency is associated with lower levels of serum BDNF and with childhood-onset obesity; thus, BDNF may be important for energy homeostasis in humans.
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Affiliation(s)
- Joan C Han
- Unit on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1103, USA
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Su YA, Wu J, Zhang L, Zhang Q, Su DM, He P, Wang BD, Li H, Webster MJ, Rennert OM, Ursano RJ. Dysregulated mitochondrial genes and networks with drug targets in postmortem brain of patients with posttraumatic stress disorder (PTSD) revealed by human mitochondria-focused cDNA microarrays. Int J Biol Sci 2008; 4:223-35. [PMID: 18690294 PMCID: PMC2500154 DOI: 10.7150/ijbs.4.223] [Citation(s) in RCA: 80] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 08/02/2008] [Indexed: 01/15/2023] Open
Abstract
Posttraumatic stress disorder (PTSD) is associated with decreased activity in the dorsolateral prefrontal cortex (DLPFC), the brain region that regulates working memory and preparation and selection of fear responses. We investigated gene expression profiles in DLPFC Brodmann area (BA) 46 of postmortem patients with (n=6) and without PTSD (n=6) using human mitochondria-focused cDNA microarrays. Our study revealed PTSD-specific expression fingerprints of 800 informative mitochondria-focused genes across all of these 12 BA46 samples, and 119 (+/->1.25, p<0.05) and 42 (+/->1.60, p<0.05) dysregulated genes between the PTSD and control samples. Quantitative RT-PCR validated the microarray results. These fingerprints can essentially distinguish the PTSD DLPFC BA46 brains from controls. Of the 119 dysregulated genes (+/-> or =125%, p<0.05), the highest percentages were associated with mitochondrial dysfunction (4.8%, p=6.61 x 10(-6)), oxidative phosphorylation (3.8%, p=9.04 x 10(-4)), cell survival-apoptosis (25.2%, p<0.05) and neurological diseases (23.5%, p<0.05). Fifty (50) dysregulated genes were present in the molecular networks that are known to be involved in neuronal function-survival and contain 7 targets for neuropsychiatric drugs. Thirty (30) of the dysregulated genes are associated with a number of neuropsychiatric disorders. Our results indicate mitochondrial dysfunction in the PTSD DLPFC BA46 and provide the expression fingerprints that may ultimately serve as biomarkers for PTSD diagnosis and the drugs and molecular targets that may prove useful for development of remedies for prevention and treatment of PTSD.
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Affiliation(s)
- Yan A Su
- Department of Biochemistry, Molecular Biology, the Catherine Birch McCormick Genomics Center, The George Washington University School of Medicine, Health Sciences, Washington, DC 20037, USA.
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Affiliation(s)
- Stephen G Kaler
- National Institute of Child Health and Human Development, National Institute of Health, Bethesda, Maryland, USA
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Meng XL, Rennert OM, Chan WY. Human chorionic gonadotropin induces neuronal differentiation of PC12 cells through activation of stably expressed lutropin/choriogonadotropin receptor. Endocrinology 2007; 148:5865-73. [PMID: 17761763 DOI: 10.1210/en.2007-0941] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human chorionic gonadotropin (hCG) and LH play an important role in reproductive physiology. Both hCG and LH bind to the same LH/choriogonadotropin receptor (LH/CG-R). Recent reports documented the temporal and spatial expression of LH/CG-R in the developing and mature mammalian brain. Administration of hCG promoted nerve regeneration in vivo and neurite outgrowth and survival of primary neurons in vitro. The function of hCG/LH and LH/CG-R in the nervous system remains unclear. In this study, we report that hCG/LH induced distinct morphological and biochemical changes, characteristic of neuronal differentiation, in PC12 cells stably expressing LH/CG-R and that the differentiation effect is ligand dose and time dependent. Western blot analysis revealed that both the ERKs and p38 MAPK are activated after hCG treatment. Inhibitor studies showed both the ERK and p38 MAPK signal transduction pathways are required for this differentiation process, which is cAMP dependent and protein kinase A independent. These findings imply a potential role for hCG/LH and LH/CG-R in the development, maintenance, and regeneration of the mammalian nervous system, and in the neuropathogenesis of genetic diseases caused by a mutated LH/CG-R.
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Affiliation(s)
- Xing-Li Meng
- Section on Developmental Genomics, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, MSC 4429, Bethesda, MD 20892-4429, USA
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