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Abstract
Metabolic labeling is a widely used tool to investigate different aspects of pre-mRNA splicing and RNA turnover. The labeling technology takes advantage of native cellular machineries where a nucleotide analog is readily taken up and incorporated into nascent RNA. One such analog is 4-thiouridine (4sU). Previous studies demonstrated that the uptake of 4sU at elevated concentrations (>50μM) and extended exposure led to inhibition of rRNA synthesis and processing, presumably induced by changes in RNA secondary structure. Thus, it is possible that 4sU incorporation may also interfere with splicing efficiency. To test this hypothesis, we carried out splicing analyses of pre-mRNA substrates with varying levels of 4sU incorporation (0-100%). We demonstrate that increased incorporation of 4sU into pre-mRNAs decreased splicing efficiency. The overall impact of 4sU labeling on pre-mRNA splicing efficiency negatively correlates with the strength of splice site signals such as the 3' and the 5' splice sites. Introns with weaker splice sites are more affected by the presence of 4sU. We also show that transcription by T7 polymerase and pre-mRNA degradation kinetics were impacted at the highest levels of 4sU incorporation. Increased incorporation of 4sU caused elevated levels of abortive transcripts, and fully labeled pre-mRNA is more stable than its uridine-only counterpart. Cell culture experiments show that a small number of alternative splicing events were modestly, but statistically significantly influenced by metabolic labeling with 4sU at concentrations considered to be tolerable (40 μM). We conclude that at high 4sU incorporation rates small, but noticeable changes in pre-mRNA splicing can be detected when splice sites deviate from consensus. Given these potential 4sU artifacts, we suggest that appropriate controls for metabolic labeling experiments need to be included in future labeling experiments.
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Affiliation(s)
- Jessie A. C. Altieri
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Klemens J. Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
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2
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Spanka DT, Klug G. Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions. Int J Mol Sci 2021; 22:ijms222212260. [PMID: 34830143 PMCID: PMC8625941 DOI: 10.3390/ijms222212260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.
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Liu T, Hu J, Han B, Tan S, Jia W, Xin Y. A positive feedback loop of lncRNA-RMRP/ZNRF3 axis and Wnt/β-catenin signaling regulates the progression and temozolomide resistance in glioma. Cell Death Dis 2021; 12:952. [PMID: 34657141 PMCID: PMC8520527 DOI: 10.1038/s41419-021-04245-y] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022]
Abstract
Drug resistance strikingly limits the therapeutic effect of temozolomide (TMZ) (a common drug for glioma). Long non-coding RNA (lncRNA) RMRP has been found to be implicated in glioma progression. However, the effect of RMRP on TMZ resistance along with related molecular mechanisms is poorly defined in glioma. In the present study, RMRP, ZNRF3, and IGF2BP3 were screened out by bioinformatics analysis. The expression levels of lncRNAs and mRNAs were measured by RT-qPCR assay. Protein levels of genes were detected by western blot and immunofluorescence assays. ZNRF3 mRNA stability was analyzed using Actinomycin D assay. Cell proliferative ability and survival rate were determined by CCK-8 assay. Cell apoptotic pattern was estimated by flow cytometry. The effect of RMRP knockdown on the growth of TMZ-treated glioma xenograft tumors was explored in vivo. The relationships of IGF2BP3, RMRP, and ZNRF3 were explored by bioinformatics prediction analysis, RNA immunoprecipitation, luciferase, and RNA pull-down, and chromatin immunoprecipitation assays. The results showed that RMRP was highly expressed in glioma. RMRP knockdown curbed cell proliferation, facilitated cell apoptosis and reduced TMZ resistance in glioma cells, and hindered the growth of TMZ-treated glioma xenograft tumors. RMRP exerted its functions by down-regulating ZNRF3 in glioma cells. IGF2BP3 interacted with RMRP and ZNRF3 mRNA. IGF2BP3 knockdown weakened the interaction of Argonaute 2 (Ago2) and ZNRF3. RMRP reduced ZNRF3 expression and mRNA stability by IGF2BP3. RMRP knockdown inhibited β-catenin expression by up-regulating ZNRF3. The inhibition of Wnt/β-catenin signaling pathway by XAV-939 weakened RMRP-mediated TMZ resistance in glioma cells. β-catenin promoted RMRP expression by TCF4 in glioma cells. In conclusion, RMRP/ZNRF3 axis and Wnt/β-catenin signaling formed a positive feedback loop to regulate TMZ resistance in glioma. The sustained activation of Wnt/β-catenin signaling by RMRP might contribute to the better management of cancers.
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Affiliation(s)
- Tie Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jie Hu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Bo Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Shishan Tan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Wenqing Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yu Xin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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Wilmore S, Rogers-Broadway KR, Taylor J, Lemm E, Fell R, Stevenson FK, Forconi F, Steele AJ, Coldwell M, Packham G, Yeomans A. Targeted inhibition of eIF4A suppresses B-cell receptor-induced translation and expression of MYC and MCL1 in chronic lymphocytic leukemia cells. Cell Mol Life Sci 2021; 78:6337-6349. [PMID: 34398253 PMCID: PMC8429177 DOI: 10.1007/s00018-021-03910-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022]
Abstract
Signaling via the B-cell receptor (BCR) is a key driver and therapeutic target in chronic lymphocytic leukemia (CLL). BCR stimulation of CLL cells induces expression of eIF4A, an initiation factor important for translation of multiple oncoproteins, and reduces expression of PDCD4, a natural inhibitor of eIF4A, suggesting that eIF4A may be a critical nexus controlling protein expression downstream of the BCR in these cells. We, therefore, investigated the effect of eIF4A inhibitors (eIF4Ai) on BCR-induced responses. We demonstrated that eIF4Ai (silvestrol and rocaglamide A) reduced anti-IgM-induced global mRNA translation in CLL cells and also inhibited accumulation of MYC and MCL1, key drivers of proliferation and survival, respectively, without effects on upstream signaling responses (ERK1/2 and AKT phosphorylation). Analysis of normal naïve and non-switched memory B cells, likely counterparts of the two main subsets of CLL, demonstrated that basal RNA translation was higher in memory B cells, but was similarly increased and susceptible to eIF4Ai-mediated inhibition in both. We probed the fate of MYC mRNA in eIF4Ai-treated CLL cells and found that eIF4Ai caused a profound accumulation of MYC mRNA in anti-IgM treated cells. This was mediated by MYC mRNA stabilization and was not observed for MCL1 mRNA. Following drug wash-out, MYC mRNA levels declined but without substantial MYC protein accumulation, indicating that stabilized MYC mRNA remained blocked from translation. In conclusion, BCR-induced regulation of eIF4A may be a critical signal-dependent nexus for therapeutic attack in CLL and other B-cell malignancies, especially those dependent on MYC and/or MCL1.
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MESH Headings
- Antibodies, Anti-Idiotypic/pharmacology
- Benzofurans/pharmacology
- Cells, Cultured
- Eukaryotic Initiation Factor-4A/antagonists & inhibitors
- Eukaryotic Initiation Factor-4A/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/metabolism
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Protein Biosynthesis/drug effects
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA Stability/drug effects
- RNA, Messenger/metabolism
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/drug effects
- Triterpenes/pharmacology
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Affiliation(s)
- Sarah Wilmore
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Karly-Rai Rogers-Broadway
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Joe Taylor
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Elizabeth Lemm
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Rachel Fell
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Freda K Stevenson
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Francesco Forconi
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Andrew J Steele
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Mark Coldwell
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK.
| | - Alison Yeomans
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
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Shen ZQ, Wang J, Tan WF, Huang TM. Berberine inhibits colorectal tumor growth by suppressing SHH secretion. Acta Pharmacol Sin 2021; 42:1190-1194. [PMID: 32958873 PMCID: PMC8209003 DOI: 10.1038/s41401-020-00514-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 04/27/2020] [Accepted: 08/17/2020] [Indexed: 01/06/2023] Open
Abstract
Hedgehog plays an important role in a wide range of physiological and pathological conditions. Paracrine activation of Hedgehog pathway in stromal cells increases the expression of VEGF, which promotes neovascularization in colorectal cancer and ultimately the growth of colorectal cancer. Berberine (BBR) has anticancer activity. In this study we investigated whether BBR inhibited the growth of colon cancer through suppressing the paracrine sonic hedgehog (SHH) signaling in vitro and in vivo. We showed that BBR (1-10 μM) dose-dependently inhibited the secretion and expression of SHH protein in HT-29 and SW480 cells. BBR did not influence the transcription of SHH, but promoted the degradation of SHH mRNA, thus decreased the SHH mRNA expression in the colorectal cancer cells. In nude mice bearing HT-29 xenograft, oral administration of BBR (100 mg · kg-1 · d-1) or a positive control drug GDC-0449 (100 mg · kg-1 · d-1) for 4 weeks markedly suppressed the growth of HT-29 tumor with BBR exhibiting a better antitumor efficacy. The tumor growth inhibition caused by BBR or GDC-0449 was comparable to their respective inhibitory effect on the mouse-specific Gli mRNA expression in the tumor. However, BBR (20 μM) did not affect the expression of human transcription factor Gli1 mRNA in HT-29 and SW480 cells. In conclusion, BBR promotes the degradation of SHH mRNA in colorectal cancer cells, interrupting the paracrine Hedgehog signaling pathway activity thus suppresses the colorectal cancer growth. This study reveals a novel molecular mechanism underlying the anticancer action of BBR.
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Affiliation(s)
- Zhu-Qing Shen
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Juan Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Wen-Fu Tan
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China.
| | - Tao-Min Huang
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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6
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Jaso-Vera ME, Domínguez-Malfavón L, Curiel-Quesada E, García-Mena J. Dynamics of the canonical RNA degradosome components during glucose stress. Biochimie 2021; 187:67-74. [PMID: 34022290 DOI: 10.1016/j.biochi.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/21/2021] [Accepted: 05/12/2021] [Indexed: 11/19/2022]
Abstract
The RNA Degradosome (RNAD) is a multi-enzyme complex, which performs important functions in post-transcriptional regulation in Escherichia coli with the assistance of regulatory sRNAs and the RNA chaperone Hfq. Although the interaction of the canonical RNAD components with RNase E has been extensively studied, the dynamic nature of the interactions in vivo remains largely unknown. In this work, we explored the rearrangements upon glucose stress using fluorescence energy transfer (hetero-FRET). Results revealed differences in the proximity of the canonical components with 1% (55.5 mM) glucose concentration, with the helicase RhlB and the glycolytic enzyme Enolase exhibiting the largest changes to the C-terminus of RNase E, followed by PNPase. We quantified ptsG mRNA decay and SgrS sRNA synthesis as they mediate bacterial adaptation to glucose stress conditions. We propose that once the mRNA degradation is completed, the RhlB, Enolase and PNPase decrease their proximity to the C-terminus of RNase E. Based on the results, we present a model where the canonical components of the RNAD coalesce when the bacteria is under glucose-6-phosphate stress and associate it with RNA decay. Our results demonstrate that FRET is a helpful tool to study conformational rearrangements in enzymatic complexes in bacteria in vivo.
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Affiliation(s)
- Marcos Emmanuel Jaso-Vera
- Departamento de Genética y Biología Molecular, Cinvestav, Unidad Zacatenco, Ciudad de México, 07360, Mexico
| | - Lilianha Domínguez-Malfavón
- Department of Biotechnology, Universidad Autónoma Metropolitana (Unidad Iztapalapa), Ciudad de México, 09340, Mexico
| | - Everardo Curiel-Quesada
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Ciudad de México, 11340, Mexico
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Cinvestav, Unidad Zacatenco, Ciudad de México, 07360, Mexico.
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7
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Tessier SN, Bookstaver LD, Angpraseuth C, Stannard CJ, Marques B, Ho UK, Muzikansky A, Aldikacti B, Reátegui E, Rabe DC, Toner M, Stott SL. Isolation of intact extracellular vesicles from cryopreserved samples. PLoS One 2021; 16:e0251290. [PMID: 33983964 PMCID: PMC8118530 DOI: 10.1371/journal.pone.0251290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/23/2021] [Indexed: 01/23/2023] Open
Abstract
Extracellular vesicles (EVs) have emerged as promising candidates in biomarker discovery and diagnostics. Protected by the lipid bilayer, the molecular content of EVs in diverse biofluids are protected from RNases and proteases in the surrounding environment that may rapidly degrade targets of interests. Nonetheless, cryopreservation of EV-containing samples to -80°C may expose the lipid bilayer to physical and biological stressors which may result in cryoinjury and contribute to changes in EV yield, function, or molecular cargo. In the present work, we systematically evaluate the effect of cryopreservation at -80°C for a relatively short duration of storage (up to 12 days) on plasma- and media-derived EV particle count and/or RNA yield/quality, as compared to paired fresh controls. On average, we found that the plasma-derived EV concentration of stored samples decreased to 23% of fresh samples. Further, this significant decrease in EV particle count was matched with a corresponding significant decrease in RNA yield whereby plasma-derived stored samples contained only 47-52% of the total RNA from fresh samples, depending on the extraction method used. Similarly, media-derived EVs showed a statistically significant decrease in RNA yield whereby stored samples were 58% of the total RNA from fresh samples. In contrast, we did not obtain clear evidence of decreased RNA quality through analysis of RNA traces. These results suggest that samples stored for up to 12 days can indeed produce high-quality RNA; however, we note that when directly comparing fresh versus cryopreserved samples without cryoprotective agents there are significant losses in total RNA. Finally, we demonstrate that the addition of the commonly used cryoprotectant agent, DMSO, alongside greater control of the rate of cooling/warming, can rescue EVs from damaging ice formation and improve RNA yield.
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Affiliation(s)
- Shannon N. Tessier
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Shriners Hospitals for Children—Boston, Boston, MA, United States of America
| | - Lauren D. Bookstaver
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Cindy Angpraseuth
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Cleo J. Stannard
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Beatriz Marques
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Uyen K. Ho
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Alona Muzikansky
- Biostatistics Center, Massachusetts General Hospital, Boston, MA, United States of America
| | - Berent Aldikacti
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Eduardo Reátegui
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Daniel C. Rabe
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Mehmet Toner
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Shriners Hospitals for Children—Boston, Boston, MA, United States of America
| | - Shannon L. Stott
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
- * E-mail:
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8
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Liu L, Liu X, Bi W, Alcorn JL. A primate-specific RNA-binding protein (RBMXL3) is involved in glucocorticoid regulation of human pulmonary surfactant protein B (SP-B) mRNA stability. Am J Physiol Lung Cell Mol Physiol 2021; 320:L942-L957. [PMID: 33719563 PMCID: PMC8174829 DOI: 10.1152/ajplung.00022.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 01/25/2021] [Accepted: 03/05/2021] [Indexed: 11/22/2022] Open
Abstract
The ability of pulmonary surfactant to reduce alveolar surface tension requires adequate levels of surfactant protein B (SP-B). Dexamethasone (DEX) increases human SP-B expression, in part, through increased SP-B mRNA stability. A 30-nt-long hairpin element (RBE) in the 3'-untranslated region of human SP-B mRNA mediates both DEX-induced and intrinsic mRNA stabilities, but the mechanism is unknown. Proteomic analysis of RBE-interacting proteins identified a primate-specific protein, RNA-binding motif X-linked-like-3 (RBMXL3). siRNA directed against RBMXL3 reduces DEX-induced SP-B mRNA expression in human bronchoalveolar cells. Human SP-B mRNA stability, measured by our dual cistronic plasmid assay, is unaffected by DEX in mouse lung epithelial cells lacking RBMXL3, but DEX increases human SP-B mRNA stability when RBMXL3 is expressed and requires the RBE. In the absence of DEX, RBE interacts with cellular proteins, reducing intrinsic SP-B mRNA stability in human and mouse lung epithelial cells. RBMXL3 specifically binds the RBE in vitro, whereas RNA immunoprecipitation and affinity chromatography analyses indicate that binding is enhanced in the presence of DEX. These results describe a model where intrinsic stability of human SP-B mRNA is reduced through binding of cellular mRNA decay factors to RBE, which is then relieved through DEX-enhanced binding of primate-specific RBMXL3.
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Affiliation(s)
- Lidan Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiangli Liu
- Department of Thoracic Surgery, First Hospital of China Medical University, Shenyang, China
| | - Weizhen Bi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Joseph L Alcorn
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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9
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Cui YH, Yang S, Wei J, Shea CR, Zhong W, Wang F, Shah P, Kibriya MG, Cui X, Ahsan H, He C, He YY. Autophagy of the m 6A mRNA demethylase FTO is impaired by low-level arsenic exposure to promote tumorigenesis. Nat Commun 2021; 12:2183. [PMID: 33846348 PMCID: PMC8041927 DOI: 10.1038/s41467-021-22469-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/16/2021] [Indexed: 12/14/2022] Open
Abstract
Here we show that FTO as an N6-methyladenosine (m6A) RNA demethylase is degraded by selective autophagy, which is impaired by low-level arsenic exposure to promote tumorigenesis. We found that in arsenic-associated human skin lesions, FTO is upregulated, while m6A RNA methylation is downregulated. In keratinocytes, chronic relevant low-level arsenic exposure upregulated FTO, downregulated m6A RNA methylation, and induced malignant transformation and tumorigenesis. FTO deletion inhibited arsenic-induced tumorigenesis. Moreover, in mice, epidermis-specific FTO deletion prevented skin tumorigenesis induced by arsenic and UVB irradiation. Targeting FTO genetically or pharmacologically inhibits the tumorigenicity of arsenic-transformed tumor cells. We identified NEDD4L as the m6A-modified gene target of FTO. Finally, arsenic stabilizes FTO protein through inhibiting p62-mediated selective autophagy. FTO upregulation can in turn inhibit autophagy, leading to a positive feedback loop to maintain FTO accumulation. Our study reveals FTO-mediated dysregulation of mRNA m6A methylation as an epitranscriptomic mechanism to promote arsenic tumorigenicity.
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Affiliation(s)
- Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Seungwon Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Christopher R Shea
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Wen Zhong
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Department of Radiation Oncology, 4th Affiliated Hospital, China Medical University, Shenyang, China
| | - Fang Wang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Muhammad G Kibriya
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Departments of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA.
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10
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Cao X, Shu Y, Chen Y, Xu Q, Guo G, Wu Z, Shao M, Zhou Y, Chen M, Gong Y, Li C, Shi Y, Bu H. Mettl14-Mediated m 6A Modification Facilitates Liver Regeneration by Maintaining Endoplasmic Reticulum Homeostasis. Cell Mol Gastroenterol Hepatol 2021; 12:633-651. [PMID: 33848642 PMCID: PMC8261664 DOI: 10.1016/j.jcmgh.2021.04.001] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND & AIMS N6-methyladenosine (m6A), the most prevalent and dynamic posttranscriptional methylation modification of mammalian mRNA, is involved in various biological processes, but its role in liver regeneration has not been characterized. METHODS We first conducted transcriptome-wide m6A mRNA sequencing and characterized the expression pattern of m6A in regenerating mouse liver. Next, we generated hepatocyte-specific Mettl3- or Mettl14-deficient mice and investigated their role in liver regeneration. A series of biochemical experiments in vitro and in vivo was further performed to investigate potential mechanisms. RESULTS We identified an overwhelming proportion of m6A-modified genes with initially up-regulated and subsequently down-regulated m6A levels as liver regeneration progressed. Loss of Mettl14 but not of Mettl3 resulted in markedly disrupted liver regeneration, and Mettl14-ablated hepatocytes were arrested in the G1 phase of the cell cycle. Most strikingly, the Mettl14-ablated regenerating liver exhibited extensive parenchymal necrosis. mRNA transcripts, such as Hsp90b1, Erp29, Stt3a, P4hb, and Lman1, encoding proteins involved in polypeptide processing and the endoplasmic reticulum (ER) stress response, were m6A-hypomethylated, and their mRNA and protein levels were subsequently decreased, resulting in unresolved ER stress, hepatocyte death, and inhibited proliferation. CONCLUSIONS We demonstrate the essential role of Mettl14 in facilitating liver regeneration by modulating polypeptide-processing proteins in the ER in an m6A-dependent manner.
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Affiliation(s)
- Xiaoyue Cao
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Yuke Shu
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Yuwei Chen
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Xu
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Guo
- Department of Talent Highland, Center for Gut Microbiome Research, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
| | - Zhenru Wu
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Mingyang Shao
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Yongjie Zhou
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Menglin Chen
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Yuping Gong
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.
| | - Chuan Li
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China.
| | - Yujun Shi
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China.
| | - Hong Bu
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, China; Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
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11
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Lucchesi CA, Zhang J, Ma B, Nussinov R, Chen X. Survivin Expression Is Differentially Regulated by a Selective Cross-talk between RBM38 and miRNAs let-7b or miR-203a. Cancer Res 2021; 81:1827-1839. [PMID: 33472892 PMCID: PMC8137528 DOI: 10.1158/0008-5472.can-20-3157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/17/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
RNA-binding motif 38 (RBM38) is a member of a protein family with a highly conserved RNA-binding motif and has been shown to regulate mRNA processing, stability, and translation. Survivin is an essential modulator of apoptotic and nonapoptotic cell death as well as a stress responder. Survivin mRNA is the fourth most frequently overexpressed transcript in the human cancer transcriptome, and its aberrant expression is associated with chemo-/radioresistance and poor prognosis. In this study, we examined whether survivin expression is regulated by RBM38. RBM38 bound to survivin 3'-untranslated region and suppressed miRNA let-7b from binding to and degrading survivin mRNA, leading to increased survivin expression. RBM38 interacted with argonaute-2 (AGO2) and facilitated miR-203a-mediated degradation of survivin mRNA, leading to decreased survivin expression. Due to the abundance of let-7b over miR-203a, RBM38 ultimately increased survivin expression in HCT116 and MCF7 cells. In addition, Ser-195 in RBM38 interacted with Glu-73/-76 in AGO2, and Pep8, an eight-amino acid peptide spanning the region of Ser-195 in RBM38, blocked the RBM38-AGO2 interaction and inhibited miR-203a-mediated mRNA degradation, leading to enhanced survivin expression. Furthermore, Pep8 cooperated with YM155, an inhibitor of survivin, to suppress tumor spheroid growth and viability. Pep8 sensitized tumor cells to YM155-induced DNA damage in an RBM38-dependent manner. Together, our data indicate that RBM38 is a dual regulator of survivin and that Pep8/YM155 may be therapeutically explored for tumor suppression. SIGNIFICANCE: These findings show that RBM38 exerts opposing effects on survivin expression via two miRNAs, and disruption of the RBM38-AGO2 complex by an eight-amino acid peptide sensitizes tumor spheroids to survivin inhibitor YM155.
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Affiliation(s)
- Christopher A Lucchesi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California.
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12
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Carvalho AF, Rocha RP, Gonçalves AP, Silva TBS, Sato HI, Vuitika L, Bagno FF, Sérgio SAR, Figueiredo MM, Martins RB, Souza JP, Arruda E, Fernandes APSM, Alves PA, Teixeira SMR, da Fonseca FG. The use of denaturing solution as collection and transport media to improve SARS-CoV-2 RNA detection and reduce infection of laboratory personnel. Braz J Microbiol 2021; 52:531-539. [PMID: 33788178 PMCID: PMC8010291 DOI: 10.1007/s42770-021-00469-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Accurate testing to detect SARS-CoV-2 RNA is key to counteract the virus spread. Nonetheless, the number of diagnostic laboratories able to perform qPCR tests is limited, particularly in developing countries. We describe the use of a virus-inactivating, denaturing solution (DS) to decrease virus infectivity in clinical specimens without affecting RNA integrity. Swab samples were collected from infected patients and from laboratory personnel using a commercially available viral transport solution and the in-house DS. Samples were tested by RT-qPCR, and exposure to infective viruses was also accessed by ELISA. The DS used did not interfere with viral genome detection and was able to maintain RNA integrity for up to 16 days at room temperature. Furthermore, virus loaded onto DS were inactivated, as attested by attempts to grow SARS-CoV-2 in cell monolayers after DS desalt filtration to remove toxic residues. The DS described here provides a strategy to maintain diagnostic accuracy and protects diagnostic laboratory personnel from accidental infection, as it has helped to protect our lab crew.
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Affiliation(s)
- Alex F Carvalho
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Raissa P Rocha
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Andreza P Gonçalves
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz/FIOCRUZ, Belo Horizonte, Minas Gerais, CEP: 30190-002, Brazil
| | - Thaís B S Silva
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz/FIOCRUZ, Belo Horizonte, Minas Gerais, CEP: 30190-002, Brazil
| | - Hugo I Sato
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Larissa Vuitika
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Flavia F Bagno
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Sarah A R Sérgio
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Maria M Figueiredo
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Ronaldo B Martins
- Virology Research Center, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, São Paulo, 14040900, Brazil
| | - Juliano P Souza
- Virology Research Center, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, São Paulo, 14040900, Brazil
| | - Eurico Arruda
- Virology Research Center, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, São Paulo, 14040900, Brazil
| | - Ana P S M Fernandes
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Pedro A Alves
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz/FIOCRUZ, Belo Horizonte, Minas Gerais, CEP: 30190-002, Brazil
| | - Santuza M R Teixeira
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil
| | - Flavio G da Fonseca
- Centro de Tecnologia em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31210-260, Brazil.
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Abstract
Myotonic dystrophy (DM) types 1 (DM1) and 2 (DM2) are caused by autosomal dominant gain-of-function RNA which are, in turn, created by the expansion of repeat sequences in the DMPK and ZNF9 genes, respectively. The expansions are highly unstable and biased for further expansion in somatic cells and across generations. Despite the different genes involved, DM1 and DM2 share several clinical features due to having the similar underlying mechanism of repetitive RNA-mediated toxicity. Both disorders manifest as multisystemic conditions with features including myotonia, cataract development, and abnormalities in cardiac conduction. At present, there is no cure for DM and treatments mostly aim at symptom management. Among the therapeutics being developed, antisense therapy using gapmers is one of the most promising. Compared to other antisense oligonucleotides, gapmers maintain the ability to induce RNase H cleavage while having enhanced target binding affinity and nuclease resistance. This chapter will consolidate the different strategies studied thus far to develop a treatment for DM1 through the targeting of toxic repetitive RNA using gapmers.
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Affiliation(s)
- Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garret Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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14
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Lai HC, James A, Luff J, De Souza P, Quek H, Ho U, Lavin MF, Roberts TL. Regulation of RNA degradation pathways during the lipopolysaccharide response in Macrophages. J Leukoc Biol 2021; 109:593-603. [PMID: 32829531 DOI: 10.1002/jlb.2ab0420-151rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 11/09/2022] Open
Abstract
The innate immune response to LPS is highly dynamic yet tightly regulated. The majority of studies of gene expression have focussed on transcription. However, it is also important to understand how post-transcriptional pathways are regulated in response to inflammatory stimuli as the rate of RNA degradation relative to new transcription is important for overall expression. RNA decay pathways include nonsense-mediated decay, the RNA decay exosome, P-body localized deadenylation, decapping and degradation, and AU-rich element targeted decay mediated by tristetraprolin. Here, bone marrow-derived Mϕs were treated with LPS over a time course of 0, 2, 6, and 24 h and the transcriptional profiles were analyzed by RNA sequencing. The data show that components of RNA degradation pathways are regulated during an LPS response. Processing body associated decapping enzyme DCP2 and regulatory subunit DCP1A, and 5' exonuclease XRN1 and sequence specific RNA decay pathways were upregulated. Nonsense mediated decay was also increased in response to LPS induced signaling, initially by increased activation and at later timepoints at the mRNA and protein levels. This leads to increased nonsense mediated decay efficiency across the 24 h following LPS treatment. These findings suggest that LPS activation of Mϕs results in targeted regulation of RNA degradation pathways in order to change how subsets of mRNAs are degraded during an inflammatory response.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
| | - John Luff
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- Medical Oncology Department, Liverpool Hospital, Liverpool, New South Wales, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
| | - Hazel Quek
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Uda Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Martin F Lavin
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, New South Wales, Australia
- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- School of Medicine, Western Sydney University, Macarthur, New South Wales, Australia
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15
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Jang D, Marcus-Samuels B, Morgan SJ, Klubo-Gwiezdzinska J, Neumann S, Gershengorn MC. Thyrotropin regulation of differentiated gene transcription in adult human thyrocytes in primary culture. Mol Cell Endocrinol 2020; 518:111032. [PMID: 32941925 PMCID: PMC7606794 DOI: 10.1016/j.mce.2020.111032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 01/05/2023]
Abstract
Thyroid transcription factors (TTFs) - NKX2-1, FOXE1, PAX8 and HHEX - regulate multiple genes involved in thyroid development in mice but little is known about TTF regulation of thyroid-specific genes - thyroglobulin (TG), thyroid peroxidase (TPO), deiodinase type 2 (DIO2), sodium/iodide symporter (NIS) and TSH receptor (TSHR) - in adult, human thyrocytes. Thyrotropin (thyroid-stimulating hormone, TSH) regulation of thyroid-specific gene expression in primary cultures of human thyrocytes is biphasic yielding an inverted U-shaped dose-response curve (IUDRC) with upregulation at low doses and decreases at high doses. Herein we show that NKX2-1, FOXE1 and PAX8 are required for TSH-induced upregulation of the mRNA levels of TG, TPO, DIO2, NIS, and TSHR whereas HHEX has little effect on the levels of these thyroid-specific gene mRNAs. We show that TSH-induced upregulation is mediated by changes in their transcription and not by changes in the degradation of their mRNAs. In contrast to the IUDRC of thyroid-specific genes, TSH effects on the levels of the mRNAs for NKX2-1, FOXE1 and PAX8 exhibit monophasic decreases at high doses of TSH whereas TSH regulation of HHEX mRNA levels exhibits an IUDRC that overlaps the IUDRC of thyroid-specific genes. In contrast to findings during mouse development, TTFs do not have major effects on the levels of other TTF mRNAs in adult, human thyrocytes. Thus, we found similarities and important differences in the regulation of thyroid-specific genes in mouse development and TSH regulation of these genes in adult, human thyrocytes.
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Affiliation(s)
- Daesong Jang
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Bernice Marcus-Samuels
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Sarah J Morgan
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Joanna Klubo-Gwiezdzinska
- Metabolic Disease Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Susanne Neumann
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Marvin C Gershengorn
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA.
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16
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Kognole AA, MacKerell AD. Contributions and competition of Mg 2+ and K + in folding and stabilization of the Twister ribozyme. RNA 2020; 26:1704-1715. [PMID: 32769092 PMCID: PMC7566569 DOI: 10.1261/rna.076851.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg2+ in a background of monovalent ions. In a recent study, we have shown how the presence of Mg2+ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic umbrella sampling and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg2+ and K+ ions around Twister RNA. Results show the presence of 100 mM Mg2+ to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states, overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K+ ions. Furthermore, K+ preferentially interacts with purine N7 atoms of helical regions in partially unfolded states, thereby potentially stabilizing the helical regions. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K+ can act as a surrogate for Mg2+ by participating in specific interactions with nonsequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at submillimolar Mg2+ concentrations.
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Affiliation(s)
- Abhishek A Kognole
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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17
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Abstract
As a naturally occurring class of gene regulators, microRNAs (miRNAs) have attracted much attention as promising targets for therapeutic development. However, RNAs including miRNAs have long been considered undruggable, and most efforts have been devoted to using synthetic oligonucleotides to regulate miRNAs. Encouragingly, recent findings have revealed that miRNAs can also be drugged with small molecules that directly target miRNAs. In this review paper, we give a summary of recently emerged small-molecule inhibitors (SMIs) and small-molecule degraders (SMDs) for miRNAs. SMIs are small molecules that directly bind to miRNAs to inhibit their biogenesis, and SMDs are bifunctional small molecules that upon binding to miRNAs induce miRNA degradation. Strategies for discovering SMIs and developing SMDs were summarized. Applications of SMIs and SMDs in miRNA inhibition and cancer therapy were also introduced. Overall, SMIs and SMDs introduced here have high potency and specificity in miRNA inhibition. We envision that these small molecules will pave the way for developing novel therapeutics toward miRNAs that were previously considered undruggable.
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Affiliation(s)
- Dejun Liu
- The Yancheng Clinical College of Xuzhou Medical University, Yancheng, 224001, China
| | - Xinqiang Wan
- Department of Gynaecology and Obstetrics, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Xiangxiang Shan
- Department of Geraeology, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Rengen Fan
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
| | - Wenzhang Zha
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
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18
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Wang Y, Yang T, Han Y, Ren Z, Zou J, Liu J, Xi S. lncRNA OTUD6B-AS1 Exacerbates As 2O 3-Induced Oxidative Damage in Bladder Cancer via miR-6734-5p-Mediated Functional Inhibition of IDH2. Oxid Med Cell Longev 2020; 2020:3035624. [PMID: 32952848 PMCID: PMC7481943 DOI: 10.1155/2020/3035624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/06/2020] [Accepted: 07/18/2020] [Indexed: 12/18/2022]
Abstract
Arsenic trioxide (As2O3) is a promising effective chemotherapeutic agent for cancer treatment; however, how and through what molecular mechanisms the oxidative damage of As2O3 is controlled remains poorly understood. Recently, the involvement of dysregulated long noncoding RNA ovarian tumor domain containing 6B antisense RNA1 (lncRNA OTUD6B-AS1) in tumorigenesis is established. Here, for the first time, we characterize the regulation of As2O3 in the oxidative damage against bladder cancer via lncRNA OTUD6B-AS1. As2O3 could activate lncRNA OTUD6B-AS1 transcription in bladder cancer cells, and these findings were validated in a xenograft tumor model. Functional assays showed that lncRNA OTUD6B-AS1 dramatically exacerbated As2O3-mediated oxidative damage by inducing oxidative stress. Mechanistically, As2O3 increased levels of metal-regulatory transcription factor 1 (MTF1), which regulates lncRNA OTUD6B-AS1, in response to oxidative stress. Further, lncRNA OTUD6B-AS1 inhibited mitochondrial NADP+-dependent isocitrate dehydrogenase 2 (IDH2) expression by stabilizing miR-6734-5p, which contributed to cytotoxicity by enhancing oxidative stress. Together, our findings offer new insights into the mechanism of As2O3-induced oxidative damage and identify important factors in the pathway, As2O3/lncRNA OTUD6B-AS1/miR-6734-5p/IDH2, expanding the knowledge of activity of As2O3 as cancer treatment.
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Affiliation(s)
- Yutong Wang
- Department of Environmental Health, China Medical University, Shenyang 110122, China
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang 110022, China
| | - Tianyao Yang
- Department of Environmental Health, China Medical University, Shenyang 110122, China
| | - Yanshou Han
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110022, China
| | - Zhaozhou Ren
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jiayun Zou
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang 110022, China
| | - Jieyu Liu
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Shuhua Xi
- Department of Environmental Health, China Medical University, Shenyang 110122, China
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19
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Walsh HL, Sperry AJ, Blazer VS. The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu). PLoS One 2020; 15:e0236104. [PMID: 32776939 PMCID: PMC7416921 DOI: 10.1371/journal.pone.0236104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
There is an increasing emphasis on effects-based monitoring to document responses associated with exposure to complex mixtures of chemicals, climate change, pathogens, parasites and other environmental stressors in fish populations. For decades aquatic monitoring programs have included the collection of tissues preserved for microscopic pathology. Consequently, formalin-fixed, paraffin-embedded (FFPE) tissue can be an important reservoir of nucleic acids as technologies emerge that utilize molecular endpoints. Despite the cross-linking effects of formalin, its impact on nucleic acid quality and concentration, amplification, and sequencing are not well described. While fresh-frozen tissue is optimal for working with nucleic acids, FFPE samples have been shown to be conducive for molecular studies. Laser capture microdissection (LCM) is one technology which allows for collection of specific regions or cell populations from fresh or preserved specimens with pathological alterations, pathogens, or parasites. In this study, smallmouth bass (Micropterus dolomieu) liver was preserved in three different fixatives, including 10% neutral buffered formalin (NBF), Z-Fix® (ZF), and PAXgene® (PG) for four time periods (24 hr, 48 hr, seven days, and 14 days). Controls consisted of pieces of liver preserved in RNALater® or 95% ethanol. Smallmouth bass were chosen as they are an economically important sportfish and have been utilized as indicators of exposure to endocrine disruptors and other environmental stressors. Small liver sections were cut out with laser microdissection and DNA and RNA were purified and analyzed for nucleic acid concentration and quality. Sanger sequencing and the NanoString nCounter® technology were used to assess the suitability of these samples in downstream molecular techniques. The results revealed that of the formalin fixatives, NBF samples fixed for 24 and 48 hr were superior to ZF samples for both Sanger sequencing and the Nanostring nCounter®. The non-formalin PAXgene® samples were equally successful and they showed greater stability in nucleic acid quality and concentration over longer fixation times. This study demonstrated that small quantities of preserved tissue from smallmouth bass can be utilized in downstream molecular techniques; however, future studies will need to optimize the methods presented here for different tissue types, fish species, and pathological conditions.
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Affiliation(s)
- Heather L. Walsh
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
- * E-mail:
| | - Adam J. Sperry
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
| | - Vicki S. Blazer
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
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20
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Zeng Z, Chen H, Cai J, Huang Y, Yue J. IL-10 regulates the malignancy of hemangioma-derived endothelial cells via regulation of PCNA. Arch Biochem Biophys 2020; 688:108404. [PMID: 32416101 DOI: 10.1016/j.abb.2020.108404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/29/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/13/2022]
Abstract
Hemangioma (HA) is the most common benign tumor and formed by the proliferating endothelial cells of blood vessels. Interleukins (ILs) have been reported to be critical for HA progression. Our present study found that the expression of IL-10 was decreased in HA cells and tissues as compared to their corresponding controls. Treatment with recombinant IL-10 (rIL-10) can suppress the proliferation of HA cells via suppression of proliferating cell nuclear antigen (PCNA), while over expression of PCNA can attenuate rIL-10-inhibited cell proliferation. Further, rIL-10 can decrease the promoter activity and mRNA stability of PCNA in HA cells. Mechanistically, rIL-10 can increase expression of miR-27b-3p to decrease mRNA stability of PCNA, while down regulation of YY1 is involved in rIL-10 suppressed transcription of PCNA. Collectively, IL-10 can suppress the expression of PCNA via miR-27b-3p mediated suppression of mRNA stability and YY1 mediated down regulation of transcription. It suggested that rIL-10 might be a potential therapeutic approach for HA development and progression.
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Affiliation(s)
- Zhaofan Zeng
- Department of Vascular Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, Hainan Province, PR China
| | - Hao Chen
- Department of Vascular Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, Hainan Province, PR China
| | - Junhong Cai
- Molecular Laboratory Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, Hainan Province, PR China
| | - Yanjing Huang
- Department of Medical Oncology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, 570311, Hainan Province, PR China
| | - Jie Yue
- Department of Cardiovascula Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong Province, PR China.
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Disney MD, Suresh BM, Benhamou RI, Childs-Disney JL. Progress toward the development of the small molecule equivalent of small interfering RNA. Curr Opin Chem Biol 2020; 56:63-71. [PMID: 32036231 PMCID: PMC7311281 DOI: 10.1016/j.cbpa.2020.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
Given that many small molecules could bind to structured regions at sites that will not affect function, approaches that trigger degradation of RNA could provide a general way to affect biology. Indeed, targeted RNA degradation is an effective strategy to selectively and potently modulate biology. We describe several approaches to endow small molecules with the power to cleave RNAs. Central to these strategies is Inforna, which designs small molecules targeting RNA from human genome sequence. Inforna deduces the uniqueness of a druggable pocket, enables generation of hypotheses about functionality of the pocket, and defines on- and off-targets to drive compound optimization. RNA-binding compounds are then converted into cleavers that degrade the target directly or recruit an endogenous nuclease to do so. Cleaving compounds have significantly contributed to understanding and manipulating biological functions. Yet, there is much to be learned about how to affect human RNA biology with small molecules.
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Affiliation(s)
- Matthew D Disney
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA.
| | - Blessy M Suresh
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA
| | - Raphael I Benhamou
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA
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22
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Workel HH, van Rooij N, Plat A, Spierings DC, Fehrmann RSN, Nijman HW, de Bruyn M. Transcriptional Activity and Stability of CD39+CD103+CD8+ T Cells in Human High-Grade Endometrial Cancer. Int J Mol Sci 2020; 21:E3770. [PMID: 32471032 PMCID: PMC7312498 DOI: 10.3390/ijms21113770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Tumor-infiltrating CD8+ T cells (TIL) are of the utmost importance in anti-tumor immunity. CD103 defines tumor-resident memory T cells (TRM cells) associated with improved survival and response to immune checkpoint blockade (ICB) across human tumors. Co-expression of CD39 and CD103 marks tumor-specific TRM with enhanced cytolytic potential, suggesting that CD39+CD103+ TRM could be a suitable biomarker for immunotherapy. However, little is known about the transcriptional activity of TRM cells in situ. We analyzed CD39+CD103+ TRM cells sorted from human high-grade endometrial cancers (n = 3) using mRNA sequencing. Cells remained untreated or were incubated with PMA/ionomycin (activation), actinomycin D (a platinum-like chemotherapeutic that inhibits transcription), or a combination of the two. Resting CD39+CD103+ TRM cells were transcriptionally active and expressed a characteristic TRM signature. Activated CD39+CD103+ TRM cells differentially expressed PLEK, TWNK, and FOS, and cytokine genes IFNG, TNF, IL2, CSF2 (GM-CSF), and IL21. Findings were confirmed using qPCR and cytokine production was validated by flow cytometry of cytotoxic TIL. We studied transcript stability and found that PMA-responsive genes and mitochondrial genes were particularly stable. In conclusion, CD39+CD103+ TRM cells are transcriptionally active TRM cells with a polyfunctional, reactivation-responsive repertoire. Secondly, we hypothesize that differential regulation of transcript stability potentiates rapid responses upon TRM reactivation in tumors.
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Affiliation(s)
- Hagma H. Workel
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Nienke van Rooij
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Annechien Plat
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Rudolf S. N. Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Hans W. Nijman
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Marco de Bruyn
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
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Shanidze N, Lenkeit F, Hartig JS, Funck D. A Theophylline-Responsive Riboswitch Regulates Expression of Nuclear-Encoded Genes. Plant Physiol 2020; 182:123-135. [PMID: 31704721 PMCID: PMC6945857 DOI: 10.1104/pp.19.00625] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/25/2019] [Indexed: 05/27/2023]
Abstract
Riboswitches are small cis-regulatory RNA elements that regulate gene expression by conformational changes in response to ligand binding. Synthetic riboswitches have been engineered as versatile and innovative tools for gene regulation by external application of their ligand in prokaryotes and eukaryotes. In plants, synthetic riboswitches were used to regulate gene expression in plastids, but the application of synthetic riboswitches for the regulation of nuclear-encoded genes in planta remains to be explored. Here, we characterize the properties of a theophylline-responsive synthetic aptazyme for control of nuclear-encoded transgenes in Arabidopsis (Arabidopsis thaliana). Activation of the aptazyme, inserted in the 3' UTR of the target gene, resulted in rapid self-cleavage and subsequent decay of the mRNA. This riboswitch allowed reversible, theophylline-dependent down-regulation of the GFP reporter gene in a dose- and time-dependent manner. Insertion of the riboswitch into the ONE HELIX PROTEIN1 gene allowed complementation of ohp1 mutants and induction of the mutant phenotype by theophylline. GFP and ONE HELIX PROTEIN1 transcript levels were downregulated by up to 90%, and GFP protein levels by 95%. These results establish artificial riboswitches as tools for externally controlled gene expression in synthetic biology in plants or functional crop design.
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Affiliation(s)
- Nana Shanidze
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Felina Lenkeit
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany
| | - Dietmar Funck
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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24
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Eshleman N, Luo X, Capaldi A, Buchan JR. Alterations of signaling pathways in response to chemical perturbations used to measure mRNA decay rates in yeast. RNA 2020; 26:10-18. [PMID: 31601735 PMCID: PMC6913126 DOI: 10.1261/rna.072892.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Assessing variations in mRNA stability typically involves inhibiting transcription either globally or in a gene-specific manner. Alternatively, mRNA pulse-labeling strategies offer a means to calculate mRNA stability without inhibiting transcription. However, key stress-responsive cell signaling pathways, which affect mRNA stability, may themselves be perturbed by the approaches used to measure mRNA stability, leading to artifactual results. Here, we have focused on common strategies to measure mRNA half-lives in yeast and determined that commonly used transcription inhibitors thiolutin and 1,10 phenanthroline inhibit TORC1 signaling, PKC signaling, and partially activate HOG signaling. Additionally, 4-thiouracil (4tU), a uracil analog used in mRNA pulse-labeling approaches, modestly induces P-bodies, mRNA-protein granules implicated in storage and decay of nontranslating mRNA. Thiolutin also induces P-bodies, whereas phenanthroline has no effect. Doxycycline, which controls "Tet On/Tet Off" regulatable promoters, shows no impact on the above signaling pathways or P-bodies. In summary, our data argues that broad-acting transcriptional inhibitors are problematic for determining mRNA half-life, particularly if studying the impacts of the TORC1, HOG, or PKC pathway on mRNA stability. Regulatable promoter systems are a preferred approach for individual mRNA half-life studies, with 4tU labeling representing a good approach to global mRNA half-life analysis, despite modestly inducing P-bodies.
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Affiliation(s)
- Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Andrew Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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25
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Santaus TM, Greenberg K, Suri P, Geddes CD. Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It. PLoS One 2019; 14:e0225475. [PMID: 31790434 PMCID: PMC6886747 DOI: 10.1371/journal.pone.0225475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/05/2019] [Indexed: 01/11/2023] Open
Abstract
Rapid sample preparation is one of the leading bottlenecks to low-cost and efficient sample component detection. To overcome this setback, a technology known as Lyse-It has been developed to rapidly (less than 60 seconds) lyse Gram-positive and-negative bacteria alike, while simultaneously fragmenting DNA/RNA and proteins into tunable sizes. This technology has been used with a variety of organisms, but the underlying mechanism behind how the technology actually works to fragment DNA/RNA and proteins has hitherto been studied. It is generally understood how temperature affects cellular lysing, but for DNA/RNA and protein degradation, the temperature and amount of energy introduced by microwave irradiation of the sample, cannot explain the degradation of the biomolecules to the extent that was being observed. Thus, an investigation into the microwave generation of reactive oxygen species, in particular singlet oxygen, hydroxyl radicals, and superoxide anion radicals, was undertaken. Herein, we probe one aspect, the generation of reactive oxygen species (ROS), which is thought to contribute to a non-thermal mechanism behind biomolecule fragmentation with the Lyse-It technology. By utilizing off/on (Photoinduced electron transfer) PET fluorescent-based probes highly specific for reactive oxygen species, it was found that as oxygen concentration in the sample and/or microwave irradiation power increases, more reactive oxygen species are generated and ultimately, more oxidation and biomolecule fragmentation occurs within the microwave cavity.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Ken Greenberg
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Prabhdeep Suri
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
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26
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Lim WQ, Phua SZF, Zhao Y. Redox-Responsive Polymeric Nanocomplex for Delivery of Cytotoxic Protein and Chemotherapeutics. ACS Appl Mater Interfaces 2019; 11:31638-31648. [PMID: 31389684 DOI: 10.1021/acsami.9b09605] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Responsive delivery of anticancer proteins into cells is an emerging field in biological therapeutics. Currently, the delivery of proteins is highly compromised by multiple successive physiological barriers that reduce the therapeutic efficacy. Hence, there is a need to design a robust and sustainable nanocarrier to provide suitable protection of proteins and overcome the physiological barriers for better cellular accumulation. In this work, polyethylenimine (PEI) cross-linked by oxaliplatin(IV) prodrug (oxliPt(IV)) was used to fabricate a redox-responsive nanocomplex (PEI-oxliPt(IV)@RNBC/GOD) for the delivery of a reactive oxygen species-cleavable, reversibly caged RNase A protein (i.e., RNase A nitrophenylboronic conjugate, RNBC) and glucose oxidase (GOD) in order to realize efficient cancer treatment. The generation of hydrogen peroxide by GOD can uncage and restore the enzymatic activity of RNBC. On account of the responsiveness of the nanocomplex to highly reducing cellular environment, it would dissociate and release the protein and active oxaliplatin drug, causing cell death by both catalyzing RNA degradation and inhibiting DNA synthesis. As assessed by the RNA degradation assay, the activity of the encapsulated RNBC was recovered by the catalytic production of hydrogen peroxide from GOD and glucose substrate overexpressed in cancer cells. Monitoring of the changes in nanoparticle size confirmed that the nanocomplex could dissociate in the reducing environment, with the release of active oxaliplatin drug and protein. Confocal laser scanning microscopy (CLSM) and flow cytometry analysis revealed highly efficient accumulation of the nanocomplex as compared to free native proteins. In vitro cytotoxicity experiments using 4T1 cancer cells showed ∼80% cell killing efficacy, with highly efficient apoptosis induction. Assisted by the cationic polymeric carrier, it was evident from CLSM images that intracellular delivery of the therapeutic protein significantly depleted the RNA level. Thus, this work provides a promising platform for the delivery of therapeutic proteins and chemotherapeutic drugs for efficient cancer treatment.
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Affiliation(s)
- Wei Qi Lim
- NTU-Northwestern Institute for Nanomedicine, Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Soo Zeng Fiona Phua
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Yanli Zhao
- NTU-Northwestern Institute for Nanomedicine, Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
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Shimo HM, Terassi C, Lima Silva CC, Zanella JDL, Mercaldi GF, Rocco SA, Benedetti CE. Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance. Mol Plant Pathol 2019; 20:1105-1118. [PMID: 31115151 PMCID: PMC6640180 DOI: 10.1111/mpp.12815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Poly(A) tail shortening is a critical step in messenger RNA (mRNA) decay and control of gene expression. The carbon catabolite repressor 4 (CCR4)-associated factor 1 (CAF1) component of the CCR4-NOT deadenylase complex plays an essential role in mRNA deadenylation in most eukaryotes. However, while CAF1 has been extensively investigated in yeast and animals, its role in plants remains largely unknown. Here, we show that the Citrus sinensis CAF1 (CsCAF1) is a magnesium-dependent deadenylase implicated in resistance against the citrus canker bacteria Xanthomonas citri. CsCAF1 interacted with proteins of the CCR4-NOT complex, including CsVIP2, a NOT2 homologue, translin-associated factor X (CsTRAX) and the poly(A)-binding proteins CsPABPN and CsPABPC. CsCAF1 also interacted with PthA4, the main X. citri effector required for citrus canker elicitation. We also present evidence suggesting that PthA4 inhibits CsCAF1 deadenylase activity in vitro and stabilizes the mRNA encoded by the citrus canker susceptibility gene CsLOB1, which is transcriptionally activated by PthA4 during canker formation. Moreover, we show that an inhibitor of CsCAF1 deadenylase activity significantly enhanced canker development, despite causing a reduction in PthA4-dependent CsLOB1 transcription. These results thus link CsCAF1 with canker development and PthA4-dependent transcription in citrus plants.
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Affiliation(s)
- Hugo Massayoshi Shimo
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Carolina Terassi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Caio Cesar Lima Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Silvana Aparecida Rocco
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
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28
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Song H, Feng X, Zhang H, Luo Y, Huang J, Lin M, Jin J, Ding X, Wu S, Huang H, Yu T, Zhang M, Hong H, Yao S, Zhao Y, Zhang Z. METTL3 and ALKBH5 oppositely regulate m 6A modification of TFEB mRNA, which dictates the fate of hypoxia/reoxygenation-treated cardiomyocytes. Autophagy 2019; 15:1419-1437. [PMID: 30870073 PMCID: PMC6613905 DOI: 10.1080/15548627.2019.1586246] [Citation(s) in RCA: 294] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/25/2019] [Accepted: 02/07/2019] [Indexed: 01/19/2023] Open
Abstract
N6-methyladenosine (m6A) mRNA modifications play critical roles in various biological processes. However, no study addresses the role of m6A in macroautophagy/autophagy. Here, we show that m6A modifications are increased in H/R-treated cardiomyocytes and ischemia/reperfusion (I/R)-treated mice heart. We found that METTL3 (methyltransferase like 3) is the primary factor involved in aberrant m6A modification. Silencing METTL3 enhances autophagic flux and inhibits apoptosis in H/R-treated cardiomyocytes. However, overexpression of METTL3 or inhibition of the RNA demethylase ALKBH5 has an opposite effect, suggesting that METTL3 is a negative regulator of autophagy. Mechanistically, METTL3 methylates TFEB, a master regulator of lysosomal biogenesis and autophagy genes, at two m6A residues in the 3'-UTR, which promotes the association of the RNA-binding protein HNRNPD with TFEB pre-mRNA and subsequently decreases the expression levels of TFEB. Further experiments show that autophagic flux enhanced by METTL3 deficiency is TFEB dependent. In turn, TFEB regulates the expression levels of METTL3 and ALKBH5 in opposite directions: it induces ALKBH5 and inhibits METTL3. TFEB binds to the ALKBH5 promoter and activates its transcription. In contrast, inhibition of METTL3 by TFEB does not involve transcriptional repression but rather downregulation of mRNA stability, thereby establishing a negative feedback loop. Together, our work uncovers a critical link between METTL3-ALKBH5 and autophagy, providing insight into the functional importance of the reversible mRNA m6A methylation and its modulators in ischemic heart disease. Abbreviations: ACTB, actin beta; ALKBH5, alkB homolog 5, RNA demethylase; ANXA5, annexin A5; ATG, autophagy-related; BafA, bafilomycin A1; CASP3, caspase 3; ELAVL1, ELAV like RNA binding protein 1; FTO, FTO, alpha-ketoglutarate dependent dioxygenase; GFP, green fluorescent protein; GST, glutathione S-transferase; HNRNPD, heterogeneous nuclear ribonucleoprotein D; H/R, hypoxia/reoxygenation; I/R, ischemia/reperfusion; LAD, left anterior descending; m6A, N6-methyladenosine; MEFs, mouse embryo fibroblasts; Mer, mutated estrogen receptor domains; METTL3, methyltransferase like 3; METTL14, methyltransferase like 14; mRFP, monomeric red fluorescent protein; MTORC1, mechanistic target of rapamycin kinase complex 1; NMVCs, neonatal mouse ventricular cardiomyocytes; PCNA, proliferating cell nuclear antigen; PE, phosphatidylethanolamine; PI, propidium iodide; PTMs, post-translational modifications; PVDF, polyvinylidenedifluoride; RIP, RNA-immunoprecipitation; siRNA, small interfering RNA; SQSTM1, sequestosome 1; TFEB, transcription factor EB; TUBA: tublin alpha; WTAP, WT1 associated protein; YTHDF, YTH N6-methyladenosine RNA binding protein.
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Affiliation(s)
- Huiwen Song
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Feng
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Heng Zhang
- Department of Histology and Embryology, Xiang Ya School of Medicine, Central South University, Changsha, China
| | - Yunmei Luo
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Juan Huang
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Meihua Lin
- Research Center of Clinical Pharmacy, State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Junfei Jin
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xue Ding
- Department of Cardiology; the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shujing Wu
- Department of Cardiology, The ChengGong Hospital Affiliated to Xiamen University, Xiamen, China
| | - He Huang
- Department of Histology and Embryology, Xiang Ya School of Medicine, Central South University, Changsha, China
- Digestive Cancer Laboratory, Second Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Tian Yu
- Department of Anesthesia, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Mukun Zhang
- Health Management Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China
| | - Haiou Hong
- Health Management Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China
| | - Shihua Yao
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yongxiang Zhao
- National Center for International Research of Biological Targeting Diagnosis and Therapy (Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research), Guangxi Medical University, Nanning, China
| | - Zhiyong Zhang
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Department of Surgery; Robert-Wood-Johnson Medical School University Hospital, Rutgers University, State University of New Jersey, New Brunswick, NJ USA
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Bjune K, Wierød L, Naderi S. Inhibitors of AKT kinase increase LDL receptor mRNA expression by two different mechanisms. PLoS One 2019; 14:e0218537. [PMID: 31216345 PMCID: PMC6583949 DOI: 10.1371/journal.pone.0218537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/04/2019] [Indexed: 11/19/2022] Open
Abstract
Protein kinase B (AKT) is a serine/threonine kinase that functions as an important downstream effector of phosphoinositide 3-kinase. We have recently shown that MK-2206 and triciribine, two highly selective AKT inhibitors increase the level of low density lipoprotein receptor (LDLR) mRNA which leads to increased amount of cell-surface LDLRs. However, whereas MK-2206 induces transcription of the LDLR gene, triciribine stabilizes LDLR mRNA, raising the possibility that the two inhibitors may actually affect other kinases than AKT. In this study, we aimed to ascertain the role of AKT in regulation of LDLR mRNA expression by examining the effect of five additional AKT inhibitors on LDLR mRNA levels. Here we show that in cultured HepG2 cells, AKT inhibitors ARQ-092, AKT inhibitor VIII, perifosine, AT7867 and CCT128930 increase LDLR mRNA levels by inducing the activity of LDLR promoter. CCT128930 also increased the stability of LDLR mRNA. To study the role of AKT isoforms on LDLR mRNA levels, we examined the effect of siRNA-mediated knockdown of AKT1 or AKT2 on LDLR promoter activity and LDLR mRNA stability. Whereas knockdown of either AKT1 or AKT2 led to upregulation of LDLR promoter activity, only knockdown of AKT2 had a stabilizing effect on LDLR mRNA. Taken together, these results provide strong evidence for involvement of AKT in regulation of LDLR mRNA expression, and point towards the AKT isoform specificity for upregulation of LDLR mRNA expression.
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Affiliation(s)
- Katrine Bjune
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- * E-mail:
| | - Lene Wierød
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Soheil Naderi
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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Tian Z, Luo Y, Zhu J, Hua X, Xu J, Huang C, Jin H, Huang H, Huang C. Transcriptionally elevation of miR-494 by new ChlA-F compound via a HuR/JunB axis inhibits human bladder cancer cell invasion. Biochim Biophys Acta Gene Regul Mech 2019; 1862:822-833. [PMID: 31167152 DOI: 10.1016/j.bbagrm.2019.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/08/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023]
Abstract
Muscle invasive bladder cancer (MIBC) is characterized by a poor overall survival rate in patients. Therefore, innovation and evaluation of idea anti-cancer compounds is of importance for reducing the mortality of MIBCs. The chemotherapeutic activity of ChlA-F, a novel C8 fluoride derivative of cheliensisin A with potent anti-neoplastic properties, was barely investigated. We reported here that ChlA-F treatment significantly induced miR-494 expression and suppressed cell invasion in human MIBC cells. Our results indicated that miR-494 was downregulated in M1 metastatic BC patients in comparison to non-metastatic (M0) BC patients, and such downregulation was also well correlated with over survival rate for MIBC patients. Mechanistically, ChlA-F-induced upregulation of miR-494 was due to a HuR-mediated increase in JunB mRNA stabilization and protein expression, which led to an increase in miR-494 transcription via directly binding to the miR-494 promoter region, while the upregulated miR-494 was able to bind the 3'-UTR region of c-Myc mRNA, resulting in decreased c-Myc mRNA stability and protein expression and further reducing the transcription of c-Myc-regulated MMP-2 and ultimately inhibiting BC invasion. Our results provide the first evidence showing that miR-494 downregulation was closely associated with BC metastatic status and overall BC survival, and ChlA-F was able to reverse the level of miR-494 with a profound inhibition of human BC invasion in human invasive BC cells. Our studies also reveal that ChlA-F is a promising therapeutic compound for BCs and miR-494 could also serve as a promising therapeutic target for the treatment of MIBC patients.
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Affiliation(s)
- Zhongxian Tian
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yisi Luo
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Junlan Zhu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Xiaohui Hua
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Jiheng Xu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Chao Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China.
| | - Chuanshu Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
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Mazloomian A, Araki S, Ohori M, El-Naggar AM, Yap D, Bashashati A, Nakao S, Sorensen PH, Nakanishi A, Shah S, Aparicio S. Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation. Commun Biol 2019; 2:165. [PMID: 31069274 PMCID: PMC6499833 DOI: 10.1038/s42003-019-0391-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
The RNA helicase EIF4A3 regulates the exon junction complex and nonsense-mediated mRNA decay functions in RNA transcript processing. However, a transcriptome-wide network definition of these functions has been lacking, in part due to the lack of suitable pharmacological inhibitors. Here we employ short-duration graded EIF4A3 inhibition using small molecule allosteric inhibitors to define the transcriptome-wide dependencies of EIF4A3. We thus define conserved cellular functions, such as cell cycle control, that are EIF4A3 dependent. We show that EIF4A3-dependent splicing reactions have a distinct genome-wide pattern of associated RNA-binding protein motifs. We also uncover an unanticipated role of EIF4A3 in the biology of RNA stress granules, which sequester and silence the translation of most mRNAs under stress conditions and are implicated in cell survival and tumour progression. We show that stress granule induction and maintenance is suppressed on the inhibition of EIF4A3, in part through EIF4A3-associated regulation of G3BP1 and TIA1 scaffold protein expression.
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Affiliation(s)
- Alborz Mazloomian
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shinsuke Araki
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Momoko Ohori
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shoichi Nakao
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Atsushi Nakanishi
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Sohrab Shah
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 417 E68th St, New York, NY 10065 USA
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
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Abstract
The therapeutic pathways that modulate transcription mechanisms currently include gene knockdown and splicing modulation. However, additional mechanisms may come into play as more understanding of molecular biology and disease etiology emerge. Building on advances in chemistry and delivery technology, oligonucleotide therapeutics is emerging as an established, validated class of drugs that can modulate a multitude of genetic targets. These targets include over 10,000 proteins in the human genome that have hitherto been considered undruggable by small molecules and protein therapeutics. The approval of five oligonucleotides within the last 2 years elicited unprecedented excitement in the field. However, there are remaining challenges to overcome and significant room for future innovation to fully realize the potential of oligonucleotide therapeutics. In this review, we focus on the translational strategies encompassing preclinical evaluation and clinical development in the context of approved oligonucleotide therapeutics. Translational approaches with respect to pharmacology, pharmacokinetics, cardiac safety evaluation, and dose selection that are specific to this class of drugs are reviewed with examples. The mechanism of action, chemical evolution, and intracellular delivery of oligonucleotide therapies are only briefly reviewed to provide a general background for this class of drugs.
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MESH Headings
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/pharmacokinetics
- Clinical Trials as Topic
- Drug Approval
- Drug Delivery Systems/methods
- Drug Evaluation, Preclinical
- Gene Expression Regulation/drug effects
- Genetic Therapy/methods
- Humans
- Oligoribonucleotides, Antisense/administration & dosage
- Oligoribonucleotides, Antisense/genetics
- Oligoribonucleotides, Antisense/pharmacokinetics
- RNA Interference
- RNA Stability/drug effects
- RNA, Messenger/agonists
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacokinetics
- Transcription, Genetic/drug effects
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Affiliation(s)
- Wei Yin
- Quantitative Clinical PharmacologyTakeda Pharmaceutical Company LtdCambridgeMassachusettsUSA
| | - Mark Rogge
- Quantitative Clinical PharmacologyTakeda Pharmaceutical Company LtdCambridgeMassachusettsUSA
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Lai WS, Arvola RM, Goldstrohm AC, Blackshear PJ. Inhibiting transcription in cultured metazoan cells with actinomycin D to monitor mRNA turnover. Methods 2019; 155:77-87. [PMID: 30625384 DOI: 10.1016/j.ymeth.2019.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 11/16/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
Decay of transcribed mRNA is a key determinant of steady state mRNA levels in cells. Global analysis of mRNA decay in cultured cells has revealed amazing heterogeneity in rates of decay under normal growth conditions, with calculated half-lives ranging from several minutes to many days. The factors that are responsible for this wide range of decay rates are largely unknown, although our knowledge of trans-acting RNA binding proteins and non-coding RNAs that can control decay rates is increasing. Many methods have been used to try to determine mRNA decay rates under various experimental conditions in cultured cells, and transcription inhibitors like actinomycin D have probably the longest history of any technique for this purpose. Despite this long history of use, the actinomycin D method has been criticized as prone to artifacts, and as ineffective for some promoters. With appropriate guidelines and controls, however, it can be a versatile, effective technique for measuring endogenous mRNA decay in cultured mammalian and insect cells, as well as the decay of exogenously-expressed transcripts. It can be used readily on a genome-wide level, and is remarkably cost-effective. In this short review, we will discuss our utilization of this approach in these cells; we hope that these methods will allow more investigators to apply this useful technique to study mRNA decay under the appropriate conditions.
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Affiliation(s)
- Wi S Lai
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Rene M Arvola
- The Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Aaron C Goldstrohm
- The Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Perry J Blackshear
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States; The Departments of Medicine and Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States.
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Hua X, Xu J, Deng X, Xu J, Li J, Zhu DQ, Zhu J, Jin H, Tian Z, Huang H, Zhao QS, Huang C. New compound ChlA-F induces autophagy-dependent anti-cancer effect via upregulating Sestrin-2 in human bladder cancer. Cancer Lett 2018; 436:38-51. [PMID: 30118841 PMCID: PMC6245652 DOI: 10.1016/j.canlet.2018.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 08/09/2018] [Indexed: 12/19/2022]
Abstract
ChlA-F is a novel conformation-derivative of Cheliensisin A, styryl-lactone isolates that show potent anti-tumor potential in vivo and vitro. However, the anti-cancer activity and its potential mechanisms underlying ChlA-F action have never been explored. In the present study, we evaluated the potency of ChlA-F on autophagy-mediated anchorage-independent growth inhibition in human high-grade invasive bladder cancer (BC) cells. We found that ChlA-F treatment significantly inhibited anchorage-independent growth of human BC cells by inducing autophagy in a Sestrin-2 (SESN2)-dependent fashion. Our results revealed that ChlA-F treatment specifically induced SESN2 expression via increasing its transcription and mRNA stability. On one hand, ChlA-F treatment markedly attenuated Dicer protein abundance, in turn abolishing miR-27a maturation and further relieving miR-27a binding directly to SESN2 mRNA 3'UTR, thereby promoting SESN2 mRNA stabilization. On the other hand, ChlA-F treatment promoted Sp1 abundance and consequently mediated SESN2 transcription. These results demonstrate that its activation of the autophagic pathway through specifically promoting SESN2 expression mediates the anti-cancer effect of ChlA-F, which offers insights into the novel anti-cancer effect of ChlA-F on BC, as well as providing therapeutic alternatives against human BC.
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Affiliation(s)
- Xiaohui Hua
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - Jiheng Xu
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xu Deng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Jiawei Xu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - Jingxia Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - David Q Zhu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - Junlan Zhu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhongxian Tian
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qin-Shi Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.
| | - Chuanshu Huang
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY, 10987, USA.
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Cheruiyot A, Li S, Nickless A, Roth R, Fitzpatrick JAJ, You Z. Compound C inhibits nonsense-mediated RNA decay independently of AMPK. PLoS One 2018; 13:e0204978. [PMID: 30289931 PMCID: PMC6173407 DOI: 10.1371/journal.pone.0204978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
The nonsense mediated RNA decay (NMD) pathway safeguards the integrity of the transcriptome by targeting mRNAs with premature translation termination codons (PTCs) for degradation. It also regulates gene expression by degrading a large number of non-mutant RNAs (including mRNAs and noncoding RNAs) that bear NMD-inducing features. Consequently, NMD has been shown to influence development, cellular response to stress, and clinical outcome of many genetic diseases. Small molecules that can modulate NMD activity provide critical tools for understanding the mechanism and physiological functions of NMD, and they also offer potential means for treating certain genetic diseases and cancer. Therefore, there is an intense interest in identifying small-molecule NMD inhibitors or enhancers. It was previously reported that both inhibition of NMD and treatment with the AMPK-selective inhibitor Compound C (CC) induce autophagy in human cells, raising the possibility that CC may be capable of inhibiting NMD. Here we show that CC indeed has a NMD-inhibitory activity. Inhibition of NMD by CC is, however, independent of AMPK activity. As a competitive ATP analog, CC does not affect the kinase activity of SMG1, an essential NMD factor and the only known kinase in the NMD pathway. However, CC treatment down-regulates the protein levels of several NMD factors. The induction of autophagy by CC treatment is independent of ATF4, a NMD target that has been shown to promote autophagy in response to NMD inhibition. Our results reveal a new activity of CC as a NMD inhibitor, which has implications for its use in basic research and drug development.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shan Li
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew Nickless
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robyn Roth
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James A. J. Fitzpatrick
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biomedical Engineering Washington University, St. Louis, Missouri, United States of America
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zhongsheng You
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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36
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Liao Y, Zhou X, Fu Y, Xing D. Graphene Oxide as a Bifunctional Material toward Superior RNA Protection and Extraction. ACS Appl Mater Interfaces 2018; 10:30227-30234. [PMID: 30129746 DOI: 10.1021/acsami.8b12522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
It is well known that graphene oxide (GO), a planar nanomaterial, is endowed with the capacity to immobilize short ssRNA via π-π stacking, thus enhancing its stability. However, whether large RNA molecules, such as total RNA, extracted from biological tissues can be protected using GO has not been investigated. It is usually believed that the protection of total RNA by GO is not effective because the lengths of total RNA, which range from a few to thousands of bases, are inclined to undergo desorption due to their complicated structure. Herein, the nanobiological effects of total RNA/GO are first investigated and demonstrate that the total RNA can be harbored on the surface of GO, thus resulting in a shield effect. This shield effect allows total RNA to highly resist RNase degradation and maintain RNA stability at room temperature up to 4 days, enabling the discovery of GO as the potential next-generation RNase nanoinhibitor. Furthermore, GO can be conjugated to nanomagnetic beads, defined as magnetic graphene oxide, enabling the rapid purification and protection of RNA from animal cells and tissues, whole blood, bacteria, and plant tissue.
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Affiliation(s)
- Yuhui Liao
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Yu Fu
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
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Zheng D, Wang R, Ding Q, Wang T, Xie B, Wei L, Zhong Z, Tian B. Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. Nat Commun 2018; 9:2268. [PMID: 29891946 PMCID: PMC5995920 DOI: 10.1038/s41467-018-04730-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
Most eukaryotic genes express alternative polyadenylation (APA) isoforms with different 3'UTR lengths, production of which is influenced by cellular conditions. Here, we show that arsenic stress elicits global shortening of 3'UTRs through preferential usage of proximal polyadenylation sites during stress and enhanced degradation of long 3'UTR isoforms during recovery. We demonstrate that RNA-binding protein TIA1 preferentially interacts with alternative 3'UTR sequences through U-rich motifs, correlating with stress granule association and mRNA decay of long 3'UTR isoforms. By contrast, genes with shortened 3'UTRs due to stress-induced APA can evade mRNA clearance and maintain transcript abundance post stress. Furthermore, we show that stress causes distinct 3'UTR size changes in proliferating and differentiated cells, highlighting its context-specific impacts on the 3'UTR landscape. Together, our data reveal a global, 3'UTR-based mRNA stability control in stressed cells and indicate that APA can function as an adaptive mechanism to preserve mRNAs in response to stress.
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Affiliation(s)
- Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Qingbao Ding
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Tianying Wang
- Department of Microbiology, Harbin Medical University, Harbin,, 150081, China
| | - Bingning Xie
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Lu Wei
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin,, 150081, China
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA.
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Habiba U, Kuroshima T, Yanagawa-Matsuda A, Kitamura T, Chowdhury A, Jehung JP, Hossain E, Sano H, Kitagawa Y, Shindoh M, Higashino F. HuR translocation to the cytoplasm of cancer cells in actin-independent manner. Exp Cell Res 2018; 369:218-225. [PMID: 29807023 DOI: 10.1016/j.yexcr.2018.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/05/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Human antigen R (HuR) is a RNA-binding protein, which binds to the AU-rich element (ARE) in the 3'-untranslated region (3'-UTR) of certain mRNA and is involved in the export and stabilization of ARE-mRNA. HuR constitutively relocates to the cytoplasm in many cancer cells, however the mechanism of intracellular HuR trafficking is poorly understood. To address this question, we examined the functional role of the cytoskeleton in HuR relocalization. We tested the effect of actin depolymerizing macrolide latrunculin A or myosin II ATPase activity inhibitor blebbistatin for HuR relocalization induced by the vasoactive hormone Angiotensin II in cancer and control normal cells. Western blot and confocal imaging data revealed that both inhibitors attenuated the cytoplasmic HuR in normal cells but no such alteration was observed in cancer cells. Concomitant with changes in intracellular HuR localization, both inhibitors markedly decreased the accumulation and half-lives of HuR target ARE-mRNAs in normal cells, whereas no change was observed in cancer cells. Furthermore, co-immunoprecipitation experiments with HuR proteins revealed clear physical interaction with ß-actin only in normal cells. The current study is the first to verify that cancer cells can implicate a microfilament independent HuR transport. We hypothesized that when cytoskeleton structure is impaired, cancer cells can acquire an alternative HuR trafficking strategy.
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Affiliation(s)
- Umma Habiba
- Department of Oral Pathology and Biology, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Takeshi Kuroshima
- Department of Oral Diagnosis and Medicine, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Aya Yanagawa-Matsuda
- Department of Oral Pathology and Biology, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Tetsuya Kitamura
- Department of Oral Pathology and Biology, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Afma Chowdhury
- Department of Restorative Dentistry, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Jumond P Jehung
- Department of Restorative Dentistry, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Elora Hossain
- Department of Molecular Oncology, Hokkaido University Faculty of Dental Medicine and Graduate School of Biomedical Science and Engineering, 060-8586,North 13, West 7, Kita ku, Sapporo, Japan
| | - Hidehiko Sano
- Department of Restorative Dentistry, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Yoshimasa Kitagawa
- Department of Oral Diagnosis and Medicine, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Masanobu Shindoh
- Department of Oral Pathology and Biology, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan
| | - Fumihiro Higashino
- Department of Oral Pathology and Biology, Hokkaido University Faculty of Dental Medicine and Graduate School of Dental Medicine, Sapporo, Japan; Department of Molecular Oncology, Hokkaido University Faculty of Dental Medicine and Graduate School of Biomedical Science and Engineering, 060-8586,North 13, West 7, Kita ku, Sapporo, Japan.
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Zou J, Wang N, Liu M, Bai Y, Wang H, Liu K, Zhang H, Xiao X, Wang K. Nucleolin mediated pro-angiogenic role of Hydroxysafflor Yellow A in ischaemic cardiac dysfunction: Post-transcriptional regulation of VEGF-A and MMP-9. J Cell Mol Med 2018; 22:2692-2705. [PMID: 29512890 PMCID: PMC5908102 DOI: 10.1111/jcmm.13552] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/02/2018] [Indexed: 01/22/2023] Open
Abstract
Hydroxysafflor Yellow A (HSYA), a most representative ingredient of Carthamus tinctorius L., had long been used in treating ischaemic cardiovascular diseases in China and exhibited prominently anticoagulant and pro-angiogenic activities, but the underlying mechanisms remained largely unknown. This study aimed to further elucidate the pro-angiogenic effect and mechanism of HSYA on ischaemic cardiac dysfunction. A C57 mouse model of acute myocardial infarction (AMI) was firstly established, and 25 mg/kg HSYA was intraperitoneally injected immediately after operation and given once, respectively, each morning and evening for 2 weeks. It was found that HSYA significantly improved ischaemia-induced cardiac haemodynamics, enhanced the survival rate, alleviated the myocardial injury and increased the expressions of CD31, vascular endothelial growth factor-A (VEGF-A) and nucleolin in the ischaemic myocardium. In addition, HSYA promoted the migration and tube formation of human umbilical vein endothelial cells (HUVECs), enhanced the expressions of nucleolin, VEGF-A and matrix metalloproteinase-9 (MMP-9) in a dose- and time-dependent manner. However, down-regulation of nucleolin expression sharply abrogated the effect mentioned above of HSYA. Further protein-RNA coimmunoprecipitation and immunoprecipitation-RT-PCR assay showed that nucleolin binded to VEGF-A and MMP-9 mRNA and overexpression of nucleolin up-regulated the mRNA expressions of VEGF-A and MMP-9 in the HUVECs through enhancing the stability of VEGF-A and MMP-9 mRNA. Furthermore, HSYA increased the mRNA expressions of VEGF-A and MMP-9 in the extract of antinucleolin antibody-precipitated protein from the heart of AMI mice. Our data revealed that nucleolin mediated the pro-angiogenic effect of HSYA through post-transcriptional regulation of VEGF-A and MMP-9 expression, which contributed to the protective effect of HSYA on ischaemic cardiac dysfunction.
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Affiliation(s)
- Jiang Zou
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Nian Wang
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Manting Liu
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Yongping Bai
- Department of Geriatric MedicineXiangya HospitalCentral South UniversityChangshaChina
| | - Hao Wang
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Ke Liu
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Huali Zhang
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Xianzhong Xiao
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
| | - Kangkai Wang
- Department of PathophysiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Translational Medicine Center of SepsisKey Lab of Hunan ProvinceCentral South UniversityChangshaChina
- Department of Laboratory AnimalsXiangya School of MedicineCentral South UniversityChangshaChina
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40
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Berger AK, Yi H, Kearns DB, Mainou BA. Bacteria and bacterial envelope components enhance mammalian reovirus thermostability. PLoS Pathog 2017; 13:e1006768. [PMID: 29211815 PMCID: PMC5734793 DOI: 10.1371/journal.ppat.1006768] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/18/2017] [Accepted: 11/23/2017] [Indexed: 12/24/2022] Open
Abstract
Enteric viruses encounter diverse environments as they migrate through the gastrointestinal tract to infect their hosts. The interaction of eukaryotic viruses with members of the host microbiota can greatly impact various aspects of virus biology, including the efficiency with which viruses can infect their hosts. Mammalian orthoreovirus, a human enteric virus that infects most humans during childhood, is negatively affected by antibiotic treatment prior to infection. However, it is not known how components of the host microbiota affect reovirus infectivity. In this study, we show that reovirus virions directly interact with Gram positive and Gram negative bacteria. Reovirus interaction with bacterial cells conveys enhanced virion thermostability that translates into enhanced attachment and infection of cells following an environmental insult. Enhanced virion thermostability was also conveyed by bacterial envelope components lipopolysaccharide (LPS) and peptidoglycan (PG). Lipoteichoic acid and N-acetylglucosamine-containing polysaccharides enhanced virion stability in a serotype-dependent manner. LPS and PG also enhanced the thermostability of an intermediate reovirus particle (ISVP) that is associated with primary infection in the gut. Although LPS and PG alter reovirus thermostability, these bacterial envelope components did not affect reovirus utilization of its proteinaceous cellular receptor junctional adhesion molecule-A or cell entry kinetics. LPS and PG also did not affect the overall number of reovirus capsid proteins σ1 and σ3, suggesting their effect on virion thermostability is not mediated through altering the overall number of major capsid proteins on the virus. Incubation of reovirus with LPS and PG did not significantly affect the neutralizing efficiency of reovirus-specific antibodies. These data suggest that bacteria enhance reovirus infection of the intestinal tract by enhancing the thermal stability of the reovirus particle at a variety of temperatures through interactions between the viral particle and bacterial envelope components.
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Affiliation(s)
- Angela K. Berger
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Hong Yi
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia, United States of America
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Bernardo A. Mainou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
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Zhou T, Block T, Liu F, Kondratowicz AS, Sun L, Rawat S, Branson J, Guo F, Steuer HM, Liang H, Bailey L, Moore C, Wang X, Cuconatti A, Gao M, Lee ACH, Harasym T, Chiu T, Gotchev D, Dorsey B, Rijnbrand R, Sofia MJ. HBsAg mRNA degradation induced by a dihydroquinolizinone compound depends on the HBV posttranscriptional regulatory element. Antiviral Res 2017; 149:191-201. [PMID: 29133129 DOI: 10.1016/j.antiviral.2017.11.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/01/2017] [Accepted: 11/07/2017] [Indexed: 12/23/2022]
Abstract
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that in the nanomolar range reduced the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage, but was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a significant reduction of serum HBsAg as soon as 4 days following the commencement of treatment. Reduction of HBV markers in both in vitro and in vivo experiments was related to the reduced amount of viral RNA including pre-genomic RNA (pgRNA) and 2.4/2.1 kb HBsAg mRNA. Nuclear run-on and subcellular fractionation experiments indicated that DHQ-1 mediated HBV RNA reduction was the result of accelerated viral RNA degradation in the nucleus, rather than the consequence of inhibition of transcription initiation. Through mutagenesis of HBsAg gene sequences, we found induction of HBsAg mRNA decay by DHQ-1 required the presence of the HBV posttranscriptional regulatory element (HPRE), with a 109 nucleotides sequence within the central region of the HPRE alpha sub-element being the most critical. Taken together, the current study shows that a small molecule can reduce the overall levels of HBV RNA, especially the HBsAg mRNA, and viral surface proteins. This may shed light on the development of a new class of HBV therapeutics.
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Affiliation(s)
- Tianlun Zhou
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States.
| | - Timothy Block
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fei Liu
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andrew S Kondratowicz
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Liren Sun
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Siddhartha Rawat
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Jeffrey Branson
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fang Guo
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | | | - Hongyan Liang
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Lauren Bailey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Chris Moore
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Xiaohe Wang
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andy Cuconatti
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Min Gao
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Amy C H Lee
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Troy Harasym
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Tim Chiu
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Dimitar Gotchev
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Bruce Dorsey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Rene Rijnbrand
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Michael J Sofia
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States.
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Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BM, Aronin N, Khvorova A. 5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res 2017; 45:7581-7592. [PMID: 28591791 PMCID: PMC5570069 DOI: 10.1093/nar/gkx507] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.
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Affiliation(s)
- Reka A. Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Andrew H. Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anton A. Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Department of Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
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Tani H, Okuda S, Nakamura K, Aoki M, Umemura T. Short-lived long non-coding RNAs as surrogate indicators for chemical exposure and LINC00152 and MALAT1 modulate their neighboring genes. PLoS One 2017; 12:e0181628. [PMID: 28719640 PMCID: PMC5515456 DOI: 10.1371/journal.pone.0181628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although accumulating evidence demonstrates that lncRNAs play important roles in regulating gene expression, the detailed mechanisms of action of most lncRNAs remain unclear. We previously reported that a novel class of lncRNAs with a short half-life (t1/2 < 4 h) in HeLa cells, termed short-lived non-coding transcripts (SLiTs), are closely associated with physiological and pathological functions. In this study, we focused on 26 SLiTs and nuclear-enriched abundant lncRNA, MALAT1(t1/2 of 7.6 h in HeLa cells) in neural stem cells (NSCs) derived from human induced pluripotent stem cells, and identified four SLiTs (TUG1, GAS5, FAM222-AS1, and SNHG15) that were affected by the following typical chemical stresses (oxidative stress, heavy metal stress and protein synthesis stress). We also found the expression levels of LINC00152 (t1/2 of 2.1 h in NSCs), MALAT1 (t1/2 of 1.8 h in NSCs), and their neighboring genes were elevated proportionally to the chemical doses. Moreover, we confirmed that the overexpression of LINC00152 or MALAT1 upregulated the expressions of their neighboring genes even in the absence of chemical stress. These results reveal that LINC00152 and MALAT1 modulate their neighboring genes, and thus provide a deeper understanding of the functions of lncRNAs.
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Affiliation(s)
- Hidenori Tani
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Sayaka Okuda
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki, Japan
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo, Japan
| | - Kaoru Nakamura
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki, Japan
| | - Motohide Aoki
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo, Japan
| | - Tomonari Umemura
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo, Japan
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Loupasakis K, Kuo D, Sokhi UK, Sohn C, Syracuse B, Giannopoulou EG, Park SH, Kang H, Rätsch G, Ivashkiv LB, Kalliolias GD. Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes. PLoS One 2017; 12:e0179762. [PMID: 28708839 PMCID: PMC5510804 DOI: 10.1371/journal.pone.0179762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 06/02/2017] [Indexed: 12/29/2022] Open
Abstract
During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches and becomes dominated by very stable transcripts. This temporal switch is due to: a) TNF-induced prolonged stabilization of previously unstable transcripts that enables progressive transcript accumulation over days and b) sustained expression and late induction of very stable transcripts. TNF-induced mRNA stabilization in RA FLS occurs during the late phase of TNF response, is MAPK-dependent, and involves several genes with pathogenic potential such as IL6, CXCL1, CXCL3, CXCL8/IL8, CCL2, and PTGS2. These results provide the first insights into genome-wide regulation of mRNA stability in RA FLS and highlight the potential contribution of dynamic regulation of the mRNA stabilome by TNF to chronic synovitis.
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Affiliation(s)
- Konstantinos Loupasakis
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - David Kuo
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, United States of America
- Computational Biology Program, Sloan Kettering Institute, New York, United States of America
| | - Upneet K. Sokhi
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Christopher Sohn
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Bethany Syracuse
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Eugenia G. Giannopoulou
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, United States of America
| | - Sung Ho Park
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Hyelim Kang
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, United States of America
| | - Gunnar Rätsch
- Computational Biology Program, Sloan Kettering Institute, New York, United States of America
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Lionel B. Ivashkiv
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - George D. Kalliolias
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
- * E-mail:
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45
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Chakraborty A, Mukherjee S, Saha S, De S, Sengupta Bandyopadhyay S. Phorbol-12-myristate-13-acetate-mediated stabilization of leukemia inhibitory factor ( lif) mRNA: involvement of Nucleolin and PCBP1. Biochem J 2017; 474:2349-2363. [PMID: 28512205 DOI: 10.1042/bcj20170051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/06/2017] [Accepted: 05/15/2017] [Indexed: 01/09/2023]
Abstract
Leukemia inhibitory factor (LIF) is a potent pleiotropic cytokine involved in diverse biological activities, thereby requiring precise spatial and temporal control of its expression. The present study reveals that enhanced expression of LIF in response to PMA (phorbol-12-myristate-13-acetate) in human histiocytic lymphoma cell line U937 largely happens through stabilization of its mRNA. Functional characterization of the long 3'-untranslated region of human lif mRNA revealed several conserved sequences with conventional cis-acting elements. A 216 nucleotide containing proximal cis-element with two AUUUA pentamers and four poly-rC sequences demonstrated significant mRNA destabilizing potential, which, on treatment with PMA, showed stabilizing activity. Affinity chromatography followed by western blot and RNA co-immunoprecipitation of PMA-treated U937 extract identified Nucleolin and PCBP1 as two protein trans-factors interacting with lif mRNA, specifically to the proximal non-conventional AU-rich region. PMA induced nucleo-cytoplasmic translocation of both Nucleolin and PCBP1. RNA-dependent in vivo co-association of both these proteins with lif mRNA was demonstrated by decreased co-precipitation in the presence of RNase. Ectopic overexpression of Nucleolin showed stabilization of both intrinsic lif mRNA and gfp reporter, whereas knockdown of Nucleolin and PCBP1 demonstrated a significant decrease in both lif mRNA and protein levels. Collectively, this report establishes the stabilization of lif mRNA by PMA, mediated by the interactions of two RNA-binding proteins, Nucleolin and PCBP1 with a proximal cis-element.
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Affiliation(s)
- Alina Chakraborty
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Srimoyee Mukherjee
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sucharita Saha
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Soumasree De
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
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Tiwari R, Haque L, Bhuiya S, Das S. Third strand stabilization of poly(U)·poly(A)* poly(U) triplex by the naturally occurring flavone luteolin: A multi-spectroscopic approach. Int J Biol Macromol 2017; 103:692-700. [PMID: 28545966 DOI: 10.1016/j.ijbiomac.2017.05.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 01/17/2023]
Abstract
Naturally occurring flavonoid luteolin (LTN) was found to interact with double stranded poly(A).poly(U) and triple stranded poly(U)·poly(A)*poly(U) with association constants of the order of 104M-1. The association was monitored by various spectroscopic and viscometric techniques. Non-cooperative binding was observed for the association of LTN with two different polymorphic forms of RNA. Intercalation mode of binding was confirmed by fluorescence quenching and viscometric experiments. Thermal melting profiles indicated greater stabilization of the Hoogsteen base paired third strand (∼16°C) compared to Watson-Crick double strand (∼5°C) of RNA by LTN. Since the interaction of naturally occurring small molecules with RNA is an active area of research, this study has led to great openings to explore LTN as RNA targeted therapeutic agent.
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Affiliation(s)
- Richa Tiwari
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by CAG repeat expansion within exon1 of the HTT gene. The gene generates two mRNA variants that carry either a short or long 3' untranslated region (3'UTR) while encoding the same protein. It remains unknown whether the two mRNA variants play distinct roles in HD pathogenesis. We found that the long HTT 3'UTR was capable of guiding mRNA to neuronal dendrites, suggesting that some long-form HTT mRNA is transported to dendrites for local protein synthesis. To assay roles of two HTT mRNA variants in cell bodies, we expressed mRNA harboring HTT exon1 containing 23x or 145x CAGs with the short or long 3'UTR. We found that mutant mRNA containing the short 3'UTR produced more protein aggregates and caused more apoptosis in both cultured neurons and HEK293 cells, compared with mutant mRNA containing the long 3'UTR. Although the two 3'UTRs did not affect mRNA stability, we detected higher levels of protein synthesis from mRNA containing the short 3'UTR than from mRNA containing the long 3'UTR. These results indicate that the long HTT 3'UTR suppresses translation. Thus, short-form mutant HTT mRNA will be more efficient in producing toxic protein than its long-form counterpart.
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Affiliation(s)
- Haifei Xu
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida, United States of America
| | - Juan Ji An
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida, United States of America
| | - Baoji Xu
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, Florida, United States of America
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Zhong T, Men Y, Lu L, Geng T, Zhou J, Mitsuhashi A, Shozu M, Maihle NJ, Carmichael GG, Taylor HS, Huang Y. Metformin alters DNA methylation genome-wide via the H19/SAHH axis. Oncogene 2017; 36:2345-2354. [PMID: 27775072 PMCID: PMC5415944 DOI: 10.1038/onc.2016.391] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/23/2016] [Accepted: 09/12/2016] [Indexed: 02/08/2023]
Abstract
The molecular mechanisms underlying the antineoplastic properties of metformin, a first-line drug for type 2 diabetes, remain elusive. Here we report that metformin induces genome-wide alterations in DNA methylation by modulating the activity of S-adenosylhomocysteine hydrolase (SAHH). Exposing cancer cells to metformin leads to hypermethylation of tumor-promoting pathway genes and concomitant inhibition of cell proliferation. Metformin acts by upregulating microRNA let-7 through AMPK activation, leading to degradation of H19 long noncoding RNA, which normally binds to and inactivates SAHH. H19 knockdown activates SAHH, enabling DNA methyltransferase 3B to methylate a subset of genes. This metformin-induced H19 repression and alteration of gene methylation are recapitulated in endometrial cancer tissue samples obtained from patients treated with antidiabetic doses of metformin. Our findings unveil a novel mechanism of action for the drug metformin with implications for the molecular basis of epigenetic dysregulation in cancer. This novel mechanism of action also may be occurring in normal cells.
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Affiliation(s)
- T Zhong
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Y Men
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Head and Neck Surgery, State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - L Lu
- Department of Chronic Diseases Epidemiology, Yale School of Public Health, Yale University School of Medicine, New Haven, CT, USA
| | - T Geng
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Endocrinology, School of Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - J Zhou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - A Mitsuhashi
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - M Shozu
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - N J Maihle
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - G G Carmichael
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - H S Taylor
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Y Huang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
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Liu Y, Nie H, Mao R, Mitra B, Cai D, Yan R, Guo JT, Block TM, Mechti N, Guo H. Interferon-inducible ribonuclease ISG20 inhibits hepatitis B virus replication through directly binding to the epsilon stem-loop structure of viral RNA. PLoS Pathog 2017; 13:e1006296. [PMID: 28399146 PMCID: PMC5388505 DOI: 10.1371/journal.ppat.1006296] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/15/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a viral RNA pregenome. We report herein that the interferon (IFN) stimulated exoribonuclease gene of 20 KD (ISG20) inhibits HBV replication through degradation of HBV RNA. ISG20 expression was observed at basal level and was highly upregulated upon IFN treatment in hepatocytes, and knock down of ISG20 resulted in elevation of HBV replication and attenuation of IFN-mediated antiviral effect. The sequence element conferring the susceptibility of HBV RNA to ISG20-mediated RNA degradation was mapped at the HBV RNA terminal redundant region containing epsilon (ε) stem-loop. Furthermore, ISG20-induced HBV RNA degradation relies on its ribonuclease activity, as the enzymatic inactive form ISG20D94G was unable to promote HBV RNA decay. Interestingly, ISG20D94G retained antiviral activity against HBV DNA replication by preventing pgRNA encapsidation, resulting from a consequence of ISG20-ε interaction. This interaction was further characterized by in vitro electrophoretic mobility shift assay (EMSA) and ISG20 was able to bind HBV ε directly in absence of any other cellular proteins, indicating a direct ε RNA binding capability of ISG20; however, cofactor(s) may be required for ISG20 to efficiently degrade ε. In addition, the lower stem portion of ε is the major ISG20 binding site, and the removal of 4 base pairs from the bottom portion of ε abrogated the sensitivity of HBV RNA to ISG20, suggesting that the specificity of ISG20-ε interaction relies on both RNA structure and sequence. Furthermore, the C-terminal Exonuclease III (ExoIII) domain of ISG20 was determined to be responsible for interacting with ε, as the deletion of ExoIII abolished in vitro ISG20-ε binding and intracellular HBV RNA degradation. Taken together, our study sheds light on the underlying mechanisms of IFN-mediated HBV inhibition and the antiviral mechanism of ISG20 in general. HBV is a DNA virus but replicates its DNA via retrotranscription of a viral RNA pregenome. ISG20, an antiviral RNase induced by interferons, inhibits the replication of many RNA viruses but the underlying molecular antiviral mechanism remains elusive. Since all the known viruses, except for prions, have RNA products in their life cycles, ISG20 can be a broad spectrum antiviral protein; but in order to distinguish viral RNA from host RNA, ISG20 may have evolved to recognize virus-specific signals as its antiviral target. We demonstrated herein that ISG20 selectively binds to a unique stem-loop structure called epsilon (ε) in all HBV RNA species and degrades viral RNA to inhibit HBV replication. Because ε is the HBV pregenomic RNA packaging signal and reverse transcription priming site, the binding of ISG20 to ε, even in the absence of ribonuclease activity, results in antiviral effect to prevent DNA replication due to preventing viral polymerase binding to pgRNA. We also determined the structure and sequence requirements of ε RNA and ISG20 protein for ISG20-ε binding and antiviral activity. Such information will aid the function study of ISG20 against viral pathogens in host innate defense, and ISG20 has potentials to be developed into a therapeutic agent for viral diseases including hepatitis B.
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Affiliation(s)
- Yuanjie Liu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Hui Nie
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Richeng Mao
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Bidisha Mitra
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Dawei Cai
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ran Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Timothy M. Block
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Nadir Mechti
- CNRS, UMR5235, DIMNP, University of Montpellier 2, Montpellier, France
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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50
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Diao F, Chen K, Wang Y, Li Y, Xu W, Lu J, Chen YX. Involvement of small G protein RhoB in the regulation of proliferation, adhesion and migration by dexamethasone in osteoblastic cells. PLoS One 2017; 12:e0174273. [PMID: 28323887 PMCID: PMC5360316 DOI: 10.1371/journal.pone.0174273] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/06/2017] [Indexed: 12/02/2022] Open
Abstract
Long-term exposure to therapeutic doses of glucocorticoids (GCs) results in bone remodeling, which frequently causes osteoporosis and fracture healing retardation because of the abnormality of osteoblastic proliferation and differentiation. The mechanisms of GCs’ effect on osteoblasts are largely unknown. In this present study, we found that dexamethasone (Dex) could induce the expression of the small G protein, RhoB, in mRNA and protein levels in the osteoblast-derived osteosarcoma cell lines MG-63. The up-regulation of RhoB mRNA by Dex mainly occurs at posttranscriptional level by increasing its mRNA stability through PI-3K/Akt and p38 mitogen-activated protein kinase signaling pathways. Over-expression of RhoB in MG-63 cells magnified while down-regulation of RhoB level by RNA interference impaired Dex-induced growth inhibition but not differentiation. What’s more, over-expression of RhoB mimicked the effect of Dex on cell adhesion and migration. And interfering RhoB expression partially suppressed Dex-induced pro-adhesion and anti-migration in MG-63 cells. In conclusion, these results indicate that RhoB plays an important role in the pathological effect of Dex on osteoblastic growth and migration, which is a part of the mechanisms of GCs’ adverse effect on bone remodeling.
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Affiliation(s)
- Fei Diao
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
| | - Kangyao Chen
- Department of Orthopedics, Changhai Hospital affiliated to Second Military Medical University, Shanghai, China
- Department of -Orthopedics, Fuzhou Second Hospital affiliated to Xiamen University, Fuzhou, Fujian Province, China
| | - Yan Wang
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
| | - Yidong Li
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
| | - Weidong Xu
- Department of Orthopedics, Changhai Hospital affiliated to Second Military Medical University, Shanghai, China
| | - Jian Lu
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
- * E-mail: (JL); (YXC)
| | - Yu-Xia Chen
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
- * E-mail: (JL); (YXC)
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