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Cuinat S, Quélin C, Effray C, Dubourg C, Le Bouar G, Cabaret-Dufour AS, Loget P, Proisy M, Sauvestre F, Sarreau M, Martin-Berenguer S, Beneteau C, Naudion S, Michaud V, Arveiler B, Trimouille A, Macé P, Sigaudy S, Glazunova O, Torrents J, Raymond L, Saint-Frison MH, Attié-Bitach T, Lefebvre M, Capri Y, Bourgon N, Thauvin-Robinet C, Tran Mau-Them F, Bruel AL, Vitobello A, Denommé-Pichon AS, Faivre L, Brehin AC, Goldenberg A, Patrier-Sallebert S, Perani A, Dauriat B, Bourthoumieu S, Yardin C, Marquet V, Barnique M, Fiorenza-Gasq M, Marey I, Tournadre D, Doumit R, Nugues F, Barakat TS, Bustos F, Jaillard S, Launay E, Pasquier L, Odent S. Extending the clinical spectrum of X-linked Tonne-Kalscheuer syndrome (TOKAS): new insights from the fetal perspective. J Med Genet 2024:jmg-2024-109854. [PMID: 38849204 DOI: 10.1136/jmg-2024-109854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/19/2024] [Indexed: 06/09/2024]
Abstract
INTRODUCTION Tonne-Kalscheuer syndrome (TOKAS) is a recessive X-linked multiple congenital anomaly disorder caused by RLIM variations. Of the 41 patients reported, only 7 antenatal cases were described. METHOD After the antenatal diagnosis of TOKAS by exome analysis in a family followed for over 35 years because of multiple congenital anomalies in five male fetuses, a call for collaboration was made, resulting in a cohort of 11 previously unpublished cases. RESULTS We present a TOKAS antenatal cohort, describing 11 new cases in 6 French families. We report a high frequency of diaphragmatic hernia (9 of 11), differences in sex development (10 of 11) and various visceral malformations. We report some recurrent dysmorphic features, but also pontocerebellar hypoplasia, pre-auricular skin tags and olfactory bulb abnormalities previously unreported in the literature. Although no clear genotype-phenotype correlation has yet emerged, we show that a recurrent p.(Arg611Cys) variant accounts for 66% of fetal TOKAS cases. We also report two new likely pathogenic variants in RLIM, outside of the two previously known mutational hotspots. CONCLUSION Overall, we present the first fetal cohort of TOKAS, describe the clinical features that made it a recognisable syndrome at fetopathological examination, and extend the phenotypical spectrum and the known genotype of this rare disorder.
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Affiliation(s)
- Silvestre Cuinat
- Service de Génétique Clinique, CRMR anomalies du développement CLAD-Ouest, CHU Rennes, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, CRMR anomalies du développement CLAD-Ouest, CHU Rennes, Rennes, France
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Pontchaillou, CHU Rennes, Rennes, France
| | - Claire Effray
- Service de Génétique Clinique, CRMR anomalies du développement CLAD-Ouest, CHU Rennes, Rennes, France
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire, Hôpital Pontchaillou, CHU Rennes, Rennes, France
- CNRS, INSERM UMR 6290, ERL U1305, F-35000, Université de Rennes, IGDR, Rennes, France
| | - Gwenaelle Le Bouar
- Unité de Médecine fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | | | - Philippe Loget
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Pontchaillou, CHU Rennes, Rennes, France
| | - Maia Proisy
- Radiology Department, CHU de Brest, Brest, France
| | - Fanny Sauvestre
- Unité de Pathologie Fœto-placentaire, Service de Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Mélie Sarreau
- Unité de Pathologie Fœto-placentaire, Service de Pathologie, CHU de Bordeaux, Bordeaux, France
| | - Sophie Martin-Berenguer
- Unité de Pathologie Fœto-placentaire, Service de Pathologie, CHU de Bordeaux, Bordeaux, France
- Department of Gynaecology and Obstetrics, Mother and Children's Hospital, CHU Limoges, Limoges, France
| | - Claire Beneteau
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Sophie Naudion
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
- INSERM U1211, Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | - Benoit Arveiler
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
- INSERM U1211, Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | - Aurélien Trimouille
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
- INSERM U1211, Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | - Pierre Macé
- Institut méditerranéen d'imagerie médicale appliquée à la gynécologie, la grossesse et l'enfance IMAGE2, Marseille, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, Hôpital Timone Enfant, AP-HM, Marseille, France
| | - Olga Glazunova
- Département de Génétique Médicale, Hôpital Timone Enfant, AP-HM, Marseille, France
| | - Julia Torrents
- Department of Pathology and Neuropathology, La Timone Hospital, Aix Marseille University, AP-HM, Marseille, France
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | | | - Tania Attié-Bitach
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, AP-HP, Paris, France
- INSERM UMR 1163, Imagine Institute, Université Paris Cité, Paris, France
| | - Mathilde Lefebvre
- Service de Pathologie fœtale, Hôpital Universitaire Armand Trousseau, AP-HP, Paris, France
| | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, AP-HP, Paris, France
| | - Nicolas Bourgon
- Service d'Obstétrique-Maternité Chirurgie, Médecine et Imagerie foetales, AP-HP, Hopital Universitaire Necker-Enfants Malades, Paris, France
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon, Dijon, France
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD, CHU Dijon, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Ange-Line Bruel
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Antonio Vitobello
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, INSERM, Université Bourgogne Franche-Comté, Dijon, France
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD, CHU Dijon, Dijon, France
| | - Anne-Claire Brehin
- Department of Pathology, Department of Genetics and Reference Center for Developmental Abnormalities, F-76000, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Alice Goldenberg
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Genetics and Reference Center for Developmental Abnormalities, F-76000, CHU de Rouen, Rouen, France
| | | | - Alexandre Perani
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
| | - Benjamin Dauriat
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
| | - Sylvie Bourthoumieu
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
- UMR 7252, CNRS, XLIM, F-87000, Université de Limoges, Limoges, France
| | - Catherine Yardin
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
- UMR 7252, CNRS, XLIM, F-87000, Université de Limoges, Limoges, France
| | - Valentine Marquet
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
| | - Marion Barnique
- Cytogenetic, Medical Genetic and Reproductive Biology Department, Hôpital de la Mère et de l'Enfant, CHU Dupuytren, CHU Limoges, Limoges, France
| | - Maryse Fiorenza-Gasq
- Department of Gynaecology and Obstetrics, Mother and Children's Hospital, CHU Limoges, Limoges, France
| | - Isabelle Marey
- INSERM U1209, Institute for Advanced Bioscience, Université Grenoble Alpes, Grenoble, France
| | - Danielle Tournadre
- CPDPN de Grenoble, Echographie obstétricale dépistage et diagnostic, CHU Grenoble Alpes, Grenoble, France
| | - Raïa Doumit
- Service d'Imagerie Pédiatrique, CHU Grenoble Alpes, Grenoble, France
| | - Frédérique Nugues
- Service d'Imagerie Pédiatrique, CHU Grenoble Alpes, Grenoble, France
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Francisco Bustos
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- EHESP, INSERM U1085 IRSET, Université de Rennes 1, Rennes, France
| | - Erika Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Laurent Pasquier
- Service de Génétique Clinique, CRMR anomalies du développement CLAD-Ouest, CHU Rennes, Rennes, France
- CNRS, INSERM UMR 6290, ERL U1305, F-35000, Université de Rennes, IGDR, Rennes, France
- FHU GenoMeds, ERN ITHACA, CHU Rennes, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, CRMR anomalies du développement CLAD-Ouest, CHU Rennes, Rennes, France
- CNRS, INSERM UMR 6290, ERL U1305, F-35000, Université de Rennes, IGDR, Rennes, France
- FHU GenoMeds, ERN ITHACA, CHU Rennes, Rennes, France
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Wang F, Mehta P, Bach I. How does the Xist activator Rlim/Rnf12 regulate Xist expression? Biochem Soc Trans 2024:BST20230573. [PMID: 38747697 DOI: 10.1042/bst20230573] [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: 01/25/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/23/2024]
Abstract
The long non-coding RNA (lncRNA) Xist is crucially involved in a process called X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female mammals to achieve X dosage compensation between the sexes. Because Xist RNA silences the X chromosome from which it is transcribed, the activation of Xist transcription marks the initiation of the XCI process and thus, mechanisms and players that activate this gene are of central importance to the XCI process. During female mouse embryogenesis, XCI occurs in two steps. At the 2-4 cell stages imprinted XCI (iXCI) silences exclusively the paternally inherited X chromosome (Xp). While extraembryonic cells including trophoblasts keep the Xp silenced, epiblast cells that give rise to the embryo proper reactivate the Xp and undergo random XCI (rXCI) around implantation. Both iXCI and rXCI are dependent on Xist. Rlim, also known as Rnf12, is an X-linked E3 ubiquitin ligase that is involved in the transcriptional activation of Xist. However, while data on the crucial involvement of Rlim during iXCI appear clear, its role in rXCI has been controversial. This review discusses data leading to this disagreement and recent evidence for a regulatory switch of Xist transcription in epiblasts of implanting embryos, partially reconciling the roles of Rlim during Xist activation.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, U.S.A
| | - Poonam Mehta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, U.S.A
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, U.S.A
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3
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Bustos F, Mathur S, Espejo-Serrano C, Toth R, Hastie CJ, Virdee S, Findlay GM. Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome. Life Sci Alliance 2022; 5:5/11/e202101248. [PMID: 35764390 PMCID: PMC9240097 DOI: 10.26508/lsa.202101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Affiliation(s)
- Francisco Bustos
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Sunil Mathur
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Carmen Espejo-Serrano
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - C James Hastie
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Greg M Findlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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Huang Y, Liu S, Shan M, Hagenaars SC, Mesker WE, Cohen D, Wang L, Zheng Z, Devilee P, Tollenaar RAEM, Li Z, Song Y, Zhang L, Li D, Ten Dijke P. RNF12 is regulated by AKT phosphorylation and promotes TGF-β driven breast cancer metastasis. Cell Death Dis 2022; 13:44. [PMID: 35013159 PMCID: PMC8748510 DOI: 10.1038/s41419-021-04493-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
Transforming growth factor-β (TGF-β) acts as a pro-metastatic factor in advanced breast cancer. RNF12, an E3 ubiquitin ligase, stimulates TGF-β signaling by binding to the inhibitory SMAD7 and inducing its proteasomal degradation. How RNF12 activity is regulated and its exact role in cancer is incompletely understood. Here we report that RNF12 was overexpressed in invasive breast cancers and its high expression correlated with poor prognosis. RNF12 promoted breast cancer cell migration, invasion, and experimental metastasis in zebrafish and murine xenograft models. RNF12 levels were positively associated with the phosphorylated AKT/protein kinase B (PKB) levels, and both displayed significant higher levels in the basal-like subtype compared with the levels in luminal-like subtype of breast cancer cells. Mechanistically, AKT-mediated phosphorylation induced the nuclear localization of RNF12, maintained its stability, and accelerated the degradation of SMAD7 mediated by RNF12. Furthermore, we demonstrated that RNF12 and AKT cooperated functionally in breast cancer cell migration. Notably, RNF12 expression strongly correlated with both phosphorylated AKT and phosphorylated SMAD2 levels in breast cancer tissues. Thus, our results uncovered RNF12 as an important determinant in the crosstalk between the TGF-β and AKT signaling pathways during breast cancer progression.
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Affiliation(s)
- Yongsheng Huang
- Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Sijia Liu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mengjie Shan
- Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sophie C Hagenaars
- Department of Surgery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lin Wang
- Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi Zheng
- Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Zhangfu Li
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongmei Song
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Long Zhang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands. .,Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Dan Li
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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Liao Y, Wang Z, Glória LS, Zhang K, Zhang C, Yang R, Luo X, Jia X, Lai SJ, Chen SY. Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model. Front Genet 2021; 12:750939. [PMID: 34691158 PMCID: PMC8531506 DOI: 10.3389/fgene.2021.750939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Growth is a complex trait with moderate to high heritability in livestock and must be described by the longitudinal data measured over multiple time points. Therefore, the used phenotype in genome-wide association studies (GWAS) of growth traits could be either the measures at the preselected time point or the fitted parameters of whole growth trajectory. A promising alternative approach was recently proposed that combined the fitting of growth curves and estimation of single-nucleotide polymorphism (SNP) effects into single-step nonlinear mixed model (NMM). In this study, we collected the body weights at 35, 42, 49, 56, 63, 70, and 84 days of age for 401 animals in a crossbred population of meat rabbits and compared five fitting models of growth curves (Logistic, Gompertz, Brody, Von Bertalanffy, and Richards). The logistic model was preferably selected and subjected to GWAS using the approach of single-step NMM, which was based on 87,704 genome-wide SNPs. A total of 45 significant SNPs distributed on five chromosomes were found to simultaneously affect the two growth parameters of mature weight (A) and maturity rate (K). However, no SNP was found to be independently associated with either A or K. Seven positional genes, including KCNIP4, GBA3, PPARGC1A, LDB2, SHISA3, GNA13, and FGF10, were suggested to be candidates affecting growth performances in meat rabbits. To the best of our knowledge, this is the first report of GWAS based on single-step NMM for longitudinal traits in rabbits, which also revealed the genetic architecture of growth traits that are helpful in implementing genome selection.
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Affiliation(s)
- Yonglan Liao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhicheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Leonardo S Glória
- Laboratory of Animal Science, State University of Northern of Rio de Janeiro, Campos dos Goytacazes, Brazil
| | - Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cuixia Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Rui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xinmao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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6
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Zhai D, Wang G, Li L, Jia X, Zheng G, Yin J. [LIM-domain binding protein 2 regulated by m 6A modification inhibits lung adenocarcinoma cell proliferation in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:329-335. [PMID: 33849822 DOI: 10.12122/j.issn.1673-4254.2021.03.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the role and expression pattern of LIM-domain binding protein 2 (LDB2) in lung adenocarcinoma. OBJECTIVE We studied the expression pattern of LDB2 in lung adenocarcinoma based on data from the online databases TCGA, GEO and CPTAC, and the results were verified in lung adenocarcinoma tissues and cells using immunohistochemistry, qRT-PCR and Western blotting. The relationship between LDB2 and the prognosis of patients with lung adenocarcinoma was analyzed using GEPIA and GEO databases. We further analyzed the role of LDB2 in regulating cell behaviors in a H1299 cell model over-expressing LDB2 using cell counting, soft agar colony forming assay and flow cytometry. The m6A binding sites on LDB2 were confirmed by bioinformatics analysis and MeRIP-qPCR assays. The effect of YTHDC2 on LDB2 was examined using qRT-PCR and Western blotting, and the binding of YTHDC2 to the transcript of LDB2 was verified with RIP-qPCR assays. Dual luciferase reporter assay was performed to verify YTHDC2 functioning via m6A sites. OBJECTIVE LDB2 expression was significantly decreased in lung adenocarcinoma in comparison with normal tissues based on data from TCGA, GEPIA and CPTAC, and the same results were obtained from 80 lung adenocarcinoma tissues and 17 adjacent normal tissues. Similarly, LDB2 expression was decreased in lung adenocarcinoma cells as compared with 16HBE cells. The data from Prognoscan and GEPIA suggested that a high LDB2 expression was positively correlated with a more favorable outcome of lung adenocarcinoma patients. LDB2-overexpressing H1299 cells showed a significant inhibition of proliferative activity with cell cycle arrest in S phage. Bioinformatics analysis and MeRIP-qPCR assay confirmed the presence of m6A sites on LDB2. The m6A reader YTHDC2 was positively related with LDB2 in lung adenocarcinoma based on data from GEPIA (r=0.22). Overexpression YTHDC2 significantly enhanced LDB2 expression in H1299 cells by about 19.35 folds. Dual luciferase reporter assay showed that YTHDC2 enhanced the promoter activity in the wild-type group but not in deletion group. OBJECTIVE LDB2 expression can be up-regulated by m6A reader YTHDC2 in lung adenocarcinoma to inhibit the proliferation of the tumor cells in vitro.
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Affiliation(s)
- D Zhai
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
| | - G Wang
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
| | - L Li
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
| | - X Jia
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
| | - G Zheng
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
| | - J Yin
- Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University//Guangzhou Key Laboratory of Translational Medicine on Cancer Treatment, Guangzhou 510095, China
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7
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Wang F, Gervasi MG, Bošković A, Sun F, Rinaldi VD, Yu J, Wallingford MC, Tourzani DA, Mager J, Zhu LJ, Rando OJ, Visconti PE, Strittmatter L, Bach I. Deficient spermiogenesis in mice lacking Rlim. eLife 2021; 10:e63556. [PMID: 33620316 PMCID: PMC7935487 DOI: 10.7554/elife.63556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The X-linked gene Rlim plays major roles in female mouse development and reproduction, where it is crucial for the maintenance of imprinted X chromosome inactivation in extraembryonic tissues of embryos. However, while females carrying a systemic Rlim knockout (KO) die around implantation, male Rlim KO mice appear healthy and are fertile. Here, we report an important role for Rlim in testis where it is highly expressed in post-meiotic round spermatids as well as in Sertoli cells. Systemic deletion of the Rlim gene results in lower numbers of mature sperm that contains excess cytoplasm, leading to decreased sperm motility and in vitro fertilization rates. Targeting the conditional Rlim cKO specifically to the spermatogenic cell lineage largely recapitulates this phenotype. These results reveal functions of Rlim in male reproduction specifically in round spermatids during spermiogenesis.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Maria Gracia Gervasi
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Vera D Rinaldi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Mary C Wallingford
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Darya A Tourzani
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Jesse Mager
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Pablo E Visconti
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Lara Strittmatter
- Electron Microscopy Core, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
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8
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Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens. Gene 2020; 761:145046. [PMID: 32781192 DOI: 10.1016/j.gene.2020.145046] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/01/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023]
Abstract
Many studies have shown that the LDB2 gene plays a regulatory role in retinal development and the cell cycle, but its biological role remains unclear. In this study, a 31-bp indel in the LDB2 gene was found for the first time on the basis of 2797 individuals from 10 different breeds, which led to different genotypes among individuals (II, ID and DD). Among these genotypes, DD was the most dominant. Association analysis of an F2 resource population crossed with the Gushi (GS) chicken and Anka chicken showed that the DD genotype conferred a significantly greater semi-evisceration weight (SEW, 1108.665 g ± 6.263), evisceration weight (EW, 927.455 g ± 5.424), carcass weight (CW, 1197.306 g ± 6.443), breast muscle weight (BMW, 71.05 g ± 0.574), and leg muscle weight (LMW, 100.303 g ± 0.677) than the ID genotype (SEW, 1059.079 g ± 16.86; EW, 879.459 g ± 14.446; CW, 1141.821 g ± 17.176; BMW, 67.164 g ± 1.523; and LMW, 96.163 g ± 1.823). In addition, LDB2 gene expression in different breeds was significantly higher in the breast muscles and leg muscles than in other tissues. The expression level in the breast muscle differed significantly among stages of GS chicken development, with the highest expression observed at 6 weeks. The expression levels in the pectoral muscles differed significantly among Ross 308 genotypes. In summary, we studied the relationships between a 31-bp indel in the LDB2 gene and economic traits in chickens. The indel was significantly correlated with multiple growth and carcass traits in the F2 resource population and affected the expression of the LDB2 gene in muscle tissue. In short, our study revealed that the LDB2 gene 31-bp indel can be used as a potential genetic marker for molecular breeding.
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9
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Abstract
The Lim domain binding proteins (LDB1 and LDB2 in human and Chip in Drosophila) play critical roles in cell fate decisions through partnership with multiple Lim-homeobox and Lim-only proteins in diverse developmental systems including cardiogenesis, neurogenesis, and hematopoiesis. In mammalian erythroid cells, LDB1 dimerization supports long-range connections between enhancers and genes involved in erythropoiesis, including the β-globin genes. Single-stranded DNA binding proteins (SSBPs) interact specifically with the LDB/Chip conserved domain (LCCD) of LDB proteins and stabilize LDBs by preventing their proteasomal degradation, thus promoting their functions in gene regulation. The structural basis for LDB1 self-interaction and interface with SSBPs is unclear. Here we report a crystal structure of the human LDB1/SSBP2 complex at 2.8-Å resolution. The LDB1 dimerization domain (DD) contains an N-terminal nuclear transport factor 2 (NTF2)-like subdomain and a small helix 4-helix 5 subdomain, which together form the LDB1 dimerization interface. The 2 LCCDs in the symmetric LDB1 dimer flank the core DDs, with each LCCD forming extensive interactions with an SSBP2 dimer. The conserved linker between LDB1 DD and LCCD covers a potential ligand-binding pocket of the LDB1 NTF2-like subdomain and may serve as a regulatory site for LDB1 structure and function. Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.
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10
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Wang F, Bach I. Rlim/Rnf12, Rex1, and X Chromosome Inactivation. Front Cell Dev Biol 2019; 7:258. [PMID: 31737626 PMCID: PMC6834644 DOI: 10.3389/fcell.2019.00258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/16/2019] [Indexed: 12/28/2022] Open
Abstract
RLIM/Rnf12 is an E3 ubiquitin ligase that has originally been identified as a transcriptional cofactor associated with LIM domain transcription factors. Indeed, this protein modulates transcriptional activities and multiprotein complexes recruited by several classes of transcription factors thereby enhancing or repressing transcription. Around 10 years ago, RLIM/Rnf12 has been identified as a major regulator for the process of X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female mice and ESCs. However, the precise roles of RLIM during XCI have been controversial. Here, we discuss the cellular and developmental functions of RLIM as an E3 ubiquitin ligase and its roles during XCI in conjunction with its target protein Rex1.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
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11
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Frints SGM, Ozanturk A, Rodríguez Criado G, Grasshoff U, de Hoon B, Field M, Manouvrier-Hanu S, E Hickey S, Kammoun M, Gripp KW, Bauer C, Schroeder C, Toutain A, Mihalic Mosher T, Kelly BJ, White P, Dufke A, Rentmeester E, Moon S, Koboldt DC, van Roozendaal KEP, Hu H, Haas SA, Ropers HH, Murray L, Haan E, Shaw M, Carroll R, Friend K, Liebelt J, Hobson L, De Rademaeker M, Geraedts J, Fryns JP, Vermeesch J, Raynaud M, Riess O, Gribnau J, Katsanis N, Devriendt K, Bauer P, Gecz J, Golzio C, Gontan C, Kalscheuer VM. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol Psychiatry 2019; 24:1748-1768. [PMID: 29728705 DOI: 10.1038/s41380-018-0065-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022]
Abstract
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.
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Affiliation(s)
- Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands. .,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands.
| | - Aysegul Ozanturk
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands.,Department of Gynaecology and Obstetrics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Michael Field
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Sylvie Manouvrier-Hanu
- Clinique de Génétique médicale Guy Fontaine, Centre de référence maladies rares Anomalies du développement Hôpital Jeanne de Flandre, Lille, 59000, France.,EA 7364 RADEME Maladies Rares du Développement et du Métabolisme, Faculté de Médecine, Université de Lille, Lille, 59000, France
| | - Scott E Hickey
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Molka Kammoun
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Karen W Gripp
- Alfred I. duPont Hospital for Children Nemours, Wilmington, DE, 19803, USA
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Theresa Mihalic Mosher
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Sungjin Moon
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Daniel C Koboldt
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Lucinda Murray
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Eric Haan
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Lynne Hobson
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Marjan De Rademaeker
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, 1090, Brussels, Belgium
| | - Joep Geraedts
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Jean-Pierre Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Martine Raynaud
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Christelle Golzio
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67400, Illkirch, France
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
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12
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Wang F, Zhao K, Yu S, Xu A, Han W, Mei Y. RNF12 catalyzes BRF1 ubiquitination and regulates RNA polymerase III-dependent transcription. J Biol Chem 2018; 294:130-141. [PMID: 30413534 DOI: 10.1074/jbc.ra118.004524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Indexed: 01/07/2023] Open
Abstract
RNA polymerase III (Pol III) is responsible for the production of small noncoding RNA species, including tRNAs and 5S rRNA. Pol III-dependent transcription is generally enhanced in transformed cells and tumors, but the underlying mechanisms remain not well-understood. It has been demonstrated that the BRF1 subunit of TFIIIB is essential for the accurate initiation of Pol III-dependent transcription. However, it is not known whether BRF1 undergoes ubiquitin modification and whether BRF1 ubiquitination regulates Pol III-dependent transcription. Here, we show that RNF12, a RING domain-containing ubiquitin E3 ligase, physically interacts with BRF1. Via direct interaction, RNF12 catalyzes Lys27- and Lys33-linked polyubiquitination of BRF1. Furthermore, RNF12 is able to negatively regulate Pol III-dependent transcription and cell proliferation via BRF1. These findings uncover a novel mechanism for the regulation of BRF1 and reveal RNF12 as an important regulator of Pol III-dependent transcription.
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Affiliation(s)
- Fang Wang
- Anhui Province Key Laboratory of Medical Physics and Technology/Center of Medical Physics and Technology, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, Anhui, China; Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Kailiang Zhao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Sixiang Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - An Xu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Wei Han
- Anhui Province Key Laboratory of Medical Physics and Technology/Center of Medical Physics and Technology, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
| | - Yide Mei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230026, Anhui, China.
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13
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Associations of canopy leaf traits with SNP markers in durum wheat (Triticum turgidum L. durum (Desf.)). PLoS One 2018; 13:e0206226. [PMID: 30352102 PMCID: PMC6198983 DOI: 10.1371/journal.pone.0206226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/09/2018] [Indexed: 11/23/2022] Open
Abstract
The canopy leaves including the top three, i.e., the flag, the 2nd and 3rd from the top, are important for photosynthesis and grain yield of wheat. Molecular markers associated with traits of these leaves should be helpful for the high-yielding breeding. In this study, 1366 single nucleotide polymorphisms (SNP) markers covering the whole genome of durum wheat were used to genotype 150 cultivars collected from 46 countries and regions in the world. Leaf length, leaf width and chlorophyll content of the top three leaves were measured, respectively, in three consecutive years. Association analyses were performed on the leaf traits and SNP markers. A total of 120 SNP marker associations were detected on 13 of the 14 chromosomes. Among these markers, 83 were associated with the canopy leaf traits, 10 with 1000-grain weight, and 29 with kernel number per spike. This study is helpful for better understanding the potential and genetic basis of functional leaves, and facilitates pyramiding of the favorable alleles using marker assisted selection for ideal plant-type and high photosynthesis efficiency in durum wheat breeding.
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14
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LDB2 inhibits proliferation and migration in liver cancer cells by abrogating HEY1 expression. Oncotarget 2017; 8:94440-94449. [PMID: 29212240 PMCID: PMC5706886 DOI: 10.18632/oncotarget.21772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/20/2017] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) was one of the most common cancers around the world, has very low 5-year survival rate. However, the mechanism of HCC occurrence and development is largely unknown. LDB2 belongs to the LIM-domain binding family and functions as an adaptor for transcriptional regulation. Here we found that LDB2 is downregulated in HCC samples. LDB2 has the ability to inhibit proliferation and migration of hepatocarcinoma cells. We found that the proliferation and migration abilities in HCC sample cells were impaired after LDB2 overexpression and vice versa. In mechanism, we found that LDB2 can recruit BRD7 to HEY1 promoter and then block its expression. HEY1 whose expression is upregulated in HCC acts as an oncogene. In brief, our research reveals a new regulatory mechanism for hepatocarcinoma cell proliferation and migration.
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15
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RLIM suppresses hepatocellular carcinogenesis by up-regulating p15 and p21. Oncotarget 2017; 8:83075-83087. [PMID: 29137325 PMCID: PMC5669951 DOI: 10.18632/oncotarget.20904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 01/22/2023] Open
Abstract
Hepatocellular carcinogenesis results from dysregulation of oncogenes and tumor suppressors that influence cellular proliferation, differentiation and apoptosis. p15 and p21 are cyclin-dependent kinase inhibitors, which arrest cell proliferation and serve as critical tumor suppressors. Here we report that the E3 ubiquitin ligase RLIM expression is downregulated in hepatocellular carcinoma patients, and correlated with p15 and p21 expression in clinical progression. In addition, we showed that RLIM overexpression suppresses the cell growth and arrests cell cycle progression of hepatocellular carcinoma. Mechanistically, we found that RLIM directly binds to MIZ1, disrupting the interaction between c-MYC and MIZ1, and enhancing p15 and p21 transcription. Our results demonstrate that RLIM is an important suppressor in hepatocellular carcinogenesis.
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16
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Liu JL, Kaddour N, Chowdhury S, Li Q, Gao ZH. Role of CCN5 (WNT1 inducible signaling pathway protein 2) in pancreatic islets. J Diabetes 2017; 9:462-474. [PMID: 27863006 DOI: 10.1111/1753-0407.12507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 12/15/2022] Open
Abstract
In search of direct targets of insulin-like growth factor (IGF)-1 action, we discovered CCN5 (WNT1 inducible signaling pathway protein 2 [WISP2]) as a novel protein expressed in pancreatic β-cells. As a member of the "CCN" ( C ysteine-rich angiogenic inducer 61 [Cyr61], C onnective tissue growth factor [CTGF in humans], and N ephroblastoma overexpressed [Nov; in chickens]) family, the expression of CCN5/WISP2 is stimulated by IGF-1 together with Wnt signaling. When overexpressed in insulinoma cells, CCN5 promotes cell proliferation and cell survival against streptozotocin-induced cell death. The cell proliferation effect seems to be caused by AKT phosphorylation and increased cyclin D1 levels. These properties resemble those of CCN2/CTGF, another isoform of the CCN family, although CCN5 is the only one within the family of six proteins that lacks the C-terminal repeat. Treatment of primary mouse islets with recombinant CCN5 protein produced similar effects to those of gene transfection, indicating that either as a matricellular protein or a secreted growth factor, CCN5 stimulates β-cell proliferation and regeneration in a paracrine fashion. This review also discusses the regulation of CCN5/WISP2 by estrogen and its involvement in angiogenesis and tumorigenesis.
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Affiliation(s)
- Jun-Li Liu
- Fraser Laboratories, Department of Medicine, The Research Institute of McGill University Health Centre, Montreal, Canada
| | - Nancy Kaddour
- Fraser Laboratories, Department of Medicine, The Research Institute of McGill University Health Centre, Montreal, Canada
| | - Subrata Chowdhury
- Fraser Laboratories, Department of Medicine, The Research Institute of McGill University Health Centre, Montreal, Canada
| | - Qing Li
- Fraser Laboratories, Department of Medicine, The Research Institute of McGill University Health Centre, Montreal, Canada
| | - Zu-Hua Gao
- Department of Pathology, The Research Institute of McGill University Health Centre, Montreal, Canada
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17
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HRG/HER2/HER3 signaling promotes AhR-mediated Memo-1 expression and migration in colorectal cancer. Oncogene 2016; 36:2394-2404. [DOI: 10.1038/onc.2016.390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 12/23/2022]
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18
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Gao R, Wang L, Cai H, Zhu J, Yu L. E3 Ubiquitin Ligase RLIM Negatively Regulates c-Myc Transcriptional Activity and Restrains Cell Proliferation. PLoS One 2016; 11:e0164086. [PMID: 27684546 PMCID: PMC5042457 DOI: 10.1371/journal.pone.0164086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
RNF12/RLIM is a RING domain-containing E3 ubiquitin ligase whose function has only begun to be elucidated recently. Although RLIM was reported to play important roles in some biological processes such as imprinted X-chromosome inactivation and regulation of TGF-β pathway etc., other functions of RLIM are largely unknown. Here, we identified RLIM as a novel E3 ubiquitin ligase for c-Myc, one of the most frequently deregulated oncoproteins in human cancers. RLIM associates with c-Myc in vivo and in vitro independently of the E3 ligase activity of RLIM. Moreover, RLIM promotes the polyubiquitination of c-Myc protein independently of Ser62 and Thr58 phosphorylation of c-Myc. However, RLIM-mediated ubiquitination does not affect c-Myc stability. Instead, RLIM inhibits the transcriptional activity of c-Myc through which RLIM restrains cell proliferation. Our results suggest that RLIM may function as a tumor suppressor by controlling the activity of c-Myc oncoprotein.
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Affiliation(s)
- Rui Gao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
- * E-mail:
| | - Lan Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine Ministry of Education, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Hao Cai
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Jingjing Zhu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
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Klein RH, Stephens DN, Ho H, Chen JK, Salmans ML, Wang W, Yu Z, Andersen B. Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function. J Biol Chem 2016; 291:13271-85. [PMID: 27129775 DOI: 10.1074/jbc.m115.709386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 11/06/2022] Open
Abstract
Cofactors of LIM domain proteins, CLIM1 and CLIM2, are widely expressed transcriptional cofactors that are recruited to gene regulatory regions by DNA-binding proteins, including LIM domain transcription factors. In the cornea, epithelium-specific expression of a dominant negative (DN) CLIM under the keratin 14 (K14) promoter causes blistering, wounding, inflammation, epithelial hyperplasia, and neovascularization followed by epithelial thinning and subsequent epidermal-like differentiation of the corneal epithelium. The defects in corneal epithelial differentiation and cell fate determination suggest that CLIM may regulate corneal progenitor cells and the transition to differentiation. Consistent with this notion, the K14-DN-Clim corneal epithelium first exhibits increased proliferation followed by fewer progenitor cells with decreased proliferative potential. In vivo ChIP-sequencing experiments with corneal epithelium show that CLIM binds to and regulates numerous genes involved in cell adhesion and proliferation, including limbally enriched genes. Intriguingly, CLIM associates primarily with non-LIM homeodomain motifs in corneal epithelial cells, including that of estrogen receptor α. Among CLIM targets is the noncoding RNA H19 whose deregulation is associated with Silver-Russell and Beckwith-Wiedemann syndromes. We demonstrate here that H19 negatively regulates corneal epithelial proliferation. In addition to cell cycle regulators, H19 affects the expression of multiple cell adhesion genes. CLIM interacts with estrogen receptor α at the H19 locus, potentially explaining the higher expression of H19 in female than male corneas. Together, our results demonstrate an important role for CLIM in regulating the proliferative potential of corneal epithelial progenitors and identify CLIM downstream target H19 as a regulator of corneal epithelial proliferation and adhesion.
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Affiliation(s)
- Rachel Herndon Klein
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | | | | | | | - Michael L Salmans
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | - Winnie Wang
- From the Departments of Biological Chemistry and
| | - Zhengquan Yu
- From the Departments of Biological Chemistry and State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bogi Andersen
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and Medicine and
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20
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Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics 2016; 17:263. [PMID: 27029813 PMCID: PMC4815211 DOI: 10.1186/s12864-016-2542-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation. RESULTS The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS). CONCLUSION The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.
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Affiliation(s)
- Matt R Paul
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd, Philadelphia, PA, USA.
| | - Nicholas P Levitt
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - David E Moore
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - Patricia M Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Robert C Wilson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Chadrick E Denlinger
- Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Surgery, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Dennis K Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
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21
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Helzer KT, Hooper C, Miyamoto S, Alarid ET. Ubiquitylation of nuclear receptors: new linkages and therapeutic implications. J Mol Endocrinol 2015; 54:R151-67. [PMID: 25943391 PMCID: PMC4457637 DOI: 10.1530/jme-14-0308] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 12/25/2022]
Abstract
The nuclear receptor (NR) superfamily is a group of transcriptional regulators that control multiple aspects of both physiology and pathology and are broadly recognized as viable therapeutic targets. While receptor-modulating drugs have been successful in many cases, the discovery of new drug targets is still an active area of research, because resistance to NR-targeting therapies remains a significant clinical challenge. Many successful targeted therapies have harnessed the control of receptor activity by targeting events within the NR signaling pathway. In this review, we explore the role of NR ubiquitylation and discuss how the expanding roles of ubiquitin could be leveraged to identify additional entry points to control receptor function for future therapeutic development.
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Affiliation(s)
- Kyle T Helzer
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Christopher Hooper
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Shigeki Miyamoto
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Elaine T Alarid
- McArdle Laboratory for Cancer ResearchDepartment of Oncology, 6151 Wisconsin Institutes for Medical Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, USA
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22
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Sun Z, Prodduturi N, Sun SY, Thompson EA, Kocher JPA. Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling. Epigenomics 2015; 7:1099-110. [PMID: 26039248 DOI: 10.2217/epi.15.43] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM Abnormal inactivation or loss of inactivated X chromosome (Xi) is implicated in women's cancer. However, the underlying mechanisms and clinical relevance are little known. MATERIALS & METHODS High-throughput sequencing was conducted on breast cancer cell lines for copy number, RNA expression and 5'-methylcytosine in ChrX. The results were examined in primary breast tumors. RESULTS & CONCLUSION Breast cancer cells demonstrated reduced or total loss of hemimethylation. Most cell lines lost part or one of X chromosomes. Cell lines without ChrX loss were more active in gene expression. DNA methylation was corroborated with Xi control lincRNA XIST. Similar transcriptome and DNA methylation changes were observed in primary breast cancer datasets with clinical phenotype associations. Dramatic genomic and epigenomic changes in ChrX may be used for potential diagnostic or prognostic markers in breast cancer.
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Affiliation(s)
- Zhifu Sun
- Department of Health Sciences Research, Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Naresh Prodduturi
- Department of Health Sciences Research, Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Susan Y Sun
- Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - E Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jean-Pierre A Kocher
- Department of Health Sciences Research, Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA
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23
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Wragg JW, Durant S, McGettrick HM, Sample KM, Egginton S, Bicknell R. Shear stress regulated gene expression and angiogenesis in vascular endothelium. Microcirculation 2015; 21:290-300. [PMID: 24471792 DOI: 10.1111/micc.12119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/22/2014] [Indexed: 01/13/2023]
Abstract
The behavior of vascular EC is greatly altered in sites of pathological angiogenesis, such as a developing tumor or atherosclerotic plaque. Until recently it was thought that this was largely due to abnormal chemical signaling, i.e., endothelial cell chemo transduction, at these sites. However, we now demonstrate that the shear stress intensity encountered by EC can have a profound impact on their gene expression and behavior. We review the growing body of evidence suggesting that mechanotransduction, too, is a major regulator of pathological angiogenesis. This fits with the evolving story of physiological angiogenesis, where a combination of metabolic and mechanical signaling is emerging as the probable mechanism by which tight feedback regulation of angiogenesis is achieved in vivo.
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Affiliation(s)
- Joseph W Wragg
- Angiogenesis Group, Centre for Cardiovascular Sciences, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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24
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Xue B, Huang W, Yuan X, Xu B, Lou Y, Zhou Q, Ran F, Ge Z, Li R, Cui J. YSY01A, a Novel Proteasome Inhibitor, Induces Cell Cycle Arrest on G2 Phase in MCF-7 Cells via ERα and PI3K/Akt Pathways. J Cancer 2015; 6:319-26. [PMID: 25767601 PMCID: PMC4349871 DOI: 10.7150/jca.10733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 11/15/2014] [Indexed: 11/05/2022] Open
Abstract
Given that the proteasome is essential for multiple cellular processes by degrading diverse regulatory proteins, inhibition of the proteasome has emerged as an attractive target for anti-cancer therapy. YSY01A is a novel small molecule compound targeting the proteasome. The compound was found to suppress viability of MCF-7 cells and cause limited cell membrane damage as determined by sulforhodamine B assay (SRB) and CytoTox 96(®) non-radioactive cytotoxicity assay. High-content screening (HCS) further shows that YSY01A treatment induces cell cycle arrest on G2 phase within 24 hrs. Label-free quantitative proteomics (LFQP), which allows extensive comparison of cellular responses following YSY01A treatment, suggests that various regulatory proteins including cell cycle associated proteins and PI3K/Akt pathway may be affected. Furthermore, YSY01A increases p-CDC-2, p-FOXO3a, p53, p21(Cip1) and p27(Kip1) but decreases p-Akt, p-ERα as confirmed by Western blotting. Therefore, YSY01A represents a potential therapeutic for breast cancer MCF-7 by inducing G2 phase arrest via ERα and PI3K/Akt pathways.
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Affiliation(s)
- Bingjie Xue
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Wei Huang
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Xia Yuan
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Bo Xu
- 2. Instrumental Analysis Center of State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Yaxin Lou
- 3. Lab of Proteomics Medical and Healthy Analytical Center, Peking University, Beijing, China
| | - Quan Zhou
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Fuxiang Ran
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
| | - Zemei Ge
- 4. Peking University School of Pharmaceutical Sciences Department of Medicinal Chemistry, Beijing, China
| | - Runtao Li
- 4. Peking University School of Pharmaceutical Sciences Department of Medicinal Chemistry, Beijing, China
| | - Jingrong Cui
- 1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100083, Beijing, China
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25
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Shchebet A, Karpiuk O, Kremmer E, Eick D, Johnsen SA. Phosphorylation by cyclin-dependent kinase-9 controls ubiquitin-conjugating enzyme-2A function. Cell Cycle 2014; 11:2122-7. [DOI: 10.4161/cc.20548] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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26
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Salmans ML, Yu Z, Watanabe K, Cam E, Sun P, Smyth P, Dai X, Andersen B. The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis. PLoS Genet 2014; 10:e1004520. [PMID: 25079073 PMCID: PMC4117441 DOI: 10.1371/journal.pgen.1004520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/03/2014] [Indexed: 12/20/2022] Open
Abstract
Mammary gland branching morphogenesis and ductal homeostasis relies on mammary stem cell function for the maintenance of basal and luminal cell compartments. The mechanisms of transcriptional regulation of the basal cell compartment are currently unknown. We explored these mechanisms in the basal cell compartment and identified the Co-factor of LIM domains (CLIM/LDB/NLI) as a transcriptional regulator that maintains these cells. Clims act within the basal cell compartment to promote branching morphogenesis by maintaining the number and proliferative potential of basal mammary epithelial stem cells. Clim2, in a complex with LMO4, supports mammary stem cells by directly targeting the Fgfr2 promoter in basal cells to increase its expression. Strikingly, Clims also coordinate basal-specific transcriptional programs to preserve luminal cell identity. These basal-derived cues inhibit epidermis-like differentiation of the luminal cell compartment and enhance the expression of luminal cell-specific oncogenes ErbB2 and ErbB3. Consistently, basal-expressed Clims promote the initiation and progression of breast cancer in the MMTV-PyMT tumor model, and the Clim-regulated branching morphogenesis gene network is a prognostic indicator of poor breast cancer outcome in humans. Recent advancements in mammary gland biology demonstrate conflicting models in maintenance of basal and luminal cell compartments by either unipotent or bipotent mammary stem cells. However, the molecular mechanisms underlying control of the basal cell compartment, including stem cells, remain poorly understood. Here we explore the currently unknown transcriptional mechanisms of basal stem cell (BSC) maintenance, in addition to addressing the role of the basal cell compartment in preserving luminal cell fate and promoting development of human breast tumors of luminal origin. We discover a novel function for the Co-factor of LIM domains (Clim) transcriptional regulator in promoting mammary gland branching morphogenesis and breast tumorigenesis through maintenance of the basal stem cell population. The transcriptional networks coordinated by Clims in basal mammary epithelial cells also preserve the identity of luminal epithelial cells, demonstrating a crosstalk between these two cellular compartments. Furthermore, we correlate developmental gene expression data with human breast cancer to investigate the role of developmental pathways during the initiation and progression of breast cancer. The gene regulatory networks identified during development, including those specifically coordinated by Clims, correlate with breast cancer patient outcome, suggesting these genes play an important role in the progression of breast cancer.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Carcinogenesis/genetics
- Cell Differentiation/genetics
- DNA-Binding Proteins/genetics
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- LIM Domain Proteins/genetics
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/pathology
- Neoplasms, Basal Cell/genetics
- Neoplasms, Basal Cell/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- Receptor, ErbB-2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Stem Cells/metabolism
- Stem Cells/pathology
- Transcription Factors/genetics
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Affiliation(s)
- Michael L. Salmans
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Zhengquan Yu
- State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, PR China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Eric Cam
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Peng Sun
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Padhraic Smyth
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, Irvine, California, United States of America
| | - Xing Dai
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Bogi Andersen
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Medicine, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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27
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Chen X, Shen J, Li X, Wang X, Long M, Lin F, Wei J, Yang L, Yang C, Dong K, Zhang H. Rlim, an E3 ubiquitin ligase, influences the stability of Stathmin protein in human osteosarcoma cells. Cell Signal 2014; 26:1532-8. [PMID: 24686088 DOI: 10.1016/j.cellsig.2014.03.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 12/21/2022]
Abstract
Stathmin is an oncoprotein and is expressed at high levels in a wide variety of human malignancies, which plays important roles in maintenance of malignant phenotypes. The regulation of Stathmin gene overexpression has been wildly explored, but the exact mechanism still needs to be elucidated. It is believed that regulation of an oncogene protein abundance through post-translational modifications is essential for maintenance of malignant phenotypes. Here we identified the Rlim, a Ring H2 zinc finger protein with intrinsic ubiquitin ligase activity, as a Stathmin-interacting protein that could increase Stathmin turnover through binding with this targeted protein and then induce its degradation by proteasome in a ubiquitin-dependent manner. Inhibition of endogenous Rlim expression by siRNA could increase the level of Stathmin protein, which further led to cell proliferation and cell cycle changes in human osteosarcoma cell lines. On the other hand, forced overexpression of Rlim could decrease the level of Stathmin protein. These results demonstrate that Rlim is involved in the negative regulation of Stathmin protein level through physical interaction and ubiquitin-mediated proteolysis. Hence, Rlim is a novel regulator of Stathmin protein in a ubiquitin-dependent manner, and represents a new pathway for malignant phenotype turnover by modulating the level of Stathmin protein in human osteosarcomas.
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Affiliation(s)
- Xi Chen
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jianjun Shen
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xingyu Li
- Department of Ophthalmology, Xi'an No. 4 Hospital, Xi'an, China
| | - Xi Wang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Min Long
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Lin
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Junxia Wei
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Longfei Yang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Chinglai Yang
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, USA
| | - Ke Dong
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
| | - Huizhong Zhang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
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28
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Jiao B, Taniguchi-Ishigaki N, Güngör C, Peters MA, Chen YW, Riethdorf S, Drung A, Ahronian LG, Shin J, Pagnis R, Pantel K, Tachibana T, Lewis BC, Johnsen SA, Bach I. Functional activity of RLIM/Rnf12 is regulated by phosphorylation-dependent nucleocytoplasmic shuttling. Mol Biol Cell 2013; 24:3085-96. [PMID: 23904271 PMCID: PMC3784382 DOI: 10.1091/mbc.e13-05-0239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In mice, the ubiquitin ligase RLIM/Rnf12 is a critical survival factor for mammary milk-producing alveolar cells, but little is known about how its activity is regulated. It is shown here that RLIM shuttles between the nucleus and cytoplasm in a phosphorylation-dependent manner, and shuttling is important for its alveolar survival function. The X-linked gene Rnf12 encodes the ubiquitin ligase really interesting new gene (RING) finger LIM domain–interacting protein (RLIM)/RING finger protein 12 (Rnf12), which serves as a major sex-specific epigenetic regulator of female mouse nurturing tissues. Early during embryogenesis, RLIM/Rnf12 expressed from the maternal allele is crucial for the development of extraembryonic trophoblast cells. In contrast, in mammary glands of pregnant and lactating adult females RLIM/Rnf12 expressed from the paternal allele functions as a critical survival factor for milk-producing alveolar cells. Although RLIM/Rnf12 is detected mostly in the nucleus, little is known about how and in which cellular compartment(s) RLIM/Rnf12 mediates its biological functions. Here we demonstrate that RLIM/Rnf12 protein shuttles between nucleus and cytoplasm and this is regulated by phosphorylation of serine S214 located within its nuclear localization sequence. We show that shuttling is important for RLIM to exert its biological functions, as alveolar cell survival activity is inhibited in cells expressing shuttling-deficient nuclear or cytoplasmic RLIM/Rnf12. Thus regulated nucleocytoplasmic shuttling of RLIM/Rnf12 coordinates cellular compartments during mammary alveolar cell survival.
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Affiliation(s)
- Baowei Jiao
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605-2324 Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605-2324 Centre for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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Role of the ubiquitin ligase E6AP/UBE3A in controlling levels of the synaptic protein Arc. Proc Natl Acad Sci U S A 2013; 110:8888-93. [PMID: 23671107 DOI: 10.1073/pnas.1302792110] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Inactivation of the ubiquitin ligase E6 associated protein (E6AP) encoded by the UBE3A gene has been associated with development of the Angelman syndrome. Recently, it was reported that in mice, loss of E6AP expression results in increased levels of the synaptic protein Arc and a concomitant impaired synaptic function, providing an explanation for some phenotypic features of Angelman syndrome patients. Accordingly, E6AP has been shown to negatively regulate activity-regulated cytoskeleton-associated protein (Arc) and it has been suggested that E6AP targets Arc for ubiquitination and degradation. In our study, we provide evidence that Arc is not a direct substrate for E6AP and binds only weakly to E6AP, if at all. Furthermore, we show that down-regulation of E6AP expression stimulates estradiol-induced transcription of the Arc gene. Thus, we propose that Arc protein levels are controlled by E6AP at the transcriptional rather than at the posttranslational level.
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miR-203 regulates cell proliferation through its influence on Hakai expression. PLoS One 2012; 7:e52568. [PMID: 23285092 PMCID: PMC3527564 DOI: 10.1371/journal.pone.0052568] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/20/2012] [Indexed: 01/08/2023] Open
Abstract
Gene expression is potently regulated through the action of microRNAs (miRNAs). Here, we present evidence of a miRNA regulating Hakai protein. Hakai was discovered as an E3 ubiquitin-ligase that mediates the posttranslational downregulation of E-cadherin, a major component of adherens junctions in epithelial cells and a potent tumour suppressor. Recent data have provided evidence that Hakai affects cell proliferation in an E-cadherin-independent manner, thus revealing a role for Hakai in the early stages of tumour progression. Furthermore, Hakai is highly up-regulated in human colon adenocarcinomas compared to normal tissues. However, the molecular mechanisms that regulate Hakai abundance are unknown. We identified two putative sites of miR-203 interaction on the Hakai mRNA, in its 3′-untranslated region (UTR). In several human carcinoma cell lines tested, overexpression of a miR-203 precursor (Pre-miR-203) reduced Hakai abundance, while inhibiting miR-203 by using an antisense RNA (Anti-miR-203) elevated Hakai levels. The repressive influence of miR-203 on the Hakai 3′-UTR was confirmed using heterologous reporter constructs. In keeping with Hakai's proliferative influence, Anti-miR-203 significantly increased cell number and BrdU incorporation, while Pre-miR-203 reduced these parameters. Importantly, the growth-promoting effects of anti-miR-203 required the presence of Hakai, because downregulation of Hakai by siRNA suppressed its proliferative action. Finally, in situ hybridization showed that miR-203 expression is attenuated in colon tumour tissues compared to normal colon tissues, suggesting that miR-203 could be a potential new prognostic marker and therapeutic target to explore in colon cancer. In conclusion, our findings reveal, for the first time, a post-transcriptional regulator of Hakai expression. Furthermore, by lowering Hakai abundance, miR-203 also reduces Hakai-regulated-cell division.
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Abstract
In order to metastasize, cancer cells must first detach from the primary tumor, migrate, invade through tissues, and attach to a second site. Hakai was discovered as an E3 ubiquitin-ligase that mediates the posttranslational downregulation of E-cadherin, a major component of adherens junctions in epithelial cells that is characterized as a potent tumor suppressor and is modulated during various processes including epithelial–mesenchymal transition. Recent data have provided evidences for novel biological functional role of Hakai during tumor progression and other diseases. Here, we will review the knowledge that has been accumulated since Hakai discovery 10 years ago and its implication in human cancer disease. We will highlight the different signaling pathways leading to the influence on Hakai and suggest its potential usefulness as therapeutic target for cancer.
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Bach I. Releasing the break on X chromosome inactivation: Rnf12/RLIM targets REX1 for degradation. Cell Res 2012; 22:1524-6. [PMID: 22785560 DOI: 10.1038/cr.2012.98] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
One of the two X chromosomes in cells of female mammals is transcriptionally silenced in a process known as X chromosome inactivation (XCI). Initiation of XCI is regulated by the ubiquitin ligase Rnf12/RLIM, but the mechanisms by which Rnf12/RLIM mediates this process has been a mystery. A recent study by Gontan et al. shows that Rnf12/RLIM targets REX1, an inhibitor of XCI, for proteasomal degradation, providing an answer to this question.
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Affiliation(s)
- Ingolf Bach
- Program in Gene Function & Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, Shin J, Lu S, Byron M, Kalantry S, Mercurio AM, Lawrence JB, Hoffmann A, Bach I. Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell 2012; 149:630-41. [PMID: 22541433 DOI: 10.1016/j.cell.2012.02.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 12/12/2011] [Accepted: 02/21/2012] [Indexed: 11/18/2022]
Abstract
In female mouse embryos, somatic cells undergo a random form of X chromosome inactivation (XCI), whereas extraembryonic trophoblast cells in the placenta undergo imprinted XCI, silencing exclusively the paternal X chromosome. Initiation of imprinted XCI requires a functional maternal allele of the X-linked gene Rnf12, which encodes the ubiquitin ligase Rnf12/RLIM. We find that knockout (KO) of Rnf12 in female mammary glands inhibits alveolar differentiation and milk production upon pregnancy, with alveolar cells that lack RLIM undergoing apoptosis as they begin to differentiate. Genetic analyses demonstrate that these functions are mediated primarily by the paternal Rnf12 allele due to nonrandom maternal XCI in mammary epithelial cells. These results identify paternal Rnf12/RLIM as a critical survival factor for milk-producing alveolar cells and, together with population models, reveal implications of transgenerational epigenetic inheritance.
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Affiliation(s)
- Baowei Jiao
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
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A regulatory potential of the Xist gene promoter in vole M. rossiaemeridionalis. PLoS One 2012; 7:e33994. [PMID: 22606223 PMCID: PMC3350511 DOI: 10.1371/journal.pone.0033994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 02/24/2012] [Indexed: 12/24/2022] Open
Abstract
X chromosome inactivation takes place in the early development of female mammals and depends on the Xist gene expression. The mechanisms of Xist expression regulation have not been well understood so far. In this work, we compared Xist promoter region of vole Microtus rossiaemeridionalis and other mammalian species. We observed three conserved regions which were characterized by computational analysis, DNaseI in vitro footprinting, and reporter construct assay. Regulatory factors potentially involved in Xist activation and repression in voles were determined. The role of CpG methylation in vole Xist expression regulation was established. A CTCF binding site was found in the 5' flanking region of the Xist promoter on the active X chromosome in both males and females. We suggest that CTCF acts as an insulator which defines an inactive Xist domain on the active X chromosome in voles.
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Zhang L, Huang H, Zhou F, Schimmel J, Pardo CG, Zhang T, Barakat TS, Sheppard KA, Mickanin C, Porter JA, Vertegaal ACO, van Dam H, Gribnau J, Lu CX, ten Dijke P. RNF12 controls embryonic stem cell fate and morphogenesis in zebrafish embryos by targeting Smad7 for degradation. Mol Cell 2012; 46:650-61. [PMID: 22560923 DOI: 10.1016/j.molcel.2012.04.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 12/12/2011] [Accepted: 04/02/2012] [Indexed: 01/10/2023]
Abstract
TGF-β members are of key importance during embryogenesis and tissue homeostasis. Smad7 is a potent antagonist of TGF-β family/Smad-mediated responses, but the regulation of Smad7 activity is not well understood. We identified the RING domain-containing E3 ligase RNF12 as a critical component of TGF-β signaling. Depletion of RNF12 dramatically reduced TGF-β/Smad-induced effects in mammalian cells, whereas ectopic expression of RNF12 strongly enhanced these responses. RNF12 specifically binds to Smad7 and induces its polyubiquitination and degradation. Smad7 levels were increased in RNF12-deficient mouse embryonic stem cells, resulting in mitigation of both BMP-mediated repression of neural induction and activin-induced anterior mesoderm formation. RNF12 also antagonized Smad7 during Nodal-dependent and BMP-dependent signaling and morphogenic events in early zebrafish embryos. The gastrulation defects induced by ectopic and depleted Smad7 were rescued in part by RNF12 gain and loss of function, respectively. These findings demonstrate that RNF12 plays a critical role in TGF-β family signaling.
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Affiliation(s)
- Long Zhang
- Department of Molecular Cell Biology and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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36
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Abstract
Telomeres are coated by shelterin, a six-subunit complex that is required for protection and replication of chromosome ends. The central subunit TIN2, with binding sites to three subunits (TRF1, TRF2, and TPP1), is essential for stability and function of the complex. Here we show that TIN2 stability is regulated by the E3 ligase Siah2. We demonstrate that TIN2 binds to Siah2 and is ubiquitylated in vivo. We show using purified proteins that Siah2 acts as an E3 ligase to directly ubiquitylate TIN2 in vitro. Depletion of Siah2 led to stabilization of TIN2 protein, indicating that Siah2 regulates TIN2 protein levels in vivo. Overexpression of Siah2 in human cells led to loss of TIN2 at telomeres that was dependent on the presence of the catalytic RING domain of Siah2. In contrast to RNAi-mediated depletion of TIN2 that led to loss of TRF1 and TRF2 at telomeres, Siah2-mediated depletion of TIN2 allowed TRF1 and TRF2 to remain on telomeres, indicating a different fate for shelterin subunits when TIN2 is depleted posttranslationally. TPP1 was lost from telomeres, although its protein level was not reduced. We speculate that Siah2-mediated removal of TIN2 may allow dynamic remodeling of the shelterin complex and its associated factors during the cell cycle.
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Huang Y, Yang Y, Gao R, Yang X, Yan X, Wang C, Jiang S, Yu L. RLIM interacts with Smurf2 and promotes TGF-β induced U2OS cell migration. Biochem Biophys Res Commun 2011; 414:181-5. [PMID: 21945933 DOI: 10.1016/j.bbrc.2011.09.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
TGF-β (transforming growth factor-β), a pleiotropic cytokine that regulates diverse cellular processes, has been suggested to play critical roles in cell proliferation, migration, and carcinogenesis. Here we found a novel E3 ubiquitin ligase RLIM which can directly bind to Smurf2, enhancing TGF-β responsiveness in osteosarcoma U2OS cells. We constructed a U2OS cell line stably over-expressing RLIM and demonstrated that RLIM promoted TGF-β-driven migration of U2OS cells as tested by wound healing assay. Our results indicated that RLIM is an important positive regulator in TGF-β signaling pathway and cell migration.
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Affiliation(s)
- Yongsheng Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
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38
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Prenzel T, Begus-Nahrmann Y, Kramer F, Hennion M, Hsu C, Gorsler T, Hintermair C, Eick D, Kremmer E, Simons M, Beissbarth T, Johnsen SA. Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer Res 2011; 71:5739-53. [PMID: 21862633 DOI: 10.1158/0008-5472.can-11-1896] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The estrogen receptor-α (ERα) determines the phenotype of breast cancers where it serves as a positive prognostic indicator. ERα is a well-established target for breast cancer therapy, but strategies to target its function remain of interest to address therapeutic resistance and further improve treatment. Recent findings indicate that proteasome inhibition can regulate estrogen-induced transcription, but how ERα function might be regulated was uncertain. In this study, we investigated the transcriptome-wide effects of the proteasome inhibitor bortezomib on estrogen-regulated transcription in MCF7 human breast cancer cells and showed that bortezomib caused a specific global decrease in estrogen-induced gene expression. This effect was specific because gene expression induced by the glucocorticoid receptor was unaffected by bortezomib. Surprisingly, we observed no changes in ERα recruitment or assembly of its transcriptional activation complex on ERα target genes. Instead, we found that proteasome inhibition caused a global decrease in histone H2B monoubiquitination (H2Bub1), leading to transcriptional elongation defects on estrogen target genes and to decreased chromatin dynamics overall. In confirming the functional significance of this link, we showed that RNA interference-mediated knockdown of the H2B ubiquitin ligase RNF40 decreased ERα-induced gene transcription. Surprisingly, RNF40 knockdown also supported estrogen-independent cell proliferation and activation of cell survival signaling pathways. Most importantly, we found that H2Bub1 levels decrease during tumor progression. H2Bub1 was abundant in normal mammary epithelium and benign breast tumors but absent in most malignant and metastatic breast cancers. Taken together, our findings show how ERα activity is blunted by bortezomib treatment as a result of reducing the downstream ubiquitin-dependent function of H2Bub1. In supporting a tumor suppressor role for H2Bub1 in breast cancer, our findings offer a rational basis to pursue H2Bub1-based therapies for future management of breast cancer.
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Affiliation(s)
- Tanja Prenzel
- Department of Molecular Oncology, Göttingen Center for Molecular Biosciences, Department of Medical Statistics, University Medical Center Göttingen, Germany
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Shin J, Bossenz M, Chung Y, Ma H, Byron M, Taniguchi-Ishigaki N, Zhu X, Jiao B, Hall LL, Green MR, Jones SN, Hermans-Borgmeyer I, Lawrence JB, Bach I. Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice. Nature 2010; 467:977-81. [PMID: 20962847 PMCID: PMC2967734 DOI: 10.1038/nature09457] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 08/26/2010] [Indexed: 11/09/2022]
Abstract
Two forms of XCI ensure the selective silencing of female sex chromosomes during mouse embryogenesis. Imprinted XCI begins with the detection of Xist RNA expression on the paternal X chromosome (Xp) around the four cell stage of embryonic development. In the embryonic tissues of the inner cell mass (ICM), a random form of XCI occurs in blastocysts which inactivates either the Xp or the maternal X chromosome (Xm) 1,2. Both forms of XCI require the non-coding Xist RNA which coats the inactive X chromosome (Xi) from which it is expressed. Xist plays crucial functions for the silencing of X-linked genes including Rnf123,4 encoding the ubiquitin ligase RLIM. Targeting a conditional knockout (KO) of Rnf12 to oocytes where RLIM accumulates to high levels, we find that the maternal transmission of the mutant X chromosome (Δm) leads to embryonic lethality due to defective imprinted XCI. We show that in Δm female embryos the initial formation of Xist clouds and Xp silencing is inhibited. In contrast, ES cells lacking RLIM are able to form Xist clouds and silence at least some X-linked genes during random XCI. These results assign crucial roles to the maternal deposit of Rnf12/RLIM for the initiation of imprinted XCI.
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Affiliation(s)
- Jongdae Shin
- Program in Gene Function and Expression, University of Massachusetts Medical School (UMMS), Worcester, Massachusetts 01605, USA
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40
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Teufel A, Maass T, Strand S, Kanzler S, Galante T, Becker K, Strand D, Biesterfeld S, Westphal H, Galle PR. Liver-specific Ldb1 deletion results in enhanced liver cancer development. J Hepatol 2010; 53:1078-84. [PMID: 20828852 PMCID: PMC5903435 DOI: 10.1016/j.jhep.2010.05.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 05/23/2010] [Accepted: 05/26/2010] [Indexed: 01/15/2023]
Abstract
BACKGROUND & AIMS LIM-domain-binding (Ldb) proteins have been demonstrated to be essential not only to key embryonic developmental processes but also to carcinogenesis. We have previously demonstrated Ldb1 to be of high biological and developmental relevance, as a targeted deletion of the Ldb1 gene in mice results in an embryonic lethal and pleiotropic phenotype. METHODS We have now established a liver-specific Ldb1 knock out to investigate the role of Ldb1 in carcinogenesis, in particular in hepatocellular carcinoma (HCC) development, in vivo. RESULTS These mice demonstrated a significantly enhanced growth of liver cancer by means of tumor size and number, advocating for an essential role of Ldb1 in HCC development. In addition, proliferation and resistance against apoptosis were increased. In order to identify the functional disturbances due to a lack of Ldb1, we performed a 15k mouse gene microarray expression analysis. We found the Myc oncogene to be regulated in the microarray analysis and were able to further confirm this regulation by demonstrating an over-expression of its downstream target Cyclin D1. Furthermore, we were able to demonstrate a down-regulation of the tumor suppressor p21. Finally, the liver stem cell marker EpCAM was also identified to be over expressed in Ldb1(-/-) knock out mice. CONCLUSIONS We have established a significant role of Ldb1 in cancer development. Furthermore, we provided evidence for a myc/cyclin D1, p21, and EpCAM-dependent signalling to be key downstream regulators of this novel concept in HCC development.
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Affiliation(s)
- Andreas Teufel
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany.
| | - Thorsten Maass
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Strand
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Stephan Kanzler
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Tiziana Galante
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Kevin Becker
- Gene Expression Unit, National Institute On Aging, National Institutes of Health, Bethesda, MD, USA
| | - Dennis Strand
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | | | - Heiner Westphal
- Laboratory of Mammalian Genes and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Peter R. Galle
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
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41
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Zhong Z, Ma H, Taniguchi-Ishigaki N, Nagarajan L, Becker CG, Bach I, Becker T. SSDP cofactors regulate neural patterning and differentiation of specific axonal projections. Dev Biol 2010; 349:213-24. [PMID: 21056553 DOI: 10.1016/j.ydbio.2010.10.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 10/25/2010] [Accepted: 10/29/2010] [Indexed: 10/18/2022]
Abstract
The developmental activity of LIM homeodomain transcription factors (LIM-HDs) is critically controlled by LIM domain-interacting cofactors of LIM-HDs (CLIM, also known as NLI or LDB). CLIM cofactors associate with single-stranded DNA binding proteins (SSDPs, also known as SSBPs) thereby recruiting SSDP1 and/or SSDP2 to LIM-HD/CLIM complexes. Although evidence has been presented that SSDPs are important for the activity of specific LIM-HD/CLIM complexes, the developmental roles of SSDPs are unclear. We show that SSDP1a and SSDP1b mRNAs are widely expressed early during zebrafish development with conspicuous expression of SSDP1b in sensory trigeminal and Rohon-Beard neurons. SSDP1 and CLIM immunoreactivity co-localize in these neuronal cell types and in other structures. Over-expression of the N-terminal portion of SSDP1 (N-SSDP1), which contains the CLIM-interaction domain, increases endogenous CLIM protein levels in vivo and impairs the formation of eyes and midbrain-hindbrain boundary. In addition, manipulation of SSDP1 via N-SSDP1 over-expression or SSDP1b knock down impairs trigeminal and Rohon-Beard sensory axon growth. We show that N-SSDP1 is able to partially rescue the inhibition of axon growth induced by a dominant-negative form of CLIM (DN-CLIM). These results reveal specific functions of SSDP in neural patterning and sensory axon growth, in part due to the stabilization of LIM-HD/CLIM complexes.
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Affiliation(s)
- Zhen Zhong
- Centre for Neuroregeneration, School of Biomedical Sciences, University of Edinburgh, The Chancellor's Building, Edinburgh EH16 4SB, UK
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42
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Russo JW, Castellot JJ. CCN5: biology and pathophysiology. J Cell Commun Signal 2010; 4:119-130. [PMID: 21063502 DOI: 10.1007/s12079-010-0098-73] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 08/19/2010] [Indexed: 05/26/2023] Open
Abstract
CCN5 is one of six proteins in the CCN family. This family of proteins has been shown to play important roles in many processes, including proliferation, migration, adhesion, extracellular matrix regulation, angiogenesis, tumorigenesis, fibrosis, and implantation. In this review, we focus on the biological and putative pathophysiological roles of CCN5. This intriguing protein is structurally unique among the CCN family members, and has a unique biological activity profile as well.
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43
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Abstract
CCN5 is one of six proteins in the CCN family. This family of proteins has been shown to play important roles in many processes, including proliferation, migration, adhesion, extracellular matrix regulation, angiogenesis, tumorigenesis, fibrosis, and implantation. In this review, we focus on the biological and putative pathophysiological roles of CCN5. This intriguing protein is structurally unique among the CCN family members, and has a unique biological activity profile as well.
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Abstract
Estrogen receptors play a key role in breast cancer development. One of the current therapeutic strategies for the treatment of estrogen receptor (ER)-α-positive breast cancers relies on the blockade of ERα transcriptional activity. In the present study, we characterized Hakai, originally characterized as an E-cadherin binding protein, as a strong blockade of ERα in breast cancer cells. We showed that Hakai inhibited the transcriptional activity of ERα by binding directly to ERα. The DNA-binding domain of ERα was found to be responsible for its interaction with Hakai. Hakai competed with ERα coactivators, such as steroid receptor coactivator-1 (SRC-1) and glucocoriticord receptor interacting protein-1 (GRIP-1), for the modulation of ERα transactivation, while its ubiquitin-ligase activity was not required. Further, overexpression of Hakai inhibited the proliferation and migration of breast cancer cells. Taken together, these results suggest that Hakai is a novel corepressor of ERα and may play a negative role in the development and progression of breast cancers.
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Affiliation(s)
- Eun-Yeung Gong
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, Korea
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45
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Regulation of LIM-domain-binding 1 protein expression by ubiquitination of Lys134. Biochem J 2010; 429:127-36. [PMID: 20423330 DOI: 10.1042/bj20091461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
LDB1 (LIM-domain-binding 1) is a cofactor that participates in formation of transcriptional regulatory complexes involving transcription factors containing LIM domains as well as other factors. The amount of LDB1 protein in cells has previously been shown to be modulated by RNF12 (RING finger protein 12). RNF12 is an E3 ubiquitin ligase that can target LDB1 for poly-ubiquitination and degradation via the proteasome. We find that in HEK (human embryonic kidney)-293 cells expression of RNF12 leads to mono-ubiquitination of LDB1 and increased levels of LDB1 protein. Mutagenesis studies identified Lys134 of LDB1 as the residue that is mono-ubiquitinated by RNF12. Mutation of Lys134 of LDB1 to arginine blocks the formation of mono-ubiquitinated LDB1 and surprisingly also increases LDB1 protein expression in HEK-293 cells. This leads to a model in which Lys134 of LDB1 can be either mono-ubiquitinated, leading to stabilization, or poly-ubiquitinated, leading to degradation by the proteasome pathway. We also find that ubiquitin-LDB1 fusion proteins are stabilized in HEK-293 cells, offering further evidence that mono-ubiquitination stabilizes LDB1 in these cells. Expression in Xenopus laevis embryos of an LDB1 protein in which Lys134 is replaced with arginine leads to enhanced expression of the mutant protein as compared with the wild-type protein. These findings provide evidence that modification of Lys134 can play a major role in regulating LDB1 expression.
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46
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Wang Y, Klumpp S, Amin HM, Liang H, Li J, Estrov Z, Zweidler-McKay P, Brandt SJ, Agulnick A, Nagarajan L. SSBP2 is an in vivo tumor suppressor and regulator of LDB1 stability. Oncogene 2010; 29:3044-53. [PMID: 20348955 PMCID: PMC2878399 DOI: 10.1038/onc.2010.78] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
SSBP proteins bind and stabilize transcriptional cofactor Lim Domain Binding protein1 (LDB1) from proteosomal degradation to promote tissue specific transcription through an evolutionarily conserved pathway. The human SSBP2 gene was isolated as a candidate tumor suppressor from a critical region of loss in chromosome 5q14.1. By gene targeting, we demonstrate increased predisposition to B cell lymphomas and carcinomas in Ssbp2−/− mice. Remarkably, loss of Ssbp2 causes increased LDB1 turnover in the thymus, a pathway exploited in Trp53−/−Ssbp2−/− mice to develop highly aggressive, immature thymic lymphomas. Using T cell differentiation as a model, we report a stage specific up regulation of Ssbp2 expression which in turn regulates LDB1 turnover under physiological conditions. Furthermore, transcript levels of pTα, a target of LDB1 containing complex, and a critical regulator T cell differentiation is reduced in Ssbp2−/− immature thymocytes. Our findings suggest disruption of the SSBP2 regulated pathways may be an infrequent but critical step in malignant transformation of multiple tissues.
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Affiliation(s)
- Y Wang
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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47
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Barakat TS, Gribnau J. X chromosome inactivation and embryonic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:132-54. [PMID: 21222204 DOI: 10.1007/978-1-4419-7037-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X chromosome inactivation (XCI) is a process required to equalize the dosage of X-encoded genes between female and male cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. The regulation of XCI involves factors that also play a crucial role in ES cell maintenance and differentiation and the XCI process therefore provides a beautiful paradigm to study ES cell biology. In this chapter we describe the important cis and trans acting regulators of XCI and introduce the models that have been postulated to explain initiation of XCI in female cells only. We also discuss the proteins involved in the establishment of the inactive X chromosome and describe the different chromatin modifications associated with the inactivation process. Finally, we describe the potential of mouse and human ES and induced pluripotent stem (iPS) cells as model systems to study the XCI process.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, University Medical Center, Room Ee 09-71, Erasmus MC, 3015 GE, Rotterdam, Netherlands
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48
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Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J. RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 2009; 139:999-1011. [PMID: 19945382 DOI: 10.1016/j.cell.2009.10.034] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 09/03/2009] [Accepted: 10/23/2009] [Indexed: 11/17/2022]
Abstract
In somatic cells of female placental mammals, one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes. Random X chromosome inactivation (XCI) in the embryo is a stochastic process, in which each X has an independent probability to initiate XCI, triggered by the nuclear concentration of one or more X-encoded XCI-activators. Here, we identify the E3 ubiquitin ligase RNF12 as an important XCI-activator. Additional copies of mouse Rnf12 or human RNF12 result in initiation of XCI in male mouse ES cells and on both X chromosomes in a substantial percentage of female mouse ES cells. This activity is dependent on an intact open reading frame of Rnf12 and correlates with the transgenic expression level of RNF12. Initiation of XCI is markedly reduced in differentiating female heterozygous Rnf12(+/-) ES cells. These findings provide evidence for a dose-dependent role of RNF12 in the XCI counting and initiation process.
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Affiliation(s)
- Iris Jonkers
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands
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Gong Y, Sweet W, Duh YJ, Greenfield L, Tarco E, Trivedi S, Symmans WF, Isola J, Sneige N. Performance of chromogenic in situ hybridization on testing HER2 Status in breast carcinomas with chromosome 17 polysomy and equivocal (2+) herceptest results: a study of two institutions using the conventional and new ASCO/CAP scoring criteria. Am J Clin Pathol 2009; 132:228-36. [PMID: 19605817 DOI: 10.1309/ajcp4m2vuzcldaln] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
This study specifically addressed the performance of chromogenic in situ hybridization (CISH) on HER2 testing in 66 breast carcinomas with chromosome 17 polysomy and 49 carcinomas with an equivocal HercepTest (DakoCytomation, Carpinteria, CA) score by comparing CISH with corresponding FISH results at 2 test sites and evaluating intersite agreement of CISH results. For tumors with chromosome 17 polysomy, when using the manufacturers' criteria, the concordance values between CISH and FISH at site A, site B, and intersite CISH agreement were 95.8%, 95.5%, and 93.5%, respectively; when using the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) criteria, the values were 100.0%, 100.0%, and 100.0%, respectively. For tumors with an equivocal HercepTest score, when using the manufacturers' criteria, the concordance values between the 2 methods at site A, site B, and intersite CISH agreement were 88.2%, 95.1%, and 91.1%, respectively; when using the ASCO/CAP criteria, the values were 96.7%, 97.3%, and 97.4%, respectively. These results indicate that CISH is reliable for testing these 2 types of tumors, especially when the ASCO/CAP criteria are used.
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CDK9 directs H2B monoubiquitination and controls replication-dependent histone mRNA 3'-end processing. EMBO Rep 2009; 10:894-900. [PMID: 19575011 DOI: 10.1038/embor.2009.108] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/09/2009] [Accepted: 04/20/2009] [Indexed: 11/08/2022] Open
Abstract
Post-translational histone modifications have essential roles in controlling nuclear processes; however, the specific mechanisms regulating these modifications and their combinatorial activities remain elusive. Cyclin-dependent kinase 9 (CDK9) regulates gene expression by phosphorylating transcriptional regulatory proteins, including the RNA polymerase II carboxy-terminal domain. Here, we show that CDK9 activity is essential for maintaining global and gene-associated levels of histone H2B monoubiquitination (H2Bub1). Furthermore, CDK9 activity and H2Bub1 help to maintain correct replication-dependent histone messenger RNA (mRNA) 3'-end processing. CDK9 knockdown consistently resulted in inefficient recognition of the correct mRNA 3'-end cleavage site and led to increased read-through of RNA polymerase II to an alternative downstream polyadenylation signal. Thus, CDK9 acts to integrate phosphorylation during transcription with chromatin modifications to control co-transcriptional histone mRNA processing.
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