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Peng X, Yang Y, Hou R, Zhang L, Shen C, Yang X, Luo Z, Yin Z, Cao Y. MTCH2 in Metabolic Diseases, Neurodegenerative Diseases, Cancers, Embryonic Development and Reproduction. Drug Des Devel Ther 2024; 18:2203-2213. [PMID: 38882047 PMCID: PMC11180440 DOI: 10.2147/dddt.s460448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Mitochondrial carrier homolog 2 (MTCH2) is a member of the solute carrier 25 family, located on the outer mitochondrial membrane. MTCH2 was first identified in 2000. The development in MTCH2 research is rapidly increasing. The most well-known role of MTCH2 is linking to the pro-apoptosis BID to facilitate mitochondrial apoptosis. Genetic variants in MTCH2 have been investigated for their association with metabolic and neurodegenerative diseases, however, no intervention or therapeutic suggestions were provided. Recent studies revealed the physiological and pathological function of MTCH2 in metabolic diseases, neurodegenerative diseases, cancers, embryonic development and reproduction via regulating mitochondrial apoptosis, metabolic shift between glycolysis and oxidative phosphorylation, mitochondrial fusion/fission, epithelial-mesenchymal transition, etc. This review endeavors to assess a total of 131 published articles to summarise the structure and physiological/pathological role of MTCH2, which has not previously been conducted. This review concludes that MTCH2 plays a crucial role in metabolic diseases, neurodegenerative diseases, cancers, embryonic development and reproduction, and the predominant molecular mechanism is regulation of mitochondrial function. This review gives a comprehensive state of current knowledgement on MTCH2, which will promote the therapeutic research of MTCH2.
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Affiliation(s)
- Xiaoqing Peng
- School of Pharmacy, Anhui Medical University, Hefei, People’s Republic of China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Hefei, Anhui, People’s Republic of China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- The Key National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, People’s Republic of China
| | - Yuanyuan Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- The Key National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, People’s Republic of China
| | - Ruirui Hou
- School of Pharmacy, Anhui Medical University, Hefei, People’s Republic of China
| | - Longbiao Zhang
- School of Pharmacy, Anhui Medical University, Hefei, People’s Republic of China
| | - Can Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Xiaoyan Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Zhigang Luo
- Department of Cardiology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Zongzhi Yin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- The Key National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, People’s Republic of China
| | - Yunxia Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- The Key National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, People’s Republic of China
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Deloulme JC, Leclercq M, Deschaux O, Flore G, Capellano L, Tocco C, Braz BY, Studer M, Lahrech H. Structural interhemispheric connectivity defects in mouse models of BBSOAS: Insights from high spatial resolution 3D white matter tractography. Neurobiol Dis 2024; 193:106455. [PMID: 38408685 DOI: 10.1016/j.nbd.2024.106455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024] Open
Abstract
White matter (WM) tract formation and axonal pathfinding are major processes in brain development allowing to establish precise connections between targeted structures. Disruptions in axon pathfinding and connectivity impairments will lead to neural circuitry abnormalities, often associated with various neurodevelopmental disorders (NDDs). Among several neuroimaging methodologies, Diffusion Tensor Imaging (DTI) is a magnetic resonance imaging (MRI) technique that has the advantage of visualizing in 3D the WM tractography of the whole brain non-invasively. DTI is particularly valuable in unpinning structural tract connectivity defects of neural networks in NDDs. In this study, we used 3D DTI to unveil brain-specific tract defects in two mouse models lacking the Nr2f1 gene, which mutations in patients have been proven to cause an emerging NDD, called Bosch-Boonstra-Schaaf Optic Atrophy (BBSOAS). We aimed to investigate the impact of the lack of cortical Nr2f1 function on WM morphometry and tract microstructure quantifications. We found in both mutant mice partial loss of fibers and severe misrouting of the two major cortical commissural tracts, the corpus callosum, and the anterior commissure, as well as the two major hippocampal efferent tracts, the post-commissural fornix, and the ventral hippocampal commissure. DTI tract malformations were supported by 2D histology, 3D fluorescent imaging, and behavioral analyses. We propose that these interhemispheric connectivity impairments are consistent in explaining some cognitive defects described in BBSOAS patients, particularly altered information processing between the two brain hemispheres. Finally, our results highlight 3DDTI as a relevant neuroimaging modality that can provide appropriate morphometric biomarkers for further diagnosis of BBSOAS patients.
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Affiliation(s)
| | | | - Olivier Deschaux
- University Côte d'Azur (UCA), CNRS, Inserm, Institute of Biology Valrose (iBV), Nice, France
| | - Gemma Flore
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Napoli, Italy
| | - Laetitia Capellano
- Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institute Neurosciences, 38000 Grenoble, France
| | - Chiara Tocco
- University Côte d'Azur (UCA), CNRS, Inserm, Institute of Biology Valrose (iBV), Nice, France
| | - Barbara Yael Braz
- Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institute Neurosciences, 38000 Grenoble, France
| | - Michèle Studer
- University Côte d'Azur (UCA), CNRS, Inserm, Institute of Biology Valrose (iBV), Nice, France.
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3
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Yasir M, Park J, Chun W. EWS/FLI1 Characterization, Activation, Repression, Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Int J Mol Sci 2023; 24:15173. [PMID: 37894854 PMCID: PMC10607184 DOI: 10.3390/ijms242015173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Despite their clonal origins, tumors eventually develop into complex communities made up of phenotypically different cell subpopulations, according to mounting evidence. Tumor cell-intrinsic programming and signals from geographically and temporally changing microenvironments both contribute to this variability. Furthermore, the mutational load is typically lacking in childhood malignancies of adult cancers, and they still exhibit high cellular heterogeneity levels largely mediated by epigenetic mechanisms. Ewing sarcomas represent highly aggressive malignancies affecting both bone and soft tissue, primarily afflicting adolescents. Unfortunately, the outlook for patients facing relapsed or metastatic disease is grim. These tumors are primarily fueled by a distinctive fusion event involving an FET protein and an ETS family transcription factor, with the most prevalent fusion being EWS/FLI1. Despite originating from a common driver mutation, Ewing sarcoma cells display significant variations in transcriptional activity, both within and among tumors. Recent research has pinpointed distinct fusion protein activities as a principal source of this heterogeneity, resulting in markedly diverse cellular phenotypes. In this review, we aim to characterize the role of the EWS/FLI fusion protein in Ewing sarcoma by exploring its general mechanism of activation and elucidating its implications for tumor heterogeneity. Additionally, we delve into potential therapeutic opportunities to target this aberrant fusion protein in the context of Ewing sarcoma treatment.
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Affiliation(s)
| | | | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.)
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Nakadai T, Shimada M, Ito K, Cevher MA, Chu CS, Kumegawa K, Maruyama R, Malik S, Roeder RG. Two target gene activation pathways for orphan ERR nuclear receptors. Cell Res 2023; 33:165-183. [PMID: 36646760 PMCID: PMC9892517 DOI: 10.1038/s41422-022-00774-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/02/2022] [Indexed: 01/18/2023] Open
Abstract
Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
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Affiliation(s)
- Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Murat Alper Cevher
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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Fang Y, Xu Y, Liao W, Ji T, Yu L, Li L, Pan M, Yang D. Multiomics analyses and machine learning of nuclear receptor coactivator 6 reveal its essential role in hepatocellular carcinoma. Cancer Sci 2022; 114:75-90. [PMID: 36086920 PMCID: PMC9807532 DOI: 10.1111/cas.15577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 01/07/2023] Open
Abstract
Nuclear receptor coactivator 6 (NCOA6), a coactivator of numerous nuclear receptors and transcription factors, regulates multiple critical cellular functions. Nuclear receptor coactivator 6 is dysregulated in various cancers, including hepatocellular carcinoma (HCC); however, its role remains largely unknown. Here we reported that NCOA6 was highly expressed in HCC compared to the adjacent liver tissue, and NCOA6 overexpression was significantly correlated with poor HCC prognosis. Experiments revealed that the knockdown of NCOA6 damaged the proliferation, migration, and invasion of HCC cells. Multiomics and immune infiltration analyses showed a close relationship between NCOA6 expression, multiple cancer-related malignant pathways, and the immunosuppressive microenvironment. Finally, we established an effective NCOA6-related microRNA (miRNA) signature to distinguish HCC from hepatitis\liver cirrhosis patients. To the best of our knowledge, this study is the first to provide a comprehensive analysis of NCOA6 expression in HCC. We found that NCOA6 plays an important role in HCC development and has a potential mechanism of action. Establishing an NCOA6-related miRNA signature will help develop novel diagnostic strategies for HCC patients.
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Affiliation(s)
- Yinghao Fang
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Yuyan Xu
- General Surgery Center, Department of Hepatobiliary Surgery IIGuangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Wei Liao
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Tao Ji
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Linyuan Yu
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Longhai Li
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Mingxin Pan
- General Surgery Center, Department of Hepatobiliary Surgery IIGuangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Dinghua Yang
- Unit of Hepatobiliary Surgery, General Surgery DepartmentNanfang Hospital, Southern Medical UniversityGuangzhouChina
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Li S, Wu S, Wang L, Li F, Jiang H, Bai F. Recent advances in predicting protein-protein interactions with the aid of artificial intelligence algorithms. Curr Opin Struct Biol 2022; 73:102344. [PMID: 35219216 DOI: 10.1016/j.sbi.2022.102344] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are essential in the regulation of biological functions and cell events, therefore understanding PPIs have become a key issue to understanding the molecular mechanism and investigating the design of drugs. Here we highlight the major developments in computational methods developed for predicting PPIs by using types of artificial intelligence algorithms. The first part introduces the source of experimental PPI data. The second part is devoted to the PPI prediction methods based on sequential information. The third part covers representative methods using structural information as the input feature. The last part is methods designed by combining different types of features. For each part, the state-of-the-art computational PPI prediction methods are reviewed in an inclusive view. Finally, we discuss the flaws existing in this area and future directions of next-generation algorithms.
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Affiliation(s)
- Shiwei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Sanan Wu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fenglei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China.
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7
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Pharmacoepigenomics circuits induced by a novel retinoid-polyamine conjugate in human immortalized keratinocytes. THE PHARMACOGENOMICS JOURNAL 2021; 21:638-648. [PMID: 34145402 DOI: 10.1038/s41397-021-00241-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/02/2021] [Accepted: 04/23/2021] [Indexed: 02/05/2023]
Abstract
Retinoids are widely used in diseases spanning from dermatological lesions to cancer, but exhibit severe adverse effects. A novel all-trans-Retinoic Acid (atRA)-spermine conjugate (termed RASP) has shown previously optimal in vitro and in vivo anti-inflammatory and anticancer efficacy, with undetectable teratogenic and toxic side-effects. To get insights, we treated HaCaT cells which resemble human epidermis with IC50 concentration of RASP and analyzed their miRNA expression profile. Gene ontology analysis of their predicted targets indicated dynamic networks involved in cell proliferation, signal transduction and apoptosis. Furthermore, DNA microarrays analysis verified that RASP affects the expression of the same categories of genes. A protein-protein interaction map produced using the most significant common genes, revealed hub genes of nodal functions. We conclude that RASP is a synthetic retinoid derivative with improved properties, which possess the beneficial effects of retinoids without exhibiting side-effects and with potential beneficial effects against skin diseases including skin cancer.
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Tran BN, Valek L, Wilken-Schmitz A, Fuhrmann DC, Namgaladze D, Wittig I, Tegeder I. Reduced exploratory behavior in neuronal nucleoredoxin knockout mice. Redox Biol 2021; 45:102054. [PMID: 34198070 PMCID: PMC8254043 DOI: 10.1016/j.redox.2021.102054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/07/2022] Open
Abstract
Nucleoredoxin is a thioredoxin-like redoxin that has been recognized as redox modulator of WNT signaling. Using a Yeast-2-Hybrid screen, we identified calcium calmodulin kinase 2a, Camk2a, as a prominent prey in a brain library. Camk2a is crucial for nitric oxide dependent processes of neuronal plasticity of learning and memory. Therefore, the present study assessed functions of NXN in neuronal Nestin-NXN-/- deficient mice. The NXN-Camk2a interaction was confirmed by coimmunoprecipitation, and by colocalization in neuropil and dendritic spines. Functionally, Camk2a activity was reduced in NXN deficient neurons and restored with recombinant NXN. Proteomics revealed reduced oxidation in the hippocampus of Nestin-NXN-/- deficient mice, including Camk2a, further synaptic and mitochondrial proteins, and was associated with a reduction of mitochondrial respiration. Nestin-NXN-/- mice were healthy and behaved normally in behavioral tests of anxiety, activity and sociability. They had no cognitive deficits in touchscreen based learning & memory tasks, but omitted more trials showing a lower interest in the reward. They also engaged less in rewarding voluntary wheel running, and in exploratory behavior in IntelliCages. Accuracy was enhanced owing to the loss of exploration. The data suggested that NXN maintained the oxidative state of Camk2a and thereby its activity. In addition, it supported oxidation of other synaptic and mitochondrial proteins, and mitochondrial respiration. The loss of NXN-dependent pro-oxidative functions manifested in a loss of exploratory drive and reduced interest in reward in behaving mice.
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Affiliation(s)
- Bao Ngoc Tran
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Lucie Valek
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Annett Wilken-Schmitz
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | | | - Dimitry Namgaladze
- Institute of Biochemistry I, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute of Cardiovascular Physiology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany.
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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10
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Tong Z, Liu Y, Yu X, Martinez JD, Xu J. The transcriptional co-activator NCOA6 promotes estrogen-induced GREB1 transcription by recruiting ERα and enhancing enhancer-promoter interactions. J Biol Chem 2019; 294:19667-19682. [PMID: 31744881 DOI: 10.1074/jbc.ra119.010704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/13/2019] [Indexed: 11/06/2022] Open
Abstract
Estrogen and its cognate receptor, ERα, regulate cell proliferation, differentiation, and carcinogenesis in the endometrium by controlling gene transcription. ERα requires co-activators to mediate transcription via mechanisms that are largely uncharacterized. Herein, using growth-regulating estrogen receptor binding 1 (GREB1) as an ERα target gene in Ishikawa cells, we demonstrate that nuclear receptor co-activator 6 (NCOA6) is essential for estradiol (E2)/ERα-activated GREB1 transcription. We found that NCOA6 associates with the GREB1 promoter and enhancer in an E2-independent manner and that NCOA6 knockout reduces chromatin looping, enhancer-promoter interactions, and basal GREB1 expression in the absence of E2. In the presence of E2, ERα bound the GREB1 enhancer and also associated with its promoter, and p300, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL4), and RNA polymerase II were recruited to the GREB1 enhancer and promoter. Consequently, the levels of the histone modifications H3K4me1/3, H3K9ac, and H3K27ac were significantly increased; enhancer and promoter regions were transcribed; and GREB1 mRNA was robustly transcribed. NCOA6 knockout reduced ERα recruitment and abolished all of the aforementioned E2-induced events, making GREB1 completely insensitive to E2 induction. We also found that GREB1-deficient Ishikawa cells are much more resistant to chemotherapy and that human endometrial cancers with low GREB1 expression predict poor overall survival. These results indicate that NCOA6 has an essential role in ERα-mediated transcription by increasing enhancer-promoter interactions through chromatin looping and by recruiting RNA polymerase II and the histone-code modifiers p300 and MLL4. Moreover, GREB1 loss may predict chemoresistance of endometrial cancer.
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Affiliation(s)
- Zhangwei Tong
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Yonghong Liu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Xiaobin Yu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Jarrod D Martinez
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Jianming Xu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
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Ochoa J, Valli A, Martín-Trillo M, Simón-Mateo C, García JA, Rodamilans B. Sterol isomerase HYDRA1 interacts with RNA silencing suppressor P1b and restricts potyviral infection. PLANT, CELL & ENVIRONMENT 2019; 42:3015-3026. [PMID: 31286514 DOI: 10.1111/pce.13610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
Plants use RNA silencing as a strong defensive barrier against virus challenges, and viruses counteract this defence by using RNA silencing suppressors (RSSs). With the objective of identifying host factors helping either the plant or the virus in this interaction, we have performed a yeast two-hybrid screen using P1b, the RSS protein of the ipomovirus Cucumber vein yellowing virus (CVYV, family Potyviridae), as a bait. The C-8 sterol isomerase HYDRA1 (HYD1), an enzyme involved in isoprenoid biosynthesis and cell membrane biology, and required for RNA silencing, was isolated in this screen. The interaction between CVYV P1b and HYD1 was confirmed in planta by Bimolecular Fluorescence Complementation assays. We demonstrated that HYD1 negatively impacts the accumulation of CVYV P1b in an agroinfiltration assay. Moreover, expression of HYD1 inhibited the infection of the potyvirus Plum pox virus, especially when antiviral RNA silencing was boosted by high temperature or by coexpression of homologous sequences. Our results reinforce previous evidence highlighting the relevance of particular composition and structure of cellular membranes for RNA silencing and viral infection. We report a new interaction of an RSS protein from the Potyviridae family with a member of the isoprenoid biosynthetic pathway.
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Affiliation(s)
- Jon Ochoa
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Adrián Valli
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Mar Martín-Trillo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Simón-Mateo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Antonio García
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Bernardo Rodamilans
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
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12
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Agbo L, Lambert JP. Proteomics contribution to the elucidation of the steroid hormone receptors functions. J Steroid Biochem Mol Biol 2019; 192:105387. [PMID: 31173874 DOI: 10.1016/j.jsbmb.2019.105387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
Steroid hormones have far-ranging biological impacts and more are continuously being uncovered. Over the last decades, proteomics approaches have become key to better understand biological processes. Due to multiple technical breakthroughs allowing for the concurrent identification and/or quantification of thousands of analytes using mass spectrometers, researchers employing proteomics tools today can now obtain truly holistic views of multiple facets of the human proteome. Here, we review how the field of proteomics has contributed to discoveries about steroid hormones, their receptors and their impact on human pathologies. In particular, the involvement of steroid receptors in cancer initiation, development, metastasis and treatment will be highlighted. Techniques at the forefront of the proteomics field will also be discussed to present how they can contribute to a better understanding of steroid hormone receptors.
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Affiliation(s)
- Lynda Agbo
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec, QC, Canada; Research Center CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec, QC, Canada; Research Center CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada.
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13
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Hughes NP, Xu L, Nielsen CH, Chang E, Hori SS, Natarajan A, Lee S, Kjær A, Kani K, Wang SX, Mallick P, Gambhir SS. A blood biomarker for monitoring response to anti-EGFR therapy. Cancer Biomark 2018; 22:333-344. [PMID: 29689709 DOI: 10.3233/cbm-171149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVE To monitor therapies targeted to epidermal growth factor receptors (EGFR) in non-small cell lung cancer (NSCLC), we investigated Peroxiredoxin 6 (PRDX6) as a biomarker of response to anti-EGFR agents. METHODS We studied cells that are sensitive (H3255, HCC827) or resistant (H1975, H460) to gefitinib. PRDX6 was examined with either gefitinib or vehicle treatment using enzyme-linked immunosorbent assays. We created xenograft models from one sensitive (HCC827) and one resistant cell line (H1975) and monitored serum PRDX6 levels during treatment. RESULTS PRDX6 levels in cell media from sensitive cell lines increased significantly after gefitinib treatment vs. vehicle, whereas there was no significant difference for resistant lines. PRDX6 accumulation over time correlated positively with gefitinib sensitivity. Serum PRDX6 levels in gefitinib-sensitive xenograft models increased markedly during the first 24 hours of treatment and then decreased dramatically during the following 48 hours. Differences in serum PRDX6 levels between vehicle and gefitinib-treated animals could not be explained by differences in tumor burden. CONCLUSIONS Our results show that changes in serum PRDX6 during the course of gefitinib treatment of xenograft models provide insight into tumor response and such an approach offers several advantages over imaging-based strategies for monitoring response to anti-EGFR agents.
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Affiliation(s)
- Nicholas P Hughes
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingyun Xu
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten H Nielsen
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Edwin Chang
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon S Hori
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Arutselvan Natarajan
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Samantha Lee
- Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Andreas Kjær
- Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kian Kani
- Lawrence J. Ellison Institute of Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shan X Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Parag Mallick
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Sanjiv Sam Gambhir
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
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14
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Deng J, Kong W, Wang S, Mou X, Zeng W. Prior Knowledge Driven Joint NMF Algorithm for ceRNA Co-Module Identification. Int J Biol Sci 2018; 14:1822-1833. [PMID: 30443186 PMCID: PMC6231218 DOI: 10.7150/ijbs.27555] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
MRNA and lncRNA serve as a type of endogenous RNA in cell, which can competitively bind to the same miRNA through miRNA response elements (MREs), thereby regulating their respective expression levels, playing an important role in post-transcriptional regulation, and regulating the progress of tumors. The proposed competing endogenous RNA (ceRNA) hypothesis provides novel clues for the occurrence and development of tumors, but the integrative analysis methods of diverse RNA data are significantly limited. In order to find out the relationship among miRNA, mRNA and lncRNA, the previous studies only used individual dataset as seeds to search two other related data in the database to construct ceRNA network, but it was difficult to identify the synchronized effects from multiple regulatory levels. Here, we developed the joint matrix factorization method integrating prior knowledge to map the three types of RNA data of lung cancer to the common coordinate system and construct the ceRNA network corresponding to the common module. The results show that more than 90% of the modules are closely related to cancer, including lung cancer. Furthermore, the resulting ceRNA network not only accurately excavates the known correlation of the three types of RNA molecular, but also further discovers the potential biological associations of them. Our work provides support and foundation for future biological validation how competitive relationships of multiple RNAs affects the development of tumors.
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Affiliation(s)
- Jin Deng
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave., Shanghai 201306, P. R. China
| | - Wei Kong
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave., Shanghai 201306, P. R. China
| | - Shuaiqun Wang
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave., Shanghai 201306, P. R. China
| | - Xiaoyang Mou
- Department of Biochemistry, Rowan University and Guava Medicine, Glassboro, New Jersey 08028, USA
| | - Weiming Zeng
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave., Shanghai 201306, P. R. China
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15
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Watkinson JI, Bowerman PA, Crosby KC, Hildreth SB, Helm RF, Winkel BSJ. Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus. PeerJ 2018; 6:e5598. [PMID: 30258711 PMCID: PMC6151112 DOI: 10.7717/peerj.5598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023] Open
Abstract
Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.
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Affiliation(s)
- Jonathan I Watkinson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Peter A Bowerman
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,BASF Plant Science LP, Research Triangle Park, NC, USA
| | - Kevin C Crosby
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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16
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Broekema MF, Hollman DAA, Koppen A, van den Ham HJ, Melchers D, Pijnenburg D, Ruijtenbeek R, van Mil SWC, Houtman R, Kalkhoven E. Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery. Endocrinology 2018; 159:2397-2407. [PMID: 29718163 DOI: 10.1210/en.2018-00149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.
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Affiliation(s)
- Marjoleine F Broekema
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Danielle A A Hollman
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Arjen Koppen
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | | | - Diana Melchers
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Dirk Pijnenburg
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Rob Ruijtenbeek
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Saskia W C van Mil
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - René Houtman
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Eric Kalkhoven
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
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17
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Nicholson P, Gkratsou A, Josi C, Colombo M, Mühlemann O. Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells. RNA (NEW YORK, N.Y.) 2018; 24:557-573. [PMID: 29348139 PMCID: PMC5855955 DOI: 10.1261/rna.063719.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%-10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1. However, the existence, dominance, and mechanistic details of these exonucleolytic pathways are divisive. Therefore, we have investigated the possible exonucleolytic modes of mRNA decay in NMD by examining the roles of UPF1, SMG5, SMG7, and PNRC2 using a combination of functional assays and interaction mapping. Confirming previous work, we detected an interaction between SMG5 and SMG7 and also a functional need for this complex in NMD. In contrast, we found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2. Instead, we show that UPF1 interacts with PNRC2 and that it triggers 5'-3' exonucleolytic decay of reporter transcripts in tethering assays. PNRC2 interacts mainly with decapping factors and its knockdown does not affect the RNA levels of NMD reporters. We conclude that PNRC2 is probably an important mRNA decapping factor but that it does not appear to be required for NMD.
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Affiliation(s)
- Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Asimina Gkratsou
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Christoph Josi
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
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18
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Hou H, Uusküla-Reimand L, Makarem M, Corre C, Saleh S, Metcalf A, Goldenberg A, Palmert MR, Wilson MD. Gene expression profiling of puberty-associated genes reveals abundant tissue and sex-specific changes across postnatal development. Hum Mol Genet 2018; 26:3585-3599. [PMID: 28911201 DOI: 10.1093/hmg/ddx246] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
The timing of human puberty is highly variable, sexually dimorphic, and associated with adverse health outcomes. Over 20 genes carrying rare mutations have been identified in known pubertal disorders, many of which encode critical components of the hypothalamic-pituitary-gonadal (HPG) axis. Recent genome-wide association studies (GWAS) have identified more than 100 candidate genes at loci associated with age at menarche or voice breaking in males. We know little about the spatial, temporal or postnatal expression patterns of the majority of these puberty-associated genes. Using a high-throughput and sensitive microfluidic quantitative PCR strategy, we profiled the gene expression patterns of the mouse orthologs of 178 puberty-associated genes in male and female mouse HPG axis tissues, the pineal gland, and the liver at five postnatal ages spanning the pubertal transition. The most dynamic gene expression changes were observed prior to puberty in all tissues. We detected known and novel tissue-enhanced gene expression patterns, with the hypothalamus expressing the largest number of the puberty-associated genes. Notably, over 40 puberty-associated genes in the pituitary gland showed sex-biased gene expression, most of which occurred peri-puberty. These sex-biased genes included the orthologs of candidate genes at GWAS loci that show sex-discordant effects on pubertal timing. Our findings provide new insight into the expression of puberty-associated genes and support the possibility that the pituitary plays a role in determining sex differences in the timing of puberty.
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Affiliation(s)
- Huayun Hou
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Liis Uusküla-Reimand
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Gene Technology, Tallinn University of Technology, 12616 Tallinn, Estonia
| | - Maisam Makarem
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Christina Corre
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Shems Saleh
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5S 2E5, Canada
| | - Ariane Metcalf
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Anna Goldenberg
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5S 2E5, Canada
| | - Mark R Palmert
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Division of Endocrinology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Departments of Paediatrics and Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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19
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Bar-Peled L, Kemper EK, Suciu RM, Vinogradova EV, Backus KM, Horning BD, Paul TA, Ichu TA, Svensson RU, Olucha J, Chang MW, Kok BP, Zhu Z, Ihle NT, Dix MM, Jiang P, Hayward MM, Saez E, Shaw RJ, Cravatt BF. Chemical Proteomics Identifies Druggable Vulnerabilities in a Genetically Defined Cancer. Cell 2017; 171:696-709.e23. [PMID: 28965760 PMCID: PMC5728659 DOI: 10.1016/j.cell.2017.08.051] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 07/07/2017] [Accepted: 08/30/2017] [Indexed: 01/11/2023]
Abstract
The transcription factor NRF2 is a master regulator of the cellular antioxidant response, and it is often genetically activated in non-small-cell lung cancers (NSCLCs) by, for instance, mutations in the negative regulator KEAP1. While direct pharmacological inhibition of NRF2 has proven challenging, its aberrant activation rewires biochemical networks in cancer cells that may create special vulnerabilities. Here, we use chemical proteomics to map druggable proteins that are selectively expressed in KEAP1-mutant NSCLC cells. Principal among these is NR0B1, an atypical orphan nuclear receptor that we show engages in a multimeric protein complex to regulate the transcriptional output of KEAP1-mutant NSCLC cells. We further identify small molecules that covalently target a conserved cysteine within the NR0B1 protein interaction domain, and we demonstrate that these compounds disrupt NR0B1 complexes and impair the anchorage-independent growth of KEAP1-mutant cancer cells. Our findings designate NR0B1 as a druggable transcriptional regulator that supports NRF2-dependent lung cancers.
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Affiliation(s)
- Liron Bar-Peled
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Esther K Kemper
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Radu M Suciu
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ekaterina V Vinogradova
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Keriann M Backus
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Benjamin D Horning
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas A Paul
- Oncology Research Unit, Pfizer Worldwide Research and Development, La Jolla, CA 92121, USA
| | - Taka-Aki Ichu
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert U Svensson
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jose Olucha
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernard P Kok
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zhou Zhu
- Oncology Research Unit, Pfizer Worldwide Research and Development, La Jolla, CA 92121, USA
| | - Nathan T Ihle
- Oncology Research Unit, Pfizer Worldwide Research and Development, La Jolla, CA 92121, USA
| | - Melissa M Dix
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ping Jiang
- Oncology Research Unit, Pfizer Worldwide Research and Development, La Jolla, CA 92121, USA
| | - Matthew M Hayward
- Oncology Research Unit, Pfizer Worldwide Research and Development, La Jolla, CA 92121, USA
| | - Enrique Saez
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Reuben J Shaw
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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20
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Lam VQ, Zheng J, Griffin PR. Unique Interactome Network Signatures for Peroxisome Proliferator-activated Receptor Gamma (PPARγ) Modulation by Functional Selective Ligands. Mol Cell Proteomics 2017; 16:2098-2110. [PMID: 28972081 DOI: 10.1074/mcp.ra117.000308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 01/18/2023] Open
Abstract
The nuclear receptor PPARγ regulates adipogenesis and plays a central role in lipid and glucose homeostasis, and is the molecular target of the glitazones (TZDs), therapeutics used to treat insulin resistance and type-2 diabetes (T2D). Although the TZDs, which are PPARγ agonists, demonstrated robust clinical efficacy in T2D, their use has been hampered by an array of untoward side effects. Paradoxically, partial agonists (e.g. MRL24), antagonists (e.g. SR1664), and inverse agonists (e.g. SR10171 and SR2595), possess similar insulin-sensitizing efficacy as the TZDs in obese diabetic mice. Given the unique pharmacology of these modulators, we sought to identify the components of the PPARγ transcriptional complex that is regulated by these ligands. To achieve this, we employed subcellular fractionation of adipocytes combined with either trapping of the receptor complex on biotinylated DNA oligonucleotide, or classical immunoprecipitation. Tandem mass spectrometry analysis revealed unique, partially overlapping, compound- and subcellular compartment-specific complexes. Components of these interactomes are putative coregulators of PPARγ. Interestingly, complexes isolated in the cytosol contain sets of proteins involve in cellular assembly and extracellular matrix. Furthermore, the interactome observed for cytosolic non-DNA bound receptor was distinct from that observed from nuclear chromatin associated PPARγ, suggesting cellular compartment-specific roles for this receptor.
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Affiliation(s)
- Vinh Q Lam
- ‡From the Department of Molecular Medicine, The Scripps Research Institute, Scripps, Florida, Jupiter, Florida 33458
| | - Jie Zheng
- ‡From the Department of Molecular Medicine, The Scripps Research Institute, Scripps, Florida, Jupiter, Florida 33458
| | - Patrick R Griffin
- ‡From the Department of Molecular Medicine, The Scripps Research Institute, Scripps, Florida, Jupiter, Florida 33458
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21
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Dierck F, Kuhn C, Rohr C, Hille S, Braune J, Sossalla S, Molt S, van der Ven PFM, Fürst DO, Frey N. The novel cardiac z-disc protein CEFIP regulates cardiomyocyte hypertrophy by modulating calcineurin signaling. J Biol Chem 2017; 292:15180-15191. [PMID: 28717008 DOI: 10.1074/jbc.m117.786764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/04/2017] [Indexed: 11/06/2022] Open
Abstract
The z-disc is a structural component at the lateral borders of the sarcomere and is important for mechanical stability and contractility of both cardiac and skeletal muscles. Of note, the sarcomeric z-disc also represents a nodal point in cardiomyocyte function and signaling. Mutations of numerous z-disc proteins are associated with cardiomyopathies and muscle diseases. To identify additional z-disc proteins that might contribute to cardiac disease, we employed an in silico screen for cardiac-enriched cDNAs. This screen yielded a previously uncharacterized protein named cardiac-enriched FHL2-interacting protein (CEFIP), which exhibited a heart- and skeletal muscle-specific expression profile. Importantly, CEFIP was located at the z-disc and was up-regulated in several models of cardiomyopathy. We also found that CEFIP overexpression induced the fetal gene program and cardiomyocyte hypertrophy. Yeast two-hybrid screens revealed that CEFIP interacts with the calcineurin-binding protein four and a half LIM domains 2 (FHL2). Because FHL2 binds calcineurin, a phosphatase controlling hypertrophic signaling, we examined the effects of CEFIP on the calcineurin/nuclear factor of activated T-cell (NFAT) pathway. These experiments revealed that CEFIP overexpression further enhances calcineurin-dependent hypertrophic signal transduction, and its knockdown repressed hypertrophy and calcineurin/NFAT activity. In summary, we report on a previously uncharacterized protein CEFIP that modulates calcineurin/NFAT signaling in cardiomyocytes, a finding with possible implications for the pathogenesis of cardiomyopathy.
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Affiliation(s)
- Franziska Dierck
- From the Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, 24105 Kiel.,the DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 24105 Kiel
| | - Christian Kuhn
- From the Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, 24105 Kiel.,the DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 24105 Kiel
| | - Claudia Rohr
- the Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, and
| | - Susanne Hille
- From the Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, 24105 Kiel.,the DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 24105 Kiel
| | - Julia Braune
- the Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Samuel Sossalla
- From the Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, 24105 Kiel.,the DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 24105 Kiel
| | - Sibylle Molt
- the Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Peter F M van der Ven
- the Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Dieter O Fürst
- the Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Norbert Frey
- From the Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, 24105 Kiel, .,the DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 24105 Kiel
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22
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Fulton J, Mazumder B, Whitchurch JB, Monteiro CJ, Collins HM, Chan CM, Clemente MP, Hernandez-Quiles M, Stewart EA, Amoaku WM, Moran PM, Mongan NP, Persson JL, Ali S, Heery DM. Heterodimers of photoreceptor-specific nuclear receptor (PNR/NR2E3) and peroxisome proliferator-activated receptor-γ (PPARγ) are disrupted by retinal disease-associated mutations. Cell Death Dis 2017; 8:e2677. [PMID: 28300834 PMCID: PMC5386588 DOI: 10.1038/cddis.2017.98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/30/2022]
Abstract
Photoreceptor-specific nuclear receptor (PNR/NR2E3) and Tailless homolog (TLX/NR2E1) are human orthologs of the NR2E group, a subgroup of phylogenetically related members of the nuclear receptor (NR) superfamily of transcription factors. We assessed the ability of these NRs to form heterodimers with other members of the human NRs representing all major subgroups. The TLX ligand-binding domain (LBD) did not appear to form homodimers or interact directly with any other NR tested. The PNR LBD was able to form homodimers, but also exhibited robust interactions with the LBDs of peroxisome proliferator-activated receptor-γ (PPARγ)/NR1C3 and thyroid hormone receptor b (TRb) TRβ/NR1A2. The binding of PNR to PPARγ was specific for this paralog, as no interaction was observed with the LBDs of PPARα/NR1C1 or PPARδ/NR1C2. In support of these findings, PPARγ and PNR were found to be co-expressed in human retinal tissue extracts and could be co-immunoprecipitated as a native complex. Selected sequence variants in the PNR LBD associated with human retinopathies, or a mutation in the dimerization region of PPARγ LBD associated with familial partial lipodystrophy type 3, were found to disrupt PNR/PPARγ complex formation. Wild-type PNR, but not a PNR309G mutant, was able to repress PPARγ-mediated transcription in reporter assays. In summary, our results reveal novel heterodimer interactions in the NR superfamily, suggesting previously unknown functional interactions of PNR with PPARγ and TRβ that have potential importance in retinal development and disease.
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Affiliation(s)
- Joel Fulton
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Bismoy Mazumder
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | | | | | - Chun M Chan
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | | | - Elizabeth A Stewart
- Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Winfried M Amoaku
- Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Paula M Moran
- School of Psychology, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Jenny L Persson
- Division of Experimental Cancer Research, Department of Translational Medicine, Lund University, Clinical Research Centre, Malmö, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - David M Heery
- School of Pharmacy, University of Nottingham, Nottingham, UK
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23
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Rottiers V, Francisco A, Platov M, Zaltsman Y, Ruggiero A, Lee SS, Gross A, Libert S. MTCH2 is a conserved regulator of lipid homeostasis. Obesity (Silver Spring) 2017; 25:616-625. [PMID: 28127879 DOI: 10.1002/oby.21751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE More than one-third of U.S. adults have obesity, causing an alarming increase in obesity-related comorbidities such as type 2 diabetes. The functional role of mitochondrial carrier homolog 2 (MTCH2), a human obesity-associated gene, in lipid homeostasis was investigated in Caenorhabditis elegans, cell culture, and mice. METHODS In C. elegans, MTCH2/MTCH-1 was depleted, using RNAi and a genetic mutant, and overexpressed to assess its effect on lipid accumulation. In cells and mice, shRNAs against MTCH2 were used for knockdown and MTCH2 overexpression vectors were used for overexpression to study the role of this gene in fat accumulation. RESULTS MTCH2 knockdown reduced lipid accumulation in adipocyte-like cells in vitro and in C. elegans and mice in vivo. MTCH2 overexpression increased fat accumulation in cell culture, C. elegans, and mice. Acute MTCH2 inhibition reduced fat accumulation in animals subjected to a high-fat diet. Finally, MTCH2 influenced estrogen receptor 1 (ESR1) activity. CONCLUSIONS MTCH2 is a conserved regulator of lipid homeostasis. MTCH2 was found to be both required and sufficient for lipid homeostasis shifts, suggesting that pharmacological inhibition of MTCH2 could be therapeutic for treatment of obesity and related disorders. MTCH2 could influence lipid homeostasis through inhibition of ESR1 activity.
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Affiliation(s)
- Veerle Rottiers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Adam Francisco
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Michael Platov
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yehudit Zaltsman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Antonella Ruggiero
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Atan Gross
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sergiy Libert
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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24
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Altmann C, Hardt S, Fischer C, Heidler J, Lim HY, Häussler A, Albuquerque B, Zimmer B, Möser C, Behrends C, Koentgen F, Wittig I, Schmidt MH, Clement AM, Deller T, Tegeder I. Progranulin overexpression in sensory neurons attenuates neuropathic pain in mice: Role of autophagy. Neurobiol Dis 2016; 96:294-311. [DOI: 10.1016/j.nbd.2016.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 12/14/2022] Open
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25
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Klimeš P, Mazura P, Turek D, Brzobohatý B. An automated method to evaluate the enzyme kinetics of β-glucosidases. Protein Sci 2016; 26:382-388. [PMID: 27862518 DOI: 10.1002/pro.3078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 11/05/2022]
Abstract
Enzyme kinetic measurements are important for the characterization and engineering of biocatalysts, with applications in a wide range of research fields. The measurement of initial reaction velocity is usually slow and laborious, which motivated us to explore the possibilities for automating this process. Our model enzyme is the maize β-glucosidase Zm-p60.1. Zm-p60.1 plays a significant role in plant growth and development by regulating levels of the active plant hormone cytokinin. Zm-p60.1 belongs to a wide group of hydrolytic enzymes. Members of this group hydrolyze several different types of glucosides, releasing glucose as a secondary product. Enzyme kinetic measurements using artificial substrates are well established, but burdensome and time-consuming. Thus, they are a suitable target for process automation. Simple optical methods for enzyme kinetic measurements using natural substrates are often impossible given the optical properties of the enzymatic reaction products. However, we have developed an automated method based on glucose detection, as glucose is released from all substrates of glucosidase reactions. The presented method can obtain 24 data points from up to 15 substrate concentrations to precisely describe the enzyme kinetics. The combination of an automated liquid handling process with assays that have been optimized for measuring the initial hydrolysis velocity of β-glucosidases yields two distinct methods that are faster, cheaper, and more accurate than the established protocols.
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Affiliation(s)
- Pavel Klimeš
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Pavel Mazura
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Dušan Turek
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
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26
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Tegeder I. Yeast-2-Hybrid data file showing progranulin interactions in human fetal brain and bone marrow libraries. Data Brief 2016; 9:1060-1062. [PMID: 27921076 PMCID: PMC5126125 DOI: 10.1016/j.dib.2016.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/13/2016] [Accepted: 11/10/2016] [Indexed: 11/28/2022] Open
Abstract
Progranulin deficiency in humans is associated with neurodegeneration. Its mechanisms are not yet fully understood. We performed a Yeast-2-Hybrid screen using human full-length progranulin as bait to assess the interactions of progranulin. Progranulin was screened against human fetal brain and human bone marrow libraries using the standard Matchmaker technology (Clontech). This article contains the full Y2H data table, including blast results and sequences, a sorted table according to selection criteria for likely positive, putatively positive, likely false and false preys, and tables showing the gene ontology terms associated with the likely and putative preys of the brain and bone marrow libraries. The interactions with autophagy proteins were confirmed and functionally analyzed in "Progranulin overexpression in sensory neurons attenuates neuropathic pain in mice: Role of autophagy" (C. Altmann, S. Hardt, C. Fischer, J. Heidler, H.Y. Lim, A. Haussler, B. Albuquerque, B. Zimmer, C. Moser, C. Behrends, F. Koentgen, I. Wittig, M.H. Schmidt, A.M. Clement, T. Deller, I. Tegeder, 2016) [1].
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27
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Weitzel JM. Impaired Repressor Function in SUMOylation-Defective Thyroid Hormone Receptor Isoforms. Eur Thyroid J 2016; 5:152-163. [PMID: 27843805 PMCID: PMC5091228 DOI: 10.1159/000447232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Many nuclear receptors are modified by posttranslational modifications. OBJECTIVES The transcriptional activity of thyroid hormone receptors (TRs) is modified by the influence of its ligand (thyroid hormones T3 and T4), but is also affected by posttranslational modifications. This study focuses on the SUMOylation of TR isoforms and the consequences on transcriptional activity and promoter occupancy. METHODS SUMOylation of TR wild-type as well as isoform-specific point mutations have been studied in vitro. The promoter occupancy of TR (wild-type and double- or triple-mutated versions) and transcriptional cofactors have been investigated in chromatin immunoprecipitation (ChIP) and Re-ChIP analysis. RESULTS TR is modified by SUMO proteins at defined residues: the isoform TRα is mainly modified at lysines 281 and 387, whereas lysines 50 and 443 are major SUMOylation sites of isoform TRβ. Lysine residues K281 (TRα) and K50 (TRβ) are isoform-specific SUMOylation sites influencing differing TR domains, whereas K387 (TRα) and K443 (TRβ) are orthologous residues. TRs are targets of all three SUMO variants (SUMO-1, -2, and -3). The transcriptional activity of SUMOylation-defective mutants of TR alters gene transcription from positively and negatively regulated T3 target genes. CONCLUSIONS The most pronounced effect is an impaired repressor function of SUMOylation-deficient TR in the absence of T3. The transcriptional properties of SUMOylation-defective TRs can be at least in part ascribed to altered interaction with transcriptional cofactors such as SRC-1 and NCoR. Thus, these data indicate that posttranslational modification of TR by SUMOylation contribute to the fine tuning of its transcriptional response maintaining effects on cellular and physiological homeostasis.
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Affiliation(s)
- Joachim M. Weitzel
- *Joachim M. Weitzel, Institute of Reproductive Biology, Leibniz Institute for Farm, Animal Biology (FBN), FBN Dummerstorf, Wilhelm-Stahl-Allee 2, DE-18196 Dummerstorf (Germany), E-Mail
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28
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Taguchi YH, Iwadate M, Umeyama H. SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer. BMC Med Genomics 2016; 9 Suppl 1:28. [PMID: 27534621 PMCID: PMC4989892 DOI: 10.1186/s12920-016-0196-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) remains a lethal disease despite many proposed treatments. Recent studies have indicated that epigenetic therapy, which targets epigenetic effects, might be a new therapeutic methodology for NSCLC. However, it is not clear which objects (e.g., genes) this treatment specifically targets. Secreted frizzled-related proteins (SFRPs) are promising candidates for epigenetic therapy in many cancers, but there have been no reports of SFRPs targeted by epigenetic therapy for NSCLC. Methods This study performed a meta-analysis of reprogrammed NSCLC cell lines instead of the direct examination of epigenetic therapy treatment to identify epigenetic therapy targets. In addition, mRNA expression/promoter methylation profiles were processed by recently proposed principal component analysis based unsupervised feature extraction and categorical regression analysis based feature extraction. Results The Wnt/β-catenin signalling pathway was extensively enriched among 32 genes identified by feature extraction. Among the genes identified, SFRP1 was specifically indicated to target β-catenin, and thus might be targeted by epigenetic therapy in NSCLC cell lines. A histone deacetylase inhibitor might reactivate SFRP1 based upon the re-analysis of a public domain data set. Numerical computation validated the binding of SFRP1 to WNT1 to suppress Wnt signalling pathway activation in NSCLC. Conclusions The meta-analysis of reprogrammed NSCLC cell lines identified SFRP1 as a promising target of epigenetic therapy for NSCLC. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0196-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, 112-8551, Tokyo, Japan.
| | - Mitsuo Iwadate
- Department of Biological Science, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, 112-8551, Tokyo, Japan
| | - Hideaki Umeyama
- Department of Biological Science, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, 112-8551, Tokyo, Japan
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29
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Hille S, Dierck F, Kühl C, Sosna J, Adam-Klages S, Adam D, Lüllmann-Rauch R, Frey N, Kuhn C. Dyrk1a regulates the cardiomyocyte cell cycle via D-cyclin-dependent Rb/E2f-signalling. Cardiovasc Res 2016; 110:381-94. [PMID: 27056896 DOI: 10.1093/cvr/cvw074] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 04/01/2016] [Indexed: 11/14/2022] Open
Abstract
AIMS Down syndrome-associated dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1A (DYRK1A) is a ubiquitously expressed protein kinase. Up to date a variety of targets have been identified, establishing a key role for Dyrk1a in selected signalling pathways. In cardiomyocytes, Dyrk1a acts as a negative regulator of hypertrophy by phosphorylating transcription factors of the NFAT family, but its mechanistic function in the heart remains poorly understood. This study was designed to investigate a potential protective role of Dyrk1a in cardiac hypertrophy in vivo. METHODS AND RESULTS We generated transgenic mice with cardiac-specific overexpression of Dyrk1a. Counterintuitively, these mice developed severe dilated cardiomyopathy associated with congestive heart failure and premature death. In search for the cause of this unexpected phenotype, we found that Dyrk1a interacts with all members of the D-cyclin family and represses their protein levels in vitro and in vivo. Particularly, forced expression of Dyrk1a leads to increased phosphorylation of Ccnd2 on Thr280 and promotes its subsequent proteasomal degradation. Accordingly, cardiomyocytes overexpressing Dyrk1a display hypo-phosphorylated Rb1, suppression of Rb/E2f-signalling, and reduced expression of E2f-target genes, which ultimately results in impaired cell cycle progression. CONCLUSIONS We identified Dyrk1a as a novel negative regulator of D-cyclin-mediated Rb/E2f-signalling. As dysregulation of this pathway with impaired cardiomyocyte proliferation leads to cardiomyopathy, dose-specific Dyrk1a expression and activity appears to be critical for the hyperplastic and hypertrophic growth of the developing heart.
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MESH Headings
- Animals
- Cardiomegaly/enzymology
- Cardiomegaly/genetics
- Cardiomegaly/pathology
- Cardiomegaly/physiopathology
- Cardiomyopathy, Dilated/enzymology
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Dilated/physiopathology
- Cell Cycle
- Cell Proliferation
- Cyclin D/genetics
- Cyclin D/metabolism
- Disease Models, Animal
- E2F Transcription Factors/metabolism
- Gene Expression Regulation
- HEK293 Cells
- Heart Failure/enzymology
- Heart Failure/genetics
- Heart Failure/pathology
- Heart Failure/physiopathology
- Humans
- Mice, Inbred C57BL
- Mice, Transgenic
- Myocytes, Cardiac/enzymology
- Myocytes, Cardiac/pathology
- Phosphorylation
- Protein Binding
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Rats, Wistar
- Retinoblastoma/metabolism
- Signal Transduction
- Time Factors
- Transfection
- Dyrk Kinases
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Affiliation(s)
- Susanne Hille
- Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Str. 3 (Building 6), 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Franziska Dierck
- Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Str. 3 (Building 6), 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Constantin Kühl
- Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Str. 3 (Building 6), 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Justyna Sosna
- Institute of Immunology, Christian-Albrechts-University Kiel, UKSH Campus Kiel, 24105 Kiel, Germany
| | - Sabine Adam-Klages
- Institute of Immunology, Christian-Albrechts-University Kiel, UKSH Campus Kiel, 24105 Kiel, Germany
| | - Dieter Adam
- Institute of Immunology, Christian-Albrechts-University Kiel, UKSH Campus Kiel, 24105 Kiel, Germany
| | | | - Norbert Frey
- Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Str. 3 (Building 6), 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Christian Kuhn
- Department of Internal Medicine III, University Medical Center of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Str. 3 (Building 6), 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
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30
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Myoscape controls cardiac calcium cycling and contractility via regulation of L-type calcium channel surface expression. Nat Commun 2016; 7:11317. [PMID: 27122098 DOI: 10.1315/11317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 03/13/2016] [Indexed: 01/29/2023] Open
Abstract
Calcium signalling plays a critical role in the pathogenesis of heart failure. Here we describe a cardiac protein named Myoscape/FAM40B/STRIP2, which directly interacts with the L-type calcium channel. Knockdown of Myoscape in cardiomyocytes decreases calcium transients associated with smaller Ca(2+) amplitudes and a lower diastolic Ca(2+) content. Likewise, L-type calcium channel currents are significantly diminished on Myoscape ablation, and downregulation of Myoscape significantly reduces contractility of cardiomyocytes. Conversely, overexpression of Myoscape increases global Ca(2+) transients and enhances L-type Ca(2+) channel currents, and is sufficient to restore decreased currents in failing cardiomyocytes. In vivo, both Myoscape-depleted morphant zebrafish and Myoscape knockout (KO) mice display impairment of cardiac function progressing to advanced heart failure. Mechanistically, Myoscape-deficient mice show reduced L-type Ca(2+)currents, cell capacity and calcium current densities as a result of diminished LTCC surface expression. Finally, Myoscape expression is reduced in hearts from patients suffering of terminal heart failure, implying a role in human disease.
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31
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Myoscape controls cardiac calcium cycling and contractility via regulation of L-type calcium channel surface expression. Nat Commun 2016. [PMID: 27122098 PMCID: PMC5438100 DOI: 10.1038/ncomms11317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Calcium signalling plays a critical role in the pathogenesis of heart failure. Here we describe a cardiac protein named Myoscape/FAM40B/STRIP2, which directly interacts with the L-type calcium channel. Knockdown of Myoscape in cardiomyocytes decreases calcium transients associated with smaller Ca2+ amplitudes and a lower diastolic Ca2+ content. Likewise, L-type calcium channel currents are significantly diminished on Myoscape ablation, and downregulation of Myoscape significantly reduces contractility of cardiomyocytes. Conversely, overexpression of Myoscape increases global Ca2+ transients and enhances L-type Ca2+ channel currents, and is sufficient to restore decreased currents in failing cardiomyocytes. In vivo, both Myoscape-depleted morphant zebrafish and Myoscape knockout (KO) mice display impairment of cardiac function progressing to advanced heart failure. Mechanistically, Myoscape-deficient mice show reduced L-type Ca2+currents, cell capacity and calcium current densities as a result of diminished LTCC surface expression. Finally, Myoscape expression is reduced in hearts from patients suffering of terminal heart failure, implying a role in human disease. Heart failure is a major public health issue but due to our poor disease understanding the current therapies are symptomatic. Here the authors identify Myoscape as a novel cardiac protein regulating membrane localization of the L-type calcium channel and heart's contractile force, thus promising new therapeutic avenues for heart failure.
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Müller M, Wasson CW, Bhatia R, Boxall S, Millan D, Goh GYS, Haas J, Stonehouse NJ, Macdonald A. YIP1 family member 4 (YIPF4) is a novel cellular binding partner of the papillomavirus E5 proteins. Sci Rep 2015; 5:12523. [PMID: 26235900 PMCID: PMC4522686 DOI: 10.1038/srep12523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/26/2015] [Indexed: 01/14/2023] Open
Abstract
E5 proteins are amongst the least understood of the Human Papillomavirus (HPV) encoded gene products. They are small, membrane-integrated proteins known to modulate a number of critical host pathways associated with pathogenesis including growth factor receptor signaling and immune evasion. Their role in the virus life cycle is less clear, indicating a role in the productive stages of the life cycle. However, a mechanism for this is currently lacking. Here we describe the identification of a novel binding partner of E5, YIPF4 using yeast two-hybrid analysis. YIPF4 is also a poorly characterized membrane spanning protein. Mutagenesis studies implicated the transmembrane regions of each protein as important for their interaction. Binding to YIPF4 was found for all E5 proteins tested suggesting that this interaction may mediate a conserved E5 function. In normal human keratinocytes YIPF4 expression was down-regulated upon differentiation and this reduction was partially rescued in cells harbouring HPV. Despite the conserved nature of the interaction with E5, siRNA mediated depletion of YIPF4 failed to impede two well-characterized functions of E5, namely EGFR trafficking or HLA class I presentation. Continued studies of YIPF4 are warranted to determine its role in the PV life cycle.
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Affiliation(s)
| | | | - Ramya Bhatia
- Division of Pathway Medicine, The University of Edinburgh, UK
| | | | - David Millan
- Department of Pathology, Southern General Hospital, Glasgow, Scotland, UK
| | | | - Jürgen Haas
- Division of Pathway Medicine, The University of Edinburgh, UK
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Cidre-Aranaz F, Alonso J. EWS/FLI1 Target Genes and Therapeutic Opportunities in Ewing Sarcoma. Front Oncol 2015; 5:162. [PMID: 26258070 PMCID: PMC4507460 DOI: 10.3389/fonc.2015.00162] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/06/2015] [Indexed: 12/31/2022] Open
Abstract
Ewing sarcoma is an aggressive bone malignancy that affect children and young adults. Ewing sarcoma is the second most common primary bone malignancy in pediatric patients. Although significant progress has been made in the treatment of Ewing sarcoma since it was first described in the 1920s, in the last decade survival rates have remained unacceptably invariable, thus pointing to the need for new approaches centered in the molecular basis of the disease. Ewing sarcoma driving mutation, EWS–FLI1, which results from a chromosomal translocation, encodes an aberrant transcription factor. Since its first characterization in 1990s, many molecular targets have been described to be regulated by this chimeric transcription factor. Their contribution to orchestrate Ewing sarcoma phenotype has been reported over the last decades. In this work, we will focus on the description of a selection of EWS/FLI1 targets, their functional role, and their potential clinical relevance. We will also discuss their role in other types of cancer as well as the need for further studies to be performed in order to achieve a broader understanding of their particular contribution to Ewing sarcoma development.
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Affiliation(s)
- Florencia Cidre-Aranaz
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III , Madrid , Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III , Madrid , Spain
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Rattay K, Claude J, Rezavandy E, Matt S, Hofmann TG, Kyewski B, Derbinski J. Homeodomain-interacting protein kinase 2, a novel autoimmune regulator interaction partner, modulates promiscuous gene expression in medullary thymic epithelial cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:921-8. [PMID: 25552543 DOI: 10.4049/jimmunol.1402694] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Promiscuous expression of a plethora of tissue-restricted Ags (TRAs) by medullary thymic epithelial cells (mTECs) plays an essential role in T cell tolerance. Although the cellular mechanisms by which promiscuous gene expression (pGE) imposes T cell tolerance have been well characterized, the underlying molecular mechanisms remain poorly understood. The autoimmune regulator (AIRE) is to date the only validated molecule known to regulate pGE. AIRE is part of higher-order multiprotein complexes, which promote transcription, elongation, and splicing of a wide range of target genes. How AIRE and its partners mediate these various effects at the molecular level is still largely unclear. Using a yeast two-hybrid screen, we searched for novel AIRE-interacting proteins and identified the homeodomain-interacting protein kinase 2 (HIPK2) as a novel partner. HIPK2 partially colocalized with AIRE in nuclear bodies upon cotransfection and in human mTECs in situ. Moreover, HIPK2 phosphorylated AIRE in vitro and suppressed the coactivator activity of AIRE in a kinase-dependent manner. To evaluate the role of Hipk2 in modulating the function of AIRE in vivo, we compared whole-genome gene signatures of purified mTEC subsets from TEC-specific Hipk2 knockout mice with control mice and identified a small set of differentially expressed genes. Unexpectedly, most differentially expressed genes were confined to the CD80(lo) mTEC subset and preferentially included AIRE-independent TRAs. Thus, although it modulates gene expression in mTECs and in addition affects the size of the medullary compartment, TEC-specific HIPK2 deletion only mildly affects AIRE-directed pGE in vivo.
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Affiliation(s)
- Kristin Rattay
- Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany; and
| | - Janine Claude
- Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany; and
| | - Esmail Rezavandy
- Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany; and
| | - Sonja Matt
- Zelluläre Seneszenz-Gruppe, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie Allianz, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
| | - Thomas G Hofmann
- Zelluläre Seneszenz-Gruppe, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie Allianz, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
| | - Bruno Kyewski
- Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany; and
| | - Jens Derbinski
- Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany; and
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Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M. The EHEC-host interactome reveals novel targets for the translocated intimin receptor. Sci Rep 2014; 4:7531. [PMID: 25519916 PMCID: PMC4269881 DOI: 10.1038/srep07531] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/21/2014] [Indexed: 12/20/2022] Open
Abstract
Enterohemorrhagic E. coli (EHEC) manipulate their human host through at least 39 effector proteins which hijack host processes through direct protein-protein interactions (PPIs). To identify their protein targets in the host cells, we performed yeast two-hybrid screens, allowing us to find 48 high-confidence protein-protein interactions between 15 EHEC effectors and 47 human host proteins. In comparison to other bacteria and viruses we found that EHEC effectors bind more frequently to hub proteins as well as to proteins that participate in a higher number of protein complexes. The data set includes six new interactions that involve the translocated intimin receptor (TIR), namely HPCAL1, HPCAL4, NCALD, ARRB1, PDE6D, and STK16. We compared these TIR interactions in EHEC and enteropathogenic E. coli (EPEC) and found that five interactions were conserved. Notably, the conserved interactions included those of serine/threonine kinase 16 (STK16), hippocalcin-like 1 (HPCAL1) as well as neurocalcin-delta (NCALD). These proteins co-localize with the infection sites of EPEC. Furthermore, our results suggest putative functions of poorly characterized effectors (EspJ, EspY1). In particular, we observed that EspJ is connected to the microtubule system while EspY1 appears to be involved in apoptosis/cell cycle regulation.
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Affiliation(s)
- Sonja Blasche
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Stefan Arens
- Institute of Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster
| | - Arnaud Ceol
- 1] Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain [2] Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan - Italy
| | - Gabriella Siszler
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - M Alexander Schmidt
- Institute of Infectiology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster
| | - Roman Häuser
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Frank Schwarz
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Stefan Wuchty
- 1] Dept. of Computer Science, Univ. of Miami, 1365 Memorial Drive, Coral Gables, FL 33146, USA [2] Center for Computational Science, Univ. of Miami, 1365 Memorial Drive, Coral Gables, FL 33146, USA
| | - Patrick Aloy
- 1] Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Theresia Stradal
- 1] Institute of Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster [2] Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig
| | - Manfred Koegl
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Peláez-García A, Barderas R, Batlle R, Viñas-Castells R, Bartolomé RA, Torres S, Mendes M, Lopez-Lucendo M, Mazzolini R, Bonilla F, García de Herreros A, Casal JI. A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation. Mol Cell Proteomics 2014; 14:303-15. [PMID: 25505127 DOI: 10.1074/mcp.m114.045328] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Adipogenesis requires a differentiation program driven by multiple transcription factors, where PPARγ and C/EBPα play a central role. Recent findings indicate that Snail inhibits adipocyte differentiation in 3T3-L1 and murine mesenchymal stem cells (mMSC). An in-depth quantitative SILAC analysis of the nuclear fraction of Snail-induced alterations of 3T3-L1 cells was carried out. In total, 2251 overlapping proteins were simultaneously quantified in forward and reverse experiments. We observed 574 proteins deregulated by Snail1 using a fold-change ≥1.5, with 111 up- and 463 down-regulated proteins, respectively. Among other proteins, multiple transcription factors such as Trip4, OsmR, Nr2f6, Cbx6, and Prrx1 were down-regulated. Results were validated in 3T3-L1 cells and mMSC cells by Western blot and quantitative PCR. Knock-down experiments in 3T3-L1 cells demonstrated that only Nr2f6 (and Trip4 at minor extent) was required for adipocyte differentiation. Ectopic expression of Nr2f6 reversed the effects of Snail1 and promoted adipogenesis. Because Nr2f6 inhibits the expression of IL-17, we tested the effect of Snail on IL-17 expression. IL-17 and TNFα were among the most up-regulated pro-inflammatory cytokines in Snail-transfected 3T3-L1 and mMSC cells. Furthermore, the blocking of IL-17 activity in Snail-transfected cells promoted adipocyte differentiation, reverting Snail inhibition. In summary, Snail inhibits adipogenesis through a down-regulation of Nr2f6, which in turn facilitates the expression of IL-17, an anti-adipogenic cytokine. These results would support a novel and important role for Snail and Nr2f6 in obesity control.
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Affiliation(s)
- Alberto Peláez-García
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Rodrigo Barderas
- §Departamento de Biochemistry and Molecular Biology Department I, Universidad Complutense de Madrid, Spain
| | | | | | - Rubén A Bartolomé
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Sofía Torres
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Marta Mendes
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - María Lopez-Lucendo
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | | | - Félix Bonilla
- ‖Hospital Puerta de Hierro, Majadahonda, Madrid, Spain
| | | | - J Ignacio Casal
- From the ‡Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain;
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37
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Bazot Q, Deschamps T, Tafforeau L, Siouda M, Leblanc P, Harth-Hertle ML, Rabourdin-Combe C, Lotteau V, Kempkes B, Tommasino M, Gruffat H, Manet E. Epstein-Barr virus nuclear antigen 3A protein regulates CDKN2B transcription via interaction with MIZ-1. Nucleic Acids Res 2014; 42:9700-16. [PMID: 25092922 PMCID: PMC4150796 DOI: 10.1093/nar/gku697] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Epstein-Barr virus (EBV) nuclear antigen 3 family of protein is critical for the EBV-induced primary B-cell growth transformation process. Using a yeast two-hybrid screen we identified 22 novel cellular partners of the EBNA3s. Most importantly, among the newly identified partners, five are known to play direct and important roles in transcriptional regulation. Of these, the Myc-interacting zinc finger protein-1 (MIZ-1) is a transcription factor initially characterized as a binding partner of MYC. MIZ-1 activates the transcription of a number of target genes including the cell cycle inhibitor CDKN2B. Focusing on the EBNA3A/MIZ-1 interaction we demonstrate that binding occurs in EBV-infected cells expressing both proteins at endogenous physiological levels and that in the presence of EBNA3A, a significant fraction of MIZ-1 translocates from the cytoplasm to the nucleus. Moreover, we show that a trimeric complex composed of a MIZ-1 recognition DNA element, MIZ-1 and EBNA3A can be formed, and that interaction of MIZ-1 with nucleophosmin (NPM), one of its coactivator, is prevented by EBNA3A. Finally, we show that, in the presence of EBNA3A, expression of the MIZ-1 target gene, CDKN2B, is downregulated and repressive H3K27 marks are established on its promoter region suggesting that EBNA3A directly counteracts the growth inhibitory action of MIZ-1.
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Affiliation(s)
- Quentin Bazot
- CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses team, Université de Lyon, Lyon 69364, France Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France
| | - Thibaut Deschamps
- CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses team, Université de Lyon, Lyon 69364, France Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France
| | - Lionel Tafforeau
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France Ecole Normale Supérieure de Lyon, Lyon 69364, France
| | - Maha Siouda
- International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Pascal Leblanc
- CNRS, UMR5308, Lyon 69364, France CNRS UMR5239, Laboratoire de Biologie de la Cellule, Lyon 69364, France
| | - Marie L Harth-Hertle
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Chantal Rabourdin-Combe
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France Ecole Normale Supérieure de Lyon, Lyon 69364, France
| | - Vincent Lotteau
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France Ecole Normale Supérieure de Lyon, Lyon 69364, France
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Massimo Tommasino
- International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Henri Gruffat
- CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses team, Université de Lyon, Lyon 69364, France Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France
| | - Evelyne Manet
- CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses team, Université de Lyon, Lyon 69364, France Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections team, Université de Lyon, Lyon 69364, France INSERM, U1111, Lyon 69364, France CNRS, UMR5308, Lyon 69364, France
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NR4A nuclear receptors are orphans but not lonesome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2543-2555. [PMID: 24975497 DOI: 10.1016/j.bbamcr.2014.06.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 01/23/2023]
Abstract
The NR4A subfamily of nuclear receptors consists of three mammalian members: Nur77, Nurr1, and NOR-1. The NR4A receptors are involved in essential physiological processes such as adaptive and innate immune cell differentiation, metabolism and brain function. They act as transcription factors that directly modulate gene expression, but can also form trans-repressive complexes with other transcription factors. In contrast to steroid hormone nuclear receptors such as the estrogen receptor or the glucocorticoid receptor, no ligands have been described for the NR4A receptors. This lack of known ligands might be explained by the structure of the ligand-binding domain of NR4A receptors, which shows an active conformation and a ligand-binding pocket that is filled with bulky amino acid side-chains. Other mechanisms, such as transcriptional control, post-translational modifications and protein-protein interactions therefore seem to be more important in regulating the activity of the NR4A receptors. For Nur77, over 80 interacting proteins (the interactome) have been identified so far, and roughly half of these interactions has been studied in more detail. Although the NR4As show some overlap in interacting proteins, less information is available on the interactome of Nurr1 and NOR-1. Therefore, the present review will describe the current knowledge on the interactomes of all three NR4A nuclear receptors with emphasis on Nur77.
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Abstract
Crystal structures represent the static picture in the life of a molecule giving a sneak preview what it might be in reality. Hence, it is very hard to extrapolate from these photos toward dynamic processes such as transcriptional regulation. Mechanistically VDR may be considered as molecular machine able to perform ligand-, DNA- and protein recognition, and interaction in a multi-task manner. Taking this into account the functional net effect will be the combination of all these processes. The long awaited answer to explain the differences in physiological effects for various ligands was one of the biggest disappointment that crystal structures provided since no substantial distinction could be made for the conformation of the active VDR-ligand complexes. This may have come from the limitation on the complexity of the available ligand-VDR structures. The recent studies with full length VDR-RXRα showed somewhat more comprehensive perspective for the 3D organization and possible function of the VDR-RXRα-cofactor complex. In addition to in vitro approaches, also computational tools had been introduced with the aim to get understanding on the mechanic and dynamic properties of the VDR complexes with some success. Using these methods and based on measurable descriptors such as pocket size and positions of side chains it is possible to note subtle differences between the structures. The meaning of these differences has not been fully understood yet but the possibility of a “butterfly effect” may have more extreme consequences in terms of VDR signaling. In this review, the three functional aspects (ligand-, DNA- and protein recognition, and binding) will be discussed with respect to available data as well as possible implication and questions that may be important to address in the future.
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Affiliation(s)
- Ferdinand Molnár
- Faculty of Health Sciences, School of Pharmacy, Institute of Biopharmacy, University of Eastern Finland Kuopio, Finland
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40
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Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells. PLoS Genet 2014; 10:e1004339. [PMID: 24811540 PMCID: PMC4014424 DOI: 10.1371/journal.pgen.1004339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 03/17/2014] [Indexed: 02/04/2023] Open
Abstract
We previously reported that TR2 and TR4 orphan nuclear receptors bind to direct repeat (DR) elements in the ε- and γ-globin promoters, and act as molecular anchors for the recruitment of epigenetic corepressors of the multifaceted DRED complex, thereby leading to ε- and γ-globin transcriptional repression during definitive erythropoiesis. Other than the ε- and γ-globin and the GATA1 genes, TR4-regulated target genes in human erythroid cells remain unknown. Here, we identified TR4 binding sites genome-wide using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) as human primary CD34+ hematopoietic progenitors differentiated progressively to late erythroid precursors. We also performed whole transcriptome analyses by RNA-seq to identify TR4 downstream targets after lentiviral-mediated TR4 shRNA knockdown in erythroid cells. Analyses from combined ChIP-seq and RNA-seq datasets indicate that DR1 motifs are more prevalent in the proximal promoters of TR4 direct target genes, which are involved in basic biological functions (e.g., mRNA processing, ribosomal assembly, RNA splicing and primary metabolic processes). In contrast, other non-DR1 repeat motifs (DR4, ER6 and IR1) are more prevalent at gene-distal TR4 binding sites. Of these, approximately 50% are also marked with epigenetic chromatin signatures (such as P300, H3K27ac, H3K4me1 and H3K27me3) associated with enhancer function. Thus, we hypothesize that TR4 regulates gene transcription via gene-proximal DR1 sites as TR4/TR2 heterodimers, while it can associate with novel nuclear receptor partners (such as RXR) to bind to distant non-DR1 consensus sites. In summary, this study reveals that the TR4 regulatory network is far more complex than previously appreciated and that TR4 regulates basic, essential biological processes during the terminal differentiation of human erythroid cells. Sequential genome-wide binding studies investigated by deep sequencing (ChIP-seq) represent a powerful tool for investigating the temporal sequence of gene activation and repression events that take place as cells differentiate. Here, we report the binding of an “orphan” nuclear receptor (one for which no ligand has been identified) to its cognate genomic regulatory sites and perform the functional analysis to validate its downstream targets as precursor cells differentiate from very early human hematopoietic progenitors into red blood cells. We discovered that when this receptor is bound at gene proximal promoters, it recognizes a different DNA sequence than when it binds to more distant regulatory sites (enhancers and silencers). Since this receptor can either activate or repress specific target genes, the data suggest the intriguing possibility that the two different modes of DNA recognition may reflect association of the receptor with different partner molecules when regulating gene expression from proximal or distal sequences.
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Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury. Proc Natl Acad Sci U S A 2014; 111:E1149-58. [PMID: 24616509 DOI: 10.1073/pnas.1402318111] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Neuronal calcium (Ca(2+))-binding proteins 1 and 2 (NECAB1/2) are members of the phylogenetically conserved EF-hand Ca(2+)-binding protein superfamily. To date, NECABs have been explored only to a limited extent and, so far, not at all at the spinal level. Here, we describe the distribution, phenotype, and nerve injury-induced regulation of NECAB1/NECAB2 in mouse dorsal root ganglia (DRGs) and spinal cord. In DRGs, NECAB1/2 are expressed in around 70% of mainly small- and medium-sized neurons. Many colocalize with calcitonin gene-related peptide and isolectin B4, and thus represent nociceptors. NECAB1/2 neurons are much more abundant in DRGs than the Ca(2+)-binding proteins (parvalbumin, calbindin, calretinin, and secretagogin) studied to date. In the spinal cord, the NECAB1/2 distribution is mainly complementary. NECAB1 labels interneurons and a plexus of processes in superficial layers of the dorsal horn, commissural neurons in the intermediate area, and motor neurons in the ventral horn. Using CLARITY, a novel, bilaterally connected neuronal system with dendrites that embrace the dorsal columns like palisades is observed. NECAB2 is present in cell bodies and presynaptic boutons across the spinal cord. In the dorsal horn, most NECAB1/2 neurons are glutamatergic. Both NECAB1/2 are transported into dorsal roots and peripheral nerves. Peripheral nerve injury reduces NECAB2, but not NECAB1, expression in DRG neurons. Our study identifies NECAB1/2 as abundant Ca(2+)-binding proteins in pain-related DRG neurons and a variety of spinal systems, providing molecular markers for known and unknown neuron populations of mechanosensory and pain circuits in the spinal cord.
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Woodsmith J, Stelzl U. Studying post-translational modifications with protein interaction networks. Curr Opin Struct Biol 2014; 24:34-44. [DOI: 10.1016/j.sbi.2013.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 12/14/2022]
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Kempf A, Tews B, Arzt ME, Weinmann O, Obermair FJ, Pernet V, Zagrebelsky M, Delekate A, Iobbi C, Zemmar A, Ristic Z, Gullo M, Spies P, Dodd D, Gygax D, Korte M, Schwab ME. The sphingolipid receptor S1PR2 is a receptor for Nogo-a repressing synaptic plasticity. PLoS Biol 2014; 12:e1001763. [PMID: 24453941 PMCID: PMC3891622 DOI: 10.1371/journal.pbio.1001763] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/02/2013] [Indexed: 01/11/2023] Open
Abstract
This study identifies a GPCR, S1PR2, as a receptor for the Nogo-A-Δ20 domain of the membrane protein Nogo-A, which inhibits neuronal growth and synaptic plasticity. Nogo-A is a membrane protein of the central nervous system (CNS) restricting neurite growth and synaptic plasticity via two extracellular domains: Nogo-66 and Nogo-A-Δ20. Receptors transducing Nogo-A-Δ20 signaling remained elusive so far. Here we identify the G protein-coupled receptor (GPCR) sphingosine 1-phosphate receptor 2 (S1PR2) as a Nogo-A-Δ20-specific receptor. Nogo-A-Δ20 binds S1PR2 on sites distinct from the pocket of the sphingolipid sphingosine 1-phosphate (S1P) and signals via the G protein G13, the Rho GEF LARG, and RhoA. Deleting or blocking S1PR2 counteracts Nogo-A-Δ20- and myelin-mediated inhibition of neurite outgrowth and cell spreading. Blockade of S1PR2 strongly enhances long-term potentiation (LTP) in the hippocampus of wild-type but not Nogo-A−/− mice, indicating a repressor function of the Nogo-A/S1PR2 axis in synaptic plasticity. A similar increase in LTP was also observed in the motor cortex after S1PR2 blockade. We propose a novel signaling model in which a GPCR functions as a receptor for two structurally unrelated ligands, a membrane protein and a sphingolipid. Elucidating Nogo-A/S1PR2 signaling platforms will provide new insights into regulation of synaptic plasticity. Recent studies have demonstrated an important role of Nogo-A signaling in the repression of structural and synaptic plasticity in mature neuronal networks of the central nervous system. These insights extended our understanding of Nogo-A's inhibitory function far beyond its well-studied role as axonal-growth inhibitor. Repression is mediated via two different Nogo-A extracellular domains: Nogo-66 and Nogo-A-Δ20. Here, we identify the G-protein coupled receptor S1PR2 as a high-affinity receptor for Nogo-A-Δ20 and demonstrate that S1PR2 binds this domain with sites different from the recently proposed S1P binding pocket. Interfering with S1PR2 activity, either pharmacologically or genetically, prevented Nogo-A-Δ20-mediated inhibitory effects. Similar results were obtained when we blocked G13, LARG, and RhoA, components of the downstream signaling pathway. These findings revealed a strong increase in hippocampal and cortical synaptic plasticity when acutely interfering with Nogo-A/S1PR2 signaling, similar to previous results obtained by blocking Nogo-A. We thus provide a novel biological concept of multi-ligand GPCR signaling in which this sphingolipid-activated GPCR is also bound and activated by the high molecular weight membrane protein Nogo-A.
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Affiliation(s)
- Anissa Kempf
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Bjoern Tews
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Michael E. Arzt
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Oliver Weinmann
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Franz J. Obermair
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Vincent Pernet
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Marta Zagrebelsky
- Zoological Institute, Division of Cellular Neurobiology, TU Braunschweig, Braunschweig, Germany
| | - Andrea Delekate
- Zoological Institute, Division of Cellular Neurobiology, TU Braunschweig, Braunschweig, Germany
| | - Cristina Iobbi
- Zoological Institute, Division of Cellular Neurobiology, TU Braunschweig, Braunschweig, Germany
| | - Ajmal Zemmar
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Zorica Ristic
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Miriam Gullo
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Peter Spies
- School of Life Sciences, University of Applied Life Sciences Northwestern Switzerland, Muttenz, Switzerland
| | - Dana Dodd
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Daniel Gygax
- School of Life Sciences, University of Applied Life Sciences Northwestern Switzerland, Muttenz, Switzerland
| | - Martin Korte
- Zoological Institute, Division of Cellular Neurobiology, TU Braunschweig, Braunschweig, Germany
| | - Martin E. Schwab
- Brain Research Institute, University of Zurich, and Dept. of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
- * E-mail:
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Teske K, Nandhikonda P, Bogart JW, Feleke B, Sidhu P, Yuan N, Preston J, Goy R, Arnold LA. Modulation of Transcription mediated by the Vitamin D Receptor and the Peroxisome Proliferator-Activated Receptor δ in the presence of GW0742 analogs. ACTA ACUST UNITED AC 2014; 3. [PMID: 25485183 DOI: 10.4172/2167-7956.1000111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herein we describe the evaluation of GW0742 analogs in respect to their ability to modulate transcription mediated by the vitamin D receptor (VDR) and the peroxisome proliferator activated receptor (PPAR) δ. The GW0742 analog bearing a carboxylic ester functionality in place of the carboxylic acid was partially activating both nuclear receptors at low concentration and inhibited transcription at higher compound concentrations. The GW0742 alcohol derivative was more active than the ester in respect to VDR but less active in regard to PPARδ. Importantly, the alcohol derivative was significantly more toxic than the corresponding acid and ester.
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Affiliation(s)
- Kelly Teske
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | | | - Jonathan W Bogart
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Belaynesh Feleke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Preetpal Sidhu
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Nina Yuan
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Joshua Preston
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Robin Goy
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Leggy A Arnold
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, WI 53211, USA
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Abstract
Continuous synthesis of all cellular components requires their constant turnover in order for a cell to achieve homeostasis. To this end, eukaryotic cells are endowed with two degradation pathways - the ubiquitin-proteasome system and the lysosomal pathway. The latter pathway is partly fed by autophagy, which targets intracellular material in distinct vesicles, termed autophagosomes, to the lysosome. Central to this pathway is a set of key autophagy proteins, including the ubiquitin-like modifier Atg8, that orchestrate autophagosome initiation and biogenesis. In higher eukaryotes, the Atg8 family comprises six members known as the light chain 3 (LC3) or γ-aminobutyric acid (GABA)-receptor-associated protein (GABARAP) proteins. Considerable effort during the last 15 years to decipher the molecular mechanisms that govern autophagy has significantly advanced our understanding of the functioning of this protein family. In this Cell Science at a Glance article and the accompanying poster, we present the current LC3 protein interaction network, which has been and continues to be vital for gaining insight into the regulation of autophagy.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry II, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Sahni N, Yi S, Zhong Q, Jailkhani N, Charloteaux B, Cusick ME, Vidal M. Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev 2013; 23:649-57. [PMID: 24287335 DOI: 10.1016/j.gde.2013.11.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/06/2013] [Accepted: 11/01/2013] [Indexed: 11/17/2022]
Abstract
Classical 'one-gene/one-disease' models cannot fully reconcile with the increasingly appreciated prevalence of complicated genotype-to-phenotype associations in human disease. Genes and gene products function not in isolation but as components of intricate networks of macromolecules (DNA, RNA, or proteins) and metabolites linked through biochemical or physical interactions, represented in 'interactome' network models as 'nodes' and 'edges', respectively. Accordingly, mechanistic understanding of human disease will require understanding of how disease-causing mutations affect systems or interactome properties. The study of 'edgetics' uncovers specific loss or gain of interactions (edges) to interpret genotype-to-phenotype relationships. We review how distinct genetic variants, the genotype, lead to distinct phenotypic outcomes, the phenotype, through edgetic perturbations in interactome networks altogether representing the 'edgotype'.
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Affiliation(s)
- Nidhi Sahni
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Li H, Dou W, Padikkala E, Mani S. Reverse yeast two-hybrid system to identify mammalian nuclear receptor residues that interact with ligands and/or antagonists. J Vis Exp 2013:e51085. [PMID: 24300333 DOI: 10.3791/51085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
As a critical regulator of drug metabolism and inflammation, Pregnane X Receptor (PXR), plays an important role in disease pathophysiology linking metabolism and inflammation (e.g. hepatic steatosis)(1,2). There has been much progress in the identification of agonist ligands for PXR, however, there are limited descriptions of drug-like antagonists and their binding sites on PXR(3,4,5). A critical barrier has been the inability to efficiently purify full-length protein for structural studies with antagonists despite the fact that PXR was cloned and characterized in 1998. Our laboratory developed a novel high throughput yeast based two-hybrid assay to define an antagonist, ketoconazole's, binding residues on PXR(6). Our method involves creating mutational libraries that would rescue the effect of single mutations on the AF-2 surface of PXR expected to interact with ketoconazole. Rescue or "gain-of-function" second mutations can be made such that conclusions regarding the genetic interaction of ketoconazole and the surface residue(s) on PXR are feasible. Thus, we developed a high throughput two-hybrid yeast screen of PXR mutants interacting with its coactivator, SRC-1. Using this approach, in which the yeast was modified to accommodate the study of the antifungal drug, ketoconazole, we could demonstrate specific mutations on PXR enriched in clones unable to bind to ketoconazole. By reverse logic, we conclude that the original residues are direct interaction residues with ketoconazole. This assay represents a novel, tractable genetic assay to screen for antagonist binding sites on nuclear receptor surfaces. This assay could be applied to any drug regardless of its cytotoxic potential to yeast as well as to cellular protein(s) that cannot be studied using standard structural biology or proteomic based methods. Potential pitfalls include interpretation of data (complementary methods useful), reliance on single Y2H method, expertise in handling yeast or performing yeast two-hybrid assays, and assay optimization.
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Affiliation(s)
- Hao Li
- Department of Genetics, Albert Einstein College of Medicine
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Chan CM, Fulton J, Montiel-Duarte C, Collins HM, Bharti N, Wadelin FR, Moran PM, Mongan NP, Heery DM. A signature motif mediating selective interactions of BCL11A with the NR2E/F subfamily of orphan nuclear receptors. Nucleic Acids Res 2013; 41:9663-79. [PMID: 23975195 PMCID: PMC3834829 DOI: 10.1093/nar/gkt761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite their physiological importance, selective interactions between nuclear receptors (NRs) and their cofactors are poorly understood. Here, we describe a novel signature motif (F/YSXXLXXL/Y) in the developmental regulator BCL11A that facilitates its selective interaction with members of the NR2E/F subfamily. Two copies of this motif (named here as RID1 and RID2) permit BCL11A to bind COUP-TFs (NR2F1;NR2F2;NR2F6) and Tailless/TLX (NR2E1), whereas RID1, but not RID2, binds PNR (NR2E3). We confirmed the existence of endogenous BCL11A/TLX complexes in mouse cortex tissue. No interactions of RID1 and RID2 with 20 other ligand-binding domains from different NR subtypes were observed. We show that RID1 and RID2 are required for BCL11A-mediated repression of endogenous γ-globin gene and the regulatory non-coding transcript Bgl3, and we identify COUP-TFII binding sites within the Bgl3 locus. In addition to their importance for BCL11A function, we show that F/YSXXLXXL/Y motifs are conserved in other NR cofactors. A single FSXXLXXL motif in the NR-binding SET domain protein NSD1 facilitates its interactions with the NR2E/F subfamily. However, the NSD1 motif incorporates features of both LXXLL and FSXXLXXL motifs, giving it a distinct NR-binding pattern in contrast to other cofactors. In summary, our results provide new insights into the selectivity of NR/cofactor complex formation.
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Affiliation(s)
- Chun Ming Chan
- Gene Regulation Group, Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK, School of Psychology, University of Nottingham, Nottingham NG7 2RD, UK and School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2RD, UK
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Griffiths SJ, Koegl M, Boutell C, Zenner HL, Crump CM, Pica F, Gonzalez O, Friedel CC, Barry G, Martin K, Craigon MH, Chen R, Kaza LN, Fossum E, Fazakerley JK, Efstathiou S, Volpi A, Zimmer R, Ghazal P, Haas J. A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PLoS Pathog 2013; 9:e1003514. [PMID: 23950709 PMCID: PMC3738494 DOI: 10.1371/journal.ppat.1003514] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/24/2013] [Indexed: 11/24/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome.
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Affiliation(s)
| | - Manfred Koegl
- Preclinical Target Development and Genomics and Proteomics Core Facilities, German Cancer Research Center, Heidelberg, Germany
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Helen L. Zenner
- Division of Virology, Department of Pathology Cambridge University, Cambridge, United Kingdom
| | - Colin M. Crump
- Division of Virology, Department of Pathology Cambridge University, Cambridge, United Kingdom
| | | | - Orland Gonzalez
- Institute for Informatics, Ludwig-Maximilians Universität München, München, Germany
| | - Caroline C. Friedel
- Institute for Informatics, Ludwig-Maximilians Universität München, München, Germany
| | - Gerald Barry
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Kim Martin
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Marie H. Craigon
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rui Chen
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Lakshmi N. Kaza
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Even Fossum
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - John K. Fazakerley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Stacey Efstathiou
- Division of Virology, Department of Pathology Cambridge University, Cambridge, United Kingdom
| | | | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians Universität München, München, Germany
| | - Peter Ghazal
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, United Kingdom
| | - Jürgen Haas
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Max von Pettenkofer Institut, Ludwig-Maximilians Universität München, München, Germany
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50
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de Chassey B, Aublin-Gex A, Ruggieri A, Meyniel-Schicklin L, Pradezynski F, Davoust N, Chantier T, Tafforeau L, Mangeot PE, Ciancia C, Perrin-Cocon L, Bartenschlager R, André P, Lotteau V. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication. PLoS Pathog 2013; 9:e1003440. [PMID: 23853584 PMCID: PMC3701712 DOI: 10.1371/journal.ppat.1003440] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/06/2013] [Indexed: 12/24/2022] Open
Abstract
Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution. Viruses are obligate intracellular parasites that rely on cellular functions for efficient replication. As most biological processes are sustained by protein-protein interactions, the identification of interactions between viral and host proteins can provide a global overview about the cellular functions engaged during viral replication. Influenza viruses express 13 viral proteins, including NS1 and NS2, which are translated from an alternatively spliced RNA derived from the same genome segment. We present here a comprehensive overview of possible interactions of cellular proteins with NS1 and NS2 from 9 viral strains. Seventy nine cellular proteins were identified to interact with NS1, NS2 or both NS1 and NS2. These interacting host cell proteins are potentially involved in many steps of the virus life cycle and 7 can directly control the viral replication. Most of the cellular targets are shared by the majority of the virus strains, especially the double-stranded RNA binding domain protein family that is strikingly targeted by NS1. One of its members, ADAR1, is essential for influenza virus replication. ADAR1 colocalizes with NS1 in nuclear structures and its editing activity is enhanced by NS1 expressed on its own and during virus infection. A similar phenomenon is observed for dengue virus whose NS3 protein also interacts with ADAR1, suggesting a parallel virus-host co-evolution.
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Affiliation(s)
- Benoît de Chassey
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
| | - Anne Aublin-Gex
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Alessia Ruggieri
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Laurène Meyniel-Schicklin
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Fabrine Pradezynski
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Nathalie Davoust
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Thibault Chantier
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Lionel Tafforeau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Philippe-Emmanuel Mangeot
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Claire Ciancia
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Patrice André
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
- * E-mail:
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