1
|
Tao Y, Budhipramono A, Huang J, Fang M, Xie S, Kim J, Khivansara V, Dominski Z, Tong L, De Brabander JK, Nijhawan D. Anticancer benzoxaboroles block pre-mRNA processing by directly inhibiting CPSF3. Cell Chem Biol 2024; 31:139-149.e14. [PMID: 37967558 PMCID: PMC10841686 DOI: 10.1016/j.chembiol.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/31/2023] [Accepted: 10/25/2023] [Indexed: 11/17/2023]
Abstract
A novel class of benzoxaboroles was reported to induce cancer cell death but the mechanism was unknown. Using a forward genetics platform, we discovered mutations in cleavage and polyadenylation specific factor 3 (CPSF3) that reduce benzoxaborole binding and confer resistance. CPSF3 is the endonuclease responsible for pre-mRNA 3'-end processing, which is also important for RNA polymerase II transcription termination. Benzoxaboroles inhibit this endonuclease activity of CPSF3 in vitro and also curb transcriptional termination in cells, which results in the downregulation of numerous constitutively expressed genes. Furthermore, we used X-ray crystallography to demonstrate that benzoxaboroles bind to the active site of CPSF3 in a manner distinct from the other known inhibitors of CPSF3. The benzoxaborole compound impeded the growth of cancer cell lines derived from different lineages. Our results suggest benzoxaboroles may represent a promising lead as CPSF3 inhibitors for clinical development.
Collapse
Affiliation(s)
- Ye Tao
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Albert Budhipramono
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ji Huang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Min Fang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shanhai Xie
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vishal Khivansara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics and Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Jef K De Brabander
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Deepak Nijhawan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
2
|
Kogaki T, Hase H, Tanimoto M, Tashiro A, Kitae K, Ueda Y, Jingushi K, Tsujikawa K. ALKBH4 is a novel enzyme that promotes translation through modified uridine regulation. J Biol Chem 2023; 299:105093. [PMID: 37507018 PMCID: PMC10465949 DOI: 10.1016/j.jbc.2023.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Epitranscriptomics studies the mechanisms of acquired RNA modifications. The epitranscriptome is dynamically regulated by specific enzymatic reactions, and the proper execution of these enzymatic RNA modifications regulates a variety of physiological RNA functions. However, the lack of experimental tools, such as antibodies for RNA modification, limits the development of epitranscriptomic research. Furthermore, the regulatory enzymes of many RNA modifications have not yet been identified. Herein, we aimed to identify new molecular mechanisms involved in RNA modification by focusing on the AlkB homolog (ALKBH) family molecules, a family of RNA demethylases. We demonstrated that ALKBH4 interacts with small RNA, regulating the formation and metabolism of the (R)-5-carboxyhydroxymethyl uridine methyl ester. We also found that the reaction of ALKBH4 with small RNA enhances protein translation efficiency in an in vitro assay system. These findings indicate that ALKBH4 is involved in the regulation of uridine modification and expand on the role of tRNA-mediated translation control through ALKBH4.
Collapse
Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Masaya Tanimoto
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Atyuya Tashiro
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
3
|
Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
Collapse
Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| |
Collapse
|
4
|
Rico-Díaz A, Barreiro-Alonso A, Rey-Souto C, Becerra M, Lamas-Maceiras M, Cerdán ME, Vizoso-Vázquez Á. The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis. Biomolecules 2021; 11:biom11091392. [PMID: 34572607 PMCID: PMC8465852 DOI: 10.3390/biom11091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
In the traditional fermentative model yeast Saccharomyces cerevisiae, ScIxr1 is an HMGB (High Mobility Group box B) protein that has been considered as an important regulator of gene transcription in response to external changes like oxygen, carbon source, or nutrient availability. Kluyveromyces lactis is also a useful eukaryotic model, more similar to many human cells due to its respiratory metabolism. We cloned and functionally characterized by different methodologies KlIXR1, which encodes a protein with only 34.4% amino acid sequence similarity to ScIxr1. Our data indicate that both proteins share common functions, including their involvement in the response to hypoxia or oxidative stress induced by hydrogen peroxide or metal treatments, as well as in the control of key regulators for maintenance of the dNTP (deoxyribonucleotide triphosphate) pool and ribosome synthesis. KlIxr1 is able to bind specific regulatory DNA sequences in the promoter of its target genes, which are well conserved between S. cerevisiae and K. lactis. Oppositely, we found important differences between ScIrx1 and KlIxr1 affecting cellular responses to cisplatin or cycloheximide in these yeasts, which could be dependent on specific and non-conserved domains present in these two proteins.
Collapse
|
5
|
McFadden MJ, McIntyre ABR, Mourelatos H, Abell NS, Gokhale NS, Ipas H, Xhemalçe B, Mason CE, Horner SM. Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine. Cell Rep 2021; 34:108798. [PMID: 33657363 PMCID: PMC7981787 DOI: 10.1016/j.celrep.2021.108798] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/18/2020] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Type I interferons (IFNs) induce hundreds of IFN-stimulated genes (ISGs) in response to viral infection. Induction of these ISGs must be regulated for an efficient and controlled antiviral response, but post-transcriptional controls of these genes have not been well defined. Here, we identify a role for the RNA base modification N6-methyladenosine (m6A) in the regulation of ISGs. Using ribosome profiling and quantitative mass spectrometry, coupled with m6A-immunoprecipitation and sequencing, we identify a subset of ISGs, including IFITM1, whose translation is enhanced by m6A and the m6A methyltransferase proteins METTL3 and METTL14. We further determine that the m6A reader YTHDF1 increases the expression of IFITM1 in an m6A-binding-dependent manner. Importantly, we find that the m6A methyltransferase complex promotes the antiviral activity of type I IFN. Thus, these studies identify m6A as having a role in post-transcriptional control of ISG translation during the type I IFN response for antiviral restriction.
Collapse
Affiliation(s)
- Michael J McFadden
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10021, USA
| | - Haralambos Mourelatos
- Weill Cornell/Rockefeller/Memorial Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Nathan S Abell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hélène Ipas
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Blerta Xhemalçe
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| |
Collapse
|
6
|
Gonella-Diaza AM, Lopes E, Ribeiro da Silva K, Perecin Nociti R, Mamede Andrade G, Atuesta-Bustos JE, Coelho da Silveira J, Vieira Meirelles F, Binelli M. Steroidal Regulation of Oviductal microRNAs Is Associated with microRNA-Processing in Beef Cows. Int J Mol Sci 2021; 22:953. [PMID: 33477993 PMCID: PMC7835783 DOI: 10.3390/ijms22020953] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
Information on molecular mechanisms through which sex-steroids regulate oviductal function to support early embryo development is lacking. Here, we hypothesized that the periovulatory endocrine milieu affects the miRNA processing machinery and miRNA expression in bovine oviductal tissues. Growth of the preovulatory follicle was controlled to obtain cows that ovulated a small follicle (SF) and subsequently bore a small corpus luteum (CL; SF-SCL) or a large follicle (LF) and large CL (LF-LCL). These groups differed in the periovulatory plasmatic sex-steroid's concentrations. Ampulla and isthmus samples were collected on day four of the estrous cycle. Abundance of DROSHA, DICER1, and AGO4 transcripts was greater in the ampulla than the isthmus. In the ampulla, transcription of these genes was greater for the SF-SCL group, while the opposite was observed in the isthmus. The expression of the 88 most abundant miRNAs and 14 miRNAs in the ampulla and 34 miRNAs in isthmus were differentially expressed between LF-LCL and SF-SCL groups. Integration of transcriptomic and miRNA data and molecular pathways enrichment showed that important pathways were inhibited in the SF-SCL group due to miRNA control. In conclusion, the endocrine milieu affects the miRNA expression in the bovine oviduct in a region-specific manner.
Collapse
Affiliation(s)
- Angela Maria Gonella-Diaza
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL 32446, USA;
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
| | - Everton Lopes
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
- Unianchieta, Av. Doutor Adoniro Ladeira, 94, (Km 55, 5 Rodovia Anhanguera), Jundiaí, SP 13210-795, Brazil
| | - Kauê Ribeiro da Silva
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
| | - Ricardo Perecin Nociti
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Gabriella Mamede Andrade
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Jorge Eduardo Atuesta-Bustos
- College of Agricultural Science—Agrarian University Foundation of Colombia-UNIAGRARIA, Calle 170 No 54a-10, Bogotá 111166, Colombia;
| | - Juliano Coelho da Silveira
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Mario Binelli
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
- Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611, USA
| |
Collapse
|
7
|
Ghazi T, Nagiah S, Chuturgoon AA. Fusaric acid decreases p53 expression by altering promoter methylation and m6A RNA methylation in human hepatocellular carcinoma (HepG2) cells. Epigenetics 2021; 16:79-91. [PMID: 32631113 PMCID: PMC7889137 DOI: 10.1080/15592294.2020.1788324] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/08/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
Fusaric acid (FA) is a food-borne mycotoxin that mediates toxicity with limited information on its epigenetic properties. p53 is a tumour suppressor protein that regulates cell cycle arrest and apoptotic cell death. The expression of p53 is regulated transcriptionally by promoter methylation and post-transcriptionally by N-6-methyladenosine (m6A) RNA methylation. We investigated the effect of FA on p53 expression and its epigenetic regulation via promoter methylation and m6A RNA methylation in human hepatocellular carcinoma (HepG2) cells. HepG2 cells were treated with FA [0, 25, 50, 104, and 150 µg/ml; 24 h] and thereafter, DNA, RNA, and protein was isolated. Promoter methylation and expression of p53 was measured using qPCR and Western blot. RNA immuno-precipitation was used to determine m6A-p53 levels. The expression of m6A methyltransferases (METTL3 and METTL14), demethylases (FTO and ALKBH5), and readers (YTHDF1-3 and YTHDC2) were measured using qPCR. FA induced p53 promoter hypermethylation (p < 0.0001) and decreased p53 expression (p < 0.0001). FA decreased m6A-p53 levels (p < 0.0001) by decreasing METTL3 (p < 0.0001) and METTL14 (p < 0.0001); and suppressed expression of YTHDF1 (p < 0.0001), YTHDF3 (p < 0.0001), and YTHDC2 (p < 0.0001) that ultimately reduced p53 translation (p < 0.0001). Taken together, the data shows that FA epigenetically decreased p53 expression by altering its promoter methylation and m6A RNA methylation in HepG2 cells. This study reveals a mechanism for p53 regulation by FA and provides insight into future therapeutic interventions.
Collapse
Affiliation(s)
- Terisha Ghazi
- Discipline of Medical Biochemistry and Chemical Pathology, School of Laboratory Medicine and Medical Science, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Savania Nagiah
- Discipline of Medical Biochemistry and Chemical Pathology, School of Laboratory Medicine and Medical Science, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Anil A. Chuturgoon
- Discipline of Medical Biochemistry and Chemical Pathology, School of Laboratory Medicine and Medical Science, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
8
|
Voelz C, Habib P, Köberlein S, Beyer C, Slowik A. Alteration of miRNA Biogenesis Regulating Proteins in the Human Microglial Cell Line HMC-3 After Ischemic Stress. Mol Neurobiol 2020; 58:1535-1549. [PMID: 33210205 DOI: 10.1007/s12035-020-02210-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNA) are small noncoding sequences that control apoptosis, proliferation, and neuroinflammatory pathways in microglia cells. The expression of distinct miRNAs is altered after ischemia in the brain. Only minor information is available about the biogenesis and maturation of miRNAs after ischemia. We aimed at examining the impact of oxygen-glucose deprivation (OGD) and hydrogen peroxide (H2O2)-induced stress on the expression of miRNA regulating proteins such as DROSHA, DGCR8, XPO5, DICER, TARBP2, and AGO2 in the cultured human microglial cell line HMC-3 (human microglial cell line clone 3). OGD duration of 2.5 h or H2O2 stimulation at a concentration of 100 μM for 24 h resulted in a marked increase of the hypoxia sensor hypoxia-inducible factor1-α in HMC-3 cells. These treatments also led to an upregulation of DROSHA, DICER1, and AGO2 detected by semiquantitative real-time PCR (qrtPCR). XPO5 and TARBP2 were only upregulated after stimulation with H2O2, while DGCR8 responded only to OGD. We found elevated DICER1, DROSHA, and AGO2 protein levels by western blot and immunohistochemistry staining. Interestingly, the latter also exposed a colocalization of AGO2 with stress granules (G3BP1) after OGD. Our data indicate that DICER, DROSHA, and AGO2 are induced in microglial cells under hypoxia-like conditions. It might be speculated that their inductions might increase the miRNA synthesis rate. Future studies should investigate this correlation to determine which miRNAs are preferably expressed by microglia cells after ischemia and which functions they could exert.
Collapse
Affiliation(s)
- Clara Voelz
- Institute of Neuroanatomy, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Pardes Habib
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Stefan Köberlein
- Institute of Neuroanatomy, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Cordian Beyer
- Institute of Neuroanatomy, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
- JARA-Brain, RWTH Aachen University, Aachen, Germany
| | - Alexander Slowik
- Institute of Neuroanatomy, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany.
- Department of Anatomy and Cell Biology, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany.
| |
Collapse
|
9
|
Yang L, Liu X, Song L, Su G, Di A, Bai C, Wei Z, Li G. Melatonin restores the pluripotency of long-term-cultured embryonic stem cells through melatonin receptor-dependent m6A RNA regulation. J Pineal Res 2020; 69:e12669. [PMID: 32415999 DOI: 10.1111/jpi.12669] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022]
Abstract
N6-methyladenosine (m6A) methylation is the most common and abundant modification on mammalian messenger RNA (mRNA) and regulates the pluripotency of embryonic stem cells (ESCs). Research has shown that melatonin plays a fundamental role in DNA and histone modifications. However, the effect of melatonin on RNA modification is unknown. Here, for the first time, we investigated the effect of melatonin on m6A modifications in long-term-cultured ESCs. Pluripotency studies indicated that 10 μmol/L melatonin sufficiently maintained ESCs with stemness features over 45 passages (more than 90 days). Notably, treatment of ESCs with melatonin led to a significant decrease in the nuclear presence of m6A methyltransferase complex and decreased global m6A modification. Depletion of melatonin receptor 1 (MT1) by CRISPR/Cas9 significantly reduced the effects of melatonin on ESC pluripotency and m6A modification. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that melatonin promotes stabilization of core pluripotency factors, such as Nanog, Sox2, Klf4, and c-Myc, by preventing m6A-dependent mRNA decay. Using cell signaling pathway profiling systems, melatonin was shown to regulate m6A modification predominantly through the MT1-JAK2/STAT3-Zfp217 signal axis. This study reveals a new dimension regarding melatonin regulation of gene expression at the RNA level.
Collapse
Affiliation(s)
- Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
| | - Xuefei Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
| | - Lishuang Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Anqi Di
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Zhuying Wei
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, Hohhot, China
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| |
Collapse
|
10
|
Drino A, Oberbauer V, Troger C, Janisiw E, Anrather D, Hartl M, Kaiser S, Kellner S, Schaefer MR. Production and purification of endogenously modified tRNA-derived small RNAs. RNA Biol 2020; 17:1104-1115. [PMID: 32138588 PMCID: PMC7549616 DOI: 10.1080/15476286.2020.1733798] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 01/20/2023] Open
Abstract
During particular stress conditions, transfer RNAs (tRNAs) become substrates of stress-induced endonucleases, resulting in the production of distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide range of biological processes, but how isoacceptor and even isodecoder-specific tsRNAs act at the molecular level is still poorly understood. Importantly, stress-induced tRNA cleavage affects only a few tRNAs of a given isoacceptor or isodecoder, raising the question as to how such limited molecule numbers could exert measurable biological impact. While the molecular function of individual tsRNAs is likely mediated through association with other molecules, addressing the interactome of specific tsRNAs has only been attempted by using synthetic RNA sequences. Since tRNAs carry post-transcriptional modifications, tsRNAs are likely modified but the extent of their modifications remains largely unknown. Here, we developed a biochemical framework for the production and purification of specific tsRNAs using human cells. Preparative scale purification of tsRNAs from biological sources should facilitate experimentally addressing as to how exactly these small RNAs mediate the multitude of reported molecular functions.
Collapse
Affiliation(s)
- Aleksej Drino
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Vienna, Austria
| | - Vera Oberbauer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Vienna, Austria
| | - Conor Troger
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Vienna, Austria
| | - Eva Janisiw
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, Max Perutz Laboratories (MPL), Vienna Biocenter (VBC), Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Laboratories (MPL), Vienna Biocenter (VBC), Vienna, Austria
| | | | | | - Matthias R. Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Vienna, Austria
| |
Collapse
|
11
|
Zhang QJ, Luan JC, Song LB, Cong R, Ji CJ, Zhou X, Xia JD, Song NH. m6A RNA methylation regulators correlate with malignant progression and have potential predictive values in clear cell renal cell carcinoma. Exp Cell Res 2020; 392:112015. [PMID: 32333907 DOI: 10.1016/j.yexcr.2020.112015] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A) has been reported to be involved in several biological processes in tumors. In this study, we found that most of the m6A RNA methylation regulators were not only differentially expressed between clear cell renal cell carcinoma (ccRCC) and normal but also among ccRCC stratified by different clinicopathologic characters. Two ccRCC subgroups, cluster 1 and 2, were identified using consensus clustering based on the expression of m6A methylation regulators. Although no obvious differences were observed between two subgroups regarding clinicopathologic characters, except gender, patients in cluster 1 had a relatively more favorable survival rate than cluster 2. Moreover, we established a risk signature with two m6A methylation regulators, METTL3 and METTL14, which was not only of great value for prognosis prediction but also closely associated with clinicopathological features. In conclusion, m6A RNA methylation regulators play an important role in ccRCC progression and are potentially favorable for prognostic stratification.
Collapse
MESH Headings
- Adenosine/metabolism
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cohort Studies
- Disease Progression
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Male
- Methylation/drug effects
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Middle Aged
- Predictive Value of Tests
- Prognosis
- RNA Processing, Post-Transcriptional/drug effects
- RNA Processing, Post-Transcriptional/physiology
- Survival Analysis
- Transcriptome
Collapse
Affiliation(s)
- Qi-Jie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiao-Chen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Le-Bin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Jian Ji
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-Dong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Ning-Hong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| |
Collapse
|
12
|
Yang C. ToxPoint: Dissecting Functional RNA Modifications in Responses to Environmental Exposure-Mechanistic Toxicology Research Enters a New Era. Toxicol Sci 2020; 174:1-2. [PMID: 32101319 PMCID: PMC7043219 DOI: 10.1093/toxsci/kfz252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
13
|
Uddin MB, Wang Z, Yang C. Dysregulations of Functional RNA Modifications in Cancer, Cancer Stemness and Cancer Therapeutics. Theranostics 2020; 10:3164-3189. [PMID: 32194861 PMCID: PMC7053189 DOI: 10.7150/thno.41687] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
More than a hundred chemical modifications in coding and non-coding RNAs have been identified so far. Many of the RNA modifications are dynamic and reversible, playing critical roles in gene regulation at the posttranscriptional level. The abundance and functions of RNA modifications are controlled mainly by the modification regulatory proteins: writers, erasers and readers. Modified RNA bases and their regulators form intricate networks which are associated with a vast array of diverse biological functions. RNA modifications are not only essential for maintaining the stability and structural integrity of the RNA molecules themselves, they are also associated with the functional outcomes and phenotypic attributes of cells. In addition to their normal biological roles, many of the RNA modifications also play important roles in various diseases particularly in cancer as evidenced that the modified RNA transcripts and their regulatory proteins are aberrantly expressed in many cancer types. This review will first summarize the most commonly reported RNA modifications and their regulations, followed by discussing recent studies on the roles of RNA modifications in cancer, cancer stemness as wells as functional RNA modification machinery as potential cancer therapeutic targets. It is concluded that, while advanced technologies have uncovered the contributions of many of RNA modifications in cancer, the underlying mechanisms are still poorly understood. Moreover, whether and how environmental pollutants, important cancer etiological factors, trigger abnormal RNA modifications and their roles in environmental carcinogenesis remain largely unknown. Further studies are needed to elucidate the mechanism of how RNA modifications promote cell malignant transformation and generation of cancer stem cells, which will lead to the development of new strategies for cancer prevention and treatment.
Collapse
Affiliation(s)
| | | | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536-0305, USA
| |
Collapse
|
14
|
Obeng EA, Stewart C, Abdel-Wahab O. Altered RNA Processing in Cancer Pathogenesis and Therapy. Cancer Discov 2019; 9:1493-1510. [PMID: 31611195 PMCID: PMC6825565 DOI: 10.1158/2159-8290.cd-19-0399] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/21/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022]
Abstract
Major advances in our understanding of cancer pathogenesis and therapy have come from efforts to catalog genomic alterations in cancer. A growing number of large-scale genomic studies have uncovered mutations that drive cancer by perturbing cotranscriptional and post-transcriptional regulation of gene expression. These include alterations that affect each phase of RNA processing, including splicing, transport, editing, and decay of messenger RNA. The discovery of these events illuminates a number of novel therapeutic vulnerabilities generated by aberrant RNA processing in cancer, several of which have progressed to clinical development. SIGNIFICANCE: There is increased recognition that genetic alterations affecting RNA splicing and polyadenylation are common in cancer and may generate novel therapeutic opportunities. Such mutations may occur within an individual gene or in RNA processing factors themselves, thereby influencing splicing of many downstream target genes. This review discusses the biological impact of these mutations on tumorigenesis and the therapeutic approaches targeting cells bearing these mutations.
Collapse
Affiliation(s)
- Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Connor Stewart
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
15
|
Oshiquiri LH, Dos Santos KRA, Ferreira Junior SA, Steindorff AS, Barbosa Filho JR, Mota TM, Ulhoa CJ, Georg RC. Trichoderma harzianum transcriptome in response to cadmium exposure. Fungal Genet Biol 2019; 134:103281. [PMID: 31626987 DOI: 10.1016/j.fgb.2019.103281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/18/2022]
Abstract
Cadmium (Cd) is a heavy metal present in the environment mainly as a result of industrial contamination that can cause toxic effects to life. Some microorganisms, as Trichoderma harzianum, a fungus used in biocontrol, are able to survive in polluted environments and act as bioremediators. Aspects about the tolerance to the metal have been widely studied in other fungi although there are a few reports about the response of T. harzianum. In this study, we determined the effects of cadmium over growth of T. harzianum and used RNA-Seq to identify significant genes and processes regulated in the metal presence. Cadmium inhibited the fungus growth proportionally to its concentration although the fungus exhibited tolerance as it continued to grow, even in the highest concentrations used. A total of 3767 (1993 up and 1774 down) and 2986 (1606 up and 1380 down) differentially expressed genes were detected in the mycelium of T. harzianum cultivated in the presence of 1.0 mg mL-1 or 2.0 mg mL-1 of CdCl2, respectively, compared to the absence of the metal. Of these, 2562 were common to both treatments. Biological processes related to cellular homeostasis, transcription initiation, sulfur compound biosynthetic and metabolic processes, RNA processing, protein modification and vesicle-mediated transport were up-regulated. Carbohydrate metabolic processes were down-regulated. Pathway enrichment analysis indicated induction of glutathione and its precursor's metabolism. Interestingly, it also indicated an intense transcriptional induction, especially by up-regulation of spliceosome components. Carbohydrate metabolism was repressed, especially the mycoparasitism-related genes, suggesting that the mycoparasitic ability of T. harzianum could be affected during cadmium exposure. These results contribute to the advance of the current knowledge about the response of T. harzianum to cadmium exposure and provide significant targets for biotechnological improvement of this fungus as a bioremediator and a biocontrol agent.
Collapse
Affiliation(s)
- Letícia Harumi Oshiquiri
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | | | | | - Andrei Stecca Steindorff
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | | | - Thuana Marcolino Mota
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Cirano José Ulhoa
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Raphaela Castro Georg
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil.
| |
Collapse
|
16
|
Alfano LN, Charleston JS, Connolly AM, Cripe L, Donoghue C, Dracker R, Dworzak J, Eliopoulos H, Frank DE, Lewis S, Lucas K, Lynch J, Milici AJ, Flynt A, Naughton E, Rodino-Klapac LR, Sahenk Z, Schnell FJ, Young GD, Mendell JR, Lowes LP. Long-term treatment with eteplirsen in nonambulatory patients with Duchenne muscular dystrophy. Medicine (Baltimore) 2019; 98:e15858. [PMID: 31261494 PMCID: PMC6617421 DOI: 10.1097/md.0000000000015858] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This analysis aims to describe the outcomes of two nonambulatory patients with Duchenne muscular dystrophy (DMD) who participated in two clinical studies. The two consecutive trials of eteplirsen (studies 201 and 202) were conducted in patients with DMD (N = 12) and confirmed genetic mutations amenable to exon 51 skipping.In study 201, 12 patients were randomized to receive once-weekly, double-blind intravenous infusions of eteplirsen 30 or 50 mg/kg or placebo for 24 weeks; patients then received open-label eteplirsen during weeks 25 through 28. All 12 patients continued onto open-label extension study 202 and received long-term treatment with eteplirsen. We compared cardiac, pulmonary, and upper limb function and dystrophin production in the nonambulatory twin patients versus the 10 ambulatory patients through 240 combined treatment weeks.Ten study patients remained ambulatory through both studies, while the identical twin patients both experienced early, rapid loss of ambulation. The twin patients had greater disease severity at baseline (6-minute walk test [6MWT], 330 and 256 m) versus the other patients (n = 10; 6MWT range, 341-418 m). They maintained cardiac and upper limb function through combined week 240, with outcomes similar to those of the patients who remained ambulatory. Dystrophin production was confirmed following eteplirsen treatment.Despite the loss of ambulation, other markers of disease progression remained relatively stable in the eteplirsen-treated twin patients and were similar to those of the ambulatory patients.
Collapse
Affiliation(s)
- Lindsay N. Alfano
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| | | | - Anne M. Connolly
- Currently: Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Linda Cripe
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| | | | - Robert Dracker
- Summerwood Pediatrics/Infusacare Medical Services, PC, Liverpool, NY
| | | | | | | | - Sarah Lewis
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| | | | | | | | | | | | - Louise R. Rodino-Klapac
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
- Currently: Sarepta Therapeutics, Inc., Cambridge, MA, USA
| | - Zarife Sahenk
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| | | | | | - Jerry R. Mendell
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| | - Linda P. Lowes
- Pediatrics, Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH
| |
Collapse
|
17
|
Begolo D, Vincent IM, Giordani F, Pöhner I, Witty MJ, Rowan TG, Bengaly Z, Gillingwater K, Freund Y, Wade RC, Barrett MP, Clayton C. The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing. PLoS Pathog 2018; 14:e1007315. [PMID: 30252911 PMCID: PMC6173450 DOI: 10.1371/journal.ppat.1007315] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/05/2018] [Accepted: 09/04/2018] [Indexed: 11/25/2022] Open
Abstract
Kinetoplastid parasites-trypanosomes and leishmanias-infect millions of humans and cause economically devastating diseases of livestock, and the few existing drugs have serious deficiencies. Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies, with candidates already in human and animal clinical trials. We investigated the mechanism of action of several benzoxaboroles, including AN7973, an early candidate for veterinary trypanosomosis. In all kinetoplastids, transcription is polycistronic. Individual mRNA 5'-ends are created by trans splicing of a short leader sequence, with coupled polyadenylation of the preceding mRNA. Treatment of Trypanosoma brucei with AN7973 inhibited trans splicing within 1h, as judged by loss of the Y-structure splicing intermediate, reduced levels of mRNA, and accumulation of peri-nuclear granules. Methylation of the spliced leader precursor RNA was not affected, but more prolonged AN7973 treatment caused an increase in S-adenosyl methionine and methylated lysine. Together, the results indicate that mRNA processing is a primary target of AN7973. Polyadenylation is required for kinetoplastid trans splicing, and the EC50 for AN7973 in T. brucei was increased three-fold by over-expression of the T. brucei cleavage and polyadenylation factor CPSF3, identifying CPSF3 as a potential molecular target. Molecular modeling results suggested that inhibition of CPSF3 by AN7973 is feasible. Our results thus chemically validate mRNA processing as a viable drug target in trypanosomes. Several other benzoxaboroles showed metabolomic and splicing effects that were similar to those of AN7973, identifying splicing inhibition as a common mode of action and suggesting that it might be linked to subsequent changes in methylated metabolites. Granule formation, splicing inhibition and resistance after CPSF3 expression did not, however, always correlate and prolonged selection of trypanosomes in AN7973 resulted in only 1.5-fold resistance. It is therefore possible that the modes of action of oxaboroles that target trypanosome mRNA processing might extend beyond CPSF3 inhibition.
Collapse
Affiliation(s)
- Daniela Begolo
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Isabel M. Vincent
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
| | - Federica Giordani
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg, Germany
| | - Michael J. Witty
- Global Alliance for Livestock and Veterinary Medicine, Doherty Building, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Timothy G. Rowan
- Global Alliance for Livestock and Veterinary Medicine, Doherty Building, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Zakaria Bengaly
- Centre International de Recherche–Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso 01, Burkina Faso
| | - Kirsten Gillingwater
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland
- University of Basel, Petersplatz 1, Basel, Switzerland
| | - Yvonne Freund
- Anacor Pharmaceuticals, Inc., Palo Alto, CA, United States of America
| | - Rebecca C. Wade
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Christine Clayton
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
| |
Collapse
|
18
|
Malainer C, Schachner D, Sangiovanni E, Atanasov AG, Schwaiger S, Stuppner H, Heiss EH, Dirsch VM. Eurycomalactone Inhibits Expression of Endothelial Adhesion Molecules at a Post-Transcriptional Level. J Nat Prod 2017; 80:3186-3193. [PMID: 29148754 PMCID: PMC5744186 DOI: 10.1021/acs.jnatprod.7b00503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The C-19 quassinoid eurycomalactone (1) has recently been shown to be a potent (IC50 = 0.5 μM) NF-κB inhibitor in a luciferase reporter model. In this study, we show that 1 with similar potency inhibited the expression of the NF-κB-dependent target genes ICAM-1, VCAM-1, and E-selectin in TNFα-activated human endothelial cells (HUVECtert) by flow cytometry experiments. Surprisingly, 1 (2 μM) did not inhibit TNFα-induced IKKα/β or IκBα phosphorylation significantly. Also, the TNFα-induced degradation of IκBα remained unchanged in response to 1 (2 μM). In addition, pretreatment of HUVECtert with 1 (2 μM) had no statistically significant effect on TNFα-mediated nuclear translocation of the NF-κB subunit p65 (RelA). Quantitative RT-PCR revealed that 1 (0.5-5 μM) exhibited diverse effects on the TNFα-induced transcription of ICAM-1, VCAM-1, and SELE genes since the mRNA level either remained unchanged (ICAM-1, E-selectin, and VCAM-1 at 0.5 μM 1), was reduced (VCAM-1 at 5 μM 1), or even increased (E-selectin at 5 μM 1). Finally, the time-dependent depletion of a short-lived protein (cyclin D1) as well as the measurement of de novo protein synthesis in the presence of 1 (2-5 μM) suggested that 1 might act as a protein synthesis inhibitor rather than an inhibitor of early NF-κB signaling.
Collapse
Affiliation(s)
- Clemens Malainer
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Daniel Schachner
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Enrico Sangiovanni
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti, 9, 20133 Milano, Italy
| | - Atanas G. Atanasov
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Institute
of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland
| | - Stefan Schwaiger
- Institute
of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Hermann Stuppner
- Institute
of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Elke H. Heiss
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Verena M. Dirsch
- Department
of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Tel: +43-1-4277-55270. Fax: +43-1-4277-55969. E-mail:
| |
Collapse
|
19
|
Zhou T, Block T, Liu F, Kondratowicz AS, Sun L, Rawat S, Branson J, Guo F, Steuer HM, Liang H, Bailey L, Moore C, Wang X, Cuconatti A, Gao M, Lee ACH, Harasym T, Chiu T, Gotchev D, Dorsey B, Rijnbrand R, Sofia MJ. HBsAg mRNA degradation induced by a dihydroquinolizinone compound depends on the HBV posttranscriptional regulatory element. Antiviral Res 2017; 149:191-201. [PMID: 29133129 DOI: 10.1016/j.antiviral.2017.11.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/01/2017] [Accepted: 11/07/2017] [Indexed: 12/23/2022]
Abstract
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that in the nanomolar range reduced the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage, but was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a significant reduction of serum HBsAg as soon as 4 days following the commencement of treatment. Reduction of HBV markers in both in vitro and in vivo experiments was related to the reduced amount of viral RNA including pre-genomic RNA (pgRNA) and 2.4/2.1 kb HBsAg mRNA. Nuclear run-on and subcellular fractionation experiments indicated that DHQ-1 mediated HBV RNA reduction was the result of accelerated viral RNA degradation in the nucleus, rather than the consequence of inhibition of transcription initiation. Through mutagenesis of HBsAg gene sequences, we found induction of HBsAg mRNA decay by DHQ-1 required the presence of the HBV posttranscriptional regulatory element (HPRE), with a 109 nucleotides sequence within the central region of the HPRE alpha sub-element being the most critical. Taken together, the current study shows that a small molecule can reduce the overall levels of HBV RNA, especially the HBsAg mRNA, and viral surface proteins. This may shed light on the development of a new class of HBV therapeutics.
Collapse
Affiliation(s)
- Tianlun Zhou
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States.
| | - Timothy Block
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fei Liu
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andrew S Kondratowicz
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Liren Sun
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Siddhartha Rawat
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Jeffrey Branson
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fang Guo
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | | | - Hongyan Liang
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Lauren Bailey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Chris Moore
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Xiaohe Wang
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andy Cuconatti
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Min Gao
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Amy C H Lee
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Troy Harasym
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Tim Chiu
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Dimitar Gotchev
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Bruce Dorsey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Rene Rijnbrand
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Michael J Sofia
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States.
| |
Collapse
|
20
|
Chen Y, Zeng L, Wang Y, Tolleson WH, Knox B, Chen S, Ren Z, Guo L, Mei N, Qian F, Huang K, Liu D, Tong W, Yu D, Ning B. The expression, induction and pharmacological activity of CYP1A2 are post-transcriptionally regulated by microRNA hsa-miR-132-5p. Biochem Pharmacol 2017; 145:178-191. [PMID: 28822783 DOI: 10.1016/j.bcp.2017.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/14/2017] [Indexed: 11/20/2022]
Abstract
Cytochrome P450 1A2 (CYP1A2) is one of the most abundant and important drug metabolizing enzymes in human liver. However, little is known about the post-transcriptional regulation of CYP1A2, especially the mechanisms involving microRNAs (miRNAs). This study applied a systematic approach to investigate the post-transcriptional regulation of CYP1A2 by miRNAs. Candidate miRNAs targeting the 3'-untranslated region (3'-UTR) of CYP1A2 were screened in silico, resulting in the selection of sixty-two potential miRNAs for further analysis. The levels of two miRNAs, hsa-miR-132-5p and hsa-miR-221-5p, were inversely correlated with the expression of CYP1A2 mRNA transcripts in normal human liver tissue samples represented in The Cancer Genome Atlas (TCGA) dataset. The interactions between these miRNAs and cognate CYP1A2 mRNA sequences were evaluated using luciferase reporter gene studies and electrophoretic mobility shift assays, by which a direct interaction was confirmed involving hsa-miR-132-5p and a cognate binding site present in the CYP1A2 3'-UTR. Experiments by which hsa-miR-132-5p or random miRNA controls were introduced into HepG2, Huh-7 and HepaRG hepatic cell lines showed that only hsa-miR-132-5p suppressed the endogenous and lansoprazole-induced expression of CYP1A2, at biological activity, protein production, and mRNA transcript levels. Furthermore, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and lactate dehydrogenase (LDH) assays showed that hsa-miR-132-5p attenuates CYP1A2-mediated, lansoprazole-enhanced, flutamide-induced hepatic cell toxicity. Results from multilayer experiments demonstrate that hsa-miR-132-5p suppresses the expression of CYP1A2 and that this suppression is able to decrease the extent of an adverse drug-drug interaction involving lansoprazole and flutamide.
Collapse
Affiliation(s)
- Yinting Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Linjuan Zeng
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yong Wang
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - William H Tolleson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Bridgett Knox
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Si Chen
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Zhen Ren
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Lei Guo
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Nan Mei
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Feng Qian
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Kaihong Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - David Liu
- Longevity Center of CHI St. Vincent Hospital, Little Rock, AR 72205, USA
| | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Dianke Yu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Baitang Ning
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| |
Collapse
|
21
|
Kos-Braun IC, Jung I, Koš M. Tor1 and CK2 kinases control a switch between alternative ribosome biogenesis pathways in a growth-dependent manner. PLoS Biol 2017; 15:e2000245. [PMID: 28282370 PMCID: PMC5345768 DOI: 10.1371/journal.pbio.2000245] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 02/06/2017] [Indexed: 01/06/2023] Open
Abstract
Ribosome biogenesis is a major energy-consuming process in the cell that has to be rapidly down-regulated in response to stress or nutrient depletion. The target of rapamycin 1 (Tor1) pathway regulates synthesis of ribosomal RNA (rRNA) at the level of transcription initiation. It remains unclear whether ribosome biogenesis is also controlled directly at the posttranscriptional level. We show that Tor1 and casein kinase 2 (CK2) kinases regulate a rapid switch between a productive and a non-productive pre-rRNA processing pathways in yeast. Under stress, the pre-rRNA continues to be synthesized; however, it is processed differently, and no new ribosomes are produced. Strikingly, the control of the switch does not require the Sch9 kinase, indicating that an unrecognized Tor Complex 1 (TORC1) signaling branch involving CK2 kinase directly regulates ribosome biogenesis at the posttranscriptional level. The yeast Saccharomyces cerevisiae must, as a single-celled microorganism, rapidly respond to changes in its environment and carefully balance its energy needs with the available resources. One of the major energy-consuming processes in the cell is the production of ribosomes. Ribosome biogenesis is highly dynamic and complex and requires the coordinated action of myriads of factors and RNAs. It begins with the synthesis of the precursor ribosomal RNA (rRNA), which is concurrently cleaved, modified, folded, and assembled together with ribosomal proteins into mature ribosomal subunits. It is known that in response to depletion of nutrients, yeast quickly represses the transcription of genes encoding rRNAs and ribosomal proteins. In this study, we reveal that yeast also rapidly switches to an alternative rRNA processing pathway, in which the precursor rRNA is cleaved differently and the ribosome biogenesis is arrested at a distinct stage. We demonstrate that the choice between the two alternative pathways is controlled by the target of rapamycin complex 1 (TORC1) and casein kinase 2 (CK2) kinase, but does not require Tap42p and Sch9p, which are currently thought to be the major effectors of TORC1. Our results indicate the existence of a so far unidentified branch of TORC1 signaling regulating ribosomes biogenesis at the posttranscriptional level.
Collapse
Affiliation(s)
| | - Ilona Jung
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Martin Koš
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
22
|
Köhler D, Helm S, Agne B, Baginsky S. Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. Plant Physiol 2016; 172:2429-2444. [PMID: 27733515 PMCID: PMC5129725 DOI: 10.1104/pp.16.01393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins. In the tic56-1 mutant, the assembly of functional ribosomes is furthermore hampered by a processing defect of the plastid 23S rRNA. Spectinomycin-treatment of wild-type plants phenocopies the molecular phenotype of plastid proteome accumulation in tic56-1 and to a smaller degree also ppi2 plastids, suggesting that a defect in plastid translation is largely responsible for the phenotype of both import mutants. Import experiments with the tic56-3 mutant revealed no significant defect in the import of small ribosomal protein 16 in the absence of full-length Tic56, suggesting that the defect in ribosome assembly in tic56-1 may be independent of a function of Tic56 in protein import. Our data establish a previously unknown link between plastid protein import, the processing of plastid rRNAs, and the assembly of plastid ribosomes and provide further knowledge on the function of the translocon components and the molecular basis for their albino phenotype.
Collapse
Affiliation(s)
- Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| |
Collapse
|
23
|
Barr I, Weitz SH, Atkin T, Hsu P, Karayiorgou M, Gogos JA, Weiss S, Guo F. Cobalt(III) Protoporphyrin Activates the DGCR8 Protein and Can Compensate microRNA Processing Deficiency. ACTA ACUST UNITED AC 2016; 22:793-802. [PMID: 26091172 DOI: 10.1016/j.chembiol.2015.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 05/01/2015] [Accepted: 05/20/2015] [Indexed: 12/31/2022]
Abstract
Processing of microRNA primary transcripts (pri-miRNAs) is highly regulated and defects in the processing machinery play a key role in many human diseases. In 22q11.2 deletion syndrome (22q11.2DS), heterozygous deletion of DiGeorge critical region gene 8 (DGCR8) causes a processing deficiency, which contributes to abnormal brain development. The DGCR8 protein is the RNA-binding partner of Drosha RNase, both essential for processing canonical pri-miRNAs. To identify an agent that can compensate reduced DGCR8 expression, we screened for metalloporphyrins that can mimic the natural DGCR8 heme cofactor. We found that Co(III) protoporphyrin IX (PPIX) stably binds DGCR8 and activates it for pri-miRNA processing in vitro and in HeLa cells. Importantly, treating cultured Dgcr8(+/-) mouse neurons with Co(III)PPIX can compensate the pri-miRNA processing defects. Co(III)PPIX is effective at concentrations as low as 0.2 μM and is not degraded by heme degradation enzymes, making it useful as a research tool and a potential therapeutic.
Collapse
Affiliation(s)
- Ian Barr
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sara H Weitz
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA, 90095, USA
| | - Talia Atkin
- Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - PeiKen Hsu
- Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Maria Karayiorgou
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Joseph A Gogos
- Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
24
|
Breitkopf SB, Yuan M, Helenius KP, Lyssiotis CA, Asara JM. Triomics Analysis of Imatinib-Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis. Anal Chem 2015; 87:10995-1006. [PMID: 26434776 PMCID: PMC5585869 DOI: 10.1021/acs.analchem.5b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of metabolomics, lipidomics, and phosphoproteomics that incorporates triple stable isotope labeling by amino acids in cell culture (SILAC) protein labeling, as well as (13)C in vivo metabolite labeling, was demonstrated on BCR-ABL-positive H929 multiple myeloma cells. From 11 880 phosphorylation sites, we confirm that H929 cells are primarily signaling through the BCR-ABL-ERK pathway, and we show that imatinib treatment not only downregulates phosphosites in this pathway but also upregulates phosphosites on proteins involved in RNA expression. Metabolomics analyses reveal that BCR-ABL-ERK signaling in H929 cells drives the pentose phosphate pathway (PPP) and RNA biosynthesis, where pathway inhibition via imatinib results in marked PPP impairment and an accumulation of RNA nucleotides and negative regulation of mRNA. Lipidomics data also show an overall reduction in lipid biosynthesis and fatty acid incorporation with a significant decrease in lysophospholipids. RNA immunoprecipitation studies confirm that RNA degradation is inhibited with short imatinib treatment and transcription is inhibited upon long imatinib treatment, validating the triomics results. These data show the utility of combining mass spectrometry-based "-omics" technologies and reveals that kinase inhibitors may not only downregulate phosphorylation of their targets but also induce metabolic events via increased phosphorylation of other cellular components.
Collapse
Affiliation(s)
- Susanne B. Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
| | - Katja P. Helenius
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology and Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
25
|
Rajendra Y, Hougland MD, Schmitt MG, Barnard GC. Transcriptional and post-transcriptional targeting for enhanced transient gene expression in CHO cells. Biotechnol Lett 2015; 37:2379-86. [PMID: 26298077 DOI: 10.1007/s10529-015-1938-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/11/2015] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To develop a simple approach to increase titers of transient gene expression in CHO cells without relying on host cell line engineering as recent reports suggest that for PEI-mediated transfections, under optimized conditions, DNA delivery into cells and nuclei is not the limiting factor. RESULTS N, N-Dimethyl acetamide (DMA) was utilized to enhance transcription. To target post-transcriptional events, we evaluated the co-expression of various genes involved in the unfolded protein response, namely XBP1S, ATF4, CHOP and HSPA5. XBP1S overexpression led to a 15-85 % increase in titer for multiple therapeutic proteins. Mechanistic studies confirmed that addition of 0.125 % DMA increased transgene mRNA levels as expected. However, overexpression of XBP1S had no effect on transgene mRNA levels, indicating that it influenced post-transcriptional events. Since DMA and XBP1S targeted different pathways, the combination of the two approaches led to an additive improvement in protein titer (150-250 % titer increase). CONCLUSION Transcriptional and post-transcriptional pathways of transient gene expression can be targeted to increase titers without resorting to host cell line engineering in a simple, short, 7 day production process.
Collapse
Affiliation(s)
- Yashas Rajendra
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Maria D Hougland
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Matthew G Schmitt
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Gavin C Barnard
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA.
| |
Collapse
|
26
|
Chen A, T-Thienprasert NP, Brown CM. Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus. World J Gastroenterol 2014; 20:7993-8004. [PMID: 25009369 PMCID: PMC4081668 DOI: 10.3748/wjg.v20.i25.7993] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/19/2014] [Accepted: 04/09/2014] [Indexed: 02/06/2023] Open
Abstract
There is a continuing need for novel antivirals to treat hepatitis B virus (HBV) infection, as it remains a major health problem worldwide. Ideally new classes of antivirals would target multiple steps in the viral lifecycle. In this review, we consider the steps in which HBV RNAs are processed, exported from the nucleus and translated. These are often overlooked steps in the HBV life-cycle. HBV, like retroviruses, incorporates a number of unusual steps in these processes, which use a combination of viral and host cellular machinery. Some of these unusual steps deserve a closer scrutiny. They may provide alternative targets to existing antiviral therapies, which are associated with increasing drug resistance. The RNA post-transcriptional regulatory element identified 20 years ago promotes nucleocytoplasmic export of all unspliced HBV RNAs. There is evidence that inhibition of this step is part of the antiviral action of interferon. Similarly, the structured RNA epsilon element situated at the 5’ end of the polycistronic HBV pregenomic RNA also performs key roles during HBV replication. The pregenomic RNA, which is the template for translation of both the viral core and polymerase proteins, is also encapsidated and used in replication. This complex process, regulated at the epsilon element, also presents an attractive antiviral target. These RNA elements that mediate and regulate gene expression are highly conserved and could be targeted using novel strategies employing RNAi, miRNAs or aptamers. Such approaches targeting these functionally constrained genomic regions should avoid escape mutations. Therefore understanding these regulatory elements, along with providing potential targets, may also facilitate the development of other new classes of antiviral drugs.
Collapse
|
27
|
Delmani FA, Torreblanca J, Moreno J, García-Herdugo G, Vilaplana R, González-Víltchez F. Biological activity and redistribution of nucleolar proteins of two different cell lines treated with cis-dichloro-1,2-propylenediamine-N,N,N',N'-tetraacetato ruthenium (III) (RAP). Indian J Exp Biol 2014; 52:579-588. [PMID: 24956888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The interaction of a newly synthesized antitumor complex cis-dichloro-1,2-propylenediamine-N,N,N',N'-tetraacetato ruthenium (III) (RAP) with DNA was investigated in vitro through a number of techniques including comet assay, immunoprecipitation, and immunolocalization of certain nucleolar proteins (the upstream binding factor (UBF) and fibrillarin) involved in DNA transcription, rRNA processing, and ribosomal assembly. The results showed that RAP binds to the DNA of two cell lines (H4 and Hs-683) causing a delay in cell proliferation rate leading to a number of cellular modifications. These modifications include DNA-damage assessed by the single cell gel electrophoresis method (comet assay) and variation in the expression of nucleolar proteins; UBF was more abundant in RAP treated cells, this was explained by the high affinity of this protein to DNA modified by RAP. On the other hand, fibrillarin was found in less quantities in RAP treated cells which was explained by a de-regulation of the ribosomal machinery caused by RAP.
Collapse
|
28
|
Holcakova J, Muller P, Tomasec P, Hrstka R, Nekulova M, Krystof V, Strnad M, Wilkinson GWG, Vojtesek B. Inhibition of post-transcriptional RNA processing by CDK inhibitors and its implication in anti-viral therapy. PLoS One 2014; 9:e89228. [PMID: 24586613 PMCID: PMC3931720 DOI: 10.1371/journal.pone.0089228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/17/2014] [Indexed: 01/31/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and RNA polymerase II mediated transcription. Several pharmacological CDK inhibitors are currently in clinical trials as potential cancer therapeutics and some of them also exhibit antiviral effects. Olomoucine II and roscovitine, purine-based inhibitors of CDKs, were described as effective antiviral agents that inhibit replication of a broad range of wild type human viruses. Olomoucine II and roscovitine show high selectivity for CDK7 and CDK9, with important functions in the regulation of RNA polymerase II transcription. RNA polymerase II is necessary for viral transcription and following replication in cells. We analyzed the effect of inhibition of CDKs by olomoucine II on gene expression from viral promoters and compared its effect to widely-used roscovitine. We found that both roscovitine and olomoucine II blocked the phosphorylation of RNA polymerase II C-terminal domain. However the repression of genes regulated by viral promoters was strongly dependent on gene localization. Both roscovitine and olomoucine II inhibited expression only when the viral promoter was not integrated into chromosomal DNA. In contrast, treatment of cells with genome-integrated viral promoters increased their expression even though there was decreased phosphorylation of the C-terminal domain of RNA polymerase II. To define the mechanism responsible for decreased gene expression after pharmacological CDK inhibitor treatment, the level of mRNA transcription from extrachromosomal DNA was determined. Interestingly, our results showed that inhibition of RNA polymerase II C-terminal domain phosphorylation increased the number of transcribed mRNAs. However, some of these mRNAs were truncated and lacked polyadenylation, which resulted in decreased translation. These results suggest that phosphorylation of RNA polymerase II C-terminal domain is critical for linking transcription and posttrancriptional processing of mRNA expressed from extrachromosomal DNA.
Collapse
Affiliation(s)
- Jitka Holcakova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Tomasec
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marta Nekulova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Krystof
- Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Institute of Experimental Botany AS CR, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Institute of Experimental Botany AS CR, Olomouc, Czech Republic
| | | | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
- * E-mail:
| |
Collapse
|
29
|
Cruz Hernández A, Millan ES, de Jesús Romero Gómez S, Antonio Cervantes Chávez J, Garcia Martínez R, Pastrana Martínez X, Gómez JLA, Jones GH, Guillén JC. Exposure of Bacillus subtilis to mercury induces accumulation of shorter tRNA Cys species. Metallomics 2013; 5:398-403. [PMID: 23529473 DOI: 10.1039/c3mt20203h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA processing is an essential pathway in the regulation of genetic expression in the cell. In this work, Bacillus subtilis was used to understand the effects of mercury on the mechanism of tRNA metabolism. The CVAAS (cold vapor atomic absorption spectroscopy) method revealed that from the addition of HgCl2 (0.75 μg ml(-1)) during the bacterial exponential phase, ca. 48% of the added mercury was taken up by the cells. This led to an immediate reduction in the rate of cell division. During this response, we observed accumulation of species shorter than mature tRNA(Cys) over a 10 h period. We did not observe this accumulation for another five tRNAs analyzed. tRNA processing is largely dependent on RNase R and PNPase in B. subtilis. Thus, when the exonuclease PNPase was absent, we found that the shorter tRNA(Cys) species increased and mature tRNA(Cys) decreased after mercury addition, but this proportion changed during the time analyzed. However, in the absence of RNase R and PNPase the accumulation of the shorter tRNA(Cys) was more pronounced and the mature form was not recovered. In the single rnr mutant strain the shorter tRNA(Cys) was not observed. All together, we provide in vivo evidence that PNPase and RNase R are indispensable in controlling tRNA(Cys) quality in the presence of mercury.
Collapse
|
30
|
Cheung ST, So EY, Chang D, Ming-Lum A, Mui ALF. Interleukin-10 inhibits lipopolysaccharide induced miR-155 precursor stability and maturation. PLoS One 2013; 8:e71336. [PMID: 23951138 PMCID: PMC3741136 DOI: 10.1371/journal.pone.0071336] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/25/2013] [Indexed: 12/16/2022] Open
Abstract
The anti-inflammatory cytokine interleukin-10 (IL-10) is essential for attenuating the inflammatory response, which includes reducing the expression of pro-inflammatory microRNA-155 (miR-155) in lipopolysaccharide (LPS) activated macrophages. miR-155 enhances the expression of pro-inflammatory cytokines such as TNFα and suppresses expression of anti-inflammatory molecules such as SOCS1. Therefore, we examined the mechanism by which IL-10 inhibits miR-155. We found that IL-10 treatment did not affect the transcription of the miR-155 host gene nor the nuclear export of pre-miR-155, but rather destabilized both pri-miR-155 and pre-miR-155 transcripts, as well as interfered with the final maturation of miR-155. This inhibitory effect of IL-10 on miR-155 expression involved the contribution of both the STAT3 transcription factor and the phosphoinositol phosphatase SHIP1. This is the first report showing evidence that IL-10 regulates miRNA expression post-transcriptionally.
Collapse
Affiliation(s)
- Sylvia T. Cheung
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Y. So
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Chang
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Ming-Lum
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice L-F. Mui
- Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
31
|
Wong RW, Balachandran A, Ostrowski MA, Cochrane A. Digoxin suppresses HIV-1 replication by altering viral RNA processing. PLoS Pathog 2013; 9:e1003241. [PMID: 23555254 PMCID: PMC3610647 DOI: 10.1371/journal.ppat.1003241] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/24/2013] [Indexed: 11/18/2022] Open
Abstract
To develop new approaches to control HIV-1 replication, we examined the capacity of recently described small molecular modulators of RNA splicing for their effects on viral RNA metabolism. Of the drugs tested, digoxin was found to induce a dramatic inhibition of HIV-1 structural protein synthesis, a response due, in part, to reduced accumulation of the corresponding viral mRNAs. In addition, digoxin altered viral RNA splice site use, resulting in loss of the essential viral factor Rev. Digoxin induced changes in activity of the CLK family of SR protein kinases and modification of several SR proteins, including SRp20 and Tra2β, which could account for the effects observed. Consistent with this hypothesis, overexpression of SRp20 elicited changes in HIV-1 RNA processing similar to those observed with digoxin. Importantly, digoxin was also highly active against clinical strains of HIV-1 in vitro, validating this novel approach to treatment of this infection.
Collapse
Affiliation(s)
- Raymond W. Wong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | | | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
| |
Collapse
|
32
|
Jia F, Rock CD. MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis. Plant Mol Biol 2013; 81:447-60. [PMID: 23341152 PMCID: PMC3581712 DOI: 10.1007/s11103-013-0015-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/15/2013] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are ~21-nucleotide long endogenous small RNAs that regulate gene expression through post-transcriptional or transcriptional gene silencing and/or translational inhibition. miRNAs can arise from the "exon" of a MIRNA gene, from an intron (e.g. mirtrons in animals), or from the antisense strand of a protein coding gene (natural antisense microRNAs, nat-miRNAs). Here we demonstrate that two functionally related miRNAs, miR842 and miR846, arise from the same transcription unit but from alternate splicing isoforms. miR846 is expressed only from Isoform1 while in Isoforms2 and -3, a part of pre-miR846 containing the miRNA* sequence is included in the intron. The splicing of the intron truncates the pre-MIRNA and disrupts the expression of the mature miR846. We name this novel phenomenon splicing-regulated miRNA. Abscisic acid (ABA) is shown to mediate the alternative splicing event by reducing the functional Isoform1 and increasing the non-functional Isoform3, thus repressing the expression of miR846 concomitant with accumulation of an ABA-inducible target jacalin At5g28520 mRNA, whose cleavage was shown by modified 5'-RACE. This regulation shows the functional importance of splicing-regulated miRNA and suggests possible mechanisms for altered ABA response phenotypes of miRNA biogenesis mutants. Arabidopsis lyrata-MIR842 and Aly-MIR846 have conserved genomic arrangements with A. thaliana and candidate target jacalins, similar primary transcript structures and intron processing, and better miRNA-miRNA* pairings, suggesting that the interactions between ABA, MIR842, MIR846 and jacalins are similar in A. lyrata. Together, splicing-regulated miRNAs, nat-miRNAs/inc-miRNAs and mirtrons illustrate the complexity of MIRNA genes, the importance of introns in the biogenesis and regulation of miRNAs, and raise questions about the processes and molecular mechanisms that drive MIRNA evolution.
Collapse
|
33
|
Hussey GS, Link LA, Brown AS, Howley BV, Chaudhury A, Howe PH. Establishment of a TGFβ-induced post-transcriptional EMT gene signature. PLoS One 2012; 7:e52624. [PMID: 23285117 PMCID: PMC3527574 DOI: 10.1371/journal.pone.0052624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/20/2012] [Indexed: 12/31/2022] Open
Abstract
A major challenge in the clinical management of human cancers is to accurately stratify patients according to risk and likelihood of a favorable response. Stratification is confounded by significant phenotypic heterogeneity in some tumor types, often without obvious criteria for subdivision. Despite intensive transcriptional array analyses, the identity and validation of cancer specific ‘signature genes’ remains elusive, partially because the transcriptome does not mirror the proteome. The simplification associated with transcriptomic profiling does not take into consideration changes in the relative expression among transcripts that arise due to post-transcriptional regulatory events. We have previously shown that TGFβ post-transcriptionally regulates epithelial-mesenchymal transition (EMT) by causing increased expression of two transcripts, Dab2 and ILEI, by modulating hnRNP E1 phosphorylation. Using a genome-wide combinatorial approach involving expression profiling and RIP-Chip analysis, we have identified a cohort of translationally regulated mRNAs that are induced during TGFβ-mediated EMT. Coordinated translational regulation by hnRNP E1 constitutes a post-transcriptional regulon inhibiting the expression of related EMT-facilitating genes, thus enabling the cell to rapidly and coordinately regulate multiple EMT-facilitating genes.
Collapse
Affiliation(s)
- George S. Hussey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Laura A. Link
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Andrew S. Brown
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Breege V. Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip H. Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
| |
Collapse
|
34
|
Garikipati DK, Rodgers BD. Myostatin inhibits myosatellite cell proliferation and consequently activates differentiation: evidence for endocrine-regulated transcript processing. J Endocrinol 2012; 215:177-87. [PMID: 22872758 DOI: 10.1530/joe-12-0260] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Myostatin is a potent negative regulator of muscle growth in mammals. Despite high structural conservation, functional conservation in nonmammalian species is only assumed. This is particularly true for fish due to the presence of several myostatin paralogs: two in most species and four in salmonids (MSTN-1a, -1b, -2a, and -2b). Rainbow trout are a rich source of primary myosatellite cells as hyperplastic muscle growth occurs even in adult fish. These cells were therefore used to determine myostatin's effects on proliferation whereas our earlier studies reported its effects on quiescent cells. As in mammals, recombinant myostatin suppressed proliferation with no changes in cell morphology. Expression of MSTN-1a was several fold higher than the other paralogs and was autoregulated by myostatin, which also upregulated the expression of key differentiation markers: Myf5, MyoD1, myogenin, and myosin light chain. Thus, myostatin-stimulated cellular growth inhibition activates rather than represses differentiation. IGF-1 stimulated proliferation but had minimal and delayed effects on differentiation and its actions were suppressed by myostatin. However, IGF-1 upregulated MSTN-2a expression and the processing of its transcript, which is normally unprocessed. Myostatin therefore appears to partly mediate IGF-stimulated myosatellite differentiation in rainbow trout. This also occurs in mammals, although the IGF-stimulated processing of MSTN-2a transcripts is highly unique and is indicative of subfunctionalization within the gene family. These studies also suggest that the myokine's actions, including its antagonistic relationship with IGF-1, are conserved and that the salmonid gene family is functionally diverging.
Collapse
Affiliation(s)
- Dilip K Garikipati
- Department of Animal Sciences, 124 ASLB, School of Molecular Biosciences, Washington Center for Muscle Biology, Washington State University, Pullman, Washington 99164, USA
| | | |
Collapse
|
35
|
Morello LG, Coltri PP, Quaresma AJC, Simabuco FM, Silva TCL, Singh G, Nickerson JA, Oliveira CC, Moore MJ, Zanchin NIT. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing. PLoS One 2011; 6:e29174. [PMID: 22195017 PMCID: PMC3241699 DOI: 10.1371/journal.pone.0029174] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/22/2011] [Indexed: 12/22/2022] Open
Abstract
NIP7 is one of the many trans-acting factors required for eukaryotic ribosome biogenesis, which interacts with nascent pre-ribosomal particles and dissociates as they complete maturation and are exported to the cytoplasm. By using conditional knockdown, we have shown previously that yeast Nip7p is required primarily for 60S subunit synthesis while human NIP7 is involved in the biogenesis of 40S subunit. This raised the possibility that human NIP7 interacts with a different set of proteins as compared to the yeast protein. By using the yeast two-hybrid system we identified FTSJ3, a putative ortholog of yeast Spb1p, as a human NIP7-interacting protein. A functional association between NIP7 and FTSJ3 is further supported by colocalization and coimmunoprecipitation analyses. Conditional knockdown revealed that depletion of FTSJ3 affects cell proliferation and causes pre-rRNA processing defects. The major pre-rRNA processing defect involves accumulation of the 34S pre-rRNA encompassing from site A′ to site 2b. Accumulation of this pre-rRNA indicates that processing of sites A0, 1 and 2 are slower in cells depleted of FTSJ3 and implicates FTSJ3 in the pathway leading to 18S rRNA maturation as observed previously for NIP7. The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells.
Collapse
Affiliation(s)
- Luis G. Morello
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | | | - Alexandre J. C. Quaresma
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Fernando M. Simabuco
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Tereza C. L. Silva
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Guramrit Singh
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey A. Nickerson
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Carla C. Oliveira
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Melissa J. Moore
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nilson I. T. Zanchin
- Instituto Carlos Chagas, Fundação Instituto Oswaldo Cruz, Curitiba, Paraná, Brazil
- * E-mail:
| |
Collapse
|
36
|
Markus MA, Marques FZ, Morris BJ. Resveratrol, by modulating RNA processing factor levels, can influence the alternative splicing of pre-mRNAs. PLoS One 2011; 6:e28926. [PMID: 22174926 PMCID: PMC3236773 DOI: 10.1371/journal.pone.0028926] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/17/2011] [Indexed: 11/18/2022] Open
Abstract
Alternative pre-mRNA splicing defects can contribute to, or result from, various diseases, including cancer. Aberrant mRNAs, splicing factors and other RNA processing factors have therefore become targets for new therapeutic interventions. Here we report that the natural polyphenol resveratrol can modulate alternative splicing in a target-specific manner. We transfected minigenes of several alternatively spliceable primary mRNAs into HEK293 cells in the presence or absence of 1, 5, 20 and 50 µM resveratrol and measured exon levels by semi-quantitative PCR after separation by agarose gel electrophoresis. We found that 20 µg/ml and 50 µg/ml of resveratrol affected exon inclusion of SRp20 and SMN2 pre-mRNAs, but not CD44v5 or tau pre-mRNAs. By Western blotting and immunofluorescence we showed that this effect may be due to the ability of resveratrol to change the protein level but not the localization of several RNA processing factors. The processing factors that increased significantly were ASF/SF2, hnRNPA1 and HuR, but resveratrol did not change the levels of RBM4, PTBP1 and U2AF35. By means of siRNA-mediated knockdown we depleted cells of SIRT1, regarded as a major target of resveratrol, and showed that the effect on splicing was not dependent on SIRT1. Our results suggest that resveratrol might be an attractive small molecule to treat diseases in which aberrant splicing has been implicated, and justify more extensive research on the effects of resveratrol on the splicing machinery.
Collapse
Affiliation(s)
- M. Andrea Markus
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Francine Z. Marques
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Brian J. Morris
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
- * E-mail:
| |
Collapse
|
37
|
Zheng J, Benbrook DM, Yu H, Ding WQ. Clioquinol suppresses cyclin D1 gene expression through transcriptional and post-transcriptional mechanisms. Anticancer Res 2011; 31:2739-2747. [PMID: 21868515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Clioquinol, a metal-binding compound, has been shown to have anticancer activity in in vitro and in vivo model systems. This study investigated the effects of clioquinol on cyclin D1 gene expression in breast cancer cells. Treatment with clioquinol significantly reduced cyclin D1 protein levels in a concentration-dependent manner, effects being more pronounced in the presence of zinc. Clioquinol reduced cyclin D1 mRNA contents in cells that had been pre-treated with actinomycin D, indicating that this compound alters cyclin D1 mRNA stability, an event associated with post-transcriptional regulation. Using a cyclin D1 3'-UTR reporter construct (CCND1-3'-UTR), we confirmed that this 3'-UTR mediates the inhibitory action of clioquinol, likely through miR-302C. This study demonstrates for the first time that clioquinol targets post-transcriptional steps of cyclin D1 gene expression in cancer cells, adding new insight into our understanding of its mechanisms of anticancer action.
Collapse
Affiliation(s)
- Jie Zheng
- Departments of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | | | | |
Collapse
|
38
|
Olson PD, Kuechenmeister LJ, Anderson KL, Daily S, Beenken KE, Roux CM, Reniere ML, Lewis TL, Weiss WJ, Pulse M, Nguyen P, Simecka JW, Morrison JM, Sayood K, Asojo OA, Smeltzer MS, Skaar EP, Dunman PM. Small molecule inhibitors of Staphylococcus aureus RnpA alter cellular mRNA turnover, exhibit antimicrobial activity, and attenuate pathogenesis. PLoS Pathog 2011; 7:e1001287. [PMID: 21347352 PMCID: PMC3037362 DOI: 10.1371/journal.ppat.1001287] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 01/10/2011] [Indexed: 11/23/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus is estimated to cause more U.S. deaths annually than HIV/AIDS. The emergence of hypervirulent and multidrug-resistant strains has further amplified public health concern and accentuated the need for new classes of antibiotics. RNA degradation is a required cellular process that could be exploited for novel antimicrobial drug development. However, such discovery efforts have been hindered because components of the Gram-positive RNA turnover machinery are incompletely defined. In the current study we found that the essential S. aureus protein, RnpA, catalyzes rRNA and mRNA digestion in vitro. Exploiting this activity, high through-put and secondary screening assays identified a small molecule inhibitor of RnpA-mediated in vitro RNA degradation. This agent was shown to limit cellular mRNA degradation and exhibited antimicrobial activity against predominant methicillin-resistant S. aureus (MRSA) lineages circulating throughout the U.S., vancomycin intermediate susceptible S. aureus (VISA), vancomycin resistant S. aureus (VRSA) and other Gram-positive bacterial pathogens with high RnpA amino acid conservation. We also found that this RnpA-inhibitor ameliorates disease in a systemic mouse infection model and has antimicrobial activity against biofilm-associated S. aureus. Taken together, these findings indicate that RnpA, either alone, as a component of the RNase P holoenzyme, and/or as a member of a more elaborate complex, may play a role in S. aureus RNA degradation and provide proof of principle for RNA catabolism-based antimicrobial therapy. The last decade has witnessed a mass downsizing in pharmaceutical antibiotic drug discovery initiatives. This has posed a major healthcare issue that will likely worsen with time; antibiotic resistant bacteria continue to emerge while advances in new therapeutic options languish. In the current body of work, we show that agents that limit bacterial RNA turnover have potential as a new class of antibiotics. More specifically, our findings indicate the essential bacterial protein, RnpA, exhibits in vitro ribonuclease activity and either alone and/or as a member of the RNase P holoenzyme, may contribute to the RNA degradation properties of Staphylococcus aureus, a predominant cause of hospital and community bacterial infections. Accordingly, using high throughput screening we identified small molecule inhibitors of RnpA's in vitro RNA degradation activity. One of these agents, RNPA1000, was shown to limit S. aureus mRNA turnover and growth. RNPA1000 also limited growth of other important Gram-positive bacterial pathogens, exhibited antimicrobial efficacy against biofilm associated S. aureus and protected against the S. aureus pathogenesis in an animal model of infection. When taken together, our results illustrate that components of the bacterial RNA degradation machinery have utility as antibiotic drug-discovery targets and that RNPA1000 may represent a progenitor of this new class of antibiotics.
Collapse
Affiliation(s)
- Patrick D. Olson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lisa J. Kuechenmeister
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kelsi L. Anderson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sonja Daily
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Christelle M. Roux
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Michelle L. Reniere
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Tami L. Lewis
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - William J. Weiss
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Mark Pulse
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Phung Nguyen
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Jerry W. Simecka
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - John M. Morrison
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Khalid Sayood
- Department of Electrical Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Oluwatoyin A. Asojo
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mark S. Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Eric P. Skaar
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Paul M. Dunman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
39
|
Abdelhamid G, Anwar-Mohamed A, Elmazar MM, El-Kadi AOS. Modulation of NAD(P)H:quinone oxidoreductase by vanadium in human hepatoma HepG2 cells. Toxicol In Vitro 2010; 24:1554-61. [PMID: 20599494 DOI: 10.1016/j.tiv.2010.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 06/21/2010] [Accepted: 06/23/2010] [Indexed: 11/19/2022]
Abstract
Recent studies demonstrated the carcinogenicity and the mutagenicity of vanadium compounds. In addition, vanadium (V(5+)) was found to enhance the effects of other genotoxic agents. However, the mechanism by which V(5+) induce toxicity remain unknown. In the current study we examined the effect of V(5+) (as ammonium metavanadate, NH(4)VO(3)) on the expression of NAD(P)H: quinone oxidoreductase 1 (NQO1) in human hepatoma HepG2 cells. Therefore, HepG2 cells were treated with increasing concentrations of V(5+) in the presence of two NQO1 inducers, the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and isothiocyanate sulforaphane (SUL). Our results showed that V(5+) inhibited the TCDD- and SUL-mediated induction of NQO1 at mRNA, protein and activity levels. Investigating the effect of V(5+) at transcriptional levels revealed that V(5+) significantly inhibited the TCDD- and SUL-mediated induction of antioxidant responsive element (ARE)-dependent luciferase reporter gene expression. In addition, V(5+) was able to decrease the TCDD- and SUL-induced nuclear accumulation of nuclear factor erythroid 2-related factor-2 (Nrf2) without affecting Nrf2 mRNA or protein levels. Looking at the post-transcriptional level, V(5+) did not affect NQO1 mRNA stability, thus eliminating the possible role of V(5+) in decreasing NQO1 mRNA levels through this mechanism. In contrast, at post-translational level, V(5+) was able to significantly decrease NQO1 protein half-life. The present study demonstrates for the first time that V(5+) down-regulates NQO1 at the transcriptional and post-translational levels in the human hepatoma HepG2 cells via AhR- and Nrf2-dependent mechanisms.
Collapse
Affiliation(s)
- Ghada Abdelhamid
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | |
Collapse
|
40
|
Ahmed M, Neville MJ, Edelmann MJ, Kessler BM, Karpe F. Proteomic analysis of human adipose tissue after rosiglitazone treatment shows coordinated changes to promote glucose uptake. Obesity (Silver Spring) 2010; 18:27-34. [PMID: 19556978 DOI: 10.1038/oby.2009.208] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aim of this study was to identify potential protein targets for insulin sensitization in human adipose tissue using unbiased proteomic approaches. Ten moderately obese, but otherwise healthy, subjects were treated with rosiglitazone 4 mg b.i.d. for 14 days and global protein and gene expression changes were monitored. Proteomic analysis revealed distinct up- or downregulation (greater than twofold) in 187 protein spots on the two-dimensional (2-D) gel images between day 0 and day 1 adipose tissue samples. When comparing the protein spots on the gels from day 0 with that of 14-day-treated samples, 122 spots showed differential expression. There was a striking increase in the expression of proteins involved in glucose transporter-4 (GLUT4) granule transport and fusion (actin, myosin-9, tubulin, vimentin, annexins, moesin, LIM, and SH3 domain protein-1), signaling (calmodulin, guanine nucleotide-binding proteins), redox regulation (superoxide dismutase, catalase, ferritin, transferrin, heat shock proteins), and adipogenesis (collagens, galectin-1, nidogen-1, laminin, lamin A/C). However, there was an intriguing absence of correlated changes in mRNA expression, suggesting adaptation at a post-transcriptional level in response to rosiglitazone. Thus, the major changes observed were among proteins involved in cytoskeletal rearrangement, insulin and calcium signaling, and inflammatory and redox signals that decisively upregulate GLUT4 granule trafficking in human adipose tissue. Such orchestrated changes in expression of multiple proteins provide insights into the mechanism underlying the increased efficiency in glucose uptake and improvement of insulin sensitivity in response to rosiglitazone treatment.
Collapse
Affiliation(s)
- Meftun Ahmed
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
| | | | | | | | | |
Collapse
|
41
|
Schmidt N, Pautz A, Art J, Rauschkolb P, Jung M, Erkel G, Goldring MB, Kleinert H. Transcriptional and post-transcriptional regulation of iNOS expression in human chondrocytes. Biochem Pharmacol 2009; 79:722-32. [PMID: 19854161 DOI: 10.1016/j.bcp.2009.10.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/13/2009] [Accepted: 10/13/2009] [Indexed: 11/18/2022]
Abstract
Chondrocytes are important for the development and maintenance of articular cartilage. However, both in osteoarthritis (OA) and rheumatoid arthritis (RA) chondrocytes are involved in the process of cartilage degradation and synthesize important immunomodulatory mediators, including nitric oxide (NO) generated by the inducible NO synthase (iNOS). To uncover the role of iNOS in the pathomechanisms of OA and RA, we analyzed the regulation of iNOS expression using immortalized human chondrocytes as a reproducible model. In C-28/I2 chondrocytes, iNOS expression was associated with the expression of the chondrocyte phenotype. Peak induction by a cytokine cocktail occurred between 6 and 8h and declined by 24h. Inhibition of p38MAPK, NF-kappaB and the JAK2-STAT-1alpha pathways resulted in a reduction of iNOS expression. In contrast to other cell types, the cytokine-mediated induction of the human iNOS promoter paralleled the induction rate of the iNOS mRNA expression in C-28/I2 chondrocytes. However, in addition post-transcriptional regulation of iNOS expression by the RNA binding protein KSRP seems to operate in these cells. As seen in other chondrocyte models, glucocorticoids were not able to inhibit cytokine-induced iNOS expression in C-28/I2 cells, due to the lack of the glucocorticoid receptor mRNA expression. In this model of glucocorticoid-resistance, the new fungal anti-inflammatory compound S-curvularin was able to inhibit cytokine-induced iNOS expression and iNOS-dependent NO-production. In summary, we demonstrate for the first time that differentiated human immortalized C-28/I2 chondrocytes are a representative cell culture model to investigate iNOS gene expression in human joint diseases.
Collapse
MESH Headings
- Anti-Inflammatory Agents/pharmacology
- Cartilage, Articular/drug effects
- Cartilage, Articular/enzymology
- Cell Line, Transformed
- Chondrocytes/drug effects
- Chondrocytes/enzymology
- Cytokines/pharmacology
- Enzyme Induction
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Enzymologic/genetics
- Humans
- Interferon-Stimulated Gene Factor 3/antagonists & inhibitors
- Janus Kinase 2/antagonists & inhibitors
- NF-kappa B p50 Subunit/antagonists & inhibitors
- Nitric Oxide Synthase Type II/biosynthesis
- Nitric Oxide Synthase Type II/genetics
- RNA Processing, Post-Transcriptional/drug effects
- RNA Processing, Post-Transcriptional/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Zearalenone/analogs & derivatives
- Zearalenone/pharmacology
- p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors
Collapse
Affiliation(s)
- Nadine Schmidt
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
RNA cleavage is a catalytic reaction which defines many types of RNA processing events, including those of metabolite-sensing riboswitch, self-splicing introns, mRNA splicing, tRNA processing, polyA-cleavage, and various small ribozymes such as hairpin and hammerhead ribozyme. In this chapter, we describe a general methodology for developing a mammalian cell-based high-throughput screening assay useful for identifying small molecules capable of inhibiting RNA cleavage in mammalian cells. In the specific assay described, a plasmid DNA vector in which the expression of a luciferase reporter gene is controlled by hammerhead ribozyme cleavage was stably introduced into the human 293 cell line. Such a cell line enabled the rapid screening of chemical compound libraries and the identification of cell membrane-permeable inhibitory molecules capable of blocking ribozyme cleavage. The general strategy described later could in principle be adapted to identify small molecule inhibitors of many types of RNA cleavage reactions.
Collapse
Affiliation(s)
- Laising Yen
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | |
Collapse
|
43
|
Abstract
Posttranscriptional regulation of gene expression plays a pivotal role as a fast control system for T-cells and B-cells operating in the defense reactions against rapidly growing infectious agents. The framework of this machinery involves cis-acting elements in the mRNAs of relevant cytokines and trans-acting factors interacting with these elements. The cis- and trans-acting factors enforce rapid mRNA decay with other proteins such as nucleases in the decay machinery. The most prominent cis-element contains A + U- rich sequence (ARE), and is located in the 3'-untranslated region of the target mRNAs. Some ARE-binding proteins promote the rapid decay, and others protect the mRNA from degradation. The 5'-end of nascent mRNA undergoes capping which protects the 5'-end together with the cap-binding protein, and the 3' end is protected with poly (A) tail and associating poly (A) binding protein. Unlike in classical drawing of linear structure of mRNA, the end structures interact with each other through a common platform composed of translation initiation factors, revealing the cross-talk of the 5'-end cap structure and 3'-end poly (A) tail on the translational machinery. The rapid degradation and stabilization of mRNA is triggered by a cellular signaling cascade through phosphorylation of associating protein factors in response to environmental stimuli, and a large nucleolytic complex for specific decay reaction called exosome is formed with the 3'-UTR of mRNA through interaction with the ARE-binding proteins. Possible therapeutic agents modifying stability of ARE-containing mRNA are being screened in order to treat immunological disorders.
Collapse
Affiliation(s)
- Junichi Nakagawa
- Junichi Nakagawa Department of Food Science and Technology, Faculty of Bio-Industry, Tokyo University of Agriculture, 196 Yasaka, Abashiri-city, Hokkaido 099-2493, Japan.
| |
Collapse
|
44
|
Kim S, Yang JY, Xu J, Jang IC, Prigge MJ, Chua NH. Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol 2008; 49:1634-44. [PMID: 18829588 PMCID: PMC2722234 DOI: 10.1093/pcp/pcn146] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) are 21 nt RNAs that regulate many biological processes in plants by mediating translational inhibition or cleavage of target transcripts. Arabidopsis mutants defective in miRNA biogenesis have overlapping and highly pleiotropic phenotypes including serrated leaves and ABA hypersensitivity. Recent evidence indicates that miRNA genes are transcribed by RNA polymerase II (Pol II). Since Pol II transcripts are capped, we hypothesized that CBP (cap-binding protein) 20 and 80 may bind to capped primary miRNA (pri-miRNA) transcripts and play a role in their processing. Here, we show that cbp20 and cbp80 mutants have reduced miRNA levels and increased pri-miRNA levels. Co-immunoprecipitation experiments revealed that pri-miRNAs 159, 166, 168 and 172 could be associated with CBP20 and CBP80. We found that CBP20 and CBP80 are stabilized by ABA by a post-translational mechanism, and these proteins are needed for ABA induction of miR159 during seed germination. The lack of miR159 accumulation in ABA-treated seeds of cbp20/80 mutants leads to increased MYB33 and MYB101 transcript levels, and presumably higher levels of these positive regulators result in ABA hypersensitivity. Genetic and molecular analyses show that CBP20 and 80 have overlapping function in the same developmental pathway as SE and HYL1. Our results identify new components in miRNA biogenesis.
Collapse
Affiliation(s)
- Sanghee Kim
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
| | - Jun-Yi Yang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
| | - Jun Xu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
| | - In-Cheol Jang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
| | - Michael J. Prigge
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
- *Corresponding author: E-mail, ; Fax, +1-212-327-8327
| |
Collapse
|
45
|
Benedetti M, Martuccio G, Fattorini D, Canapa A, Barucca M, Nigro M, Regoli F. Oxidative and modulatory effects of trace metals on metabolism of polycyclic aromatic hydrocarbons in the Antarctic fish Trematomus bernacchii. Aquat Toxicol 2007; 85:167-175. [PMID: 17923160 DOI: 10.1016/j.aquatox.2007.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 08/24/2007] [Accepted: 08/28/2007] [Indexed: 05/25/2023]
Abstract
Biological interactions between various classes of pollutants are of great relevance for the Antarctic marine environment, where the naturally elevated bioavailability of metals like cadmium might indirectly influence sensitivity of endemic organisms toward other environmental pollutants, e.g. polycyclic aromatic hydrocarbons (PAHs). To further investigate reciprocal effects of different chemicals, the fish Trematomus bernacchii was exposed to trace metals (Cd, Cu, Hg, Ni, Pb) and benzo[a]pyrene (BaP, as a model PAH), dosed alone and in combinations. Co-exposures revealed that BaP did not influence the accumulation of metals, while these elements caused significant changes on tissue levels of the PAH. The marked EROD induction caused by BaP was completely suppressed by co-exposure with Cd and Cu, but no effects were observed with Ni, Hg and Pb. Similar results were confirmed at the protein level by Western blot analyses while CYP1A1 mRNA levels were reduced only during Cd co-exposures. Clear evidence of oxidative perturbations was observed in fish co-treated with Cd and BaP and the reduced capability to absorb peroxyl and hydroxyl radicals suggested some oxidative pathways by which this element might indirectly modulate the biotransformation efficiency of Cytochrome P450. Partly different and post-transcriptional mechanisms of action could be hypothesized for Cu, while moderate oxidative effects of Hg, Ni and Pb during co-exposures would confirm their limited influence on metabolism of PAHs. In general, the overall results revealed a complex pathway of interactions between different chemicals during co-exposures and the importance of oxidative status in modulating induction and expression of CYP1A1.
Collapse
Affiliation(s)
- Maura Benedetti
- Istituto di Biologia e Genetica, Università Politecnica delle Marche, Ancona, Via Ranieri Monte d'Ago, 60100 Ancona, Italy
| | | | | | | | | | | | | |
Collapse
|
46
|
Cahill AL, Moore JM, Sabar FI, Harkins AB. Variability in RNA interference in neuroendocrine PC12 cell lines stably transfected with an shRNA plasmid. J Neurosci Methods 2007; 166:236-40. [PMID: 17767962 DOI: 10.1016/j.jneumeth.2007.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
RNA interference (RNAi) has quickly become a very powerful technique for specifically suppressing or knocking down the expression of any desired gene. Many fields of research, including neuroscience, have benefitted from RNAi methods. It has been well documented that different small interfering RNAs (siRNAs) and small hairpin RNAs (shRNAs) vary greatly in terms of their effectiveness, and much attention has been focused on guidelines and algorithms for the selection of effective siRNAs. However, it has not been widely appreciated that a single shRNA-expressing plasmid can also produce widely varying levels of knockdown in different stably transfected cell lines derived from the same transfection. Here we report that knockdown of three distinct target proteins varies from minimal to almost complete in independent, stably transfected PC12 cell lines. This variability in knockdown among cell lines emphasizes the importance of characterizing a number of cell lines when attempting to establish stable knockdown cell lines, but also offers the possibility of studying the effects of graded levels of protein expression.
Collapse
Affiliation(s)
- Anne L Cahill
- Department of Neurobiology, Pharmacology and Physiology, The University of Chicago, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
47
|
Falahatpisheh H, Nanez A, Montoya-Durango D, Qian Y, Tiffany-Castiglioni E, Ramos KS. Activation profiles of HSPA5 during the glomerular mesangial cell stress response to chemical injury. Cell Stress Chaperones 2007; 12:209-18. [PMID: 17915553 PMCID: PMC1971237 DOI: 10.1379/csc-259.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Environmental injury has been associated with endoplasmic reticulum (ER) stress, a response characterized by activation of the unfolded protein response, proteasomal degradation of proteins, and induction of HSPA5, also known as GRP78 or BiP. Although HSPA5 has been implicated in the stress response to environmental injury in several cell types, its role in the glomerular ER stress response is unknown. In this study, we evaluated HSPA5 activation profiles in rat glomerular mesangial cells (rGMCs) challenged with heavy metals (HgCl2 or Pb2+ acetate) or polycyclic aromatic hydrocarbons (PAHs, ie, benzo(a)pyrene [BaP]). Challenge of rGMCs with 1 or 10 microM HgCl2 or Pb2+ acetate increased HSPA5 mRNA and protein levels. The induction response was sensitive to transcriptional and translational inhibition by actinomycin D (AD) and cyclohexamide, respectively. HSPA5 mRNA was induced by 3 microM BaP in an AD-sensitive manner, but this response was unaffected by the presence of heavy metals. A promoter construct containing sequences that mediate thapsigargin (TH) inducibility of the HSPA5 promoter was refractory to both heavy metals and BaP. The HSPA5 induction response in rGMCs is conserved because it was reproduced with fidelity in immunolocalization experiments of HSPA5 protein in M15 and HEK293 cells in embryonic lines of murine and human origin, respectively. Collectively, these findings identify HSPA5 in the stress response of rGMCs and implicate regulatory mechanisms that are distinct from those involved in TH inducibility.
Collapse
Affiliation(s)
- Hadi Falahatpisheh
- Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville, Louisville, KY 40292, USA
| | | | | | | | | | | |
Collapse
|
48
|
Kralj A, Gurgui M, König GM, van Echten-Deckert G. Trichothecenes induce accumulation of glucosylceramide in neural cells by interfering with lactosylceramide synthase activity. Toxicol Appl Pharmacol 2007; 225:113-22. [PMID: 17889095 DOI: 10.1016/j.taap.2007.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 08/09/2007] [Accepted: 08/13/2007] [Indexed: 11/28/2022]
Abstract
Trichothecenes are sesquiterpenoid metabolites produced by several fungal strains that impair human and animal health. Since sphingolipids were connected with fungal toxicity the aim of the present study was to test the influence of fungal metabolites on sphingolipid metabolism in neural cells. The crude extract of fungal strain Spicellum roseum induced accumulation of glucosylceramide (GlcCer), and simultaneous reduction of the formation of lactosylceramide (LacCer) and complex gangliosides in primary cultured neurons. Following a bioassay-guided fractionation of the respective fungal extract we could demonstrate that the two isolated trichothecene derivatives, 8-deoxy-trichothecin (8-dT) and trichodermol (Td-ol) were responsible for this effect. Thus, incubation of primary cultured neurons as well as of neuroblastoma B104 cells for 24 h with 30 microM of either of the two fungal metabolites resulted in uncoupling of sphingolipid biosynthesis at the level of LacCer. For the observed reduction of LacCer synthase activity by about 90% cell integrity was crucial in both cell types. In neuroblastoma cells the amount of LacCer synthase mRNA was reduced in the presence of trichothecenes, whereas in primary cultured neurons this was not the case, suggesting a post-transcriptional mechanism of action in the latter cell type. The data also show that the compounds did not interfere with the translocation of GlcCer in neuroblastoma cells. Collectively, our results demonstrate that trichodermol and 8-deoxy-trichothecin inhibit LacCer synthase activity in a cell-type-specific manner.
Collapse
Affiliation(s)
- Ana Kralj
- Institute for Pharmaceutical Biology, University of Bonn, Germany
| | | | | | | |
Collapse
|
49
|
Mezaki Y, Yoshikawa K, Yamaguchi N, Miura M, Imai K, Kato S, Senoo H. Rat hepatic stellate cells acquire retinoid responsiveness after activation in vitro by post-transcriptional regulation of retinoic acid receptor alpha gene expression. Arch Biochem Biophys 2007; 465:370-9. [PMID: 17693386 DOI: 10.1016/j.abb.2007.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 06/13/2007] [Accepted: 06/18/2007] [Indexed: 10/23/2022]
Abstract
Activation of hepatic stellate cells (HSCs) is a key process in liver fibrogenesis and retinoid loss is a remarkable feature of activated HSCs. However, roles of retinoids in liver fibrogenesis are obscure. We show that mRNA levels of RARalpha, beta and gamma were decreased during rat HSC activation in vitro. However, protein levels of RARalpha and beta were increased during HSC activation. A retinoic acid response element-containing luciferase assay indicated that HSCs became responsive to retinoids only after activation in vitro and that this response was mediated by, at least in part, RARalpha subtype. Immunocytochemical analysis showed that RARalpha proteins were mainly distributed in cytosol as many spots. All-trans retinoic acid treatment strongly lowered the cytosolic RARalpha protein levels. These results indicate that rat HSCs become retinoid responsive after activation in vitro, through post-transcriptional up-regulation of RARalpha gene expression.
Collapse
Affiliation(s)
- Yoshihiro Mezaki
- Department of Cell Biology and Histology, Akita University School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | | | | | | | | | | | | |
Collapse
|
50
|
Kuner R, Vogt M, Sultmann H, Buness A, Dymalla S, Bulkescher J, Fellmann M, Butz K, Poustka A, Hoppe-Seyler F. Identification of cellular targets for the human papillomavirus E6 and E7 oncogenes by RNA interference and transcriptome analyses. J Mol Med (Berl) 2007; 85:1253-62. [PMID: 17589817 DOI: 10.1007/s00109-007-0230-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/23/2007] [Indexed: 01/06/2023]
Abstract
Specific types of human papillomaviruses (HPVs) cause cervical cancer, the second most common tumor in women worldwide. Both cellular transformation and the maintenance of the oncogenic phenotype of HPV-positive tumor cells are linked to the expression of the viral E6 and E7 oncogenes. To identify downstream cellular target genes for the viral oncogenes, we silenced endogenous E6 and E7 expression in HPV-positive HeLa cells by RNA interference (RNAi). Subsequently, we assessed changes of the cellular transcriptome by genome-wide microarray analysis. We identified 648 genes, which were either downregulated (360 genes) or upregulated (288 genes), upon inhibition of E6/E7 expression. A large fraction of these genes is involved in tumor-relevant processes, such as apoptosis control, cell cycle regulation, or spindle formation. Others may represent novel cellular targets for the HPV oncogenes, such as a large group of C-MYC-associated genes involved in RNA processing and splicing. Comparison with published microarray data revealed a substantial concordance between the genes repressed by RNAi-mediated E6/E7 silencing in HeLa cells and genes reported to be upregulated in HPV-positive cervical cancer biopsies.
Collapse
Affiliation(s)
- Ruprecht Kuner
- Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|