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Zhu Y, Wang Y, Ma Z, Wang D, Yan F, Liu Y, Li J, Yang X, Gao Z, Liu X, Wang L, Wang Q. Genome-Wide Identification of CHYR Gene Family in Sophora alopecuroides and Functional Analysis of SaCHYR4 in Response to Abiotic Stress. Int J Mol Sci 2024; 25:6173. [PMID: 38892361 PMCID: PMC11173228 DOI: 10.3390/ijms25116173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Sophora alopecuroides has important uses in medicine, wind breaking, and sand fixation. The CHY-zinc-finger and RING-finger (CHYR) proteins are crucial for plant growth, development, and environmental adaptation; however, genetic data regarding the CHYR family remain scarce. We aimed to investigate the CHYR gene family in S. alopecuroides and its response to abiotic stress, and identified 18 new SaCHYR genes from S. alopecuroides whole-genome data, categorized into 3 subclasses through a phylogenetic analysis. Gene structure, protein domains, and conserved motifs analyses revealed an exon-intron structure and conserved domain similarities. A chromosome localization analysis showed distribution across 12 chromosomes. A promoter analysis revealed abiotic stress-, light-, and hormone-responsive elements. An RNA-sequencing expression pattern analysis revealed positive responses of SaCHYR genes to salt, alkali, and drought stress. SaCHYR4 overexpression considerably enhanced alkali and drought tolerance in Arabidopsis thaliana. These findings shed light on SaCHYR's function and the resistance mechanisms of S. alopecuroides, presenting new genetic resources for crop resistance breeding.
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Affiliation(s)
- Youcheng Zhu
- College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China;
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Ying Wang
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Zhipeng Ma
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Di Wang
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Fan Yan
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Jingwen Li
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Xuguang Yang
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Ziwei Gao
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Xu Liu
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Le Wang
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun 130062, China; (Y.W.); (Z.M.); (D.W.); (F.Y.); (Y.L.); (J.L.); (X.Y.); (Z.G.); (X.L.)
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Yellajoshyula D. Transcriptional regulatory network for neuron-glia interactions and its implication for DYT6 dystonia. DYSTONIA (LAUSANNE, SWITZERLAND) 2023; 2:11796. [PMID: 38737544 PMCID: PMC11087070 DOI: 10.3389/dyst.2023.11796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Advances in sequencing technologies have identified novel genes associated with inherited forms of dystonia, providing valuable insights into its genetic basis and revealing diverse genetic pathways and mechanisms involved in its pathophysiology. Since identifying genetic variation in the transcription factor coding THAP1 gene linked to isolated dystonia, numerous investigations have employed transcriptomic studies in DYT-THAP1 models to uncover pathogenic molecular mechanisms underlying dystonia. This review examines key findings from transcriptomic studies conducted on in vivo and in vitro DYT-THAP1 models, which demonstrate that the THAP1-regulated transcriptome is diverse and cell-specific, yet it is bound and co-regulated by a common set of proteins. Prominent among its functions, THAP1 and its co-regulatory network target molecular pathways critical for generating myelinating oligodendrocytes that ensheath axons and generate white matter in the central nervous system. Several lines of investigation have demonstrated the importance of myelination and oligodendrogenesis in motor function during development and in adults, emphasizing the non-cell autonomous contributions of glial cells to neural circuits involved in motor function. Further research on the role of myelin abnormalities in motor deficits in DYT6 models will enhance our understanding of axon-glia interactions in dystonia pathophysiology and provide potential therapeutic interventions targeting these pathways.
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Aljabban J, Syed S, Syed S, Rohr M, Mukhtar M, Aljabban H, Cottini F, Mohammed M, Hughes T, Gonzalez T, Panahiazr M, Hadley D, Benson D. Characterization of monoclonal gammopathy of undetermined significance progression to multiple myeloma through meta-analysis of GEO data. Heliyon 2023; 9:e17298. [PMID: 37539132 PMCID: PMC10394915 DOI: 10.1016/j.heliyon.2023.e17298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 08/05/2023] Open
Abstract
The etiology of monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma (MM) is still obscure as are the processes that enable the progression of MGUS to MM. Understanding the unique vs. shared transcriptomes can potentially elucidate why individuals develop one or the other. Furthermore, highlighting key pathways and genes involved in the pathogenesis of MM or the development of MGUS to MM may allow the discovery of novel drug targets and therapies. We employed STARGEO platform to perform three separate meta-analysis to compare MGUS and MM transcriptomes. For these analyses we tagged (1) 101 MGUS patient plasma cells from bone marrow samples and 64 plasma cells from healthy controls (2) 383 MM patient CD138+ cells from bone marrow and the 101 MGUS samples in the first analysis as controls (3) 517 MM patient peripheral blood samples and 97 peripheral blood samples from healthy controls. We then utilized Ingenuity Pathway Analysis (IPA) to analyze the unique genomic signatures within and across these samples. Our study identified genes that may have unique roles in MGUS (GADD45RA and COMMD3), but also newly identified signaling pathways (EIF2, JAK/STAT, and MYC) and gene activity (NRG3, RBFOX2, and PARP15) in MGUS that have previously been shown to be involved in MM suggesting a spectrum of molecular overlap. On the other hand, genes such as DUSP4, RN14, LAMP5, differentially upregulated in MM, may be seen as tipping the scales from benignity to malignancy and could serve as drug targets or novel biomarkers for risk of progression. Furthermore, our analysis of MM identified newly associated gene/pathway activity such as inhibition of Wnt-signaling and defective B cell development. Finally, IPA analysis, suggests the multifactorial, oncogenic qualities of IFNγ signaling in MM may be a unifying pathway for these diverse mechanisms and prompts the need for further studies.
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Affiliation(s)
- Jihad Aljabban
- University of Wisconsin Hospital and Clinics, Department of Medicine, United States
| | - Sharjeel Syed
- University of Chicago Medical Center, Department of Medicine, United States
| | - Saad Syed
- Northwestern Memorial Hospital, Department of Medicine, United States
| | - Michael Rohr
- University of Central Florida College of Medicine, United States
| | - Mohamed Mukhtar
- Michigan State University College of Human Medicine, United States
| | | | - Francesca Cottini
- Ohio State University Wexner Medical Center, United States
- James Cancer Hospital Solove Research Institute, United States
| | | | - Tiffany Hughes
- Ohio State University Wexner Medical Center, United States
| | | | - Maryam Panahiazr
- University of California San Francisco, Department of Surgery, United States
| | - Dexter Hadley
- University of Central Florida College of Medicine, United States
- University of Central Florida, Chief of the Department of Artificial Intelligence, United States
| | - Don Benson
- Ohio State University Wexner Medical Center, United States
- James Cancer Hospital Solove Research Institute, United States
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Sharifnia T, Wawer MJ, Goodale A, Lee Y, Kazachkova M, Dempster JM, Muller S, Levy J, Freed DM, Sommer J, Kalfon J, Vazquez F, Hahn WC, Root DE, Clemons PA, Schreiber SL. Mapping the landscape of genetic dependencies in chordoma. Nat Commun 2023; 14:1933. [PMID: 37024492 PMCID: PMC10079670 DOI: 10.1038/s41467-023-37593-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
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Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Mathias J Wawer
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Kojin Therapeutics, Boston, MA, 02210, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Mariya Kazachkova
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Sandrine Muller
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joan Levy
- Chordoma Foundation, Durham, NC, 27702, USA
- Melanoma Research Alliance, Washington, D.C., 20005, USA
| | | | | | - Jérémie Kalfon
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Harvard University, Cambridge, MA, 02138, USA.
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5
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Mukherjee K, Moroz LL. Transposon-derived transcription factors across metazoans. Front Cell Dev Biol 2023; 11:1113046. [PMID: 36960413 PMCID: PMC10027918 DOI: 10.3389/fcell.2023.1113046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Transposable elements (TE) could serve as sources of new transcription factors (TFs) in plants and some other model species, but such evidence is lacking for most animal lineages. Here, we discovered multiple independent co-options of TEs to generate 788 TFs across Metazoa, including all early-branching animal lineages. Six of ten superfamilies of DNA transposon-derived conserved TF families (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were identified across nine phyla encompassing the entire metazoan phylogeny. The most extensive convergent domestication of potentially TE-derived TFs occurred in the hydroid polyps, polychaete worms, cephalopods, oysters, and sea slugs. Phylogenetic reconstructions showed species-specific clustering and lineage-specific expansion; none of the identified TE-derived TFs revealed homologs in their closest neighbors. Together, our study established a framework for categorizing TE-derived TFs and informing the origins of novel genes across phyla.
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Affiliation(s)
- Krishanu Mukherjee
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
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6
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Li H, Peng H, Hong W, Wei Y, Tian H, Huang X, Jia L, Zheng J, Duan T, He Q, Wang K. Human Placental Endothelial Cell and Trophoblast Heterogeneity and Differentiation Revealed by Single-Cell RNA Sequencing. Cells 2022; 12:cells12010087. [PMID: 36611882 PMCID: PMC9818681 DOI: 10.3390/cells12010087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The placenta is an important organ for fetal and maternal health during pregnancy and impacts offspring health late in life. Defects in placental vasculature and trophoblast have been identified in several pregnancy complications. Thus, the detailed molecular profile and heterogeneity of endothelial cells and trophoblasts in placentas will aid us in better understanding placental behaviors and improving pregnancy outcomes. METHODS Single-cell RNA sequencing (scRNA-seq) was performed to profile the transcriptomics of human placental villous tissues from eleven patients with normal pregnancies in the first and second trimesters (6-16 weeks of gestation). RESULTS The transcriptomic landscape of 52,179 single cells was obtained, and the cells were classified as trophoblasts, fibroblasts, endothelial cells, erythroid cells, Hofbauer cells, and macrophages. Our analysis further revealed the three subtypes of placental endothelial cells, with distinct metabolic signatures and transcription factor regulatory networks. We also determined the transcriptomic features of the trophoblast subpopulations and characterized two distinct populations of progenitor cells in cytotrophoblasts, which were capable of differentiating to extravillous trophoblasts and syncytiotrophoblasts, respectively. CONCLUSIONS Our study provided a high-resolution molecular profile of the human placenta between 6 and 16 weeks of gestation. Our data revealed the placental cell complexity and demonstrated the transcriptional networks and signaling involved in placental endothelial and trophoblast differentiation during early pregnancy, which will be a resource for future studies of the human placental development.
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Affiliation(s)
- Han Li
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Hao Peng
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Wei Hong
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Yingying Wei
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Haojun Tian
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Xiaojie Huang
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Linyan Jia
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Jing Zheng
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Tao Duan
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
- Correspondence: (Q.H.); (K.W.)
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
- Correspondence: (Q.H.); (K.W.)
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Cheng F, Zheng W, Barbuti PA, Bonsi P, Liu C, Casadei N, Ponterio G, Meringolo M, Admard J, Dording CM, Yu-Taeger L, Nguyen HP, Grundmann-Hauser K, Ott T, Houlden H, Pisani A, Krüger R, Riess O. DYT6 mutated THAP1 is a cell type dependent regulator of the SP1 family. Brain 2022; 145:3968-3984. [PMID: 35015830 DOI: 10.1093/brain/awac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
DYT6 dystonia is caused by mutations in the transcription factor THAP1. THAP1 knock-out or knock-in mouse models revealed complex gene expression changes, which are potentially responsible for the pathogenesis of DYT6 dystonia. However, how THAP1 mutations lead to these gene expression alterations and whether the gene expression changes are also reflected in the brain of THAP1 patients are still unclear. In this study we used epigenetic and transcriptomic approaches combined with multiple model systems [THAP1 patients' frontal cortex, THAP1 patients' induced pluripotent stem cell (iPSC)-derived midbrain dopaminergic neurons, THAP1 heterozygous knock-out rat model, and THAP1 heterozygous knock-out SH-SY5Y cell lines] to uncover a novel function of THAP1 and the potential pathogenesis of DYT6 dystonia. We observed that THAP1 targeted only a minority of differentially expressed genes caused by its mutation. THAP1 mutations lead to dysregulation of genes mainly through regulation of SP1 family members, SP1 and SP4, in a cell type dependent manner. Comparing global differentially expressed genes detected in THAP1 patients' iPSC-derived midbrain dopaminergic neurons and THAP1 heterozygous knock-out rat striatum, we observed many common dysregulated genes and 61 of them were involved in dystonic syndrome-related pathways, like synaptic transmission, nervous system development, and locomotor behaviour. Further behavioural and electrophysiological studies confirmed the involvement of these pathways in THAP1 knock-out rats. Taken together, our study characterized the function of THAP1 and contributes to the understanding of the pathogenesis of primary dystonia in humans and rats. As SP1 family members were dysregulated in some neurodegenerative diseases, our data may link THAP1 dystonia to multiple neurological diseases and may thus provide common treatment targets.
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Affiliation(s)
- Fubo Cheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Wenxu Zheng
- Institute for Ophthalmic Research Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Peter Antony Barbuti
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Paola Bonsi
- Laboratory of Neurophysiology and Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Giulia Ponterio
- Laboratory of Neurophysiology and Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Maria Meringolo
- Laboratory of Neurophysiology and Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Claire Marie Dording
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Libo Yu-Taeger
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Department of Human Genetics, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | | | - Thomas Ott
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Antonio Pisani
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- IRCCS C. Mondino Foundation, Pavia, Italy
| | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
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8
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Hale MD, Koal T, Pham TH, Bowden JA, Parrott BB. Transcriptional networks underlying a primary ovarian insufficiency disorder in alligators naturally exposed to EDCs. Mol Cell Endocrinol 2022; 557:111751. [PMID: 35963581 DOI: 10.1016/j.mce.2022.111751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Interactions between the endocrine system and environmental contaminants are responsible for impairing reproductive development and function. Despite the taxonomic diversity of affected species and attendant complexity inherent to natural systems, the underlying signaling pathways and cellular consequences are mostly studied in lab models. To resolve the genetic and endocrine pathways that mediate affected ovarian function in organisms exposed to endocrine disrupting contaminants in their natural environments, we assessed broad-scale transcriptional and steroidogenic responses to exogenous gonadotropin stimulation in juvenile alligators (Alligator missippiensis) originating from a lake with well-documented pollution (Lake Apopka, FL) and a nearby reference site (Lake Woodruff, FL). We found that individuals from Lake Apopka are characterized by hyperandrogenism and display hyper-sensitive transcriptional responses to gonadotropin stimulation when compared to individuals from Lake Woodruff. Site-specific transcriptomic divergence appears to be driven by wholly distinct subsets of transcriptional regulators, indicating alterations to fundamental genetic pathways governing ovarian function. Consistent with broad-scale transcriptional differences, ovaries of Lake Apopka alligators displayed impediments to folliculogenesis, with larger germinal beds and decreased numbers of late-stage follicles. After resolving the ovarian transcriptome into clusters of co-expressed genes, most site-associated modules were correlated to ovarian follicule phenotypes across individuals. However, expression of two site-specific clusters were independent of ovarian cellular architecture and are hypothesized to represent alterations to cell-autonomous transcriptional programs. Collectively, our findings provide high resolution mapping of transcriptional patterns to specific reproductive function and advance our mechanistic understanding regarding impaired reproductive health in an established model of environmental endocrine disruption.
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Affiliation(s)
- Matthew D Hale
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA, USA; Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, USA; Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | | | - John A Bowden
- Center for Environmental and Human Toxicology, Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Benjamin B Parrott
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA, USA; Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, USA.
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Diaw SH, Ott F, Münchau A, Lohmann K, Busch H. Emerging role of a systems biology approach to elucidate factors of reduced penetrance: transcriptional changes in THAP1-linked dystonia as an example. MED GENET-BERLIN 2022; 34:131-141. [PMID: 38835919 PMCID: PMC11006298 DOI: 10.1515/medgen-2022-2126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Pathogenic variants in THAP1 can cause dystonia with a penetrance of about 50 %. The underlying mechanisms are unknown and can be considered as means of endogenous disease protection. Since THAP1 encodes a transcription factor, drivers of this variability putatively act at the transcriptome level. Several transcriptome studies tried to elucidate THAP1 function in diverse cellular and mouse models, including mutation carrier-derived cells and iPSC-derived neurons, unveiling various differentially expressed genes and affected pathways. These include nervous system development, dopamine signalling, myelination, or cell-cell adhesion. A network diffusion analysis revealed mRNA splicing, mitochondria, DNA repair, and metabolism as significant pathways that may represent potential targets for therapeutic interventions.
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Affiliation(s)
- Sokhna Haissatou Diaw
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Fabian Ott
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Hauke Busch
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
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10
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Kou L, Yang N, Dong B, Yang J, Song Y, Li Y, Qin Q. Circular RNA testis-expressed 14 overexpression induces apoptosis and suppresses migration of ox-LDL-stimulated vascular smooth muscle cells via regulating the microRNA 6509-3p/thanatos-associated domain-containing apoptosis-associated protein 1 axis. Bioengineered 2022; 13:13150-13161. [PMID: 35635088 PMCID: PMC9275967 DOI: 10.1080/21655979.2022.2070582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Affiliation(s)
- Lu Kou
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
| | - Ning Yang
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
| | - Bo Dong
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
| | - Jingyu Yang
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
| | - Yanqiu Song
- Institute of Cardiology Research, Tianjin Chest Hospital, Tianjin, China
| | - Yang Li
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
| | - Qin Qin
- Cardiovascular Department, Tianjin Chest Hospital, Tianjin, China
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11
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Liu H, Yang W, Zhao X, Kang G, Li N, Xu H. Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:204. [PMID: 35443615 PMCID: PMC9019960 DOI: 10.1186/s12870-022-03589-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND CHY zinc-finger and RING finger (CHYR) proteins have been functionally characterized in plant growth, development and various stress responses. However, the genome-wide analysis was not performed in wheat. RESULTS In this study, a total of 18 TaCHYR genes were identified in wheat and classified into three groups. All TaCHYR genes contained CHY-zinc finger, C3H2C3-type RING finger and zinc ribbon domains, and group III members included 1-3 hemerythrin domains in the N-terminus regions. TaCHYR genes in each group shared similar conserved domains distribution. Chromosomal location, synteny and cis-elements analysis of TaCHYRs were also analyzed. Real-time PCR results indicated that most of selected 9 TaCHYR genes exhibited higher expression levels in leaves during wheat seedling stage. All these TaCHYR genes were up-regulated after PEG treatment, and these TaCHYRs exhibited differential expression patterns in response to salt, cold and heat stress in seedling leaves. The growth of yeast cells expressing TaCHYR2.1, TaCHYR9.2 and TaCHYR11.1 were inhibited under salt and dehydration stress. Moreover, gene ontology (GO) annotation, protein interaction and miRNA regulatory network of TaCHYR genes were analyzed. CONCLUSIONS These results increase our understanding of CHYR genes and provide robust candidate genes for further functional investigations aimed at crop improvement.
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Affiliation(s)
- Hao Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, Henan, People's Republic of China
| | - Wenbo Yang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450046, Henan, People's Republic of China
| | - Xingli Zhao
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, Henan, People's Republic of China
| | - Guozhang Kang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Na Li
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, Henan, People's Republic of China.
| | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, Henan, People's Republic of China.
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12
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Yellajoshyula D, Rogers AE, Kim AJ, Kim S, Pappas SS, Dauer WT. A pathogenic DYT-THAP1 dystonia mutation causes hypomyelination and loss of YY1 binding. Hum Mol Genet 2022; 31:1096-1104. [PMID: 34686877 PMCID: PMC8976427 DOI: 10.1093/hmg/ddab310] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
Dystonia is a disabling disease that manifests as prolonged involuntary twisting movements. DYT-THAP1 is an inherited form of isolated dystonia caused by mutations in THAP1 encoding the transcription factor THAP1. The phe81leu (F81L) missense mutation is representative of a category of poorly understood mutations that do not occur on residues critical for DNA binding. Here, we demonstrate that the F81L mutation (THAP1F81L) impairs THAP1 transcriptional activity and disrupts CNS myelination. Strikingly, THAP1F81L exhibits normal DNA binding but causes a significantly reduced DNA binding of YY1, its transcriptional partner that also has an established role in oligodendrocyte lineage progression. Our results suggest a model of molecular pathogenesis whereby THAP1F81L normally binds DNA but is unable to efficiently organize an active transcription complex.
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Affiliation(s)
| | - Abigail E Rogers
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Audrey J Kim
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sumin Kim
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel S Pappas
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - William T Dauer
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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13
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Park TY, Leiserson MD, Klau GW, Raphael BJ. SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. CELL GENOMICS 2022; 2. [PMID: 35382456 PMCID: PMC8979493 DOI: 10.1016/j.xgen.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent genome-wide CRISPR-Cas9 loss-of-function screens have identified genetic dependencies across many cancer cell lines. Associations between these dependencies and genomic alterations in the same cell lines reveal phenomena such as oncogene addiction and synthetic lethality. However, comprehensive identification of such associations is complicated by complex interactions between genes across genetically heterogeneous cancer types. We introduce and apply the algorithm SuperDendrix to CRISPR-Cas9 loss-of-function screens from 769 cancer cell lines, to identify differential dependencies across cell lines and to find associations between differential dependencies and combinations of genomic alterations and cell-type-specific markers. These associations respect the position and type of interactions within pathways: for example, we observe increased dependencies on downstream activators of pathways, such as NFE2L2, and decreased dependencies on upstream activators of pathways, such as CDK6. SuperDendrix also reveals dozens of dependencies on lineage-specific transcription factors, identifies cancer-type-specific correlations between dependencies, and enables annotation of individual mutated residues. Using SuperDendrix, Park et al. examine associations between genetic dependencies in 769 cancer cell lines. They report 127 genetic dependencies explained by combinations of mutually exclusive somatic mutations congregating into a few oncogenic pathways across cancer subtypes. These present a small number of prominent and highly specific genetic vulnerabilities in cancer. Graphical abstract
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14
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Comprehensive Statistical and Bioinformatics Analysis in the Deciphering of Putative Mechanisms by Which Lipid-Associated GWAS Loci Contribute to Coronary Artery Disease. Biomedicines 2022; 10:biomedicines10020259. [PMID: 35203469 PMCID: PMC8868589 DOI: 10.3390/biomedicines10020259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
The study was designed to evaluate putative mechanisms by which lipid-associated loci identified by genome-wide association studies (GWAS) are involved in the molecular pathogenesis of coronary artery disease (CAD) using a comprehensive statistical and bioinformatics analysis. A total of 1700 unrelated individuals of Slavic origin from the Central Russia, including 991 CAD patients and 709 healthy controls were examined. Sixteen lipid-associated GWAS loci were selected from European studies and genotyped using the MassArray-4 system. The polymorphisms were associated with plasma lipids such as total cholesterol (rs12328675, rs4846914, rs55730499, and rs838880), LDL-cholesterol (rs3764261, rs55730499, rs1689800, and rs838880), HDL-cholesterol (rs3764261) as well as carotid intima-media thickness/CIMT (rs12328675, rs11220463, and rs1689800). Polymorphisms such as rs4420638 of APOC1 (p = 0.009), rs55730499 of LPA (p = 0.0007), rs3136441 of F2 (p < 0.0001), and rs6065906 of PLTP (p = 0.002) showed significant associations with the risk of CAD, regardless of sex, age, and body mass index. A majority of the observed associations were successfully replicated in large independent cohorts. Bioinformatics analysis allowed establishing (1) phenotype-specific and shared epistatic gene–gene and gene–smoking interactions contributing to all studied cardiovascular phenotypes; (2) lipid-associated GWAS loci might be allele-specific binding sites for transcription factors from gene regulatory networks controlling multifaceted molecular mechanisms of atherosclerosis.
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15
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Domingo A, Yadav R, Shah S, Hendriks WT, Erdin S, Gao D, O'Keefe K, Currall B, Gusella JF, Sharma N, Ozelius LJ, Ehrlich ME, Talkowski ME, Bragg DC. Dystonia-specific mutations in THAP1 alter transcription of genes associated with neurodevelopment and myelin. Am J Hum Genet 2021; 108:2145-2158. [PMID: 34672987 PMCID: PMC8595948 DOI: 10.1016/j.ajhg.2021.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/27/2021] [Indexed: 12/28/2022] Open
Abstract
Dystonia is a neurologic disorder associated with an increasingly large number of genetic variants in many genes, resulting in characteristic disturbances in volitional movement. Dissecting the relationships between these mutations and their functional outcomes is critical in understanding the pathways that drive dystonia pathogenesis. Here we established a pipeline for characterizing an allelic series of dystonia-specific mutations. We used this strategy to investigate the molecular consequences of genetic variation in THAP1, which encodes a transcription factor linked to neural differentiation. Multiple pathogenic mutations associated with dystonia cluster within distinct THAP1 functional domains and are predicted to alter DNA-binding properties and/or protein interactions differently, yet the relative impact of these varied changes on molecular signatures and neural deficits is unclear. To determine the effects of these mutations on THAP1 transcriptional activity, we engineered an allelic series of eight alterations in a common induced pluripotent stem cell background and differentiated these lines into a panel of near-isogenic neural stem cells (n = 94 lines). Transcriptome profiling followed by joint analysis of the most robust signatures across mutations identified a convergent pattern of dysregulated genes functionally related to neurodevelopment, lysosomal lipid metabolism, and myelin. On the basis of these observations, we examined mice bearing Thap1-disruptive alleles and detected significant changes in myelin gene expression and reduction of myelin structural integrity relative to control mice. These results suggest that deficits in neurodevelopment and myelination are common consequences of dystonia-associated THAP1 mutations and highlight the potential role of neuron-glial interactions in the pathogenesis of dystonia.
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Affiliation(s)
- Aloysius Domingo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shivangi Shah
- The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - William T Hendriks
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Michelle E Ehrlich
- Departments of Neurology, Pediatrics, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-Linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA.
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16
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Gal C, Carelli FN, Appert A, Cerrato C, Huang N, Dong Y, Murphy J, Frapporti A, Ahringer J. DREAM represses distinct targets by cooperating with different THAP domain proteins. Cell Rep 2021; 37:109835. [PMID: 34686342 PMCID: PMC8552245 DOI: 10.1016/j.celrep.2021.109835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/03/2021] [Accepted: 09/24/2021] [Indexed: 01/09/2023] Open
Abstract
The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell-cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline-specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell-cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
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Affiliation(s)
- Csenge Gal
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesco Nicola Carelli
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alex Appert
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ni Huang
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jane Murphy
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Andrea Frapporti
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK.
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17
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Shinkai H, Takahagi Y, Matsumoto T, Toki D, Takenouchi T, Kitani H, Sukegawa S, Suzuki K, Uenishi H. A specific promoter-type in ribonuclease L gene is associated with phagocytic activity in pigs. J Vet Med Sci 2021; 83:1407-1415. [PMID: 34321379 PMCID: PMC8498842 DOI: 10.1292/jvms.21-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We have previously generated Large White pigs with high immune competence using a selection strategy based on phagocytic activity (PA), capacity of alternative complement pathway, and
antibody response after vaccination against swine erysipelas. In this study, to identify the genetic changes caused by the immune selection pressure, we compared gene expression and
polymorphisms in the promoter region between pigs subjected to the immune selection (immune-selected pigs) and those that were not (non-selected pigs). After lipid A stimulation, using a
microarray analysis, 37 genes related to immune function and transcription factor activity showed a greater than three-fold difference in expression between macrophages derived from
immune-selected and non-selected pigs. We further performed a polymorphic analysis of the promoter region of the differentially expressed genes, and elucidated the predominant promoter-types
in the immune-selected and non-selected pigs, respectively, in the genes encoding ribonuclease L (RNASEL), sterile α motif and histidine-aspartate domain containing
deoxynucleoside triphosphate triphosphohydrolase 1, signal transducer and activator of transcription 3, and tripartite motif containing 21. Analysis of the association between these promoter
genotypes and the immune phenotypes revealed that the immune-selected promoter-type in RNASEL was associated with increased PA and was inherited recessively. Considering
that RNASEL has been reported to be involved in antimicrobial immune response of mice, it may be possible to enhance the PA of macrophages and improve disease resistance in
pig populations using RNASEL promoter-type as a DNA marker for selection.
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Affiliation(s)
- Hiroki Shinkai
- Clinical Biochemistry Unit, Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO).,Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | | | - Toshimi Matsumoto
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | - Daisuke Toki
- Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries (JATAFF)
| | - Takato Takenouchi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | - Hiroshi Kitani
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | | | - Keiichi Suzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University
| | - Hirohide Uenishi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
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18
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Sanghavi HM, Majumdar S. Oligomerization of THAP9 Transposase via Amino-Terminal Domains. Biochemistry 2021; 60:1822-1835. [PMID: 34033475 DOI: 10.1021/acs.biochem.1c00010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Active DNA transposases like the Drosophila P element transposase (DmTNP) undergo oligomerization as a prerequisite for transposition. Human THAP9 (hTHAP9) is a catalytically active but functionally uncharacterized homologue of DmTNP. Here we report (using co-immunoprecipitation, pull down, colocalization, and proximity ligation assays) that both full length and truncated hTHAP9 (corresponding to amino-terminal DNA binding and predicted coiled coil domains) undergo homo-oligomerization, predominantly in the nuclei of HEK293T cells. Interestingly, the oligomerization is shown to be partially mediated by DNA. However, mutating the leucines (either individually or together) or deleting the predicted coiled coil region did not significantly affect oligomerization. Thus, we highlight the importance of DNA and the amino-terminal regions of hTHAP9 for their ability to form higher-order oligomeric states. We also report that Hcf-1, THAP1, THAP10, and THAP11 are possible protein interaction partners of hTHAP9. Elucidating the functional relevance of the different putative oligomeric state(s) of hTHAP9 would help answer questions about its interaction partners as well as its unknown physiological roles.
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Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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19
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Staege S, Kutschenko A, Baumann H, Glaß H, Henkel L, Gschwendtberger T, Kalmbach N, Klietz M, Hermann A, Lohmann K, Seibler P, Wegner F. Reduced Expression of GABA A Receptor Alpha2 Subunit Is Associated With Disinhibition of DYT-THAP1 Dystonia Patient-Derived Striatal Medium Spiny Neurons. Front Cell Dev Biol 2021; 9:650586. [PMID: 34095114 PMCID: PMC8176025 DOI: 10.3389/fcell.2021.650586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022] Open
Abstract
DYT-THAP1 dystonia (formerly DYT6) is an adolescent-onset dystonia characterized by involuntary muscle contractions usually involving the upper body. It is caused by mutations in the gene THAP1 encoding for the transcription factor Thanatos-associated protein (THAP) domain containing apoptosis-associated protein 1 and inherited in an autosomal-dominant manner with reduced penetrance. Alterations in the development of striatal neuronal projections and synaptic function are known from transgenic mice models. To investigate pathogenetic mechanisms, human induced pluripotent stem cell (iPSC)-derived medium spiny neurons (MSNs) from two patients and one family member with reduced penetrance carrying a mutation in the gene THAP1 (c.474delA and c.38G > A) were functionally characterized in comparison to healthy controls. Calcium imaging and quantitative PCR analysis revealed significantly lower Ca2+ amplitudes upon GABA applications and a marked downregulation of the gene encoding the GABAA receptor alpha2 subunit in THAP1 MSNs indicating a decreased GABAergic transmission. Whole-cell patch-clamp recordings showed a significantly lower frequency of miniature postsynaptic currents (mPSCs), whereas the frequency of spontaneous action potentials (APs) was elevated in THAP1 MSNs suggesting that decreased synaptic activity might have resulted in enhanced generation of APs. Our molecular and functional data indicate that a reduced expression of GABAA receptor alpha2 subunit could eventually lead to limited GABAergic synaptic transmission, neuronal disinhibition, and hyperexcitability of THAP1 MSNs. These data give pathophysiological insight and may contribute to the development of novel treatment strategies for DYT-THAP1 dystonia.
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Affiliation(s)
- Selma Staege
- Department of Neurology, Hannover Medical School, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
| | - Anna Kutschenko
- Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Hauke Baumann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Hannes Glaß
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University of Rostock, Rostock, Germany
| | - Lisa Henkel
- Department of Neurology, Hannover Medical School, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
| | - Thomas Gschwendtberger
- Department of Neurology, Hannover Medical School, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
| | - Norman Kalmbach
- Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Martin Klietz
- Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University of Rostock, Rostock, Germany.,German Center for Neurodegenerative Diseases Rostock/Greifswald, Rostock, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Florian Wegner
- Department of Neurology, Hannover Medical School, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
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20
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Ma H, Qu J, Ye L, Shu Y, Qu Q. Blepharospasm, Oromandibular Dystonia, and Meige Syndrome: Clinical and Genetic Update. Front Neurol 2021; 12:630221. [PMID: 33854473 PMCID: PMC8039296 DOI: 10.3389/fneur.2021.630221] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
Meige syndrome (MS) is cranial dystonia characterized by the combination of upper and lower cranial involvement and including binocular eyelid spasms (blepharospasm; BSP) and involuntary movements of the jaw muscles (oromandibular dystonia; OMD). The etiology and pathogenesis of this disorder of the extrapyramidal system are not well-understood. Neurologic and ophthalmic examinations often reveal no abnormalities, making diagnosis difficult and often resulting in misdiagnosis. A small proportion of patients have a family history of the disease, but to date no causative genes have been identified to date and no cure is available, although botulinum toxin A therapy effectively mitigates the symptoms and deep brain stimulation is gaining increasing attention as a viable alternative treatment option. Here we review the history and progress of research on MS, BSP, and OMD, as well as the etiology, pathology, diagnosis, and treatment.
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Affiliation(s)
- Hongying Ma
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Institute for Rational and Safe Medication Practices, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Liangjun Ye
- Department of Pharmacy, Hunan Provincial Corps Hospital of Chinese People's Armed Police Force, Changsha, China
| | - Yi Shu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Institute for Rational and Safe Medication Practices, Xiangya Hospital, Central South University, Changsha, China
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21
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Gonzalez-Latapi P, Marotta N, Mencacci NE. Emerging and converging molecular mechanisms in dystonia. J Neural Transm (Vienna) 2021; 128:483-498. [DOI: 10.1007/s00702-020-02290-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/13/2020] [Indexed: 02/06/2023]
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22
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Ali A, Al-Tobasei R, Lourenco D, Leeds T, Kenney B, Salem M. Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout. BMC Genomics 2020; 21:529. [PMID: 32736521 PMCID: PMC7393730 DOI: 10.1186/s12864-020-06932-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture make up about ~ 80% of the tissue weight. The genetic architecture underlying the fat and moisture content of the muscle is still to be fully explored in fish. A 50 K gene transcribed SNP chip was used for genotyping 789 fish with available phenotypic data for fat and moisture content. Genotyped fish were obtained from two consecutive generations produced in the National Center for Cool and Cold Water Aquaculture (NCCCWA) growth-selective breeding program. Estimates of SNP effects from weighted single-step GBLUP (WssGBLUP) were used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with the studied traits. RESULTS Using genomic sliding windows of 50 adjacent SNPs, 137 and 178 SNPs were identified as associated with fat and moisture content, respectively. Chromosomes 19 and 29 harbored the highest number of SNPs explaining at least 2% of the genetic variation in fat and moisture content. A total of 61 common SNPs on chromosomes 19 and 29 affected the aforementioned traits; this association suggests common mechanisms underlying intramuscular fat and moisture content. Additionally, based on single-marker GWA analyses, 8 and 24 SNPs were identified in association with fat and moisture content, respectively. CONCLUSION SNP-harboring genes were primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work provides putative SNP markers that could be prioritized and used for genomic selection in breeding programs.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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23
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Dong C, Liu J, Chen SX, Dong T, Jiang G, Wang Y, Wu H, Reiter JL, Liu Y. Highly robust model of transcription regulator activity predicts breast cancer overall survival. BMC Med Genomics 2020; 13:49. [PMID: 32241272 PMCID: PMC7118819 DOI: 10.1186/s12920-020-0688-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND While several multigene signatures are available for predicting breast cancer prognosis, particularly in early stage disease, effective molecular indicators are needed, especially for triple-negative carcinomas, to improve treatments and predict diagnostic outcomes. The objective of this study was to identify transcriptional regulatory networks to better understand mechanisms giving rise to breast cancer development and to incorporate this information into a model for predicting clinical outcomes. METHODS Gene expression profiles from 1097 breast cancer patients were retrieved from The Cancer Genome Atlas (TCGA). Breast cancer-specific transcription regulatory information was identified by considering the binding site information from ENCODE and the top co-expressed targets in TCGA using a nonlinear approach. We then used this information to predict breast cancer patient survival outcome. RESULT We built a multiple regulator-based prediction model for breast cancer. This model was validated in more than 5000 breast cancer patients from the Gene Expression Omnibus (GEO) databases. We demonstrated our regulator model was significantly associated with clinical stage and that cell cycle and DNA replication related pathways were significantly enriched in high regulator risk patients. CONCLUSION Our findings demonstrate that transcriptional regulator activities can predict patient survival. This finding provides additional biological insights into the mechanisms of breast cancer progression.
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Affiliation(s)
- Chuanpeng Dong
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jiannan Liu
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Steven X Chen
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Tianhan Dong
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Guanglong Jiang
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Huanmei Wu
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jill L Reiter
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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24
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Unraveling Molecular Mechanisms of THAP1 Missense Mutations in DYT6 Dystonia. J Mol Neurosci 2020; 70:999-1008. [PMID: 32112337 PMCID: PMC7334247 DOI: 10.1007/s12031-020-01490-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 12/12/2022]
Abstract
Mutations in THAP1 (THAP domain-containing apoptosis-associated protein 1) are responsible for DYT6 dystonia. Until now, more than eighty different mutations in THAP1 gene have been found in patients with primary dystonia, and two third of them are missense mutations. The potential pathogeneses of these missense mutations in human are largely elusive. In the present study, we generated stable transfected human neuronal cell lines expressing wild-type or mutated THAP1 proteins found in DYT6 patients. Transcriptional profiling using microarrays revealed a set of 28 common genes dysregulated in two mutated THAP1 (S21T and F81L) overexpression cell lines suggesting a common mechanism of these mutations. ChIP-seq showed that THAP1 can bind to the promoter of one of these genes, superoxide dismutase 2 (SOD2). Overexpression of THAP1 in SK-N-AS cells resulted in increased SOD2 protein expression, whereas fibroblasts from THAP1 patients have less SOD2 expression, which indicates that SOD2 is a direct target gene of THAP1. In addition, we show that some THAP1 mutations (C54Y and F81L) decrease the protein stability which might also be responsible for altered transcription regulation due to dosage insufficiency. Taking together, the current study showed different potential pathogenic mechanisms of THAP1 mutations which lead to the same consequence of DYT6 dystonia.
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25
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dos Santos PWDS, Machado ART, De Grandis RA, Ribeiro DL, Tuttis K, Morselli M, Aissa AF, Pellegrini M, Antunes LMG. Transcriptome and DNA methylation changes modulated by sulforaphane induce cell cycle arrest, apoptosis, DNA damage, and suppression of proliferation in human liver cancer cells. Food Chem Toxicol 2020; 136:111047. [DOI: 10.1016/j.fct.2019.111047] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/30/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
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26
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Chen CP, Sang Y, Liu L, Feng ZQ, Liang Z, Pei X. THAP7 promotes cell proliferation by regulating the G1/S phase transition via epigenetically silencing p21 in lung adenocarcinoma. Onco Targets Ther 2019; 12:5651-5660. [PMID: 31372002 PMCID: PMC6634299 DOI: 10.2147/ott.s208908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Lung adenocarcinoma (LUAD) is one of the most common cancers worldwide. The THanatos-Associated Proteins (THAP) family plays an essential role in multiple cancers. However, the role of THAP7 in cancers has remained elusive. METHODS THAP7 expression status in LUAD tissues was analysed by using the Oncomine database and qRT-PCR, and its expression level in LUAD cell lines was detected by qRT-PCR and Western blotting. The role of THAP7 in LUAD cells was determined by proliferation, colony formation, and cell cycle analyses. In vivo role of THAP7 was studied on xenograft models. Luciferase reporter assays and chromatin immunoprecipitation (ChIP) were used to determine the activity and acetylation of the p21 promoter. RESULTS THAP7 expression was increased in LUAD tissues and cell lines. Moreover, the high expression of THAP7 was correlated with poor prognosis. The overexpression of THAP7 accelerated the G1/S phase transition and promoted tumour growth both in vitro and in vivo. A mechanistic study revealed that THAP7 reduced the acetylation of histone H3 on the p21 promoter to suppress p21 transcription. CONCLUSION For the first time, we demonstrated the function of THAP7 in LUAD, and our findings suggested that THAP7 may be a potential molecular therapy target in LUAD.
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Affiliation(s)
- Cai-Ping Chen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, People’s Republic of China
| | - Yi Sang
- Department of Center Laboratory, Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi330008, People’s Republic of China
| | - Lijuan Liu
- Department of Pharmacy, Jiangxi Cancer Hospital, Nanchang, Jiangxi330029, People’s Republic of China
| | - Zhi-Qi Feng
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, People’s Republic of China
| | - Zibin Liang
- Department of Thoracic Oncology, The Cancer Center of the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong519000, People’s Republic of China
| | - Xiaofeng Pei
- Department of Thoracic Oncology, The Cancer Center of the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong519000, People’s Republic of China
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27
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Sanghavi HM, Mallajosyula SS, Majumdar S. Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC STRUCTURAL BIOLOGY 2019; 19:4. [PMID: 30836974 PMCID: PMC6402169 DOI: 10.1186/s12900-019-0102-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022]
Abstract
Background The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like cancers and hemophilia. The human THAP protein family which consists of twelve members of different lengths has a well characterized amino terminal, zinc-coordinating, DNA-binding domain called the THAP domain. However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. A coiled coil region is known to help in protein oligomerization in THAP1 and THAP11. It is not known if other human THAP proteins oligomerize. We have used bioinformatic tools to explore the possibility of dimerization of THAP proteins via a coiled coil region. Results Classification of human THAP protein into three size based groups led to the identification of an evolutionarily conserved alpha helical region, downstream of the amino terminal THAP domain. Secondary structure predictions, alpha helical wheel plots and protein models demonstrated the strong possibility of coiled coil formation in this conserved, leucine rich region of all THAP proteins except THAP10. Conclusions The identification of a predicted oligomerization region in the human THAP protein family opens new directions to investigate the members of this protein family. Electronic supplementary material The online version of this article (10.1186/s12900-019-0102-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.
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28
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He F, Wang H, Li H, Su Y, Li S, Yang Y, Feng C, Yin W, Xia X. PeCHYR1, a ubiquitin E3 ligase from Populus euphratica, enhances drought tolerance via ABA-induced stomatal closure by ROS production in Populus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1514-1528. [PMID: 29406575 PMCID: PMC6041450 DOI: 10.1111/pbi.12893] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/28/2017] [Accepted: 01/28/2018] [Indexed: 05/11/2023]
Abstract
Drought, a primary abiotic stress, seriously affects plant growth and productivity. Stomata play a vital role in regulating gas exchange and drought adaptation. However, limited knowledge exists of the molecular mechanisms underlying stomatal movement in trees. Here, PeCHYR1, a ubiquitin E3 ligase, was isolated from Populus euphratica, a model of stress adaptation in forest trees. PeCHYR1 was preferentially expressed in young leaves and was significantly induced by ABA (abscisic acid) and dehydration treatments. To study the potential biological functions of PeCHYR1, transgenic poplar 84K (Populus alba × Populus glandulosa) plants overexpressing PeCHYR1 were generated. PeCHYR1 overexpression significantly enhanced H2 O2 production and reduced stomatal aperture. Transgenic lines exhibited increased sensitivity to exogenous ABA and greater drought tolerance than that of WT (wild-type) controls. Moreover, up-regulation of PeCHYR1 promoted stomatal closure and decreased transpiration, resulting in strongly elevated WUE (water use efficiency). When exposed to drought stress, transgenic poplar maintained higher photosynthetic activity and biomass accumulation. Taken together, these results suggest that PeCHYR1 plays a crucial role in enhancing drought tolerance via ABA-induced stomatal closure caused by hydrogen peroxide (H2 O2 ) production in transgenic poplar plants.
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Affiliation(s)
- Fang He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Hou‐Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Hui‐Guang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yanyan Su
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Shuang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yanli Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Cong‐Hua Feng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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29
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Li Y, Ning Q, Shi J, Chen Y, Jiang M, Gao L, Huang W, Jing Y, Huang S, Liu A, Hu Z, Liu D, Wang L, Nervi C, Dai Y, Zhang MQ, Yu L. A novel epigenetic AML1-ETO/THAP10/miR-383 mini-circuitry contributes to t(8;21) leukaemogenesis. EMBO Mol Med 2018; 9:933-949. [PMID: 28539478 PMCID: PMC5577530 DOI: 10.15252/emmm.201607180] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
DNA methylation patterns are frequently deregulated in t(8;21) acute myeloid leukaemia (AML), but little is known of the mechanisms by which specific gene sets become aberrantly methylated. Here, we found that the promoter DNA methylation signature of t(8;21)+ AML blasts differs from that of t(8;21)- AMLs. This study demonstrated that a novel hypermethylated zinc finger-containing protein, THAP10, is a target gene and can be epigenetically suppressed by AML1-ETO at the transcriptional level in t(8;21) AML. Our findings also show that THAP10 is a bona fide target of miR-383 that can be epigenetically activated by the AML1-ETO recruiting co-activator p300. In this study, we demonstrated that epigenetic suppression of THAP10 is the mechanistic link between AML1-ETO fusion proteins and tyrosine kinase cascades. In addition, we showed that THAP10 is a nuclear protein that inhibits myeloid proliferation and promotes differentiation both in vitro and in vivo Altogether, our results revealed an unexpected and important epigenetic mini-circuit of AML1-ETO/THAP10/miR-383 in t(8;21) AML, in which epigenetic suppression of THAP10 predicts a poor clinical outcome and represents a novel therapeutic target.
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Affiliation(s)
- Yonghui Li
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Qiaoyang Ning
- Department of Haematology, Chinese PLA General Hospital, Beijing, China.,Nankai University School of Medicine, Tianjin, China
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, China
| | - Yang Chen
- Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Mengmeng Jiang
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Li Gao
- Department of Haematology, China-Japan Friendship Hospital, Beijing, China
| | - Wenrong Huang
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Yu Jing
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Sai Huang
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Anqi Liu
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Zhirui Hu
- Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Daihong Liu
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Lili Wang
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
| | - Clara Nervi
- Department of Medico-Surgical Sciences and Biotechnologies, University of Rome "La Sapienza" Polo Pontino, Latina, Italy
| | - Yun Dai
- Cancer Centre, The First Hospital of Jilin University, Changchun, China.,Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael Q Zhang
- Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Li Yu
- Department of Haematology, Chinese PLA General Hospital, Beijing, China
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30
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Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions. PLoS Genet 2018; 14:e1007169. [PMID: 29364887 PMCID: PMC5798844 DOI: 10.1371/journal.pgen.1007169] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 02/05/2018] [Accepted: 12/25/2017] [Indexed: 12/14/2022] Open
Abstract
Dystonia is characterized by involuntary muscle contractions. Its many forms are genetically, phenotypically and etiologically diverse and it is unknown whether their pathogenesis converges on shared pathways. Mutations in THAP1 [THAP (Thanatos-associated protein) domain containing, apoptosis associated protein 1], a ubiquitously expressed transcription factor with DNA binding and protein-interaction domains, cause dystonia, DYT6. There is a unique, neuronal 50-kDa Thap1-like immunoreactive species, and Thap1 levels are auto-regulated on the mRNA level. However, THAP1 downstream targets in neurons, and the mechanism via which it causes dystonia are largely unknown. We used RNA-Seq to assay the in vivo effect of a heterozygote Thap1 C54Y or ΔExon2 allele on the gene transcription signatures in neonatal mouse striatum and cerebellum. Enriched pathways and gene ontology terms include eIF2α Signaling, Mitochondrial Dysfunction, Neuron Projection Development, Axonal Guidance Signaling, and Synaptic LongTerm Depression, which are dysregulated in a genotype and tissue-dependent manner. Electrophysiological and neurite outgrowth assays were consistent with those enrichments, and the plasticity defects were partially corrected by salubrinal. Notably, several of these pathways were recently implicated in other forms of inherited dystonia, including DYT1. We conclude that dysfunction of these pathways may represent a point of convergence in the pathophysiology of several forms of inherited dystonia. Dystonia is a brain disorder that causes disabling involuntary muscle contractions and abnormal postures. Mutations in THAP1, a zinc-finger transcription factor, cause DYT6, but its neuronal targets and functions are unknown. In this study, we sought to determine the effects of Thap1C54Y and ΔExon2 alleles on the gene transcription signatures at postnatal day 1 (P1) in the mouse striatum and cerebellum in order to correlate function with specific genes or pathways. Our unbiased transcriptomics approach showed that Thap1 mutants revealed multiple signaling pathways involved in neuronal plasticity, axonal guidance, and oxidative stress response, which are also present in other forms of dystonia, particularly DYT1. We conclude that dysfunction of these pathways may represent a point of convergence on the pathogenesis of unrelated forms of inherited dystonia.
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Weisheit CE, Pappas SS, Dauer WT. Inherited dystonias: clinical features and molecular pathways. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:241-254. [PMID: 29325615 DOI: 10.1016/b978-0-444-63233-3.00016-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent decades have witnessed dramatic increases in understanding of the genetics of dystonia - a movement disorder characterized by involuntary twisting and abnormal posture. Hampered by a lack of overt neuropathology, researchers are investigating isolated monogenic causes to pinpoint common molecular mechanisms in this heterogeneous disease. Evidence from imaging, cellular, and murine work implicates deficiencies in dopamine neurotransmission, transcriptional dysregulation, and selective vulnerability of distinct neuronal populations to disease mutations. Studies of genetic forms of dystonia are also illuminating the developmental dependence of disease symptoms that is typical of many forms of the disease. As understanding of monogenic forms of dystonia grows, a clearer picture will develop of the abnormal motor circuitry behind this relatively common phenomenology. This chapter focuses on the current data covering the etiology and epidemiology, clinical presentation, and pathogenesis of four monogenic forms of isolated dystonia: DYT-TOR1A, DYT-THAP1, DYT-GCH1, and DYT-GNAL.
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Affiliation(s)
- Corinne E Weisheit
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Samuel S Pappas
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - William T Dauer
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States.
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32
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Akan I, Olivier-Van Stichelen S, Bond MR, Hanover JA. Nutrient-driven O-GlcNAc in proteostasis and neurodegeneration. J Neurochem 2017; 144:7-34. [PMID: 29049853 DOI: 10.1111/jnc.14242] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/28/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022]
Abstract
Proteostasis is essential in the mammalian brain where post-mitotic cells must function for decades to maintain synaptic contacts and memory. The brain is dependent on glucose and other metabolites for proper function and is spared from metabolic deficits even during starvation. In this review, we outline how the nutrient-sensitive nucleocytoplasmic post-translational modification O-linked N-acetylglucosamine (O-GlcNAc) regulates protein homeostasis. The O-GlcNAc modification is highly abundant in the mammalian brain and has been linked to proteopathies, including neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's. C. elegans, Drosophila, and mouse models harboring O-GlcNAc transferase- and O-GlcNAcase-knockout alleles have helped define the role O-GlcNAc plays in development as well as age-associated neurodegenerative disease. These enzymes add and remove the single monosaccharide from protein serine and threonine residues, respectively. Blocking O-GlcNAc cycling is detrimental to mammalian brain development and interferes with neurogenesis, neural migration, and proteostasis. Findings in C. elegans and Drosophila model systems indicate that the dynamic turnover of O-GlcNAc is critical for maintaining levels of key transcriptional regulators responsible for neurodevelopment cell fate decisions. In addition, pathways of autophagy and proteasomal degradation depend on a transcriptional network that is also reliant on O-GlcNAc cycling. Like the quality control system in the endoplasmic reticulum which uses a 'mannose timer' to monitor protein folding, we propose that cytoplasmic proteostasis relies on an 'O-GlcNAc timer' to help regulate the lifetime and fate of nuclear and cytoplasmic proteins. O-GlcNAc-dependent developmental alterations impact metabolism and growth of the developing mouse embryo and persist into adulthood. Brain-selective knockout mouse models will be an important tool for understanding the role of O-GlcNAc in the physiology of the brain and its susceptibility to neurodegenerative injury.
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Affiliation(s)
- Ilhan Akan
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michelle R Bond
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
| | - John A Hanover
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
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33
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Yellajoshyula D, Liang CC, Pappas SS, Penati S, Yang A, Mecano R, Kumaran R, Jou S, Cookson MR, Dauer WT. The DYT6 Dystonia Protein THAP1 Regulates Myelination within the Oligodendrocyte Lineage. Dev Cell 2017; 42:52-67.e4. [PMID: 28697333 DOI: 10.1016/j.devcel.2017.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 04/25/2017] [Accepted: 06/07/2017] [Indexed: 11/30/2022]
Abstract
The childhood-onset motor disorder DYT6 dystonia is caused by loss-of-function mutations in the transcription factor THAP1, but the neurodevelopmental processes in which THAP1 participates are unknown. We find that THAP1 is essential for the timing of myelination initiation during CNS maturation. Conditional deletion of THAP1 in the CNS retards maturation of the oligodendrocyte (OL) lineage, delaying myelination and causing persistent motor deficits. The CNS myelination defect results from a cell-autonomous requirement for THAP1 in the OL lineage and is recapitulated in developmental assays performed on OL progenitor cells purified from Thap1 null mice. Loss of THAP1 function disrupts a core set of OL maturation genes and reduces the DNA occupancy of YY1, a transcription factor required for OL maturation. These studies establish a role for THAP1 transcriptional regulation at the inception of myelination and implicate abnormal timing of myelination in the pathogenesis of childhood-onset dystonia.
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Affiliation(s)
- Dhananjay Yellajoshyula
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Chun-Chi Liang
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Samuel S Pappas
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Silvia Penati
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Angela Yang
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Rodan Mecano
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Ravindran Kumaran
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Stephanie Jou
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - William T Dauer
- Department of Neurology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; VAAAHS, University of Michigan Medical School, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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Aguilo F, Zakirova Z, Nolan K, Wagner R, Sharma R, Hogan M, Wei C, Sun Y, Walsh MJ, Kelley K, Zhang W, Ozelius LJ, Gonzalez-Alegre P, Zwaka TP, Ehrlich ME. THAP1: Role in Mouse Embryonic Stem Cell Survival and Differentiation. Stem Cell Reports 2017; 9:92-107. [PMID: 28579396 PMCID: PMC5511047 DOI: 10.1016/j.stemcr.2017.04.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
THAP1 (THAP [Thanatos-associated protein] domain-containing, apoptosis-associated protein 1) is a ubiquitously expressed member of a family of transcription factors with highly conserved DNA-binding and protein-interacting regions. Mutations in THAP1 cause dystonia, DYT6, a neurologic movement disorder. THAP1 downstream targets and the mechanism via which it causes dystonia are largely unknown. Here, we show that wild-type THAP1 regulates embryonic stem cell (ESC) potential, survival, and proliferation. Our findings identify THAP1 as an essential factor underlying mouse ESC survival and to some extent, differentiation, particularly neuroectodermal. Loss of THAP1 or replacement with a disease-causing mutation results in an enhanced rate of cell death, prolongs Nanog, Prdm14, and/or Rex1 expression upon differentiation, and results in failure to upregulate ectodermal genes. ChIP-Seq reveals that these activities are likely due in part to indirect regulation of gene expression. Wild-type THAP1 regulates ESC potential, survival, and proliferation THAP1 is essential for ESC differentiation, particularly neuroectodermal Thap1C54Y or ΔExon2 ESCs prolong expression of pluripotent genes upon differentiation Thap1C54Y or ΔExon2 EBs show increased cell death and abnormal differentiation
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Affiliation(s)
- Francesca Aguilo
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Zuchra Zakirova
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katie Nolan
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ryan Wagner
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajal Sharma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan Hogan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chengguo Wei
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kevin Kelley
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijia Zhang
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laurie J Ozelius
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Pedro Gonzalez-Alegre
- Perelman Center for Cellular & Molecular Therapeutics, Department of Neurology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas P Zwaka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle E Ehrlich
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Hollstein R, Reiz B, Kötter L, Richter A, Schaake S, Lohmann K, Kaiser FJ. Dystonia-causing mutations in the transcription factor THAP1 disrupt HCFC1 cofactor recruitment and alter gene expression. Hum Mol Genet 2017; 26:2975-2983. [DOI: 10.1093/hmg/ddx187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/05/2017] [Indexed: 12/14/2022] Open
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Genetic screening of THAP1 in primary dystonia patients of India. Neurosci Lett 2016; 637:31-37. [PMID: 27913194 DOI: 10.1016/j.neulet.2016.11.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Primary Dystonia is a common movement disorder manifested by dystonic symptoms only. DYT6, a major genetic factor, plays a significant role in primary pure dystonia pathogenesis. In this study we analyzed THAP1 (DYT 6) gene in primary pure dystonia patients, which has been widely studied in other populations but not in Indians. METHODS The study cohort contained 227 index primary pure dystonia patients with the involvement of cervical region and 254 neurologically control individuals collected from East Indian population. All three exons of THAP1 and their flanking sequences, including exon-intron boundaries, were screened by PCR, DNA sequencing and/or RFLP analysis. RESULTS A total of three nucleotide variants were detected, which include a reported missense mutation (c.427 A>G; p.Met143Val) in a juvenile onset generalized dystonia patient, a novel frameshift deletion mutation (c.208-209 ΔAA; p.K70VfsX15) in a juvenile onset cervical dystonia patient and a rare variant in 3' UTR of THAP1 (c.*157 T>C) in an adult-onset blepharospasm patient. In addition, two SNPs (rs71521601 and rs111989331) were detected both in the patients and controls with the major allele of the latter being significantly over represented in the patients. CONCLUSIONS Our study suggests that the THAP1 is likely to have a causative role in the pathogenesis of Indian primary pure dystonia patients. Though the phenotypic spectrum is extensively diverse, the cervical involvement with dystonic tremor and speech problem is common amongst the patients harboring mutations.
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Camargos S, Cardoso F. Understanding dystonia: diagnostic issues and how to overcome them. ARQUIVOS DE NEURO-PSIQUIATRIA 2016; 74:921-936. [DOI: 10.1590/0004-282x20160140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/07/2016] [Indexed: 08/30/2023]
Abstract
ABSTRACT The diagnosis and treatment of dystonia are challenging. This is likely due to gaps in the complete understanding of its pathophysiology, lack of animal models for translational studies, absence of a consistent pathological substrate and highly variable phenotypes and genotypes. The aim of this review article is to provide an overview of the clinical, neurophysiological and genetic features of dystonia that can help in the identification of this movement disorder, as well as in the differential diagnosis of the main forms of genetic dystonia. The variation of penetrance, age of onset, and topographic distribution of the disease in carriers of the same genetic mutation indicates that other factors – either genetic or environmental – might be involved in the development of symptoms. The growing knowledge of cell dysfunction in mutants may give insights into more effective therapeutic targets.
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Deng Y, Zhao J, Sakurai D, Sestak AL, Osadchiy V, Langefeld CD, Kaufman KM, Kelly JA, James JA, Petri MA, Bae SC, Alarcón-Riquelme ME, Alarcón GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, Merrill JT, Gaffney PM, Sivils KM, Niewold TB, Ramsey-Goldman R, Reveille JD, Scofield RH, Stevens AM, Boackle SA, Vilá LM, Sohn W, Lee S, Chang DM, Song YW, Vyse TJ, Harley JB, Brown EE, Edberg JC, Kimberly RP, Cantor RM, Hahn BH, Grossman JM, Tsao BP. Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production. Ann Rheum Dis 2016; 75:2007-2013. [PMID: 26783109 PMCID: PMC4949149 DOI: 10.1136/annrheumdis-2015-208441] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/14/2015] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Following up the systemic lupus erythematosus (SLE) genome-wide association studies (GWAS) identification of NMNAT2 at rs2022013, we fine-mapped its 150 kb flanking regions containing NMNAT2 and SMG7 in a 15 292 case-control multi-ancestry population and tested functions of identified variants. METHODS We performed genotyping using custom array, imputation by IMPUTE 2.1.2 and allele specific functions using quantitative real-time PCR and luciferase reporter transfections. SLE peripheral blood mononuclear cells (PBMCs) were cultured with small interfering RNAs to measure antinuclear antibody (ANA) and cyto/chemokine levels in supernatants using ELISA. RESULTS We confirmed association at NMNAT2 in European American (EA) and Amerindian/Hispanic ancestries, and identified independent signal at SMG7 tagged by rs2702178 in EA only (p=2.4×10-8, OR=1.23 (95% CI 1.14 to 1.32)). In complete linkage disequilibrium with rs2702178, rs2275675 in the promoter region robustly associated with SMG7 mRNA levels in multiple expression quantitative trait locus (eQTL) datasets. Its risk allele was dose-dependently associated with decreased SMG7 mRNA levels in PBMCs of 86 patients with SLE and 119 controls (p=1.1×10-3 and 6.8×10-8, respectively) and conferred reduced transcription activity in transfected HEK-293 (human embryonic kidney cell line) and Raji cells (p=0.0035 and 0.0037, respectively). As a critical component in the nonsense-mediated mRNA decay pathway, SMG7 could regulate autoantigens including ribonucleoprotein (RNP) and Smith (Sm). We showed SMG7 mRNA levels in PBMCs correlated inversely with ANA titres of patients with SLE (r=-0.31, p=0.01), and SMG7 knockdown increased levels of ANA IgG and chemokine (C-C motif) ligand 19 in SLE PBMCs (p=2.0×10-5 and 2.0×10-4, respectively). CONCLUSION We confirmed NMNAT2 and identified independent SMG7 association with SLE. The inverse relationship between levels of the risk allele-associated SMG7 mRNAs and ANA suggested the novel contribution of mRNA surveillance pathway to SLE pathogenesis.
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Affiliation(s)
- Yun Deng
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jian Zhao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daisuke Sakurai
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrea L. Sestak
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Vadim Osadchiy
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Carl D. Langefeld
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kenneth M. Kaufman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle A. Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joan T Merrill
- Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kathy Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Anne M Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- US Department of Veterans Affairs Medical Center, Denver, CO, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Woong Sohn
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Seung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | | | - Yeong Wook Song
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea
| | - Timothy J. Vyse
- Division of Genetics and Molecular Medicine and Immunology, King’s College London, London, UK
| | - John B. Harley
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Elizabeth E. Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rita M. Cantor
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bevra H. Hahn
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer M. Grossman
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Betty P. Tsao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Dhivya S, Premkumar K. Nomadic genetic elements contribute to oncogenic translocations: Implications in carcinogenesis. Crit Rev Oncol Hematol 2015; 98:81-93. [PMID: 26548742 DOI: 10.1016/j.critrevonc.2015.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 10/05/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
Chromosomal translocations as molecular signatures have been reported in various malignancies but, the mechanism behind which is largely unknown. Swapping of chromosomal fragments occurs by induction of double strand breaks (DSBs), most of which were initially assumed de novo. However, decoding of human genome proved that transposable elements (TE) might have profound influence on genome integrity. TEs are highly conserved mobile genetic elements that generate DSBs, subsequently resulting in large chromosomal rearrangements. Previously TE insertions were thought to be harmless, but recently gains attention due to the origin of spectrum of post-insertional genomic alterations and subsequent transcriptional alterations leading to development of deleterious effects mainly carcinogenesis. Though the existing knowledge on the cancer-associated TE dynamics is very primitive, exploration of underlying mechanism promises better therapeutic strategies for cancer. Thus, this review focuses on the prevalence of TE in the genome, associated genomic instability upon transposition activation and impact on tumorigenesis.
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Affiliation(s)
- Sridaran Dhivya
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Kumpati Premkumar
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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Ruiz M, Perez-Garcia G, Ortiz-Virumbrales M, Méneret A, Morant A, Kottwitz J, Fuchs T, Bonet J, Gonzalez-Alegre P, Hof PR, Ozelius LJ, Ehrlich ME. Abnormalities of motor function, transcription and cerebellar structure in mouse models of THAP1 dystonia. Hum Mol Genet 2015; 24:7159-70. [PMID: 26376866 DOI: 10.1093/hmg/ddv384] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/14/2015] [Indexed: 01/07/2023] Open
Abstract
DYT6 dystonia is caused by mutations in THAP1 [Thanatos-associated (THAP) domain-containing apoptosis-associated protein] and is autosomal dominant and partially penetrant. Like other genetic primary dystonias, DYT6 patients have no characteristic neuropathology, and mechanisms by which mutations in THAP1 cause dystonia are unknown. Thap1 is a zinc-finger transcription factor, and most pathogenic THAP1 mutations are missense and are located in the DNA-binding domain. There are also nonsense mutations, which act as the equivalent of a null allele because they result in the generation of small mRNA species that are likely rapidly degraded via nonsense-mediated decay. The function of Thap1 in neurons is unknown, but there is a unique, neuronal 50-kDa Thap1 species, and Thap1 levels are auto-regulated on the mRNA level. Herein, we present the first characterization of two mouse models of DYT6, including a pathogenic knockin mutation, C54Y and a null mutation. Alterations in motor behaviors, transcription and brain structure are demonstrated. The projection neurons of the deep cerebellar nuclei are especially altered. Abnormalities vary according to genotype, sex, age and/or brain region, but importantly, overlap with those of other dystonia mouse models. These data highlight the similarities and differences in age- and cell-specific effects of a Thap1 mutation, indicating that the pathophysiology of THAP1 mutations should be assayed at multiple ages and neuronal types and support the notion of final common pathways in the pathophysiology of dystonia arising from disparate mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pedro Gonzalez-Alegre
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Patrick R Hof
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA and
| | - Laurie J Ozelius
- Department of Genetics and Genomic Sciences, Department of Neurology
| | - Michelle E Ehrlich
- Department of Pediatrics, Department of Genetics and Genomic Sciences, Department of Neurology,
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Edelmann MJ, Shack LA, Naske CD, Walters KB, Nanduri B. SILAC-based quantitative proteomic analysis of human lung cell response to copper oxide nanoparticles. PLoS One 2014; 9:e114390. [PMID: 25470785 PMCID: PMC4255034 DOI: 10.1371/journal.pone.0114390] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/09/2014] [Indexed: 12/03/2022] Open
Abstract
Copper (II) oxide (CuO) nanoparticles (NP) are widely used in industry and medicine. In our study we evaluated the response of BEAS-2B human lung cells to CuO NP, using Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics and phosphoproteomics. Pathway modeling of the protein differential expression showed that CuO NP affect proteins relevant in cellular function and maintenance, protein synthesis, cell death and survival, cell cycle and cell morphology. Some of the signaling pathways represented by BEAS-2B proteins responsive to the NP included mTOR signaling, protein ubiquitination pathway, actin cytoskeleton signaling and epithelial adherens junction signaling. Follow-up experiments showed that CuO NP altered actin cytoskeleton, protein phosphorylation and protein ubiquitination level.
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Affiliation(s)
- Mariola J. Edelmann
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, 240 Wise Center Drive, Mississippi State University, Mississippi, United States of America
| | - Leslie A. Shack
- Department of Basic Sciences, College of Veterinary Medicine, 240 Wise Center Drive, Mississippi State University, Mississippi, United States of America
| | - Caitlin D. Naske
- Department of Chemical Engineering, Mississippi State University, Mississippi, United States of America
| | - Keisha B. Walters
- Department of Chemical Engineering, Mississippi State University, Mississippi, United States of America
| | - Bindu Nanduri
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, 240 Wise Center Drive, Mississippi State University, Mississippi, United States of America
- * E-mail:
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Morais DR, Reis ST, Viana N, Piantino CB, Massoco C, Moura C, Dip N, Silva IA, Srougi M, Leite KR. The involvement of miR-100 in bladder urothelial carcinogenesis changing the expression levels of mRNA and proteins of genes related to cell proliferation, survival, apoptosis and chromosomal stability. Cancer Cell Int 2014; 14:119. [PMID: 25493074 PMCID: PMC4260205 DOI: 10.1186/s12935-014-0119-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/30/2014] [Indexed: 11/23/2022] Open
Abstract
Introduction MicroRNAs (miRNA) are small non-coding RNAs that play an important role in the control of gene expression by inhibiting protein translation or promoting messenger RNA degradation. Today, miRNAs have been shown to be involved in various physiological and pathological cellular processes, including cancer, where they can act as oncogenes or tumor suppressor genes. Recently, lowered expression of miR-100, resulting in upregulation of FGFR3, has been correlated with low-grade, non-invasive bladder urothelial cancer, as an alternative oncogenesis pathway to the typical FGFR3 gene mutation. Our aim is to analyze the role of miR-100 in bladder cancer cell lines in controlling the expression of some of its possible target genes, including FGFR3 and its relationship with proliferation, apoptosis and DNA ploidy. Methods The bladder cancer cell lines RT4 and T24 were transfected with pre-miR 100, anti-miR 100 and their respective controls using a lipid-based formulation. After transfection mRNA and protein levels of its supposed target genes THAP2, BAZ2A, mTOR, SMARCA5 and FGFR3 were analyzed by quantitative real time polymerase chain reaction (qRT-PCR) and western blotting. Cell proliferation, apoptosis and DNA ploidy were analyzed by flow cytometry. For statistical analysis, a t-test was applied, p < 0.05 was considered significant. Results After miR-100 transfection, there was a significant reduction in the mRNA of mTOR (p = 0.006), SMARCA5 (p = 0.007) and BAZ2A (p = 0.029) in RT4, mTOR (p = 0.023) and SMARCA5 (p = 0.015) in T24. There was a reduction in the expression of all proteins, variable from 22.5% to 57.1% in both cell lines. In T24 miR-100 promoted an increase in cell proliferation and anti-miR 100 promoted apoptosis characterizing miR-100 as an oncomiR in this cell line representative of a high-grade urothelial carcinoma. Conclusion miR-100 transfection reduces expression of BAZ2A, mTOR and SMARCA5 mRNA and protein in BC cell lines. miR-100 would be classified as an oncomiR in T24 cells representative of high grade urothelial carcinoma promoting increase in cell proliferation and reduction in apoptosis. The knowledge of miRNA role in tumors will allow their use as tumor markers and targets for new therapies.
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Affiliation(s)
- Denis R Morais
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil ; Department of Pathology, University of Sao Paulo Veterinary Medicine and Zootechnics School, Sao Paulo, Brazil
| | - Sabrina T Reis
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Nayara Viana
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Camila Berfort Piantino
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Cristina Massoco
- Department of Pathology, University of Sao Paulo Veterinary Medicine and Zootechnics School, Sao Paulo, Brazil
| | - Caio Moura
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Nelson Dip
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Iran A Silva
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Miguel Srougi
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Katia Rm Leite
- Laboratory of Medical Research, Department of Urology - LIM55, University of Sao Paulo Medical School, Sao Paulo, Brazil
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Reingold V, Luria N, Robichon A, Dombrovsky A. Adenine methylation may contribute to endosymbiont selection in a clonal aphid population. BMC Genomics 2014; 15:999. [PMID: 25406741 PMCID: PMC4246565 DOI: 10.1186/1471-2164-15-999] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 11/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pea aphid Acyrthosiphon pisum has two modes of reproduction: parthenogenetic during the spring and summer and sexual in autumn. This ability to alternate between reproductive modes and the emergence of clonal populations under favorable conditions make this organism an interesting model for genetic and epigenetic studies. The pea aphid hosts different types of endosymbiotic bacteria within bacteriocytes which help the aphids survive and adapt to new environmental conditions and habitats. The obligate endosymbiont Buchnera aphidicola has a drastically reduced and stable genome, whereas facultative endosymbionts such as Regiella insecticola have large and dynamic genomes due to phages, mobile elements and high levels of genetic recombination. In previous work, selection toward cold adaptation resulted in the appearance of parthenogenetic A. pisum individuals characterized by heavier weights and remarkable green pigmentation. RESULTS Six adenine-methylated DNA fragments were isolated from genomic DNA (gDNA) extracted from the cold-induced green variant of A. pisum using deoxyadenosine methylase (Dam) by digesting the gDNA with the restriction enzymes DpnI and DpnII, which recognize the methylated and unmethylated GATC sites, respectively. The six resultant fragments did not match any sequence in the A. pisum or Buchnera genomes, implying that they came from facultative endosymbionts. The A1 fragment encoding a putative transposase and the A6 fragment encoding a putative helicase were selected for further comparison between the two A. pisum variants (green and orange) based on Dam analysis followed by PCR amplification. An association between adenine methylation and the two A. pisum variants was demonstrated by higher adenine methylation levels on both genes in the green variant as compared to the orange one. CONCLUSION Temperature selection may affect the secondary endosymbiont and the sensitive Dam involved in the survival and adaptation of aphids to cold temperatures. There is a high degree of adenine methylation at the GATC sites of the endosymbiont genes at 8°C, an effect that disappears at 22°C. We suggest that endosymbionts can be modified or selected to increase host fitness under unfavorable climatic conditions, and that the phenotype of the newly adapted aphids can be inherited.
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Affiliation(s)
| | | | | | - Aviv Dombrovsky
- INRA/CNRS/UNSA University Nice Sophia Antipolis, 400 routes de Chappes, BP 167, Sophia Antipolis 06903, France.
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Gajos A, Golańska E, Sieruta M, Szybka M, Liberski PP, Bogucki A. High variability of clinical symptoms in a Polish family with a novelTHAP1mutation. Int J Neurosci 2014; 125:755-9. [DOI: 10.3109/00207454.2014.981749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Abstract
Isolated inherited dystonia-formerly referred to as primary dystonia-is characterized by abnormal motor functioning of a grossly normal appearing brain. The disease manifests as abnormal involuntary twisting movements. The absence of overt neuropathological lesions, while intriguing, has made it particularly difficult to unravel the pathogenesis of isolated inherited dystonia. The explosion of genetic techology enabling the identification of the causative gene mutations is transforming our understanding of dystonia pathogenesis, as the molecular, cellular and circuit level consequences of these mutations are identified in experimental systems. Here, I review the clinical genetics and cell biology of three forms of inherited dystonia for which the causative mutation is known: DYT1 (TOR1A), DYT6 (THAP1), DYT25 (GNAL).
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Affiliation(s)
- William Dauer
- Department of Neurology, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109-220, USA,
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Ortiz-Virumbrales M, Ruiz M, Hone E, Dolios G, Wang R, Morant A, Kottwitz J, Ozelius LJ, Gandy S, Ehrlich ME. Dystonia type 6 gene product Thap1: identification of a 50 kDa DNA-binding species in neuronal nuclear fractions. Acta Neuropathol Commun 2014; 2:139. [PMID: 25231164 PMCID: PMC4177242 DOI: 10.1186/s40478-014-0139-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/05/2014] [Indexed: 01/04/2023] Open
Abstract
Mutations in THAP1 result in dystonia type 6, with partial penetrance and variable phenotype. The goal of this study was to examine the nature and expression pattern of the protein product(s) of the Thap1 transcription factor (DYT6 gene) in mouse neurons, and to study the regional and developmental distribution, and subcellular localization of Thap1 protein. The goal was accomplished via overexpression and knock-down of Thap1 in the HEK293T cell line and in mouse striatal primary cultures and western blotting of embryonic Thap1-null tissue. The endogenous and transduced Thap1 isoforms were characterized using three different commercially available anti-Thap1 antibodies and validated by immunoprecipitation and DNA oligonucleotide affinity chromatography. We identified multiple, novel Thap1 species of apparent Mr 32 kDa, 47 kDa, and 50–52 kDa in vitro and in vivo, and verified the previously identified species at 29–30 kDa in neurons. The Thap1 species at the 50 kDa size range was exclusively detected in murine brain and testes and were located in the nuclear compartment. Thus, in addition to the predicted 25 kDa apparent Mr, we identified Thap1 species with greater apparent Mr that we speculate may be a result of posttranslational modifications. The neural localization of the 50 kDa species and its nuclear compartmentalization suggests that these may be key Thap1 species controlling neuronal gene transcription. Dysfunction of the neuronal 50 kDa species may therefore be implicated in the pathogenesis of DYT6.
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Mondal BC, Shim J, Evans CJ, Banerjee U. Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. eLife 2014; 3:e03626. [PMID: 25201876 PMCID: PMC4185420 DOI: 10.7554/elife.03626] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/05/2014] [Indexed: 12/18/2022] Open
Abstract
Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the 'equilibrium signal' in order to distinguish it from the 'niche signal'. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr.
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Affiliation(s)
- Bama Charan Mondal
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Jiwon Shim
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Cory J Evans
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Utpal Banerjee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
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The potential role of O-GlcNAc modification in cancer epigenetics. Cell Mol Biol Lett 2014; 19:438-60. [PMID: 25141978 PMCID: PMC6275943 DOI: 10.2478/s11658-014-0204-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/01/2014] [Indexed: 12/20/2022] Open
Abstract
There is no doubt that cancer is not only a genetic disease but that it can also occur due to epigenetic abnormalities. Diet and environmental factors can alter the scope of epigenetic regulation. The results of recent studies suggest that O-GlcNAcylation, which involves the addition of N-acetylglucosamine on the serine or threonine residues of proteins, may play a key role in the regulation of the epigenome in response to the metabolic status of the cell. Two enzymes are responsible for cyclic O-GlcNAcylation: O-GlcNAc transferase (OGT), which catalyzes the addition of the GlcNAc moiety to target proteins; and O-GlcNAcase (OGA), which removes the sugar moiety from proteins. Aberrant expression of O-GlcNAc cycling enzymes, especially OGT, has been found in all studied human cancers. OGT can link the cellular metabolic state and the epigenetic status of cancer cells by interacting with and modifying many epigenetic factors, such as HCF-1, TET, mSin3A, HDAC, and BAP1. A growing body of evidence from animal model systems also suggests an important role for OGT in polycomb-dependent repression of genes activity. Moreover, O-GlcNAcylation may be a part of the histone code: O-GlcNAc residues are found on all core histones.
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Erogullari A, Hollstein R, Seibler P, Braunholz D, Koschmidder E, Depping R, Eckhold J, Lohnau T, Gillessen-Kaesbach G, Grünewald A, Rakovic A, Lohmann K, Kaiser FJ. THAP1, the gene mutated in DYT6 dystonia, autoregulates its own expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1196-204. [PMID: 25088175 DOI: 10.1016/j.bbagrm.2014.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023]
Abstract
THAP1 encodes a transcription factor but its regulation is largely elusive. TOR1A was shown to be repressed by THAP1 in vitro. Notably, mutations in both of these genes lead to dystonia (DYT6 or DYT1). Surprisingly, expressional changes of TOR1A in THAP1 mutation carriers have not been detected indicating additional levels of regulation. Here, we investigated whether THAP1 is able to autoregulate its own expression. Using in-silico prediction, luciferase reporter gene assays, and (quantitative) chromatin immunoprecipitation (ChIP), we defined the THAP1 minimal promoter to a 480bp-fragment and demonstrated specific binding of THAP1 to this region which resulted in repression of the THAP1 promoter. This autoregulation was disturbed by different DYT6-causing mutations. Two mutants (Ser6Phe, Arg13His) were shown to be less stable than wildtype THAP1 adding to the effect of reduced binding to the THAP1 promoter. Overexpressed THAP1 is preferably degraded through the proteasome. Notably, endogenous THAP1 expression was significantly reduced in cells overexpressing wildtype THAP1 as demonstrated by quantitative PCR. In contrast, higher THAP1 levels were detected in induced pluripotent stem cell (iPS)-derived neurons from THAP1 mutation carriers. Thus, we identified a feedback-loop in the regulation of THAP1 expression and demonstrated that mutant THAP1 leads to higher THAP1 expression levels. This compensatory autoregulation may contribute to the mean age at onset in the late teen years or even reduced penetrance in some THAP1 mutation carriers.
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Affiliation(s)
- Alev Erogullari
- Sektion für Funktionelle Genetik am Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany
| | - Ronja Hollstein
- Sektion für Funktionelle Genetik am Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany
| | - Philip Seibler
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany
| | - Diana Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany
| | - Eva Koschmidder
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany
| | - Reinhard Depping
- Institute of Physiology, Center of Structural and Cell Biology in Medicine, University of Luebeck, Luebeck 23538, Germany
| | - Juliane Eckhold
- Sektion für Funktionelle Genetik am Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany; Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany
| | - Thora Lohnau
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany
| | | | - Anne Grünewald
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, Luebeck 23538, Germany.
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik, University of Luebeck, Luebeck 23538, Germany
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Kong XZ, Yin RH, Ning HM, Zheng WW, Dong XM, Yang Y, Xu FF, Li JJ, Zhan YQ, Yu M, Ge CH, Zhang JH, Chen H, Li CY, Yang XM. Effects of THAP11 on erythroid differentiation and megakaryocytic differentiation of K562 cells. PLoS One 2014; 9:e91557. [PMID: 24637716 PMCID: PMC3956667 DOI: 10.1371/journal.pone.0091557] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 02/13/2014] [Indexed: 12/16/2022] Open
Abstract
Hematopoiesis is a complex process regulated by sets of transcription factors in a stage-specific and context-dependent manner. THAP11 is a transcription factor involved in cell growth, ES cell pluripotency, and embryogenesis. Here we showed that THAP11 was down-regulated during erythroid differentiation but up-regulated during megakaryocytic differentiation of cord blood CD34+ cells. Overexpression of THAP11 in K562 cells inhibited the erythroid differentiation induced by hemin with decreased numbers of benzidine-positive cells and decreased mRNA levels of α-globin (HBA) and glycophorin A (GPA), and knockdown of THAP11 enhanced the erythroid differentiation. Conversely, THAP11 overexpression accelerated the megakaryocytic differentiation induced by phorbol myristate acetate (PMA) with increased percentage of CD41+ cells, increased numbers of 4N cells, and elevated CD61 mRNA levels, and THAP11 knockdown attenuated the megakaryocytic differentiation. The expression levels of transcription factors such as c-Myc, c-Myb, GATA-2, and Fli1 were changed by THAP11 overexpression. In this way, our results suggested that THAP11 reversibly regulated erythroid and megakaryocytic differentiation.
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Affiliation(s)
- Xiang-Zhen Kong
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Rong-Hua Yin
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
| | - Hong-Mei Ning
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital to Academy of Military Medical Sciences, Beijing, China
| | - Wei-Wei Zheng
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiao-Ming Dong
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
| | - Yang Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Fei-Fei Xu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jian-Jie Li
- Department of Pulmonary Neoplasms Internal Medicine, Affiliated Hospital to Academy of Military Medicine Sciences, Beijing, China
| | - Yi-Qun Zhan
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Miao Yu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chang-Hui Ge
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jian-Hong Zhang
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hui Chen
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chang-Yan Li
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
- * E-mail: (XMY); (CYL)
| | - Xiao-Ming Yang
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
- * E-mail: (XMY); (CYL)
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