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Chen K, Huang X, Distler U, Tenzer S, Günay-Esiyok Ö, Gupta N. Apically-located P4-ATPase1-Lem1 complex internalizes phosphatidylserine and regulates motility-dependent invasion and egress in Toxoplasma gondii. Comput Struct Biotechnol J 2023; 21:1893-1906. [PMID: 36936814 PMCID: PMC10015115 DOI: 10.1016/j.csbj.2023.02.032] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The membrane asymmetry regulated by P4-ATPases is crucial for the functioning of eukaryotic cells. The underlying spatial translocation or flipping of specific lipids is usually assured by respective P4-ATPases coupled to conforming non-catalytic subunits. Our previous work has identified five P4-ATPases (TgP4-ATPase1-5) and three non-catalytic partner proteins (TgLem1-3) in the intracellular protozoan pathogen, Toxoplasma gondii. However, their flipping activity, physiological relevance and functional coupling remain unknown. Herein, we demonstrate that TgP4-ATPase1 and TgLem1 work together to translocate phosphatidylserine (PtdSer) during the lytic cycle of T. gondii. Both proteins localize in the plasma membrane at the invasive (apical) end of its acutely-infectious tachyzoite stage. The genetic knockout of P4-ATPase1 and conditional depletion of Lem1 in tachyzoites severely disrupt the asexual reproduction and translocation of PtdSer across the plasma membrane. Moreover, the phenotypic analysis of individual mutants revealed a requirement of lipid flipping for the motility, egress and invasion of tachyzoites. Not least, the proximity-dependent biotinylation and reciprocal immunoprecipitation assays demonstrated the physical interaction of P4-ATPase1 and Lem1. Our findings disclose the mechanism and significance of PtdSer flipping during the lytic cycle and identify the P4-ATPase1-Lem1 heterocomplex as a potential drug target in T. gondii.
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Key Words
- BSA, bovine serum albumin
- CDC50, Cell Division Control 50
- COS, crossover sequence
- Cdc50
- DAPI, 4′,6-diamidino-2-phenylindole
- DHFR-TS, dihydrofolate reductase – thymidylate synthase
- HFF, human foreskin fibroblast
- HXGPRT, hypoxanthine-xanthine-guanine phosphoribosyltransferase
- IAA, indole-3-acetic acid
- LEM, Ligand Effector Module
- Lem1
- NBD, nitrobenzoxadiazole
- NBD-lipid
- P4-ATPase1
- PBS, phosphate-buffered saline
- Phosphatidylserine
- Phospholipid flipping
- PtdCho, phosphatidylcholine
- PtdEtn, phosphatidylethanolamine
- PtdSer, phosphatidylserine
- PtdThr, phosphatidylthreonine
- UTR, untranslated region
- cGMP, cyclic Guanosine Monophosphate
- mAID, (mini) auxin-inducible degron
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Affiliation(s)
- Kai Chen
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Xiyu Huang
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Özlem Günay-Esiyok
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
- Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-P), Hyderabad, India
- Corresponding author at: Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany.
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Abstract
BACKGROUND Emergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. METHODS We have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. RESULTS Whole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). CONCLUSION Delta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.
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Key Words
- NSP, non-structural protein
- SARS-CoV-2, COVID-19, genome-wide, evolution, variants, VOC, VOI, VUM, SNP, mutation, non-synonymous, silent mutation, spike, RNA dependent RNA polymerase, NSP, UTR: Abbreviations: VOC, variant of concern
- UTR, untranslated region
- VOI, variant of interest
- VUM, variant under monitoring
- rdrp, RNA dependent RNA polymerase
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Affiliation(s)
- Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, India.
| | - Sanjeet Kumar
- Gangadhar Meher University, Sambalpur, Odisha, India.
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Nagar PR, Gajjar ND, Dhameliya TM. In search of SARS CoV-2 replication inhibitors: Virtual screening, molecular dynamics simulations and ADMET analysis. J Mol Struct 2021; 1246:131190. [PMID: 34334813 DOI: 10.1016/j.molstruc.2021.131190] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/11/2021] [Accepted: 07/24/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome has relapsed recently as novel coronavirus causing a life threat to the entire world in the absence of an effective therapy. To hamper the replication of the deadly SARS CoV-2 inside the host cells, systematic in silico virtual screening of total 267,324 ligands from Asinex EliteSynergy and BioDesign libraries has been performed using AutoDock Vina against RdRp. The molecular modeling studies revealed the identification of twenty-one macrocyclic hits (2-22) with better binding energy than remdesivir (1), marketed SARS CoV-2 inhibitor. Further, the analysis using rules for drug-likeness and their ADMET profile revealed the candidature of these hits due to superior oral bioavailability and druggability. Further, the MD simulation studies of top two hits (2 and 3) performed using GROMACS 2020.1 for 10 ns revealed their stability into the docked complexes. These results provide an important breakthrough in the design of macrocyclic hits as SARS CoV-2 RNA replicase inhibitor.
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Key Words
- ACE2, angiotensin converting enzyme 2
- ADMET assay
- ADMET, absorption, distribution, metabolism, excretion and toxicity
- BBB, blood-brain barrier
- BOILED, brain or intestinal estimated permeation method
- COVID-19
- COVID-19, corona virus disease 2019
- E, envelope protein
- FDA, food and drugs administration
- HBA, hydrogen bond acceptor
- HBD, hydrogen bond donor
- HERG, human ether-a-go-go-related gene
- LOAEL, oral rat chronic toxicity
- M, membrane protein
- MD simulations
- MD, molecular dynamics
- Molecular docking
- N, nucleocapsid protein
- NSPs, non-structural proteins
- RdRp
- RdRp, RNA dependent RNA polymerase
- S, spike glycoprotein
- SARS CoV-2
- SARS CoV-2, severe acute respiratory syndrome 2
- UTR, untranslated region
- WHO, world health organization
- pp1a/b, polyproteins
- ssRNA, single stranded ribonucleic acid
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Setaro AC, Gaglia MM. All hands on deck: SARS-CoV-2 proteins that block early anti-viral interferon responses. Curr Res Virol Sci 2021; 2:100015. [PMID: 34786565 PMCID: PMC8588586 DOI: 10.1016/j.crviro.2021.100015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is responsible for the current pandemic coronavirus disease of 2019 (COVID-19). Like other pathogens, SARS-CoV-2 infection can elicit production of the type I and III interferon (IFN) cytokines by the innate immune response. A rapid and robust type I and III IFN response can curb viral replication and improve clinical outcomes of SARS-CoV-2 infection. To effectively replicate in the host, SARS-CoV-2 has evolved mechanisms for evasion of this innate immune response, which could also modulate COVID-19 pathogenesis. In this review, we discuss studies that have reported the identification and characterization of SARS-CoV-2 proteins that inhibit type I IFNs. We focus especially on the mechanisms of nsp1 and ORF6, which are the two most potent and best studied SARS-CoV-2 type I IFN inhibitors. We also discuss naturally occurring mutations in these SARS-CoV-2 IFN antagonists and the impact of these mutations in vitro and on clinical presentation. As SARS-CoV-2 continues to spread and evolve, researchers will have the opportunity to study natural mutations in IFN antagonists and assess their role in disease. Additional studies that look more closely at previously identified antagonists and newly arising mutants may inform future therapeutic interventions for COVID-19.
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Key Words
- 3CLpro, 3-chymotrypsin like protease
- COVID-19, coronavirus disease of 2019
- IFN, interferon
- IFNAR, interferon alpha/beta receptor
- IFNLR, interferon lambda receptor
- IRF, interferon response factor
- ISRE, interferon stimulated response element
- Immune evasion
- MAVS, mitochondrial antiviral-signaling protein
- MDA-5, melanoma differentiation-associated protein 5
- ORF, open reading frame
- ORF6
- PLpro, papain-like protease
- RIG-I, retinoic acid-inducible gene I
- SARS-CoV-2
- SARS-CoV-2, SARS coronavirus 2
- SRP, signal recognition particle
- STAT, signal transducer and regulator of transcription
- SeV, Sendai virus
- TAB1, TGF-beta activated kinase 1 binding protein 1
- TAK1, TGF-beta activated kinase 1
- TBK1, TANK-binding kinase 1
- TLR, toll-like receptor
- TRIF, TIR domain-containing adapter-inducing interferon beta
- Type I interferon
- UTR, untranslated region
- eIF, eukaryotic initiation factor
- nsp, non-structural protein
- nsp1
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Affiliation(s)
- Alessandra C Setaro
- Program in Immunology, Tufts Graduate School of Biomedical Sciences, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Tufts University, MA, USA
| | - Marta M Gaglia
- Program in Immunology, Tufts Graduate School of Biomedical Sciences, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Tufts University, MA, USA
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Faure-Dupuy S, Riedl T, Rolland M, Hizir Z, Reisinger F, Neuhaus K, Schuehle S, Remouchamps C, Gillet N, Schönung M, Stadler M, Wettengel J, Barnault R, Parent R, Schuster LC, Farhat R, Prokosch S, Leuchtenberger C, Öllinger R, Engleitner T, Rippe K, Rad R, Unger K, Tscharahganeh D, Lipka DB, Protzer U, Durantel D, Lucifora J, Dejardin E, Heikenwälder M. Control of APOBEC3B induction and cccDNA decay by NF-κB and miR-138-5p. JHEP Rep 2021; 3:100354. [PMID: 34704004 PMCID: PMC8523871 DOI: 10.1016/j.jhepr.2021.100354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/28/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background & Aims Immune-mediated induction of cytidine deaminase APOBEC3B (A3B) expression leads to HBV covalently closed circular DNA (cccDNA) decay. Here, we aimed to decipher the signalling pathway(s) and regulatory mechanism(s) involved in A3B induction and related HBV control. Methods Differentiated HepaRG cells (dHepaRG) knocked-down for NF-κB signalling components, transfected with siRNA or micro RNAs (miRNA), and primary human hepatocytes ± HBV or HBVΔX or HBV-RFP, were treated with lymphotoxin beta receptor (LTβR)-agonist (BS1). The biological outcomes were analysed by reverse transcriptase-qPCR, immunoblotting, luciferase activity, chromatin immune precipitation, electrophoretic mobility-shift assay, targeted-bisulfite-, miRNA-, RNA-, genome-sequencing, and mass-spectrometry. Results We found that canonical and non-canonical NF-κB signalling pathways are mandatory for A3B induction and anti-HBV effects. The degree of immune-mediated A3B production is independent of A3B promoter demethylation but is controlled post-transcriptionally by the miRNA 138-5p expression (hsa-miR-138-5p), promoting A3B mRNA decay. Hsa-miR-138-5p over-expression reduced A3B levels and its antiviral effects. Of note, established infection inhibited BS1-induced A3B expression through epigenetic modulation of A3B promoter. Twelve days of treatment with a LTβR-specific agonist BS1 is sufficient to reduce the cccDNA pool by 80% without inducing significant damages to a subset of cancer-related host genes. Interestingly, the A3B-mediated effect on HBV is independent of the transcriptional activity of cccDNA as well as on rcDNA synthesis. Conclusions Altogether, A3B represents the only described enzyme to target both transcriptionally active and inactive cccDNA. Thus, inhibiting hsa-miR-138-5p expression should be considered in the combinatorial design of new therapies against HBV, especially in the context of immune-mediated A3B induction. Lay summary Immune-mediated induction of cytidine deaminase APOBEC3B is transcriptionally regulated by NF-κB signalling and post-transcriptionally downregulated by hsa-miR-138-5p expression, leading to cccDNA decay. Timely controlled APOBEC3B-mediated cccDNA decay occurs independently of cccDNA transcriptional activity and without damage to a subset of cancer-related genes. Thus, APOBEC3B-mediated cccDNA decay could offer an efficient therapeutic alternative to target hepatitis B virus chronic infection. Impairment of NF-κB signalling prevents APOBEC3B induction and cccDNA decay. APOBEC3B is post-transcriptionally regulated by the hsa-miR-138-5p. Over-expression of the hsa-miR-138-5p inhibits APOBEC3B expression and cccDNA decay. A3B timely induces cccDNA decay without damage to cancer-related genes. APOBEC3B-mediated cccDNA decay is independent of cccDNA transcriptional activity.
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Key Words
- A20, tumour necrosis factor alpha-induced protein 3
- APOBEC3A/A3A, apolipoprotein B mRNA editing catalytic polypeptide-like A
- APOBEC3B
- APOBEC3B/A3B, apolipoprotein B mRNA editing catalytic polypeptide-like B
- APOBEC3G/A3G, apolipoprotein B mRNA editing catalytic polypeptide-like G
- BCA, bicinchoninic acid assay
- CHB, chronic hepatitis B
- CXCL10, C-X-C motif chemokine ligand 10
- ChIP, chromatin immune precipitation
- EMSA, electrophoretic mobility-shift assay
- H3K4Me3, histone 3 lysine 4 trimethylation
- HBx
- Hepatitis B virus
- IFNα/γ, interferon alpha/gamma
- IKKα/β, IκB kinase alpha/beta
- JMJD8, jumonji domain containing 8
- LPS, lipopolysaccharide
- LTβR, lymphotoxin beta receptor
- MAPK, mitogen-activated protein kinase
- NEMO, NF-κB essential modulator
- NF-κB
- NF-κB, nuclear factor kappa B
- NIK, NF-κB inducing kinase
- NT, non-treated
- RT-qPCR, reverse transcription-quantitative PCR
- RelA, NF-κB p65 subunit
- TNF, tumour necrosis factor
- UBE2V1, ubiquitin conjugating enzyme E2 V1
- UTR, untranslated region
- cccDNA
- cccDNA, covalently closed circular DNA
- d.p.i., days post infection
- miRNA
- miRNA, micro RNA
- siCTRL, siRNA control
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Affiliation(s)
- Suzanne Faure-Dupuy
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maude Rolland
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Zoheir Hizir
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Florian Reisinger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Neuhaus
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Caroline Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Nicolas Gillet
- Integrated Veterinary Research Unit, Namur Research Institute for Life Sciences, Namur, Belgium
| | - Maximilian Schönung
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen Wettengel
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Romain Barnault
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Romain Parent
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Linda Christina Schuster
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rayan Farhat
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Sandra Prokosch
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Leuchtenberger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Darjus Tscharahganeh
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, Heidelberg, Germany
| | - Daniel B. Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - David Durantel
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Julie Lucifora
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
- Corresponding authors. Addresses: Laboratory of Molecular Immunology and Signal Transduction, University of Liège, GIGA-Institute, Avenue de l'Hôpital, 1, CHU, B34, 4000 Liege, Belgium. Tel.: +32 4 366 4472; fax: +32 4 366 4534
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany. Tel.: +49 6221 42 3891; Fax: +49 6221 42 3899
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Hasan M, Ashik AI, Chowdhury MB, Tasnim AT, Nishat ZS, Hossain T, Ahmed S. Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2. Inform Med Unlocked 2021; 24:100569. [PMID: 33846694 PMCID: PMC8028608 DOI: 10.1016/j.imu.2021.100569] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by an RNA virus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 possesses an almost 30kbp long genome. The genome contains open-reading frame 1ab (ORF1ab) gene, the largest one of SARS-CoV-2, encoding polyprotein PP1ab and PP1a responsible for viral transcription and replication. Several vaccines have already been approved by the respective authorities over the world to develop herd immunity among the population. In consonance with this effort, RNA interference (RNAi) technology holds the possibility to strengthen the fight against this virus. Here, we have implemented a computational approach to predict potential short interfering RNAs including small interfering RNAs (siRNAs) and microRNAs (miRNAs), which are presumed to be intrinsically active against SARS-CoV-2. In doing so, we have screened miRNA library and siRNA library targeting the ORF1ab gene. We predicted the potential miRNA and siRNA candidate molecules utilizing an array of bioinformatic tools. By extending the analysis, out of 24 potential pre-miRNA hairpins and 131 siRNAs, 12 human miRNA and 10 siRNA molecules were sorted as potential therapeutic agents against SARS-CoV-2 based on their GC content, melting temperature (Tm), heat capacity (Cp), hybridization and minimal free energy (MFE) of hybridization. This computational study is focused on lessening the extensive time and labor needed in conventional trial and error based wet lab methods and it has the potential to act as a decent base for future researchers to develop a successful RNAi therapeutic.
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Key Words
- ACE-2, Angiotensin-converting enzyme 2
- COVID-19
- COVID-19, coronavirus disease 2019
- Cp, heat capacity
- Gene silencing
- ORF, open reading frame
- Posttranscriptional regulation
- RNAi Therapeutics
- RNAi, RNA interference
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane protease serine 2
- Tm, melting temperature
- UTR, untranslated region
- hsa-miR, human microRNA
- miRNA
- miRNA, microRNA
- sgRNA, sub-genomic RNA
- siRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Mahedi Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Arafat Islam Ashik
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Belal Chowdhury
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Atiya Tahira Tasnim
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zakia Sultana Nishat
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Shamim Ahmed
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Zhang W, Feng J, Zeng W, Zhou Z, Wang Y, Lu H. Characterization of Single Nucleotide Variants of OPN3 Gene in Melanocytic Nevi and Melanoma. JID Innov 2021; 1:100006. [PMID: 34909710 PMCID: PMC8659391 DOI: 10.1016/j.xjidi.2021.100006] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/03/2022] Open
Abstract
In this study, we examined single nucleotide variants (SNVs) of the OPN3 gene in malignant melanoma and melanocytic nevi. A total of 20 variants of SNVs were detected. Of these variants, five nonsynonymous mutations of OPN3 were identified, including c.T152C, c.T401C, c.G547A, c.G768A, and c.G992A. Three prediction tools, MutationTaster2, Polymorphism Phenotyping version 2, and PROVEAN (Protein Variation Effect Analyzer), which predict possible impact of an amino acid substitution, suggested that the mutations could be deleterious. Nine SNVs occurred in 3' untranslated regions, whereas two were observed in 5' untranslated regions. In all cases, four intronic variants were identified. In addition, we identified nine 3' untranslated region SNVs in OPN3; one of them (OPN3[NM_014322:c.∗83C>T]) is predicted to disrupt a conserved microRNA (has-miR-376c-3p) target site, located in position 86-93 of OPN3 3' untranslated region. Our findings suggest that there is a strong possibility that OPN3 SNVs play a role in the pathogenesis of melanocytic tumors via prediction of functional phenotype.
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Affiliation(s)
- Wei Zhang
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jianglong Feng
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wen Zeng
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhixu Zhou
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, China
| | - Yu Wang
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Hongguang Lu
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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Zhang P, Li J. Down-regulation of circular RNA hsa_circ_0007534 suppresses cell growth by regulating miR-219a-5p/SOX5 axis in osteosarcoma. J Bone Oncol 2021; 27:100349. [PMID: 33552887 PMCID: PMC7844569 DOI: 10.1016/j.jbo.2021.100349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
The interaction between circ_0007534 and miR-219a-5p is confirmed for the first time. The interaction between miR-219a-5p and SOX5 is confirmed for the first time. Circ_0007534 knockdown inhibits the progression of osteosarcoma cells. Circ_0007534 regulates the growth of osteosarcoma cells through modulating miR-219a-5p/SOX5 axis.
Introduction Circular RNA circ_0007534 and microRNA-219a (miR-219a-5p) were reported to be involved in osteosarcoma (OS) development. Osteosarcoma (OS) is one of the most common malignant bone tumors, which was more prone to occur in the metaphysis of long bones, including distal femur and proximal tibia. However, the detailed mechanisms were not fully clear. The purpose of this research was to reveal the functional mechanisms of circ_0007534 and miR-219a-5p in OS. Methods The levels of genes were determined by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot assay. Cell proliferation ability was detected by cell counting kit-8 (CCK-8) and colony formation assay. Cell migration and invasion abilities were measured using the transwell assay. Furthermore, the interaction between miR-219a-5p and circ_0007534 or SRY (sex-determining region Y)-box 5 (SOX5) was predicted by starbaseV3.0, and confirmed by the dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Besides, tumor xenograft experiment was performed to analyze the effect of circ_0007534 depletion on tumor growth in vivo. Results The levels of circ_0007534 and SOX5 were increased, while the miR-219a-5p level was decreased in OS tissues and cells. Circ_0007534 knockdown repressed the proliferation, colony formation, migration, and invasion in OS cells. Circ_0007534 targeted miR-219a-5p, and miR-219a-5p interacted with SOX5. Furthermore, circ_0007534 regulated the growth of OS cells through modulating the levels of miR-219a-5p and SOX5. Conclusion Our finding demonstrated that circ_0007534 knockdown suppressed the growth of OS cells via regulating miR-219a-5p/SOX5 axis, providing a potential target for OS treatment and diagnosis.
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Key Words
- ATCC, American Type Culture Collection
- CCK-8, cell counting kit-8
- Circ_0007534
- EMT, epithelial mesenchymal transformation
- EZH2, zeste homolog 2
- OS, osteosarcoma
- Osteosarcoma
- PAGE, polyacrylamide gel electrophoresis
- PVDF, polyvinylidene difluoride
- RIP, RNA immunoprecipitation
- SD, standard deviation
- SOX5
- UTR, untranslated region
- hFOB1.19, human osteoblast cell line
- mRNA, message RNA
- miR-219a-5p
- qRT-PCR, quantitative real-time polymerase chain reaction
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Affiliation(s)
- Peng Zhang
- Department of Orthopedics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jun Li
- Department of Orthopedics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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Abstract
T cells are critical to fight pathogenic microbes and combat malignantly transformed cells in the fight against cancer. To exert their effector function, T cells produce effector molecules, such as the pro-inflammatory cytokines IFN-γ, TNF-α and IL-2. Tumors possess many inhibitory mechanisms that dampen T cell effector function, limiting the secretion of cytotoxic molecules. As a result, the control and elimination of tumors is impaired. Through recent advances in genomic editing, T cells can now be successfully modified via CRISPR/Cas9 technology. For instance, engaging (post-)transcriptional mechanisms to enhance T cell cytokine production, the retargeting of T cell antigen specificity or rendering T cells refractive to inhibitory receptor signaling can augment T cell effector function. Therefore, CRISPR/Cas9-mediated genome editing might provide novel strategies for cancer immunotherapy. Recently, the first-in-patient clinical trial was successfully performed with CRISPR/Cas9-modified human T cell therapy. In this review, a brief overview of currently available techniques is provided, and recent advances in T cell genomic engineering for the enhancement of T cell effector function for therapeutic purposes are discussed.
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Key Words
- AP-1, activator protein 1
- ARE, AU-rich element
- ARE-Del, deletion of the 3′UTR AREs from the Ifng/IFNG gene
- CAR T cells
- CAR, Chimeric Antigen Receptor
- CRISPR
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeat
- CRS, cytokine release syndrome
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- Cas, CRISPR-associated
- Cas9
- Cytokines
- DGK, Diacylglycerol kinase
- DHX37, DEAH-box helicase 37
- EBV, Epstein Barr virus
- FOXP3, Forkhead box P3
- GATA, GATA binding protein
- Genome editing
- IFN, interferon
- IL, interleukin
- LAG-3, Lymphocyte Activating 3
- NF-κB, nuclear factor of activated B cells
- PD-1, Programmed cell Death 1
- PD-L1, Programmed Death Ligand 1
- PTPN2, Protein Tyrosine Phosphatase Non-Receptor 2
- Pdia3, Protein Disulfide Isomerase Family A Member 3
- RBP, RNA-binding protein
- RNP, ribonuclear protein
- T cell effector function
- T cells
- TCR, T cell receptor
- TGF, transforming growth factor
- TIL, Tumor Infiltrating Lymphocyte
- TLRs, Toll-like receptors
- TNF, tumor necrosis factor
- TRAC, TCR-α chain
- TRBC, TCR-β chain
- UTR, untranslated region
- tTCR, transgenic TCR
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Kolenda T, Guglas K, Kopczyńska M, Sobocińska J, Teresiak A, Bliźniak R, Lamperska K. Good or not good: Role of miR-18a in cancer biology. Rep Pract Oncol Radiother 2020; 25:808-819. [PMID: 32884453 DOI: 10.1016/j.rpor.2020.07.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
miR-18a is a member of primary transcript called miR-17-92a (C13orf25 or MIR17HG) which also contains five other miRNAs: miR-17, miR-19a, miR-20a, miR-19b and miR-92a. This cluster as a whole shows specific characteristics, where miR-18a seems to be unique. In contrast to the other members, the expression of miR-18a is additionally controlled and probably functions as its own internal controller of the cluster. miR-18a regulates many genes involved in proliferation, cell cycle, apoptosis, response to different kinds of stress, autophagy and differentiation. The disturbances of miR-18a expression are observed in cancer as well as in different diseases or pathological states. The miR-17-92a cluster is commonly described as oncogenic and it is known as 'oncomiR-1', but this statement is a simplification because miR-18a can act both as an oncogene and a suppressor. In this review we summarize the current knowledge about miR-18a focusing on its regulation, role in cancer biology and utility as a potential biomarker.
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Key Words
- 5-FU, 5-fluorouracyl
- ACVR2A, activin A receptor type 2A
- AKT, AKT serine/threonine kinase
- AR, androgen receptor
- ATG7, autophagy related 7
- ATM, ATM serine/threonine kinase
- BAX, BCL2 associated Xapoptosis regulator
- BCL2, BCL2 apoptosis regulator
- BCL2L10, BCL2 like 10
- BDNF, brain derived neurotrophic factor
- BLCA, bladder urothelial carcinoma
- BRCA, breast cancer
- Biomarker
- Bp, base pair
- C-myc (MYCBP), MYC binding protein
- CASC2, cancer susceptibility 2
- CD133 (PROM1), prominin 1
- CDC42, cell division cycle 42
- CDKN1, Bcyclin dependent kinase inhibitor 1B
- COAD, colon adenocarcinoma
- Cancer
- Circulating miRNA
- DDR, DNA damage repair
- E2F family (E2F1, E2F2, E2F3), E2F transcription factors
- EBV, Epstein-Barr virus
- EMT, epithelial-to-mesenchymal transition
- ER, estrogen receptor
- ERBB (EGFR), epidermal growth factor receptor
- ESCA, esophageal carcinoma
- FENDRR, FOXF1 adjacent non-coding developmental regulatory RNA
- FER1L4, fer-1 like family member 4 (pseudogene)
- GAS5, growth arrest–specific 5
- HIF-1α (HIF1A), hypoxia inducible factor 1 subunit alpha
- HNRNPA1, heterogeneous nuclear ribonucleoprotein A1
- HNSC, head and neck squamous cell carcinoma
- HRR, homologous recombination-based DNA repair
- IFN-γ (IFNG), interferon gamma
- IGF1, insulin like growth factor 1
- IL6, interleukin 6
- IPMK, inositol phosphate multikinase
- KIRC, clear cell kidney carcinoma
- KIRP, kidney renal papillary cell carcinoma
- KRAS, KRAS proto-oncogene, GTPase
- LIHC, liver hepatocellular carcinoma
- LMP1, latent membrane protein 1
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Liquid biopsy
- MAPK, mitogen-activated protein kinase
- MCM7, minichromosome maintenance complex component 7
- MET, mesenchymal-to-epithelial transition
- MTOR, mechanistic target of rapamycin kinase
- N-myc (MYCN), MYCN proto-oncogene, bHLH transcription factor
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOTCH2, notch receptor 2
- Oncogene
- PAAD, pancreatic adenocarcinoma
- PERK (EIF2AK3), eukaryotic translation initiation factor 2 alpha kinase 3
- PI3K (PIK3CA), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
- PIAS3, protein inhibitor of activated STAT 3
- PRAD, prostate adenocarcinoma
- RISC, RNA-induced silencing complex
- SMAD2, SMAD family member 2
- SMG1, SMG1 nonsense mediated mRNA decay associated PI3K related kinase
- SNHG1, small nucleolar RNA host gene 1
- SOCS5, suppressor of cytokine signaling 5
- STAD, stomach adenocarcinoma
- STAT3, signal transducer and activator of transcription 3
- STK4, serine/threonine kinase 4
- Suppressor
- TCGA
- TCGA, The Cancer Genome Atlas
- TGF-β (TGFB1), transforming growth factor beta 1
- TGFBR2, transforming growth factor beta receptor 2
- THCA, papillary thyroid carcinoma
- TNM, Classification of Malignant Tumors: T - tumor / N - lymph nodes / M – metastasis
- TP53, tumor protein p53
- TP53TG1, TP53 target 1
- TRIAP1, p53-regulating inhibitor of apoptosis gene
- TSC1, TSC complex subunit 1
- UCA1, urothelial cancer associated 1
- UCEC, uterine corpus endometrial carcinoma
- UTR, untranslated region
- WDFY3-AS2, WDFY3 antisense RNA 2
- WEE1, WEE1 G2 checkpoint kinase
- WNT family, Wingless-type MMTV integration site family/Wnt family ligands
- ZEB1/ZEB2, zinc finger E-box binding homeobox 1 and 2
- ceRNA, competitive endogenous RNA
- cncRNA, protein coding and non-coding RNA
- lncRNA, long-non coding RNA
- miR-17-92a
- miR-18a
- miRNA
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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Ozturk K, Onal MS, Efiloglu O, Nikerel E, Yildirim A, Telci D. Association of 5'UTR polymorphism of secretory phospholipase A2 group IIA (PLA2G2A) gene with prostate cancer metastasis. Gene 2020; 742:144589. [PMID: 32179174 DOI: 10.1016/j.gene.2020.144589] [Citation(s) in RCA: 8] [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: 11/20/2019] [Revised: 02/19/2020] [Accepted: 03/12/2020] [Indexed: 01/21/2023]
Abstract
Phospholipase A2 (PLA2) enzymes are small lipolytic hydrolases that can regulate immune responses through generation of Arachidonic Acid (AA), a precursor molecule of lipid mediators like prostaglandins, leukotrienes and thromboxanes. One of the family members of PLA2, secretory Phospholipase A2 Group IIA (PLA2G2A), was associated with different types of malignancies including prostate cancer. Elevated serum levels of PLA2G2A was found in prostate cancer (PCa) patients and associated with increased tumor grade in literature. 5'UTR regions have regulatory role in protein expression by controlling the accessibility of factors necessary for the translation initiation. Single nucleotide polymorphisms at 5'UTR regions have the potential to affect mRNA translation efficiency resulting in altered protein levels depending on structure and nucleotide content. Given that the 5'UTR polymorphism in PLA2G2A gene (rs11573156) is associated with increased serum levels of PLA2G2A, the association of this 5'UTR polymorphism with PCa susceptibility and metastasis was investigated in this study. Total of 261 PCa patients and 128 control individuals were genotyped with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Individuals with heterozygous CG genotype was found to have significantly reduced risk of PCa metastasis with an Odds Ratio (OR) of 0.405 (p = 0.028, 95%CI = 0.181-0.906), compared to the carriers of homozygous CC genotype (p > 0.05) suggesting an anti-metastatic effect for the G allele. No association was found between PCa susceptibility and Gleason score (p > 0.05) in Turkish population.
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Affiliation(s)
- Kaan Ozturk
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Meltem Selen Onal
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Ozgur Efiloglu
- Department of Urology, Faculty of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Asif Yildirim
- Department of Urology, Faculty of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | - Dilek Telci
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey.
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12
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Taneja S, Dutta T. On a stake-out: Mycobacterial small RNA identification and regulation. Noncoding RNA Res 2019; 4:86-95. [PMID: 32083232 DOI: 10.1016/j.ncrna.2019.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/30/2019] [Accepted: 05/12/2019] [Indexed: 12/23/2022] Open
Abstract
Persistence of mycobacteria in the hostile environment of human macrophage is pivotal for its successful pathogenesis. Rapid adaptation to diverse stresses is the key aspect for their survival in the host cells. A range of heterogeneous mechanisms operate in bacteria to retaliate stress conditions. Small RNAs (sRNA) have been implicated in many of those mechanisms in either a single or multiple regulatory networks to post-transcriptionally modulate bacterial gene expression. Although small RNA profiling in mycobacteria by advanced technologies like deep sequencing, tilling microarray etc. have identified hundreds of sRNA, however, a handful of those small RNAs have been unearthed with precise regulatory mechanism. Extensive investigations on sRNA-mediated gene regulations in eubacteria like Escherichia coli revealed the existence of a plethora of distinctive sRNA mechanisms e.g. base pairing, protein sequestration, RNA decoy etc. Increasing studies on mycobacterial sRNA also discovered several eccentric mechanisms where sRNAs act at the posttranscriptional stage to either activate or repress target gene expression that lead to promote mycobacterial survival in stresses. Several intrinsic features like high GC content, absence of any homologue of abundant RNA chaperones, Hfq and ProQ, isolate sRNA mechanisms of mycobacteria from that of other bacteria. An insightful approach has been taken in this review to describe sRNA identification and its regulations in mycobacterial species especially in Mycobacterium tuberculosis.
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Key Words
- Anti-antisense
- Antisense
- Base pairing
- CDS, coding sequence
- Gene regulation by sRNA
- IGR, intergenic region
- ORF, open reading frame
- RBS, Ribosome binding site
- RNAP, RNA polymerase
- SD, Shine Dalgarno sequence
- Small RNAs
- TF, transcription factor
- TIR, translation initiation region
- UTR, untranslated region
- nt, nucleotide
- sRNA, small RNA
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13
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Wang H, Zhao F, Cai S, Pu Y. MiR-193a regulates chemoresistance of human osteosarcoma cells via repression of IRS2. J Bone Oncol 2019; 17:100241. [PMID: 31193934 PMCID: PMC6543196 DOI: 10.1016/j.jbo.2019.100241] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022] Open
Abstract
Chemoresistance prevents curative potential of chemotherapy in most cases. MicroRNAs (miRNAs) are key players in regulating chemoresistance in osteosarcoma, which is the most common primary bone cancer. Bisulfite sequencing and quantitative real time PCR analyses showed that miR-193a expression is downregulated by DNA hypermethylation at its promoter region in a chemoresistant cell line, SJSA-1, compared to a chemosensitive cell line G-292. Introduction of a miR-193a mimic in SJSA-1 cells or an antagomir into G-292 cells confirmed the role of miR-193a in osteosarcoma chemoresistance. Bioinformatics together with biochemical assays showed that insulin receptor substrate 2 (IRS2) is a target of miR-193a. Our data concludes that miR-193a plays a role in the osteosarcoma chemoresistance and thus might serve as a useful biomarker for osteosarcoma prognosis.
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Key Words
- 3PA, miR-193a-3p-antagomir
- 3PM, miR-193a-3p-mimic
- Ago, miR-193a-3p's agomir
- Anta, miR-193a-3p's antagomir
- BSP, Bisulfite Sequencing PCR
- CDDP, cisplatin
- Carb, carboplatin
- Chemoresistance
- DNA methylation
- Dox, doxorubicin
- Etop, etoposide
- IRS2
- IRS2, Insulin Receptor Substrate 2
- MTX, methotrexate
- Mut, mutation-type vector
- OS, osteosarcoma
- Osteosarcoma
- UTR, untranslated region
- WT, wild-type vector
- miR, microRNA
- miR-193a-3p
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Affiliation(s)
- Haiyan Wang
- Department of Clinical Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, PR China
| | - Fangfang Zhao
- Department of Laboratory Research Center, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, PR China
| | - Shanbao Cai
- Department of Orthopedic Surgery, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, PR China
| | - Youguang Pu
- Department of Laboratory Research Center, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, PR China
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Liu M, Kong JQ. The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity. Acta Pharm Sin B 2018; 8:981-994. [PMID: 30505666 PMCID: PMC6251810 DOI: 10.1016/j.apsb.2018.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 12/27/2022] Open
Abstract
Herein we describe the discovery and functional characterization of a steroidal glycosyltransferase (SGT) from Ornithogalum saundersiae and a steroidal glycoside acyltransferase (SGA) from Escherichia coli and their application in the biosynthesis of acylated steroidal glycosides (ASGs). Initially, an SGT gene, designated as OsSGT1, was isolated from O. saundersiae. OsSGT1-containing cell free extract was then used as the biocatalyst to react with 49 structurally diverse drug-like compounds. The recombinant OsSGT1 was shown to be active against both 3β- and 17β-hydroxyl steroids. Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. Finally, a novel enzymatic two-step synthesis of two ASGs, acetylated testosterone-17-O-β-glucosides (AT-17β-Gs) and acetylated estradiol-17-O-β-glucosides (AE-17β-Gs), from the abundantly available free steroids using OsSGT1 and EcSGA1 as the biocatalysts was developed. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. The improved cytotoxic activities of 3′-acetylated testosterone17-O-β-glucoside towards seven human tumor cell lines were thus observable.
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Key Words
- 6′-AE-17β-G, 6′-acetylated estradiol 17-O-β-glucoside
- 6′-AT-17β-G, 6′-acetylated testosterone 17-O-β-glucoside
- AE-17β-G, acetylated estradiol-17-O-β-glucoside
- ASGs, acylated steroidal glycosides
- AT-17β-G, acetylated testosterone-17-O-β-glucoside
- Acylated steroidal glyco sides
- E-17β-G, estradiol-17-O-β-glucoside
- EcSGA1, E. coli steroidal glucoside acetyltransferase
- HPLC—SPE—NMR, high-performance liquid chromatography–solid phase extraction–NMR spectroscopy
- IPTG, isopropyl-β-D-thiogalactoside
- LacA
- ORF, open reading frame
- Ornithogalum saunder siae
- PSBD, putative steroid-binding domain
- PSPG, plant secondary product glycosyltranferase box
- RIN, RNA integrity number
- RP-HPLC, reversed phase high-performance liquid chromatography
- SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis
- SGAs, steroidal glycoside acyltransferases
- SGEs, steroidal glycoside esters
- SGTs, steroidal glycosyltransferases
- SGs, steroidal glycosides
- Steroidal glycoside acyl transferase
- Steroidal glycosyltrans ferase
- T-17β-G, testosterone-17-O-β-glucoside
- UDP-Ara, UDP-l-arabinose
- UDP-Gal, UDP-D-galactose
- UDP-GalA, UDP-D-Galacturonic acid
- UDP-Glc, UDP-D-glucose
- UDP-GlcA, UDP-D-glucuronic acid
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-Xyl, UDP-D-xylose
- UTR, untranslated region
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Virtanen E, Mannonen L, Lappalainen M, Auvinen E. Genotyping of hepatitis C virus by nucleotide sequencing: A robust method for a diagnostic laboratory. MethodsX 2018; 5:414-418. [PMID: 30050759 PMCID: PMC6060086 DOI: 10.1016/j.mex.2018.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hepatitis C virus (HCV) is a globally significant blood-borne agent causing liver diseases, and it has infected over 170 million people worldwide. HCV is a diverse group of RNA viruses currently divided into genotypes 1-7 as well as subtypes. HCV infection can be treated with antiviral drugs, but the HCV genotype has to be determined for optimal selection of treatment strategy. The aim of this study was to set up a sequencing-based HCV genotyping method suitable for the workflow of a diagnostic laboratory. The established method is robust and stable, and it utilizes a one-step reverse transcription and PCR amplification of the 5' untranslated region (5'UTR) and partial Core region of the HCV genome. Amplification products are sequenced using the standard Sanger method, and the genotype is determined by using a freely accessible web-based genotyping tool. The method was validated at the Helsinki University Hospital Laboratory using 238 previously genotyped serum samples. •A new one-step RT-PCR method for the amplification of the 5' untranslated region and partial Core region of hepatitis C virus was established.•HCV genotype is determined using Sanger sequencing and a freely accessible, easy-to-use web-based genotyping tool.•The method is robust, reproducible and suitable for diagnostic laboratory workflow, and it requires no costly instrumentation or specialized sequence analysis skills.
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16
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Jonchere V, Marisa L, Greene M, Virouleau A, Buhard O, Bertrand R, Svrcek M, Cervera P, Goloudina A, Guillerm E, Coulet F, Landman S, Ratovomanana T, Job S, Ayadi M, Elarouci N, Armenoult L, Merabtene F, Dumont S, Parc Y, Lefèvre JH, André T, Fléjou JF, Guilloux A, Collura A, de Reyniès A, Duval A. Identification of Positively and Negatively Selected Driver Gene Mutations Associated With Colorectal Cancer With Microsatellite Instability. Cell Mol Gastroenterol Hepatol 2018; 6:277-300. [PMID: 30116770 PMCID: PMC6089198 DOI: 10.1016/j.jcmgh.2018.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Recent studies have shown that cancers arise as a result of the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role, if any. However, these investigations were concerned with alterations at nonrepetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors showing microsatellite instability (MSI) resulting from mismatch repair deficiency investigated in the present study. METHODS We performed whole-exome sequencing of 47 MSI colorectal cancers (CRCs) and confirmed results in an independent cohort of 53 MSI CRCs. We used a probabilistic model of mutational events within microsatellites, while adapting pre-existing models to analyze nonrepetitive DNA sequences. Negatively selected coding alterations in MSI CRCs were investigated for their functional and clinical impact in CRC cell lines and in a third cohort of 164 MSI CRC patients. RESULTS Both positive and negative selection of somatic mutations in DNA repeats was observed, leading us to identify the expected true driver genes associated with the MSI-driven tumorigenic process. Several coding negatively selected MSI-related mutational events (n = 5) were shown to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations were observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio, 3; 95% CI, 1.1-7.9; P = .03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to a poor prognosis. CONCLUSIONS The present results identify the positive and negative driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation. Exome sequencing data have been deposited in the European genome-phenome archive (accession: EGAS00001002477).
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Key Words
- CRC, colorectal cancer
- Colorectal Cancer
- Driver Gene Mutations
- HR, hazard ratio
- MLH1, MutL Homolog 1
- MMR, mismatch repair
- MSH, MutS Homolog
- MSI, microsatellite instability
- Microsatellite Instability
- NR, nonrepetitive
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- Positive and Negative Selection
- R, repetitive
- RFS, relapse-free survival
- RTCA, Real-Time Cell Analyzer
- Tumorigenic Process
- UTR, untranslated region
- WES, whole-exome sequencing
- WGA, whole-genome amplification
- bp, base pair
- indel, insertion/deletion
- mRNA, messenger RNA
- shRNA, short hairpin RNA
- siRNA, small interfering RNA
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Affiliation(s)
- Vincent Jonchere
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Laetitia Marisa
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Malorie Greene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Alain Virouleau
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Olivier Buhard
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Romane Bertrand
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Magali Svrcek
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Pascale Cervera
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anastasia Goloudina
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Inovarion, Collaborative research Department Paris, France
| | - Erell Guillerm
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Florence Coulet
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Genetics Department, Assistance publique - Hôpitaux de Paris, Pitié Salpêtrière Hôpital, Paris, France
| | - Samuel Landman
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Toky Ratovomanana
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Lucile Armenoult
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Fatiha Merabtene
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Sylvie Dumont
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,University Pierre and Marie CURIE Paris 06, Unité Mixte de Service 30 L'Unité Mixte de service Imagerie Cytométrie, Plateforme d’Histomorphologie, Sorbonne Université Paris, France
| | - Yann Parc
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Jérémie H. Lefèvre
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service de Chirurgie Générale et Digestive, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Thierry André
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Department of Oncology, Assistance publique - Hôpitaux de Paris, Hôpital Saint Antoine, Paris, France
| | - Jean-François Fléjou
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Service d’Anatomie et Cytologie Pathologiques, Assistance publique - Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Agathe Guilloux
- Laboratoire de Mathématiques et Modélisation d’Évry, University Évry, Évry, France,Centre National de la Recherche Scientifique, Université Paris-Saclay, Evry, France
| | - Ada Collura
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Alex Duval
- Sorbonne Université, University Pierre and Marie CURIE Paris 06, INSERM, Unité Mixte de Recherche938, Equipe Instabilité des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France,Correspondence Address correspondence to: Alex Duval, MD, PhD, Sorbonne Universite, UPMC Univ Paris 06, Inserm, UMR938, Equipe Instabilite Des Microsatellites et Cancer, Centre de Recherche Saint Antoine, Paris, France. fax: (33) 149284603.
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17
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Burns R, Pechenik J. Transcriptomic Basis of Metamorphic Competence in the Salt-Marsh-Dwelling Polychaete Capitella teleta. Biol Bull 2017; 232:158-170. [PMID: 28898599 DOI: 10.1086/692829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Marine invertebrate larvae typically take hours to weeks after being released into the plankton before becoming "competent" to metamorphose. The mechanisms that govern this transition between the precompetent and metamorphically competent states are unknown. We studied gene expression patterns in precompetent and competent larvae of the salt-marsh-dwelling polychaete worm Capitella teleta (Blake, Grassle & Eckelbarger, 2009)-a species in which precompetent larvae are unusually easy to distinguish from competent larvae-to determine differences in gene expression associated with the onset of metamorphic competence. More than 1530 genes were more highly expressed in precompetent larvae, while more than 1060 genes were more highly expressed in competent larvae. Competent larvae downregulated the expression of genes belonging to gene ontologies relating to growth and development and upregulated those associated with ligand-binding transmembrane channels with possible chemo- and mechanosensory functions. Most of these channels were annotated as being from the degenerin/epithelial sodium channel family or the G-protein-coupled receptor family; proteins from these families can have chemosensory functions. Serotonin and GABA (γ-aminobutyric acid) receptors are among the genes that were upregulated in competent larvae; both have been shown to induce larvae of C. teleta and other marine invertebrates to metamorphose and are thought to be components of the signal transduction pathway that leads to metamorphosis. Overall, it appears that once larvae of C. teleta have completed development of the internal structures and physiology required for juvenile life during the precompetent period, they then upregulate the expression of chemosensory proteins and neurotransmitter receptors that will enable them to detect and transduce a settlement cue signal.
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Key Words
- 5-HT6, 5-hydroxytryptamine 6
- ASW, artificial seawater
- DEG/ENaC, degenerin/epithelial sodium channel
- FDR, false discovery rate
- GABA, γ-aminobutyric acid
- GPCR, G-protein-coupled receptor
- HSP, heat-shock protein
- NCBI, National Center for Biotechnology Information
- NOS, nitric oxide synthase
- PKD, polycystic kidney disease
- UTR, untranslated region
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18
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Ling TY, Wang XL, Chai Q, Lu T, Stulak JM, Joyce LD, Daly RC, Greason KL, Wu LQ, Shen WK, Cha YM, Lee HC. Regulation of cardiac CACNB2 by microRNA-499: Potential role in atrial fibrillation. BBA Clin 2017; 7:78-84. [PMID: 28239561 DOI: 10.1016/j.bbacli.2017.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 12/19/2022]
Abstract
The L-type calcium channel (LTCC) is one of the major ion channels that are known to be associated with the electrical remodeling of atrial fibrillation (AF). In AF, there is significant downregulation of the LTCC, but the underlying mechanism for such downregulation is not clear. We have previously reported that microRNA-499 (miR-499) is significantly upregulated in patients with permanent AF and that KCNN3, the gene that encodes the small-conductance calcium-activated potassium channel 3 (SK3), is a target of miR-499. We found that CACNB2, an important subunit of the LTCC, is also a target of miR-499. We hypothesize that miR-499 plays an important role in AF electrical remodeling by regulating the expression of CACNB2 and the LTCC. In atrial tissue from patients with permanent AF, CACNB2 was significantly downregulated by 67% (n = 4, p < 0.05) compared to those from patients with no history of AF. Transfection of miR-499 mimic into HL-1 cells, a mouse hyperplastic atrial cardiac myocyte cell-line, resulted in the downregulation of CACNB2 protein expression, while that of miR-499 inhibitor upregulated CACNB2 protein expression. Binding of miR-499 to the 3′ untranslated region of CACNB2 was confirmed by luciferase reporter assay and by the increased presence of CACNB2 mRNA in Argonaute pulled-down microRNA-induced silencing complexes after transfection with the miR-499 mimic. In addition, downregulation of CACNB2 resulted in the downregulation of protein levels of the pore-forming α-subunit (CACNA1C). In conclusion, upregulation of atrial miR-499 induces the downregulation of CACNB2 expression and may contribute to the electrical remodeling in AF. LTCC is downregulated with electrical remodeling of atrial fibrillation. MiR-499 is increased and CACNB2 is reduced in atria from patients with atrial fibrillation. MiR-499 binds to the 3′UTR of CACNB2 and inhibits its protein expression. Downregulation of CACNB2 results in the downregulation of LTCC pore-forming subunit. MiR-499 contributes to the electrical remodeling of AF through regulation of CACNB2.
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Key Words
- AF, atrial fibrillation
- Ago, Argonaute
- CACNA1C, voltage-dependent calcium channel α-1C subunit
- CACNB2, voltage-dependent calcium channel β-2 subunit
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- LTCC, L-type calcium channel
- SR, sinus rhythm
- UTR, untranslated region
- miR-499, microRNA-499
- miRISC, microRNA-inducing silencing complex
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19
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Franchi N, Ballin F, Ballarin L. Protection from Oxidative Stress in Immunocytes of the Colonial Ascidian Botryllus schlosseri: Transcript Characterization and Expression Studies. Biol Bull 2017; 232:45-57. [PMID: 28445096 DOI: 10.1086/691694] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Botryllus schlosseri is a cosmopolitan colonial ascidian that undergoes cyclical generation changes, or take-overs, during which adult zooids are resorbed and replaced by their buds. At take-over, adult tissues undergo diffuse apoptosis and effete cells are massively ingested by circulating phagocytes, with a consequent increase in oxygen consumption and in production of reactive oxygen species (ROS). The latter are responsible for the death of phagocytes involved in the clearance of apoptotic cells and corpses by phagocytosis-induced apoptosis. However, the majority of phagocytes and hemocytes do not die, even if they experience oxidative stress. This fact suggests the presence of detoxification mechanisms assuring their protection. To test this assumption, we searched for transcripts of genes involved in detoxification in the transcriptome of B. schlosseri. We identified and characterized transcripts for Cu/Zn superoxide dismutase (SOD), γ-glutamyl-cysteine ligase modulatory subunit (GCLM), glutathione synthase (GS), and two glutathione peroxidases (i.e., GPx3 and GPx5), all involved in protection from ROS. We also carried out a phylogenetic analysis of the putative amino acid sequences, confirming their similarity to their vertebrate counterparts, and studied the location of their mRNAs by in situ hybridization on hemocyte monolayers. We also analyzed gene transcription during the colonial blastogenetic cycle, which is the interval of time between one take-over and the next, by qRT-PCR. In addition, we investigated the effects of cadmium (Cd), an inducer of oxidative stress, on gene transcription. Our results indicated that i) antioxidant gene expression is modulated in the course of the blastogenetic cycle and upon exposure to Cd, and ii) hemocytes synthesize both enzymatic and nonenzymatic antioxidants, in line with the idea that they represent a major detoxification system for ascidians.
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Key Words
- AG, adenine guanine (splicing consensus signal)
- ATG, start signal
- CDS, coding sequences
- Cd, cadmium
- Cu/Zn SOD, Cu-Zn superoxide dismutase
- EST, expressed sequence tag
- FSW, filtered seawater
- GCL, γ-glutamyl-cysteine ligase
- GCLC, catalytic subunit of γ-glutamyl-cysteine ligase
- GCLM, modulatory subunit of γ-glutamyl-cysteine ligase
- GPx, glutathione peroxidase
- GS, glutathione synthase
- GSH, glutathione
- GSSG, oxidized glutathione
- GT, guanine timine (splicing consensus signal)
- ISH, in situ hybridization
- MC, mid-cycle
- ME, minimum evolution
- ML, maximum likelihood
- MP, maximum parsimony
- NADPH, nicotinamide adenine dinucleotide phosphate
- NJ, neighbor-joining
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- PO, phenoloxidase
- RACE, rapid amplification of the cDNA ends
- ROS: reactive oxygen species
- SEC, selenocysteine
- SECIS, selenocysteine insertion sequence
- SOD, superoxide dismutase
- SODb, type B SOD
- TAG, stop codon
- TGA, thymine, guanine, and adenine nucleotides (stop codon)
- TO, take-over
- UPGMA, unweighted pair group with arithmetic mean
- UTR, untranslated region
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20
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Ackermann AM, Zhang J, Heller A, Briker A, Kaestner KH. High-fidelity Glucagon-CreER mouse line generated by CRISPR-Cas9 assisted gene targeting. Mol Metab 2017; 6:236-244. [PMID: 28271030 PMCID: PMC5323890 DOI: 10.1016/j.molmet.2017.01.003] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE α-cells are the second most prominent cell type in pancreatic islets and are responsible for producing glucagon to increase plasma glucose levels in times of fasting. α-cell dysfunction and inappropriate glucagon secretion occur in both type 1 and type 2 diabetes. Thus, there is growing interest in studying both normal function and pathophysiology of α-cells. However, tools to target gene ablation or activation specifically of α-cells have been limited, compared to those available for β-cells. Previous Glucagon-Cre and Glucagon-CreER transgenic mouse lines have suffered from transgene silencing, and the only available Glucagon-CreER "knock-in" mouse line results in glucagon haploinsufficiency, which can confound the interpretation of gene deletion analyses. Therefore, we sought to develop a Glucagon-CreERT2 mouse line that would maintain normal glucagon expression and would be less susceptible to transgene silencing. METHODS We utilized CRISPR-Cas9 technology to insert an IRES-CreERT2 sequence into the 3' UTR of the Glucagon (Gcg) locus in mouse embryonic stem cells (ESCs). Targeted ESC clones were then injected into mouse blastocysts to obtain Gcg-CreERT2 mice. Recombination efficiency in GCG+ pancreatic α-cells and glucagon-like peptide 1 positive (GLP1+) enteroendocrine L-cells was measured in Gcg-CreERT2 ;Rosa26-LSL-YFP mice injected with tamoxifen during fetal development and adulthood. RESULTS Tamoxifen injection of Gcg-CreERT2 ;Rosa26-LSL-YFP mice induced high recombination efficiency of the Rosa26-LSL-YFP locus in perinatal and adult α-cells (88% and 95%, respectively), as well as in first-wave fetal α-cells (36%) and adult enteroendocrine L-cells (33%). Mice homozygous for the Gcg-CreERT2 allele were phenotypically normal. CONCLUSIONS We successfully derived a Gcg-CreERT2 mouse line that expresses CreERT2 in pancreatic α-cells and enteroendocrine L-cells without disrupting preproglucagon gene expression. These mice will be a useful tool for performing temporally controlled genetic manipulation specifically in these cell types.
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Key Words
- CRISPR
- CRISPR, clustered regularly interspaced short palindromic repeat
- Cre, Cre recombinase
- CreERT2, tamoxifen-inducible Cre recombinase-estrogen receptor fusion protein
- DAPI, 4′,6-diamidino-2-phenylindole
- ESC, embryonic stem cell
- Enteroendocrine L-cell
- FACS, fluorescence-activated cell sorting
- GCG, glucagon
- GLP1
- GLP1, glucagon-like peptide 1
- Glucagon
- IRES, internal ribosomal entry site
- Islet
- LSL, loxP-stop-loxP
- UTR, untranslated region
- YFP, yellow fluorescent protein
- gRNA, guide RNA
- α-cell
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Affiliation(s)
- Amanda M Ackermann
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA; Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
| | - Jia Zhang
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA; Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
| | - Aryel Heller
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA; Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
| | - Anna Briker
- Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
| | - Klaus H Kaestner
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA; Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
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21
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Brewer CT, Chen T. PXR variants: the impact on drug metabolism and therapeutic responses. Acta Pharm Sin B 2016; 6:441-449. [PMID: 27709012 PMCID: PMC5045535 DOI: 10.1016/j.apsb.2016.07.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/21/2016] [Accepted: 05/04/2016] [Indexed: 01/30/2023] Open
Abstract
The pregnane X receptor (PXR) plays an important and diverse role in mediating xenobiotic induction of drug-metabolizing enzymes and transporters. Several protein isoforms of PXR exist, and they have differential transcriptional activity upon target genes; transcript variants 3 (PXR3) and 4 (PXR4) do not induce target gene expression, whereas transcript variants 1 (PXR1) and 2 (PXR2) respond to agonist by activating target gene expression. PXR protein variants also display differences in protein-protein interactions; PXR1 interacts with p53, whereas PXR3 does not. Furthermore, the transcript variants of PXR that encode these protein isoforms are differentially regulated by methylation and deletions in the respective promoters of the variants, and their expression differs in various human cancers and also in cancerous tissue compared to adjacent normal tissues. PXR1 and PXR4 mRNA are downregulated by methylation in cancerous tissue and have divergent effects on cellular proliferation when ectopically overexpressed. Additional detailed and comparative mechanistic studies are required to predict the effect of PXR transcript variant expression on carcinogenesis, therapeutic response, and the development of toxicity.
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Key Words
- AF, activating function
- BAMCA, bacterial artificial chromosome array–based methylated CpG island amplification
- CYP, cytochrome P450
- Drug metabolism
- GST, glutathione S-transferase
- MDR, multidrug resistance protein
- NHR, nuclear hormone receptor
- P-gp, P-glycoprotein
- PXR1, PXR transcript variant 1 (434 residues)
- PXR2, transcript variant 2 (473 residues)
- PXR3, transcript variant 3 (397 residues)
- PXR4, transcript variant 4 (322 residues;AK122990)
- Pregnane X receptor
- RACE, 5′ rapid amplification of cDNA ends
- Therapeutic responses
- Toxicity
- Transcript variants
- UGT, UDP-glucuronosyltransferase
- UTR, untranslated region
- shRNA, short hairpin RNA
- siRNA, small interfering RNA
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Affiliation(s)
- C. Trent Brewer
- Department of Chemical Biology and Therapeutics, St. Jude Children′s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children′s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Corresponding author at: Department of Chemical Biology and Therapeutics, St. Jude Children′s Research Hospital, Mail Stop #1000, 262 Danny Thomas Place, Memphis, TN 38105, USA. Tel.: +1 901 595 5937; fax: +1 901 595 5715.Department of Chemical Biology and Therapeutics, St. Jude Children′s Research Hospital, Mail Stop #1000, 262 Danny Thomas PlaceMemphisTN38105USA
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22
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Larsen K, Momeni J, Farajzadeh L, Callesen H, Bendixen C. Molecular characterization and analysis of the porcine NURR1 gene. Biochim Open 2016; 3:26-39. [PMID: 29450128 PMCID: PMC5801910 DOI: 10.1016/j.biopen.2016.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022]
Abstract
Orphan receptor NURR1 (also termed NR4A2) belongs to the nuclear receptor superfamily and functions as a regulatory factor of differentiation, migration, maturation and maintenance of mesencephalic dopaminergic neurons. NURR1 plays an important role in nigrostriatal dopamine neuron development and is therefore implicated in the pathogenesis of neurodegenerative diseases linked to the dopamine system of the midbrain. Here we report the isolation and characterization of porcine NURR1 cDNA. The NURR1 cDNA was RT-PCR cloned using NURR1-specific oligonucleotide primers derived from in silico sequences. The porcine NURR1 cDNA encodes a polypeptide of 598 amino acids, displaying a very high similarity with bovine, human and mouse (99%) NURR1 protein. Expression analysis revealed a differential NURR1 mRNA expression in various organs and tissues. NURR1 transcripts could be detected as early as at 60 days of embryo development in different brain tissues. A significant increase in NURR1 transcript in the cerebellum and a decrease in NURR1 transcript in the basal ganglia was observed during embryo development. The porcine NURR1 gene was mapped to chromosome 15. Two missense mutations were found in exon 3, the first coding exon of NURR1. Methylation analysis of the porcine NURR1 gene body revealed a high methylation degree in brain tissue, whereas methylation of the promoter was very low. A decrease in DNA methylation in a discrete region of the NURR1 promoter was observed in pig frontal cortex during pig embryo development. This observation correlated with an increase in NURR1 transcripts. Therefore, methylation might be a determinant of NURR1 expression at certain time points in embryo development. The porcine NURR1 gene was cloned and characterized. NURR1 transcript was detected early in pig embryo brain development. Methylation status of NURR1 may be a determinant for its expression.
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Key Words
- CNS, central nervous system
- DAN, dopaminergic neuron
- DAT, dopamin transporter
- DBD, DNA binding domain
- DNA methylation
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- NTD, N-terminal domain
- NURR1
- PCR, polymerase chain reaction
- Parkinson's disease
- Pig
- RT-PCR, reverse transcriptase polymerase chain reaction
- SNP
- SNP, Single nucleotide polymorphism
- TSS, transcription start site
- Transcription factor
- UTR, untranslated region
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Affiliation(s)
- Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Jamal Momeni
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Leila Farajzadeh
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Henrik Callesen
- Department of Animal Science, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Christian Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
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Lahlali T, Plissonnier ML, Romero-López C, Michelet M, Ducarouge B, Berzal-Herranz A, Zoulim F, Mehlen P, Parent R. Netrin-1 Protects Hepatocytes Against Cell Death Through Sustained Translation During the Unfolded Protein Response. Cell Mol Gastroenterol Hepatol 2016; 2:281-301.e9. [PMID: 28174720 PMCID: PMC5042567 DOI: 10.1016/j.jcmgh.2015.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/21/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Netrin-1, a multifunctional secreted protein, is up-regulated in cancer and inflammation. Netrin-1 blocks apoptosis induced by the prototypical dependence receptors deleted in colorectal carcinoma and uncoordinated phenotype-5. Although the unfolded protein response (UPR) triggers apoptosis on exposure to stress, it first attempts to restore endoplasmic reticulum homeostasis to foster cell survival. Importantly, UPR is implicated in chronic liver conditions including hepatic oncogenesis. Netrin-1's implication in cell survival on UPR in this context is unknown. METHODS Isolation of translational complexes, determination of RNA secondary structures by selective 2'-hydroxyl acylation and primer extension/dimethyl sulfate, bicistronic constructs, as well as conventional cell biology and biochemistry approaches were used on in vitro-grown hepatocytic cells, wild-type, and netrin-1 transgenic mice. RESULTS HepaRG cells constitute a bona fide model for UPR studies in vitro through adequate activation of the 3 sensors of the UPR (protein kinase RNA-like endoplasmic reticulum kinase (PERK)), inositol requiring enzyme 1α (IRE1α), and activated transcription factor 6 (ATF6). The netrin-1 messenger RNA 5'-end was shown to fold into a complex double pseudoknot and bear E-loop motifs, both of which are representative hallmarks of related internal ribosome entry site regions. Cap-independent translation of netrin 5' untranslated region-driven luciferase was observed on UPR in vitro. Unlike several structurally related oncogenic transcripts (l-myc, c-myc, c-myb), netrin-1 messenger RNA was selected for translation during UPR both in human hepatocytes and in mice livers. Depletion of netrin-1 during UPR induces apoptosis, leading to cell death through an uncoordinated phenotype-5A/C-mediated involvement of protein phosphatase 2A and death-associated protein kinase 1 in vitro and in netrin transgenic mice. CONCLUSIONS UPR-resistant, internal ribosome entry site-driven netrin-1 translation leads to the inhibition of uncoordinated phenotype-5/death-associated protein kinase 1-mediated apoptosis in the hepatic context during UPR, a hallmark of chronic liver disease.
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Key Words
- ATF6, activated transcription factor 6
- CMV, cytomegalovirus
- DAPK, death-associated protein kinase
- DMS, dimethyl sulfate
- DR, dependence receptor
- DTT, dithiothreitol
- ER, endoplasmic reticulum
- FLuc, Firefly luciferase
- HBV, hepatitis B virus
- HCC, hepatocellular carcinoma
- HCV, hepatitis C virus
- Hepatocyte
- IRE1α, inositol requiring enzyme 1α
- IRES, internal ribosome entry site
- LSL, (Lox-Stop-Lox)
- NMIA, N-methyl-isatoic anhydride
- Netrin
- PBS, phosphate-buffered saline
- PERK, protein kinase RNA (PKR)-like endoplasmic reticulum kinase
- PP2A, protein phosphatase 2A
- PR65β, erine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
- RLuc, Renilla lucerifase
- TUNEL, terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate nick-end labeling
- Translation
- Tu, tunicamycin
- UNC5, uncoordinated phenotype-5
- UPR
- UPR, unfolded protein response
- UTR, untranslated region
- VR1, vanilloid receptor 1
- eIF2α, Eukaryotic translation initiation factor 2A
- mRNA, messenger RNA
- pBic, Bicistronic plasmid
- qRT-PCR, quantitative reverse-transcription polymerase chain reaction
- siRNA, small interfering RNA
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Affiliation(s)
- Thomas Lahlali
- Inserm U1052-UMR CNRS 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Marie-Laure Plissonnier
- Inserm U1052-UMR CNRS 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra Consejo Superior de Investigaciones Científicas, Ciencia e Investigación (IPBLN-CSIC), Parque Tecnológico Ciencias de la Salud Granada, Armilla, Granada, Spain
| | - Maud Michelet
- Inserm U1052-UMR CNRS 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Benjamin Ducarouge
- Inserm U1052-UMR Centre National de la Recherche Scientifique 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra Consejo Superior de Investigaciones Científicas, Ciencia e Investigación (IPBLN-CSIC), Parque Tecnológico Ciencias de la Salud Granada, Armilla, Granada, Spain
| | - Fabien Zoulim
- Inserm U1052-UMR CNRS 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Patrick Mehlen
- Inserm U1052-UMR Centre National de la Recherche Scientifique 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France
| | - Romain Parent
- Inserm U1052-UMR CNRS 5286, Centre Léon Berard, Centre de Recherche en Cancérologie, Lyon, France,Correspondence Address correspondence to: Romain Parent, PharmD, PhD, Inserm U1052, 151 Cours Albert Thomas, F-69424 Lyon Cedex 03, France. fax: (33) 4-72-68-19-71.Inserm U1052151 Cours Albert ThomasF-69424 Lyon Cedex 03France
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Abstract
Oncogene MYC is deregulated in many human cancers, especially in lymphoma. Previously, we showed that inauhzin (INZ) activates p53 and inhibits tumor growth. However, whether INZ could suppress cancer cell growth independently of p53 activity is still elusive. Here, we report that INZ(c), a second generation of INZ, suppresses c-Myc activity and thus inhibits growth of human lymphoma cells in a p53-independent manner. INZ(c) treatment decreased c-Myc expression at both mRNA and protein level, and suppressed c-Myc transcriptional activity in human Burkitt's lymphoma Raji cells with mutant p53. Also, we showed that overexpressing ectopic c-Myc rescues the inhibition of cell proliferation by INZ(c) in Raji cells, implicating c-Myc activity is targeted by INZ(c). Interestingly, the effect of INZ(c) on c-Myc expression was impaired by disrupting the targeting of c-Myc mRNA by miRNAs via knockdown of ribosomal protein (RP) L5, RPL11, or Ago2, a subunit of RISC complex, indicating that INZ(c) targets c-Myc via miRNA pathways. These results reveal a new mechanism that INZ
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Key Words
- Dox, doxorubicin
- FACS, Fluorescence-activated cell sorting
- GTP, guanosine triphosphate
- INZ, inauhzin
- Inauhzin
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- PBS, Phosphate Buffered Saline
- PI, propidium iodide
- RISC, RNA-induced silencing complex
- RP, ribosomal protein
- RPL11
- RPL5
- UTR, untranslated region
- c-Myc
- lymphoma
- microRNA
- q-RT-PCR, Real-time reverse transcription polymerase chain reaction
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Affiliation(s)
- Ji Hoon Jung
- a Department of Biochemistry & Molecular Biology and Cancer Center ; Tulane University School of Medicine ; New Orleans , LA USA
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Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. RNA Biol 2015; 12:162-74. [PMID: 25826568 DOI: 10.1080/15476286.2015.1017220] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
ADARs (Adenosine deaminases that act on RNA) "edit" RNA by converting adenosines to inosines within double-stranded regions. The primary targets of ADARs are long duplexes present within noncoding regions of mRNAs, such as introns and 3' untranslated regions (UTRs). Because adenosine and inosine have different base-pairing properties, editing within these regions can alter splicing and recognition by small RNAs. However, despite numerous studies identifying multiple editing sites in these genomic regions, little is known about the extent to which editing sites co-occur on individual transcripts or the functional output of these combinatorial editing events. To begin to address these questions, we performed an ultra-deep sequencing analysis of 4 Caenorhabditis elegans 3' UTRs that are known ADAR targets. Synchronous editing events were determined for the long duplexes in vivo. Furthermore, the validity of each editing event was confirmed by sequencing the same regions of mRNA from worms that lack A-to-I editing. This analysis identified a large number of editing sites that can occur within each 3' UTR, but interestingly, each individual transcript contained only a small fraction of these A-to-I editing events. In addition, editing patterns were not random, indicating that an editing event can affect the efficiency of editing at subsequent adenosines. Furthermore, we identified specific sites that can be both positively and negatively correlated with additional sites leading to mutually exclusive editing patterns. These results suggest that editing in noncoding regions is selective and hyper-editing of cellular RNAs is rare.
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Affiliation(s)
- Emily C Wheeler
- a Medical Sciences Program ; Indiana University ; Bloomington , IN USA
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26
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Kim JJ, Yu J, Bag J, Bakovic M, Cant JP. Translation attenuation via 3' terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk. RNA Biol 2015; 12:354-67. [PMID: 25826667 DOI: 10.1080/15476286.2015.1017231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The rate of secretion of αs2-casein into bovine milk is approximately 25% of that of β-casein, yet mammary expression of their respective mRNA transcripts (csn1s2 and csn2) is not different. Our objective was to identify molecular mechanisms that explain the difference in translation efficiency between csn1s2 and csn2. Cell-free translational efficiency of csn2 was 5 times that of csn1s2. Transcripts of csn1s2 distributed into heavier polysomes than csn2 transcripts, indicating an attenuation of elongation and/or termination. Stimulatory and inhibitory effects of the 5' and 3' UTRs on translational efficiency were different with luciferase and casein sequences in the coding regions. Substituting the 5' and 3' UTRs from csn2 into csn1s2 did not improve csn1s2 translation, implicating the coding region itself in the translation difference. Deletion of a 28-codon fragment from the 3' terminus of the csn1s2 coding region, which displays codons with low correlations to cell fitness, increased translation to a par with csn2. We conclude that the usage of the last 28 codons of csn1s2 is the main regulatory element that attenuates its expression and is responsible for the differential translational expression of csn1s2 and csn2.
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Key Words
- 40S, small ribosomal subunit
- 60S, large ribosomal subunit
- AA, amino acid
- ARE, AU-rich element
- Apaf-1, apoptosis protease activating factor 1
- DLG1, disc large 1 ncosuppressor
- FMR1, fragile X mental retardation 1
- HRP, horseradish eroxidase
- IE, inhibitory element
- IRE, iron-responsive element
- IRES, nternal ribosome entry site
- IRP, iron-regulatory protein
- MACT, bovine mammary epithelial cell
- PABP, poly(A) binding protein
- PAGE, polyacrylamide gel electrophoresis
- PCR, polymerase chain reaction
- PVDF, polyvinylidene fluoride
- RACE, rapid amplification of cDNA ends
- RBP, RNA-binding protein
- RRL, rabbit reticulocyte lysate
- RT, reverse transcription
- SDS, sodium dodecyl sulfate
- SE, standard error
- STR, single-stranded nucleic acid binding protein
- TBS-T, Tris-buffered saline containing 0.5%
- TfR, transferrin receptor
- Tween 20
- UTR, untranslated region
- aa-tRNA, aminoacyl-tRNA
- aaRS, aminoacyl-tRNA synthetase
- bovine casein
- cDNA, complementary DNA
- cell-free translation
- coding region
- codon usage
- eEF, eukaryotic elongation factor
- eIF, eukaryotic initiation factor
- eRF, eukaryotic termination factor
- m7G, 7-methylated uanidine
- mRNA, messenger RNA
- qPCR, real-time polymerase chain reaction
- sAUG, start codon
- tRNA, transfer RNA
- translational efficiency
- uAUG, upstream start codon
- uORF, open reading frame
- untranslated region
- ΔG, free energy
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Affiliation(s)
- Julie J Kim
- a Animal and Poultry Science; University of Guelph ; Guelph , Ontario , Canada
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Daniels SM, Sinck L, Ward NJ, Melendez-Peña CE, Scarborough RJ, Azar I, Rance E, Daher A, Pang KM, Rossi JJ, Gatignol A. HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs. RNA Biol 2015; 12:123-35. [PMID: 25668122 DOI: 10.1080/15476286.2015.1014759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Several proteins and RNAs expressed by mammalian viruses have been reported to interfere with RNA interference (RNAi) activity. We investigated the ability of the HIV-1-encoded RNA elements Trans-Activation Response (TAR) and Rev-Response Element (RRE) to alter RNAi. MicroRNA let7-based assays showed that RRE is a potent suppressor of RNAi activity, while TAR displayed moderate RNAi suppression. We demonstrate that RRE binds to TAR-RNA Binding Protein (TRBP), an essential component of the RNA Induced Silencing Complex (RISC). The binding of TAR and RRE to TRBP displaces small interfering (si)RNAs from binding to TRBP. Several stem-deleted RRE mutants lost their ability to suppress RNAi activity, which correlated with a reduced ability to compete with siRNA-TRBP binding. A lentiviral vector expressing TAR and RRE restricted RNAi, but RNAi was restored when Rev or GagPol were coexpressed. Adenoviruses are restricted by RNAi and encode their own suppressors of RNAi, the Virus-Associated (VA) RNA elements. RRE enhanced the replication of wild-type and VA-deficient adenovirus. Our work describes RRE as a novel suppressor of RNAi that acts by competing with siRNAs rather than by disrupting the RISC. This function is masked in lentiviral vectors co-expressed with viral proteins and thus will not affect their use in gene therapy. The potent RNAi suppressive effects of RRE identified in this study could be used to enhance the expression of RNAi restricted viruses used in oncolysis such as adenoviruses.
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Key Words
- Ago2, Argonaute-2
- EGFP, enhanced green fluorescent protein
- EMSA, electrophoresis mobility shift assay
- FL, firefly luciferase
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HIV, human immunodeficiency virus
- HIV-1
- IP, immunoprecipitation
- NC, nucleocapsid
- PAGE, polyacrylamide gel electrophoresis
- RISC, RNA-Induced Silencing Complex
- RL, Renilla luciferase
- RNA interference
- RNA silencing suppressor
- RNAi, RNA interference
- RRE, Rev Response Element
- RSS, RNA silencing suppressor
- RT, reverse transcription
- Rev-Response Element RNA
- TAR RNA Binding Protein (TRBP)
- TAR, trans-activation responsive element
- TRBP, TAR RNA Binding Protein
- Trans-Activation Response Element
- UTR, untranslated region
- VA, virus-associated
- WT, wild-type
- adenovirus
- ds, double-stranded
- lentiviral vectors
- miRNA, micro RNA
- pre-miRNA, precursor miRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Sylvanne M Daniels
- a Virus-Cell Interactions Laboratory ; Lady Davis Institute for Medical Research ; Montréal , Québec , Canada
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28
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Abstract
Extracellular matrix proteins of the tenascin family resemble each other in their domain structure, and also share functions in modulating cell adhesion and cellular responses to growth factors. Despite these common features, the 4 vertebrate tenascins exhibit vastly different expression patterns. Tenascin-R is specific to the central nervous system. Tenascin-C is an “oncofetal” protein controlled by many stimuli (growth factors, cytokines, mechanical stress), but with restricted occurrence in space and time. In contrast, tenascin-X is a constituitive component of connective tissues, and its level is barely affected by external factors. Finally, the expression of tenascin-W is similar to that of tenascin-C but even more limited. In accordance with their highly regulated expression, the promoters of the tenascin-C and -W genes contain TATA boxes, whereas those of the other 2 tenascins do not. This article summarizes what is currently known about the complex transcriptional regulation of the 4 tenascin genes in development and disease.
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Key Words
- AKT, v-akt murine thymoma viral oncogene homolog
- ALK, anaplastic lymphoma kinase
- AP-1, activator protein-1
- ATF, activating transcription factor
- BMP, bone morphogenetic protein
- CBP, CREB binding protein
- CREB, cAMP response element-binding protein
- CREB-RP, CREB-related protein
- CYP21A2, cytochrome P450 family 21 subfamily A polypeptide 2
- ChIP, chromatin immunoprecipitation
- EBS, Ets binding site
- ECM, extracellular matrix
- EGF, epidermal growth factor
- ERK1/2, extracellular signal-regulated kinase 1/2
- ETS, E26 transformation-specific
- EWS-ETS, Ewing sarcoma-Ets fusion protein
- Evx1, even skipped homeobox 1
- FGF, fibroblast growth factor
- HBS, homeodomain binding sequence
- IL, interleukin
- ILK, integrin-linked kinase
- JAK, Janus kinase
- JNK, c-Jun N-terminal kinase
- MHCIII, major histocompatibility complex class III
- MKL1, megakaryoblastic leukemia-1
- NFκB, nuclear factor kappa B
- NGF, nerve growth factor; NFAT, nuclear factor of activated T-cells
- OTX2, orthodenticle homolog 2
- PDGF, platelet-derived growth factor
- PI3K, phosphatidylinositol 3-kinase
- POU3F2, POU domain class 3 transcription factor 2
- PRRX1, paired-related homeobox 1
- RBPJk, recombining binding protein suppressor of hairless
- ROCK, Rho-associated, coiled-coil-containing protein kinase
- RhoA, ras homolog gene family member A
- SAP, SAF-A/B, Acinus, and PIAS
- SCX, scleraxix
- SEAP, secreted alkaline phosphatase
- SMAD, small body size - mothers against decapentaplegic
- SOX4, sex determining region Y-box 4
- SRE, serum response element
- SRF, serum response factor
- STAT, signal transducer and activator of transcription
- TGF-β, transforming growth factor-β
- TNC, tenascin-C
- TNF-α, tumor necrosis factor-α
- TNR, tenascin-R
- TNW, tenascin-W
- TNX, tenascin-X
- TSS, transcription start site
- UTR, untranslated region
- WNT, wingless-related integration site
- cancer
- cytokine
- development
- extracellular matrix
- gene promoter
- gene regulation
- glucocorticoid
- growth factor
- homeobox gene
- matricellular
- mechanical stress
- miR, micro RNA
- p38 MAPK, p38 mitogen activated protein kinase
- tenascin
- transcription factor
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Affiliation(s)
- Francesca Chiovaro
- a Friedrich Miescher Institute for Biomedical Research ; Basel , Switzerland
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29
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Abstract
The VLPNPV 2014 Conference that was convened at the Salk institute was the second conference of its kind to focus on advances in production, purification, and delivery of virus-like particles (VLPs) and nanoparticles. Many exciting developments were reported and discussed in this interdisciplinary arena, but here we report specifically on the contributions of plant-based platforms to VLP vaccine technology as reported in the section of the conference devoted to the topic as well in additional presentations throughout the meeting. The increasing popularity of plant production platforms is due to their lower cost, scalability, and lack of contaminating animal pathogens seen with other systems. Reports include production of complex VLPs consisting of 4 proteins expressed at finely-tuned expression levels, a prime-boost strategy for HIV vaccination using plant-made VLPs and a live viral vector, and the characterization and development of plant viral nanoparticles for use in cancer vaccines, drug delivery, and bioimaging.
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Key Words
- Ab, antibody
- BPV, bovine papillomavirus
- BTV, Bluetongue virus
- CPMV, cowpea mosaic virus
- ELISA, enzyme-linked immunosorbent assay
- HBV, Hepatitis B virus
- HER2, human epidermal growth factor receptor 2 (also called c-ErbB-2)
- HIV, human immunodeficiency virus
- HIV-1
- HT, HyperTrans
- Hepatitis B core antigen
- Ig, immunoglobulin
- MPR, membrane proximal region
- NPV, nano-particle vaccine
- PEG, polyethylene glycol
- PVX, potato virus X
- SNP, spherical nanoparticle
- TMV, tobacco mosaic virus
- UTR, untranslated region
- VLP, virus-like particle
- VNP, viral nanoparticle
- bluetongue virus
- c-Erbb-2 (human epidermal growth factor receptor 2)
- cowpea mosaic virus
- i.p., intraperitoneal
- live viral vectors
- potato virus X
- tobacco mosaic virus
- viral nanoparticles
- virus-like particles
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Affiliation(s)
- Lydia R Meador
- a School of Life Sciences and The Biodesign Institute ; Arizona State University ; Tempe , AZ USA
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Podszywalow-Bartnicka P, Wolczyk M, Kusio-Kobialka M, Wolanin K, Skowronek K, Nieborowska-Skorska M, Dasgupta Y, Skorski T, Piwocka K. Downregulation of BRCA1 protein in BCR-ABL1 leukemia cells depends on stress-triggered TIAR-mediated suppression of translation. Cell Cycle 2015; 13:3727-41. [PMID: 25483082 DOI: 10.4161/15384101.2014.965013] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BRCA1 tumor suppressor regulates crucial cellular processes involved in DNA damage repair and cell cycle control. We showed that expression of BCR-ABL1 correlates with decreased level of BRCA1 protein, which promoted aberrant mitoses and aneuploidy as well as altered DNA damage response. Using polysome profiling and luciferase-BRCA1 3'UTR reporter system here we demonstrate that downregulation of BRCA1 protein in CML is caused by inhibition of BRCA1 mRNA translation, but not by increased protein degradation or reduction of mRNA level and half-life. We investigated 2 mRNA-binding proteins - HuR and TIAR showing specificity to AU-Rich Element (ARE) sites in 3'UTR of mRNA. BCR-ABL1 promoted cytosolic localization of TIAR and HuR, their binding to BRCA1 mRNA and formation of the TIAR-HuR complex. HuR protein positively regulated BRCA1 mRNA stability and translation, conversely TIAR negatively regulated BRCA1 translation and was found localized predominantly in the cytosolic stress granules in CML cells. TIAR-dependent downregulation of BRCA1 protein level was a result of ER stress, which is activated in BCR-ABL1 expressing cells, as we previously shown. Silencing of TIAR in CML cells strongly elevated BRCA1 level. Altogether, we determined that TIAR-mediated repression of BRCA1 mRNA translation is responsible for downregulation of BRCA1 protein level in BCR-ABL1 -positive leukemia cells. This mechanism may contribute to genomic instability and provide justification for targeting PARP1 and/or RAD52 to induce synthetic lethality in "BRCAness" CML and BCR-ABL1 -positive ALL cells.
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Key Words
- ARE, AU-rich element
- ATM, Ataxia telangiectasia mutated kinase
- ATR, Ataxia telangiectasia and Rad3-related kinase
- BCR-ABL
- BRCA1
- BRCA1, Breast cancer type 1 susceptibility
- CML, chronic myeloid leukemia
- DNA damage response
- HuR
- HuR, Hu antigen R (alternative name: ELAV-like protein 1)
- TIAR
- TIAR, TIA1 cytotoxic granule-associated RNA-binding protein-like 1
- UPR, unfolded protein response
- UTR, untranslated region
- cell cycle
- eIF, eukaryotic initiation factor
- mRNA binding protein
- stress response
- synthetic lethality
- translation
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Abstract
It has been reported that persistent or excessive autophagy promotes cancer cell death during chemotherapy, either by enhancing the induction of apoptosis or mediating autophagic cell death. Here, we show that miR-15a and miR-16 are potent inducers of autophagy. Rictor, a component of mTORC2 complex, is directly targeted by miR-15a/16. Overexpression of miR-15a/16 or depletion of endogenous Rictor attenuates the phosphorylation of mTORC1 and p70S6K, inhibits cell proliferation and G1/S cell cycle transition in human cervical carcinoma HeLa cells. Moreover, miR-15a/16 dramatically enhances anticancer drug camptothecin (CPT)-induced autophagy and apoptotic cell death in HeLa cells. Collectively, these data demonstrate that miR-15a/16 induced autophagy contribute partly to their inhibition of cell proliferation and enhanced chemotherapeutic efficacy of CPT.
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Affiliation(s)
- Nunu Huang
- a School of Life Sciences; Tsinghua University ; Beijing , China
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32
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Jasinski-Bergner S, Stoehr C, Bukur J, Massa C, Braun J, Hüttelmaier S, Spath V, Wartenberg R, Legal W, Taubert H, Wach S, Wullich B, Hartmann A, Seliger B. Clinical relevance of miR-mediated HLA-G regulation and the associated immune cell infiltration in renal cell carcinoma. Oncoimmunology 2015; 4:e1008805. [PMID: 26155421 DOI: 10.1080/2162402x.2015.1008805] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 01/07/2023] Open
Abstract
In human tumors of distinct origin including renal cell carcinoma (RCC), the non-classical human leukocyte antigen G (HLA-G) is frequently expressed, thereby inhibiting the cytotoxic activity of T and natural killer (NK) cells. Recent studies demonstrated a strong post-transcriptional gene regulation of the HLA-G by miR-152, -148A, -148B and -133A. Standard methods were applied to characterize the expression and function of HLA-G, HLA-G-regulatory microRNAs (miRs) and the immune cell infiltration in 453 RCC lesions using a tissue microarray and five RCC cell lines linking these results to clinical parameters. Direct interactions with HLA-G regulatory miRs and the HLA-G 3' untranslated region (UTR) were detected and the affinities of these different miRs to the HLA-G 3'-UTR compared. qPCR analyses and immunohistochemical staining revealed an inverse expression of miR-148A and -133A with the HLA-G protein in situ and in vitro. Stable miR overexpression caused a downregulation of HLA-G protein enhancing the NK and LAK cell-mediated cytotoxicity in in vitro CD107a activation assays revealing a HLA-G-dependent cytotoxic activity of immune effector cells. A significant higher frequency of CD3+/CD8+ T cell lymphocytes, but no differences in the activation markers CD69, CD25 or in the presence of CD56+, FoxP3+ and CD4+ immune cells were detected in HLA-G+ compared to HLA-G- RCC lesions. This could be associated with higher WHO grade, but not with a disease-specific survival. These data suggest a miR-mediated control of HLA-G expression in RCC, which is associated with a distinct pattern of immune cell infiltration.
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Key Words
- ACTB, β-actin
- APM, antigen processing machinery
- B7-H1, B7 homolog 1
- CDS, coding sequence; Cr, chromium
- COPZ2, coatomer protein complex, subunit zeta 2
- DAC, 5′-aza-2′-desoxycytidine, GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HLA-G, human leukocyte antigen G
- HRP, horseradish peroxidase
- IFNγ, interferon gamma
- IHC, immunohistochemistry
- IL, interleukin
- ILT, immunoglobulin-like transcript
- LAK, lymphokine-activated killer cell
- MDSC, myeloid-derived suppressor cells
- MFI, mean-specific fluorescence intensity
- NK, natural killer cell
- RCC, renal cell carcinoma
- SNP, single nucleotide polymorphism
- TGF-β, transforming growth factor β
- TIL, tumor infiltrating lymphocyte
- TMA, tissue microarray
- Treg, regulatory T cell
- UTR, untranslated region
- WB, Western blot analysis
- WT, wild type
- immune escape
- luc, luciferase
- mAb, monoclonal antibody
- miR, microRNA
- miTRAP, miRNA trapping by RNA in vitro affinity purification
- microRNA
- n.d., not determined
- n.o.s., not otherwise specified; ntc., non-template control
- non-classical HLA class I molecules
- renal cell carcinoma
- sHLA-G, soluble HLA-G
- tumor-infiltrating lymphocytes
- β-gal, β-galactosidase
- β2-m, β-2-microglobulin
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Affiliation(s)
- Simon Jasinski-Bergner
- Institute of Medical Immunology; Martin Luther University Halle-Wittenberg ; Halle, Germany
| | - Christine Stoehr
- Institute of Pathology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Juergen Bukur
- Institute of Medical Immunology; Martin Luther University Halle-Wittenberg ; Halle, Germany
| | - Chiara Massa
- Institute of Medical Immunology; Martin Luther University Halle-Wittenberg ; Halle, Germany
| | - Juliane Braun
- Institute of Molecular Medicine; Martin Luther University Halle-Wittenberg ; Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine; Martin Luther University Halle-Wittenberg ; Halle, Germany
| | - Verena Spath
- Institute of Pathology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Roland Wartenberg
- Institute of Pathology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Wolfgang Legal
- Clinic of Urology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Helge Taubert
- Clinic of Urology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Sven Wach
- Clinic of Urology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Bernd Wullich
- Clinic of Urology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology; Friedrich Alexander University Erlangen-Nuremberg ; Erlangen, Germany
| | - Barbara Seliger
- Institute of Medical Immunology; Martin Luther University Halle-Wittenberg ; Halle, Germany
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Abstract
The drug metabolism is a biochemical process on modification of pharmaceutical substances through specialized enzymatic systems. Changes in the expression of drug-metabolizing enzyme genes can affect drug metabolism. Recently, epigenetic regulation of drug-metabolizing enzyme genes has emerged as an important mechanism. Epigenetic regulation refers to heritable factors of genomic modifications that do not involve changes in DNA sequence. Examples of such modifications include DNA methylation, histone modifications, and non-coding RNAs. This review examines the widespread effect of epigenetic regulations on genes involved in drug metabolism, and also suggests a network perspective of epigenetic regulation. The epigenetic mechanisms have important clinical implications and may provide insights into effective drug development and improve safety of drug therapy.
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Key Words
- CAR, constitutive androstane receptor
- DNA methylation
- DNMTs, DNA methyltransferases
- Drug metabolism
- Epigenetics
- H3K27me3, histone 3 lysine 27 trimethylation
- H3K36me3, histone 3 lysine 36 trimethylation
- H3K4me1, histone 3 lysine 4 monomethylation
- H3K4me2, histone 3 lysine 4 dimethylation
- H3K4me3, histone 3 lysine 4 trimethylation
- H3K9me2, histone 3 lysine 9 dimethylation
- H3K9me3, histone 3 lysine 9 trimethylation
- HATs, histone acetyltransferases
- HDAC, histone deacetylases
- Histone modification
- Non-coding RNA
- P450s, cytochrome P450s
- SULTs, sulfotransferases
- TSS, transcription start sites
- Transporter
- UGTs, UDP-glucuronosyltransferases
- UTR, untranslated region
- lncRNAs, long non-coding RNAs
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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Usme-Ciro JA, Méndez JA, Laiton KD, Páez A. The relevance of dengue virus genotypes surveillance at country level before vaccine approval. Hum Vaccin Immunother 2014; 10:2674-8. [PMID: 25483495 PMCID: PMC4975057 DOI: 10.4161/hv.29563] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Dengue is a major threat for public health in tropical and subtropical countries around the world. In the absence of a licensed vaccine and effective antiviral therapies, control measures have been based on education activities and vector elimination. Current efforts for developing a vaccine are both promising and troubling. At the advent of the introduction of a tetravalent dengue vaccine, molecular surveillance of the circulating genotypes in different geographical regions has gained considerable importance. A growing body of in vitro, preclinical, and clinical phase studies suggest that vaccine conferred protection in a geographical area could depends on the coincidence of the dengue virus genotypes included in the vaccine and those circulating. In this review we present the state-of-the-art in this field, highlighting the need of deeper knowledge on neutralizing immune response for making decisions about future vaccine approval and the potential need for different vaccine composition for regional administration.
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Key Words
- ADE, antibody-dependent enhancement
- DC-SIGN, Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin
- DENV, dengue viruses
- E, envelope protein
- Hsp70, heat shock protein 70
- Hsp90, heat shock protein 90
- M, membrane protein
- MRCA, more recent common ancestor
- NS1, non-structural protein 1
- UTR, untranslated region
- dengue virus
- genotypes
- neutralizing antibodies
- ssRNA+, single-stranded positive-sense RNA viruses
- surveillance
- vaccines
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Affiliation(s)
- José A Usme-Ciro
- a Grupo de Virología; Subdirección Red Nacional de Laboratorios ; Dirección de Redes en Salud Pública; Instituto Nacional de Salud ; Bogotá DC , Colombia
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Brant JO, Riva A, Resnick JL, Yang TP. Influence of the Prader-Willi syndrome imprinting center on the DNA methylation landscape in the mouse brain. Epigenetics 2014; 9:1540-56. [PMID: 25482058 PMCID: PMC4623435 DOI: 10.4161/15592294.2014.969667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 04/29/2014] [Revised: 07/23/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
Reduced representation bisulfite sequencing (RRBS) was used to analyze DNA methylation patterns across the mouse brain genome in mice carrying a deletion of the Prader-Willi syndrome imprinting center (PWS-IC) on either the maternally- or paternally-inherited chromosome. Within the ~3.7 Mb imprinted Angelman/Prader-Willi syndrome (AS/PWS) domain, 254 CpG sites were interrogated for changes in methylation due to PWS-IC deletion. Paternally-inherited deletion of the PWS-IC increased methylation levels ~2-fold at each CpG site (compared to wild-type controls) at differentially methylated regions (DMRs) associated with 5' CpG island promoters of paternally-expressed genes; these methylation changes extended, to a variable degree, into the adjacent CpG island shores. Maternal PWS-IC deletion yielded little or no changes in methylation at these DMRs, and methylation of CpG sites outside of promoter DMRs also was unchanged upon maternal or paternal PWS-IC deletion. Using stringent ascertainment criteria, ~750,000 additional CpG sites were also interrogated across the entire mouse genome. This analysis identified 26 loci outside of the imprinted AS/PWS domain showing altered DNA methylation levels of ≥25% upon PWS-IC deletion. Curiously, altered methylation at 9 of these loci was a consequence of maternal PWS-IC deletion (maternal PWS-IC deletion by itself is not known to be associated with a phenotype in either humans or mice), and 10 of these loci exhibited the same changes in methylation irrespective of the parental origin of the PWS-IC deletion. These results suggest that the PWS-IC may affect DNA methylation at these loci by directly interacting with them, or may affect methylation at these loci through indirect downstream effects due to PWS-IC deletion. They further suggest the PWS-IC may have a previously uncharacterized function outside of the imprinted AS/PWS domain.
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Key Words
- AS, Angelman Syndrome
- AS-IC, Angelman Syndrome Imprinting Center
- AS-SRO, Angelman Syndrome Shortest Region of deletion Overlap
- BGS, Sodium Bisulfite Genomic Sequencing
- BISSCA, Bisulfite Sequencing Comparative Analysis
- CGI, CpG Island
- DH, DNase I Hypersensitive
- DMR, Differentially Methylated Region
- DNA methylation
- EtOH, Ethanol
- GO, gene ontology
- IC, Imprinting Center
- ICR, Imprinting Control Region
- IPA, Ingenuity Pathway Analysis ®
- PWS, Prader-Willi Syndrome
- PWS-IC, Prader-Willi Syndrome Imprinting Center
- PWS-SRO, Prader-Willi Syndrome Shortest Region of deletion Overlap
- RRBS, Reduced Representation Bisulfite Sequencing
- SDS, Sodium Dodecyl Sulfate
- SLIM, Sliding Linear Model
- TBE, Tris/Borate/EDTA
- Tris, Trisaminomethane
- UTR, untranslated region
- angelman syndrome
- genomic imprinting
- imprinting center
- lncRNA, long non-coding RNA
- mat, maternally-inherited allele
- pat, paternally-inherited allele
- prader-Willi syndrome
- reduced representation bisulfite sequencing
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Affiliation(s)
- Jason O Brant
- Department of Biochemistry and Molecular Biology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
| | - Alberto Riva
- Department of Molecular Genetics and Microbiology; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
| | - James L Resnick
- Department of Molecular Genetics and Microbiology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
| | - Thomas P Yang
- Department of Biochemistry and Molecular Biology; University of Florida; Gainesville, FL USA
- Center for Epigenetics; University of Florida; Gainesville, FL USA
- Genetics Institute; University of Florida; Gainesville, FL USA
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Abstract
Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an endonucleolytic cleavage of the pre-mRNA at the 3'-end and the polymerization of a polyadenosine (polyA) tail, which is fundamental for mRNA stability, nuclear export and efficient translation during development. The core molecular machinery responsible for the definition of a polyA site includes several recognition, cleavage and polyadenylation factors that identify and act on a given polyA signal present in a pre-mRNA, usually an AAUAAA hexamer or similar sequence. This mechanism is tightly regulated by other cis-acting elements and trans-acting factors, and its misregulation can cause inefficient gene expression and may ultimately lead to disease. The majority of genes generate multiple mRNAs as a result of alternative polyadenylation in the 3'-untranslated region. The variable lengths of the 3' untranslated regions created by alternative polyadenylation are a recognizable target for differential regulation and clearly affect the fate of the transcript, ultimately modulating the expression of the gene. Over the past few years, several studies have highlighted the importance of polyadenylation and alternative polyadenylation in gene expression and their impact in a variety of physiological conditions, as well as in several illnesses. Abnormalities in the 3'-end processing mechanisms thus represent a common feature among many oncological, immunological, neurological and hematological disorders, but slight imbalances can lead to the natural establishment of a specific cellular state. This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3' end formation.
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Key Words
- 3′ untranslated region
- 3′READS, 3′ Region Extraction and Deep Sequencing
- AD, Alzheimer disease
- APA, Alternative polyadenylation
- AREs, Au-rich elements
- BPV, bovine papilloma virus
- CAH, congenital adrenal hyperplasia
- CFIm25, Cleavage Factor Im 25 kDa
- COX-2, cyclooxygenase 2
- CPSF, Cleavage and Polyadenylation Specificity Factor
- CSTF2, cleavage stimulatory factor-64kDa
- DMKN, dermokine
- DSE, downstream sequence element
- ESC, embryonic stem cells
- FMR1, Fragil X mental retardation 1
- FOXP3, forkhead box P3
- FXPOI, fragile X-associated immature ovarian insufficiency
- FXS, Fragile X syndrome
- FXTAS, fragile X-associated tremor/ataxia syndrome
- HGRG-14, high-glucose-regulated gene
- IMP-1, Insulin-like growth factor 2 mRNA binding protein 1
- IPEX, immune dysfunction, polyendocrinopathy, enteropathy, X-linked
- LPS, lipopolysaccharide
- OPMD, oculopharyngeal muscular dystrophy
- PABPN1, poly(A) binding protein
- PAP, polyA polymerase
- PAS, polyA site
- PD, Parkinson disease
- PDXK, pyridoxal kinase
- PPIE, peptidylpropylisomerase E
- RBP, RNA-binding protein
- RNA Pol II, RNA polymerase II
- SLE, systemic lupus erythematosus
- SMA, Spinal Muscular Atrophy
- SMN, Survival Motor Neuron
- SNP, single nucleotide polymorphism
- StAR, steroigogenic acute regulatory
- TCF/LEF, T cell factor/lymphoid enhancer factor.
- TCF7L2, transcription factor 7-like 2
- TCR, T cell receptor
- TLI, tandem UTR length index
- TNF-α, tumor necrosis factor-α
- USE, upstream sequence element
- UTR, untranslated region
- WAS, Wiskott-Aldrich syndrome
- WASP, Wiskott-Aldrich syndrome protein
- aSyn, α-Synuclein
- aSynL, longest aSyn isoform
- alternative polyadenylation
- cell state
- disease
- gene expression
- miRNA, microRNA
- nuclear 1
- pA signal, polyA signal
- pA tail, polyA tail
- polyadenylation
- siRNAs, small interfering RNAs
- snRNPs, spliceosomal small nuclear ribonucleoproteins
- α-GalA, α-galactosidase A
- μ, IgM heavy-chain mRNA
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Affiliation(s)
- Ana Curinha
- a Gene Regulation Group; IBMC-Instituto de Biologia Molecular e Celular ; Universidade do Porto ; Porto , Portugal
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Knoch KP, Nath-Sain S, Petzold A, Schneider H, Beck M, Wegbrod C, Sönmez A, Münster C, Friedrich A, Roivainen M, Solimena M. PTBP1 is required for glucose-stimulated cap-independent translation of insulin granule proteins and Coxsackieviruses in beta cells. Mol Metab 2014; 3:518-30. [PMID: 25061557 DOI: 10.1016/j.molmet.2014.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 12/15/2022] Open
Abstract
Glucose and GLP-1 stimulate not only insulin secretion, but also the post-transcriptional induction of insulin granule biogenesis. This process involves the nucleocytoplasmic translocation of the RNA binding protein PTBP1. Binding of PTBP1 to the 3'-UTRs of mRNAs for insulin and other cargoes of beta cell granules increases their stability. Here we show that glucose enhances also the binding of PTBP1 to the 5'-UTRs of these transcripts, which display IRES activity, and their translation exclusively in a cap-independent fashion. Accordingly, glucose-induced biosynthesis of granule cargoes was unaffected by pharmacological, genetic or Coxsackievirus-mediated inhibition of cap-dependent translation. Infection with Coxsackieviruses, which also depend on PTBP1 for their own cap-independent translation, reduced instead granule stores and insulin release. These findings provide insight into the mechanism for glucose-induction of insulin granule production and on how Coxsackieviruses, which have been implicated in the pathogenesis of type 1 diabetes, can foster beta cell failure.
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Key Words
- Beta cells
- CV, Coxsackievirus
- Diabetes
- ER, endoplasmic reticulum
- EV, Enterovirus
- F, Faulkner
- FL, firefly luciferase
- IRES, internal ribosomal entry site
- ITAF, IRES-trans-acting factor
- Insulin
- MCA, MIN6 cell adapted
- PABP, poly(A)-binding protein
- PC, prohormone convertase
- PTBP1, polypyrimidine tract-binding protein 1
- Polypyrimidine tract-binding protein
- S6K1, p70S6 Kinase 1
- Secretory granules
- T1D, type 1 diabetes
- Translation
- UTR, untranslated region
- Virus
- eIF4E-V5, eIF4E tagged at its C-terminus with a V5-epitope
- mTORC1, mammalian Target Of Rapamycin Complex 1
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Fernandez-Twinn DS, Alfaradhi MZ, Martin-Gronert MS, Duque-Guimaraes DE, Piekarz A, Ferland-McCollough D, Bushell M, Ozanne SE. Downregulation of IRS-1 in adipose tissue of offspring of obese mice is programmed cell-autonomously through post-transcriptional mechanisms. Mol Metab 2014; 3:325-33. [PMID: 24749062 PMCID: PMC3986586 DOI: 10.1016/j.molmet.2014.01.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023] Open
Abstract
We determined the effects of maternal diet-induced obesity on offspring adipose tissue insulin signalling and miRNA expression in the aetiology of insulin resistance in later life. Although body composition and glucose tolerance of 8-week-old male offspring of obese dams were not dysregulated, serum insulin was significantly (p<0.05) elevated. Key insulin signalling proteins in adipose tissue were down-regulated, including the insulin receptor, catalytic (p110β) and regulatory (p85α) subunits of PI3K as well as AKT1 and 2 (all p<0.05). The largest reduction observed was in IRS-1 protein (p<0.001), which was regulated post-transcriptionally. Concurrently, miR-126, which targets IRS-1, was up-regulated (p<0.05). These two features were maintained in isolated primary pre-adipocytes and differentiated adipocytes in-vitro. We have therefore established that maternal diet-induced obesity programs adipose tissue insulin resistance. We hypothesise that maintenance of the phenotype in-vitro strongly suggests that this mechanism is cell autonomous and may drive insulin resistance in later life.
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Affiliation(s)
- Denise S Fernandez-Twinn
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Maria Z Alfaradhi
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Malgorzata S Martin-Gronert
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Daniella E Duque-Guimaraes
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Ana Piekarz
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - David Ferland-McCollough
- MRC Toxicology Unit, Hodgkin Building, PO Box 138, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Martin Bushell
- MRC Toxicology Unit, Hodgkin Building, PO Box 138, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Susan E Ozanne
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
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Szeto CYY, Lin CH, Choi SC, Yip TTC, Ngan RKC, Tsao GSW, Li Lung M. Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA-microRNA regulatory network in nasopharyngeal carcinoma model systems. FEBS Open Bio 2014; 4:128-40. [PMID: 24490137 PMCID: PMC3907684 DOI: 10.1016/j.fob.2014.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 01/28/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV)-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV) to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL), single nucleotide variant (SNV), and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies. Using RNASeq we characterized the mRNA and miRNA transcriptomes in NPC and NP models. 2812 Genes and 149 miRNAs (human and EBV) were differentially expressed in NPC vs NP models. 533 miRNA–mRNA target pairs were inversely regulated in HK1, C666, and X666 vs NP460. ECM, β1 integrin, PI3K/AKT, EGFR, ErbB, and Wnt pathways appeared to be deregulated in NPC. A novel TP53 mutation was identified in NP460, HK1, and C666.
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Key Words
- AIP, aryl hydrocarbon receptor interacting protein
- BAX, BCL2-asscoiated X protein
- CIITA, class II, major histocompatibility complex, transactivator
- DKK1, Dickkopf-Like protein 1
- EBV, Epstein–Barr virus
- ECM, extracellular matrix
- EGFR, epidermal growth factor receptor
- EGR1, early growth response 1
- FBLN2, fibulin 2
- GADD45, growth arrest and DNA-damage-inducible
- GNG11, guanine nucleotide binding protein (G protein), Gamma 11
- GO, gene ontology
- GSTP1, glutathione S-transferase pi 1
- IL18, interleukin 18
- INDEL, insertion and deletion
- LMP1, Epstein–Barr virus latent membrane protein 1
- LTBP2, latent transforming growth factor beta binding protein 2
- MDM2, MDM2 oncogene, E3 ubiquitin protein ligase
- MET, met proto-oncogene
- MMP19, matrix metallopeptidase 19
- NGS, next-generation sequencing
- NPC, nasopharyngeal carcinoma
- Nasopharyngeal carcinoma
- Nasopharyngeal cell lines/xenograft (NP460, HK1, C666, X666)
- PI3K, phosphoinositide 3-kinase
- PTEN, phosphatase and tensin homolog
- RNA sequencing
- RNASeq, RNA sequencing
- SNP, single nucleotide polymorphism
- TNFRSF9, tumour necrosis factor receptor superfamily, member 9
- TP53
- Transcriptome analysis
- UTR, untranslated region
- miRNA, microRNA
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Affiliation(s)
- Carol Ying-Ying Szeto
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, The University of Hong Kong, PR China
| | - Chi Ho Lin
- Centre for Genomic Sciences, The University of Hong Kong, PR China
| | - Siu Chung Choi
- Centre for Genomic Sciences, The University of Hong Kong, PR China
| | - Timothy T C Yip
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, Queen Elizabeth Hospital, PR China
| | - Roger Kai-Cheong Ngan
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, Queen Elizabeth Hospital, PR China
| | - George Sai-Wah Tsao
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Anatomy, The University of Hong Kong, PR China
| | - Maria Li Lung
- Center for Nasopharyngeal Cancer Research, The University of Hong Kong, PR China ; Department of Clinical Oncology, The University of Hong Kong, PR China
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Zou J, Zhang D, Qin G, Chen X, Wang H, Zhang D. BRCA1 and FancJ cooperatively promote interstrand crosslinker induced centrosome amplification through the activation of polo-like kinase 1. Cell Cycle 2014; 13:3685-97. [PMID: 25483079 PMCID: PMC4612125 DOI: 10.4161/15384101.2014.964973] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 05/01/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 12/15/2022] Open
Abstract
DNA damage response (DDR) and the centrosome cycle are 2 of the most critical cellular processes affecting the genome stability in animal cells. Yet the cross-talks between DDR and the centrosome are poorly understood. Here we showed that deficiency of the breast cancer 1, early onset gene (BRCA1) induces centrosome amplification in non-stressed cells as previously reported while attenuating DNA damage-induced centrosome amplification (DDICA) in cells experiencing prolonged genotoxic stress. Mechanistically, the function of BRCA1 in promoting DDICA is through binding and recruiting polo-like kinase 1 (PLK1) to the centrosome. In a recent study, we showed that FancJ also suppresses centrosome amplification in non-stressed cells while promoting DDICA in both hydroxyurea and mitomycin C treated cells. FancJ is a key component of the BRCA1 B-complex. Here, we further demonstrated that, in coordination with BRCA1, FancJ promotes DDICA by recruiting both BRCA1 and PLK1 to the centrosome in the DNA damaged cells. Thus, we have uncovered a novel role of BRCA1 and FancJ in the regulation of DDICA. Dysregulation of DDR or centrosome cycle leads to aneuploidy, which is frequently seen in both solid and hematological cancers. BRCA1 and FancJ are known tumor suppressors and have well-recognized functions in DNA damage checkpoint and DNA repair. Together with our recent findings, we demonstrated here that BRCA1 and FancJ also play an important role in centrosome cycle especially in DDICA. DDICA is thought to be an alternative fail-safe mechanism to prevent cells experiencing severe DNA damage from becoming carcinogenic. Therefore, BRCA1 and FancJ are potential liaisons linking early DDR with the DDICA. We propose that together with their functions in DDR, the role of BRCA1 and FancJ in the activation of DDICA is also crucial for their tumor suppression functions in vivo.
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Key Words
- ATM, ataxia telangiectasia mutated
- ATR, ataxia telangiectasia Rad3-related
- BRCA1
- BRCA1, breast cancer gene 1
- CIN, chromosome instability
- DDICA, DNA damage induced centrosome amplification
- DDR, DNA damage response
- DNA damage response
- FancJ
- GFP, green fluorescent protein
- HR, homologous recombination
- HU, hydroxyurea
- ICL, interstrand cross-linkers
- MIN, microsatellite instability
- MMC, mitomycin C
- MT, microtubule
- PCM, pericentriolar materials
- PLK1
- PLK1, Polo-like kinase 1
- UTR, untranslated region
- WCL, whole-cell lysate
- centrosome amplification
- interstrand cross-link
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Affiliation(s)
- Jianqiu Zou
- Basic Biomedical Science Division; Sanford School of Medicine; University of South Dakota; Vermillion, SD USA
| | - Deli Zhang
- WeiFang Medical University; WeiFang, Shandong, China
| | - Guang Qin
- Department of Oncology; Central Hospital of TaiAn; TaiAn, Shandong, China
| | - Xiangming Chen
- Department of Oncology; Central Hospital of TaiAn; TaiAn, Shandong, China
| | - Hongmin Wang
- Basic Biomedical Science Division; Sanford School of Medicine; University of South Dakota; Vermillion, SD USA
| | - Dong Zhang
- Basic Biomedical Science Division; Sanford School of Medicine; University of South Dakota; Vermillion, SD USA
- Department of Biomedical Sciences; College of Osteopathic Medicine; New York Institute of Technology; Old Westbury, NY USA
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Siebert M, Westbroek W, Chen YC, Moaven N, Li Y, Velayati A, Saraiva-Pereira ML, Martin SE, Sidransky E. Identification of miRNAs that modulate glucocerebrosidase activity in Gaucher disease cells. RNA Biol 2014; 11:1291-300. [PMID: 25584808 PMCID: PMC4615671 DOI: 10.1080/15476286.2014.996085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 06/06/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022] Open
Abstract
Gaucher disease is an autosomal recessive disorder caused by deficiency of the enzyme glucocerebrosidase. Although it is a monogenic disease, there is vast phenotypic heterogeneity, even among patients with the same genotype. MicroRNAs (miRNAs) are small non-coding RNAs involved in many biological processes and diseases. To determine whether miRNAs can affect glucocerebrosidase activity, we performed a screen of 875 different miRNA mimics. The screen was performed using Gaucher fibroblasts, and glucocerebrosidase activity was used as the initial outcome parameter. We found several miRNAs that either up- or down-regulated glucocerebrosidase activity. In follow-up assays, we confirmed that one specific miRNA (miR-127-5p) down-regulated both glucocerebrosidase activity and protein levels by down-regulation of LIMP-2, the receptor involved in proper trafficking of glucocerebrosidase from the endoplasmic reticulum to the lysosome. A conditioned media assay demonstrated that cells treated with this miRNA secreted glucocerebrosidase into the extracellular environment, supporting impaired LIMP-2 function. Two other miRNAs, miR-16-5p and miR-195-5p, were found to up-regulate glucocerebrosidase activity by greater than 40% and to enhance expression and protein levels of the enzyme. In conclusion, we show that miRNAs can alter glucocerebrosidase activity in patient cells, indicating that miRNAs can potentially act as modifiers in Gaucher disease.
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Affiliation(s)
- Marina Siebert
- Section on Molecular Neurogenetics; Medical Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
- Postgraduate Program in Cellular and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre, RS Brazil
- Laboratory of Genetic Identification and Medical Genetics Service; Hospital de Clínicas de Porto Alegre; Porto Alegre, RS Brazil
| | - Wendy Westbroek
- Section on Molecular Neurogenetics; Medical Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Yu-Chi Chen
- RNAi Screening Facility; National Center for Advancing Translational Sciences; National Institutes of Health; Rockville, MD USA
| | - Nima Moaven
- Section on Molecular Neurogenetics; Medical Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Yan Li
- Protein/Peptide Sequencing Facility; National Institute of Neurological Disorders and Stroke; National Institutes of Health; Bethesda, MD USA
| | - Arash Velayati
- Section on Molecular Neurogenetics; Medical Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Maria Luiza Saraiva-Pereira
- Postgraduate Program in Cellular and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre, RS Brazil
- Laboratory of Genetic Identification and Medical Genetics Service; Hospital de Clínicas de Porto Alegre; Porto Alegre, RS Brazil
- Department of Biochemistry; Universidade Federal do Rio Grande do Sul; Porto Alegre, RS Brazil
| | - Scott E Martin
- RNAi Screening Facility; National Center for Advancing Translational Sciences; National Institutes of Health; Rockville, MD USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics; Medical Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
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Horn T, Reddy Kakularam K, Anton M, Richter C, Reddanna P, Kuhn H. Functional characterization of genetic enzyme variations in human lipoxygenases. Redox Biol 2013; 1:566-77. [PMID: 24282679 PMCID: PMC3840004 DOI: 10.1016/j.redox.2013.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 11/01/2013] [Indexed: 01/09/2023] Open
Abstract
Mammalian lipoxygenases play a role in normal cell development and differentiation but they have also been implicated in the pathogenesis of cardiovascular, hyperproliferative and neurodegenerative diseases. As lipid peroxidizing enzymes they are involved in the regulation of cellular redox homeostasis since they produce lipid hydroperoxides, which serve as an efficient source for free radicals. There are various epidemiological correlation studies relating naturally occurring variations in the six human lipoxygenase genes (SNPs or rare mutations) to the frequency for various diseases in these individuals, but for most of the described variations no functional data are available. Employing a combined bioinformatical and enzymological strategy, which included structural modeling and experimental site-directed mutagenesis, we systematically explored the structural and functional consequences of non-synonymous genetic variations in four different human lipoxygenase genes (ALOX5, ALOX12, ALOX15, and ALOX15B) that have been identified in the human 1000 genome project. Due to a lack of a functional expression system we resigned to analyze the functionality of genetic variations in the hALOX12B and hALOXE3 gene. We found that most of the frequent non-synonymous coding SNPs are located at the enzyme surface and hardly alter the enzyme functionality. In contrast, genetic variations which affect functional important amino acid residues or lead to truncated enzyme variations (nonsense mutations) are usually rare with a global allele frequency<0.1%. This data suggest that there appears to be an evolutionary pressure on the coding regions of the lipoxygenase genes preventing the accumulation of loss-of-function variations in the human population. Non-synonymous coding variations in human lipoxygenases are mostly rare with a global allele frequency <1%. Common ALOX SNPs are mainly localized on the enzyme surface and hardly effect the enzyme functionality. hALOX15B Ala416Asp is a newly discovered loss-of-function mutation in the hALOX gene family while inactivity seems to be caused by severe structural alterations. Our data indicate that there is evolutionary pressure on these redox enzymes preventing the accumulation of loss-of-function variations in the human population. 1000 Genome database is a useful tool to analyze the distribution and functionality of variations in genes of interest.
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Key Words
- 12-H(p)ETE, (5Z,8Z,10E,14Z)-12-hydroperoxyeicosa-5,8,10,14-tetraenoic acid
- 15-H(p)ETE, (5Z,8Z,11Z,13E)-15-hydroperoxyeicosa-5,8,11,13-tetraenoic acid
- 5-H(p)ETE, (6E,8Z,11Z,14Z)-5-hydroperoxyeicosa-6,8,11,14-tetraenoic acid
- 8-H(p)ETE, (5Z,9E,11Z,14Z)-8-hydroperoxyeicosa-5,9,11,14-tetraenoic acid
- ALOX, arachidonate lipoxygenase
- Eicosanoids
- Gene polymorphism
- H(p)ETE, hydroperoxyeicosatetraenoic acid
- HETE, hydroxyeicosatetraenoic acid
- IPTG, Isopropyl-β-D-thiogalactopyranosid
- LOXs, lipoxygenases
- LTA4, 4-[(2S,3S)-3-[(1E,3E,5Z,8Z)-tetradeca-1,3,5,8-tetraen-1-yl]oxiran-2-yl]butanoic acid
- LTB4, 5(S),12(R)-dihydroxy-6,8,10,14-(Z,E,E,Z)-eicosatetraenoic acid
- LTC4, (5S,6R,7E,9E,11Z,14Z)-6-{[(2R)-2-[(4S)-4-amino-4-carboxybutanamido]-2-[(carboxymethyl) carbamoyl]ethyl]sulfanyl}-5-hydroxyeicosa-7,9,11,14-tetraenoic acid
- Leukotrienes
- Lipoxygenases
- SNP
- UTR, untranslated region
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Affiliation(s)
- Thomas Horn
- Institute of Biochemistry, University Medicine Berlin-Charité, Charitéplatz 1, D-10117 Berlin, Germany
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Abstract
MicroRNAs (miRs) are small non-coding RNAs that negatively regulate gene expression by pairing with partially complementary target sequences in the 3'UTRs of mRNAs to promote degradation and/or block translation. Aberrant miR expression is associated with development of multiple diseases including hepatic diseases. The role of miRs in the regulation of gene expression and rapid progress in the field of microRNA research are resulting in momentum toward development of diagnostic markers and novel therapeutic strategies for human liver diseases. Recent studies provide clear evidence that miRs are abundant in the liver and modulate a diverse spectrum of biological functions, thereby supporting an association between alterations of miR homeostasis and pathological liver diseases. Here we review the role of miRs in liver as their physiological and pathological importance has been demonstrated in metabolism, immunity, viral hepatitis, oncogenesis, fatty liver diseases (alcoholic and non-alcoholic), drug-induced liver injury, fibrosis as well as acute liver failure.
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Key Words
- ALD, alcoholic liver disease
- ALF, acute liver failure
- DILI, drug-induced liver injury
- HBV, hepatitis B virus
- HCC, hepatocellular carcinoma
- HCV, hepatitis C virus
- HSC, hepatic stellate cell
- IFN, interferon
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- PPAR γ, peroxisome proliferator-activated receptor γ
- TGF, transforming growth factor
- TNF, tumor necrosis factor
- UTR, untranslated region
- down-regulation
- liver
- miR-122
- miRs/miRNA, microRNA
- microRNA
- up-regulation
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Affiliation(s)
- Nihar Shah
- Liver Center of Excellence, Digestive Disease Institute, Virginia Mason Medical Center, Seattle, WA, United States
| | - James E. Nelson
- Benaroya Research Institute, Virginia Mason Medical Center, Seattle, WA, United States
| | - Kris V. Kowdley
- Liver Center of Excellence, Digestive Disease Institute, Virginia Mason Medical Center, Seattle, WA, United States,Benaroya Research Institute, Virginia Mason Medical Center, Seattle, WA, United States,Address for correspondence: Kris V. Kowdley, MD, 1201 9th Ave., Seattle, WA 98101, United States. Tel.: +1 (206) 287 1083; fax: +1 (206) 341 1934.
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Abstract
Hepatitis E virus is a single, positive-sense, capped and poly A tailed RNA virus classified under the family Hepeviridae. Enteric transmission, acute self-limiting hepatitis, frequent epidemic and sporadic occurrence, high mortality in affected pregnants are hallmarks of hepatitis E infection. Lack of an efficient culture system and resulting reductionist approaches for the study of replication and pathogenesis of HEV made it to be a less understood agent. Early studies on animal models, sub-genomic expression of open reading frames (ORF) and infectious cDNA clones have helped in elucidating the genome organization, important stages in HEV replication and pathogenesis. The genome contains three ORF's and three untranslated regions (UTR). The 5' distal ORF, ORF1 is translated by host ribosomes in a cap dependent manner to form the non-structural polyprotein including the viral replicase. HEV replicates via a negative-sense RNA intermediate which helps in the formation of the positive-sense genomic RNA and a single bi-cistronic sub-genomic RNA. The 3' distal ORF's including the major structural protein pORF2 and the multifunctional host interacting protein pORF3 are translated from the sub-genomic RNA. Pathogenesis in HEV infections is not well articulated, and remains a concern due to the many aspects like host dependent and genotype specific variations. Animal HEV, zoonosis, chronicity in immunosuppressed patients, and rapid decompensation in affected chronic liver diseased patients warrants detailed investigation of the underlying pathogenesis. Recent advances about structure, entry, egress and functional characterization of ORF1 domains has furthered our understanding about HEV. This article is an effort to review our present understanding about molecular biology and pathogenesis of HEV.
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Affiliation(s)
- Subrat K. Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India,Address for correspondence. Subrat K. Panda, JC Bose Fellow, Professor & Head, Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India. Tel.: +91 11 26594924 (off.); fax: +91 11 26588663, +91 11 26588641.
| | - Satya P.K. Varma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
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Schneeberger M, Altirriba J, García A, Esteban Y, Castaño C, García-Lavandeira M, Alvarez CV, Gomis R, Claret M. Deletion of miRNA processing enzyme Dicer in POMC-expressing cells leads to pituitary dysfunction, neurodegeneration and development of obesity. Mol Metab 2012; 2:74-85. [PMID: 24199146 DOI: 10.1016/j.molmet.2012.10.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/05/2012] [Accepted: 10/07/2012] [Indexed: 10/27/2022] Open
Abstract
MicroRNAs (miRNAs) have recently emerged as key regulators of metabolism. However, their potential role in the central regulation of whole-body energy homeostasis is still unknown. In this study we show that the expression of Dicer, an essential endoribonuclease for miRNA maturation, is modulated by nutrient availability and excess in the hypothalamus. Conditional deletion of Dicer in POMC-expressing cells resulted in obesity, characterized by hyperphagia, increased adiposity, hyperleptinemia, defective glucose metabolism and alterations in the pituitary-adrenal axis. The development of the obese phenotype was paralleled by a POMC neuron degenerative process that started around 3 weeks of age. Hypothalamic transcriptomic analysis in presymptomatic POMCDicerKO mice revealed the downregulation of genes implicated in biological pathways associated with classical neurodegenerative disorders, such as MAPK signaling, ubiquitin-proteosome system, autophagy and ribosome biosynthesis. Collectively, our results highlight a key role for miRNAs in POMC neuron survival and the consequent development of neurodegenerative obesity.
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Key Words
- 3V, third ventricle
- ACTH, adrenocorticotropic hormone
- AP, adenopituitary
- ARC, arcuate nucleus of the hypothalamus
- AUC, area under the curve
- Acp2, acid phosphatase 2, lysosomal
- AgRP, agouti-related protein
- Ago2, Argonaute 2
- CART, cocaine and amphetamine-related transcript
- CNS, central nervous system
- CRH, corticotropin releasing hormone
- Crhr1, corticotrophin releasing hormone receptor 1
- Cx, Cortex
- DIO, diet-induced obesity
- Dicer
- Fa, Fascicular zone
- GFP, green fluorescent protein
- Gapdh, Glyceraldehyde 3-phosphate dehydrogenase
- Gh, growth hormone
- Gl, Glomerular zone
- Hprt, Hypoxanthine guanine phosphoribosyl transferase
- Hypothalamus
- IL, intermediate lobe
- IP, intraperitoneal
- LH, lateral hypothalamus
- MC3R, melanocortin receptor 3
- MC4R, melanocortin receptor 4
- MZ, Marginal Zone
- Me, Medula
- Myc, myelocytomatosis oncogene
- NP, neurohypophysis
- NPY, neuropeptide Y
- NS, not significant
- Naglu, alpha-N-acetylglucosaminidase
- Neurodegeneration
- Nhlrc1, NHL repeat containing 1
- Ntrk2, Neurotrophic tyrosine kinase, receptor, type 2
- Obesity
- POMC
- POMC, pro-opiomelanocortin
- POMCDicerKO, mice lacking Dicer in POMC-expressing cells
- PVN, paraventricular nucleus
- Park2, Parkin
- Pit1, pituitary-specific transcription factor 1
- Re, Reticular zone
- Rps24, ribosomal protein S24
- Rps9, ribosomal protein S9
- Tpit, T box transcription factor
- Tshβ, thyroid-stimulating hormone β chain
- UD, undetectable
- UPS, ubiquitin proteosome system
- UTR, untranslated region
- VMH, ventromedial hypothalamus
- YFP, yellow fluorescent protein.
- miRISC, miRNA-induced silencing complexes
- miRNA, microRNA
- microRNA
- qPCR, quantitative real-time PCR
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Affiliation(s)
- Marc Schneeberger
- Diabetes and Obesity Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain ; Department of Endocrinology and Nutrition, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
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