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  • 1
    Publication Date: 2012-09-25
    Description: In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705913/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Manqing -- Kao, Elaine -- Gao, Xia -- Sandig, Hilary -- Limmer, Kirsten -- Pavon-Eternod, Mariana -- Jones, Thomas E -- Landry, Sebastien -- Pan, Tao -- Weitzman, Matthew D -- David, Michael -- AI074967/AI/NIAID NIH HHS/ -- AI81019/AI/NIAID NIH HHS/ -- P01 AI090935/AI/NIAID NIH HHS/ -- P01AI090935/AI/NIAID NIH HHS/ -- P30AI36214/AI/NIAID NIH HHS/ -- R01 GM101982/GM/NIGMS NIH HHS/ -- R01GM101982/GM/NIGMS NIH HHS/ -- R21 AI088490/AI/NIAID NIH HHS/ -- R21AI088490/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 1;491(7422):125-8. doi: 10.1038/nature11433. Epub 2012 Sep 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23000900" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Cells, Cultured ; Codon/*genetics/immunology ; Gene Expression Regulation, Viral/*genetics ; HEK293 Cells ; HIV-1/*genetics/growth & development/immunology/metabolism ; Humans ; Immunity, Innate ; Nuclear Proteins/immunology/*metabolism ; Protein Biosynthesis/*genetics/immunology ; RNA, Transfer/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reverse Transcription ; Species Specificity ; Substrate Specificity ; Viral Proteins/*biosynthesis/*genetics ; Virus Integration
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2016-02-11
    Description: Gene expression can be regulated post-transcriptionally through dynamic and reversible RNA modifications. A recent noteworthy example is N(6)-methyladenosine (m(6)A), which affects messenger RNA (mRNA) localization, stability, translation and splicing. Here we report on a new mRNA modification, N(1)-methyladenosine (m(1)A), that occurs on thousands of different gene transcripts in eukaryotic cells, from yeast to mammals, at an estimated average transcript stoichiometry of 20% in humans. Employing newly developed sequencing approaches, we show that m(1)A is enriched around the start codon upstream of the first splice site: it preferentially decorates more structured regions around canonical and alternative translation initiation sites, is dynamic in response to physiological conditions, and correlates positively with protein production. These unique features are highly conserved in mouse and human cells, strongly indicating a functional role for m(1)A in promoting translation of methylated mRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dominissini, Dan -- Nachtergaele, Sigrid -- Moshitch-Moshkovitz, Sharon -- Peer, Eyal -- Kol, Nitzan -- Ben-Haim, Moshe Shay -- Dai, Qing -- Di Segni, Ayelet -- Salmon-Divon, Mali -- Clark, Wesley C -- Zheng, Guanqun -- Pan, Tao -- Solomon, Oz -- Eyal, Eran -- Hershkovitz, Vera -- Han, Dali -- Dore, Louis C -- Amariglio, Ninette -- Rechavi, Gideon -- He, Chuan -- GM113194/GM/NIGMS NIH HHS/ -- GM71440/GM/NIGMS NIH HHS/ -- HG006699/HG/NHGRI NIH HHS/ -- HG008688/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2016 Feb 25;530(7591):441-6. doi: 10.1038/nature16998. Epub 2016 Feb 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel. ; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. ; Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26863196" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2013-11-29
    Description: N(6)-methyladenosine (m(6)A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes. Although essential to cell viability and development, the exact role of m(6)A modification remains to be determined. The recent discovery of two m(6)A demethylases in mammalian cells highlighted the importance of m(6)A in basic biological functions and disease. Here we show that m(6)A is selectively recognized by the human YTH domain family 2 (YTHDF2) 'reader' protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m(6)A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies. The carboxy-terminal domain of YTHDF2 selectively binds to m(6)A-containing mRNA, whereas the amino-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m(6)A modification is recognized by selectively binding proteins to affect the translation status and lifetime of mRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877715/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877715/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Xiao -- Lu, Zhike -- Gomez, Adrian -- Hon, Gary C -- Yue, Yanan -- Han, Dali -- Fu, Ye -- Parisien, Marc -- Dai, Qing -- Jia, Guifang -- Ren, Bing -- Pan, Tao -- He, Chuan -- GM071440/GM/NIGMS NIH HHS/ -- GM088599/GM/NIGMS NIH HHS/ -- K01 HG006699/HG/NHGRI NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- R01 GM088599/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Jan 2;505(7481):117-20. doi: 10.1038/nature12730. Epub 2013 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA. ; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. ; 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2] Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24284625" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/metabolism/pharmacology ; Base Sequence ; DNA-Binding Proteins/genetics ; HeLa Cells ; Humans ; Nucleotide Motifs ; Organelles/genetics/metabolism ; Protein Binding ; Protein Biosynthesis ; *RNA Stability/drug effects ; RNA Transport ; RNA, Messenger/*chemistry/*metabolism ; RNA, Untranslated/chemistry/metabolism ; RNA-Binding Proteins/chemistry/classification/*metabolism ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2018-02-25
    Description: Background : Risk analysis of cold ischemia time (CIT) in liver transplantation has largely focused on patient and graft survival. Post-transplant length of stay is a sensitive marker of morbidity and cost. We hypothesize that CIT is a risk factor for post-transplant prolonged length of stay (PLOS) and aim to conduct an hour-by-hour analysis of CIT and PLOS. Methods : We retrospectively reviewed all adult, first-time liver transplants between March 2002 and September 2016 in the United Network for Organ Sharing database. 67,426 recipients were categorized by hourly CIT increments. Multivariable logistic regression of PLOS (defined as 〉 30 days), CIT groups, and an extensive list of confounding variables was performed. Linear regression between length of stay and CIT as continuous variables was also performed. Results : CIT 1-6 hours was protective against PLOS, while CIT greater than 7 hours was associated with increased odds for PLOS. The lowest odds for PLOS were observed with 1-2 (odds ratio (OR) = 0.65, 95% confidence interval (CI) 0.45-0.92) and 2-3 hours (OR = 0.65, 95% CI 0.55-0.78) of CIT. OR for PLOS steadily increased with increasing CIT, reaching the greatest odds for PLOS with 13-14 hours (OR = 2.05, 95% CI 1.57-2.67) and 15-16 hours (OR = 2.06, 95% CI 1.27-3.33) of CIT. Linear regression revealed a positive correlation between length of stay and cold ischemia time with a correlation coefficient of +0.35 (p 〈 0.001). Conclusion : Post-liver transplant length of stay is sensitive to CIT, with substantial increase in the odds of PLOS observed with nearly every additional hour of cold ischemia. We conclude that CIT should be minimized to protect against the morbidity and cost associated with post-transplant PLOS. This article is protected by copyright. All rights reserved.
    Print ISSN: 1527-6465
    Electronic ISSN: 1527-6473
    Topics: Medicine
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  • 5
    Publication Date: 2018-05-16
    Description: Purpose: Wnt/β-catenin signaling is required for leukemic stem cell function. FLT3 mutations are frequently observed in acute myeloid leukemia (AML). Anomalous FLT3 signaling increases β-catenin nuclear localization and transcriptional activity. FLT3 tyrosine kinase inhibitors (TKI) are used clinically to treat FLT3 -mutated AML patients, but with limited efficacy. We investigated the antileukemia activity of combined Wnt/β-catenin and FLT3 inhibition in FLT3 -mutant AML. Experimental Design: Wnt/β-catenin signaling was inhibited by the β-catenin/CBP antagonist C-82/PRI-724 or siRNAs, and FLT3 signaling by sorafenib or quizartinib. Treatments on apoptosis, cell growth, and cell signaling were assessed in cell lines, patient samples, and in vivo in immunodeficient mice by flow cytometry, Western blot, RT-PCR, and CyTOF. Results: We found significantly higher β-catenin expression in cytogenetically unfavorable and relapsed AML patient samples and in the bone marrow–resident leukemic cells compared with circulating blasts. Disrupting Wnt/β-catenin signaling suppressed AML cell growth, induced apoptosis, abrogated stromal protection, and synergized with TKIs in FLT3 -mutated AML cells and stem/progenitor cells in vitro . The aforementioned combinatorial treatment improved survival of AML-xenografted mice in two in vivo models and impaired leukemia cell engraftment. Mechanistically, the combined inhibition of Wnt/β-catenin and FLT3 cooperatively decreased nuclear β-catenin and the levels of c-Myc and other Wnt/β-catenin and FLT3 signaling proteins. Importantly, β-catenin inhibition abrogated the microenvironmental protection afforded the leukemic stem/progenitor cells. Conclusions: Disrupting Wnt/β-catenin signaling exerts potent activities against AML stem/progenitor cells and synergizes with FLT3 inhibition in FLT3 -mutant AML. These findings provide a rationale for clinical development of this strategy for treating FLT3 -mutated AML patients. Clin Cancer Res; 24(10); 2417–29. ©2018 AACR .
    Print ISSN: 1078-0432
    Electronic ISSN: 1557-3265
    Topics: Medicine
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  • 6
    Publication Date: 2018-03-30
    Description: Background/Aim: In a previous study, we showed that amentoflavone promotes sorafenib-induced apoptosis in hepatocellular carcinoma (HCC) cells in vitro. However, whether amentoflavone augments anticancer efficacy of sorafenib in HCC in vivo is unknown. The aim of the present study was to verify the anticancer effect of amentoflavone combined with sorafenib in HCC in vivo. Materials and Methods: HCC SK-Hep1 tumor-bearing mice were treated with vehicle, sorafenib, amentoflavone, or combination for 14 days, respectively. Effect of sorafenib, amentoflavone, or their combination on tumor growth, anti-apoptotic potential, apoptotic signaling and general toxicity were evaluated with digital caliper, immunohistochemistry staining and body weight. Results: Our results demonstrated that amentoflavone significantly enhanced sorafenib-inhibited tumor growth and expression of ERK/AKT phosphorylation and anti-apoptotic proteins compared to single-agent treatment. Additionally, amentoflavone also triggered sorafenib-induced apoptosis through extrinsic and intrinsic apoptotic pathways. Conclusion: Amentoflavone boosts therapeutic efficacy of sorafenib through blockage of anti-apoptotic potential and induction of apoptosis in HCC in vivo.
    Print ISSN: 0250-7005
    Electronic ISSN: 1791-7530
    Topics: Medicine
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  • 7
    Publication Date: 2015-02-27
    Description: RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism 'the m(6)A-switch'. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing. Combining photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and anti-m(6)A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m(6)A-switches among HNRNPC-binding sites; and global m(6)A reduction decreased HNRNPC binding at 2,798 high-confidence m(6)A-switches. We determined that these m(6)A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355918/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355918/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Nian -- Dai, Qing -- Zheng, Guanqun -- He, Chuan -- Parisien, Marc -- Pan, Tao -- GM088599/GM/NIGMS NIH HHS/ -- K01 HG006699/HG/NHGRI NIH HHS/ -- K01HG006699/HG/NHGRI NIH HHS/ -- R01 GM088599/GM/NIGMS NIH HHS/ -- UL1 TR000430/TR/NCATS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Feb 26;518(7540):560-4. doi: 10.1038/nature14234.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA. ; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA. ; 1] Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA [2] Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA [3] Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA [4] Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA. ; 1] Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA [2] Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25719671" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/metabolism ; Alternative Splicing/genetics ; Base Sequence ; Cross-Linking Reagents ; HEK293 Cells ; HeLa Cells ; Heterogeneous-Nuclear Ribonucleoprotein Group C/*metabolism ; Humans ; Immunoprecipitation ; *Nucleic Acid Conformation ; Nucleotide Motifs ; Protein Binding ; RNA, Messenger/analysis/*chemistry/*metabolism ; Transcriptome
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-06-30
    Description: Effective immune surveillance by cytotoxic T cells requires newly synthesized polypeptides for presentation by major histocompatibility complex (MHC) class I molecules. These polypeptides are produced not only from conventional AUG-initiated, but also from cryptic non-AUG-initiated, reading frames by distinct translational mechanisms. Biochemical analysis of ribosomal initiation complexes at CUG versus AUG initiation codons revealed that cells use an elongator leucine-bound transfer RNA (Leu-tRNA) to initiate translation at cryptic CUG start codons. CUG/Leu-tRNA initiation was independent of the canonical initiator tRNA (AUG/Met-tRNA(i)(Met)) pathway but required expression of eukaryotic initiation factor 2A. Thus, a tRNA-based translation initiation mechanism allows non-AUG-initiated protein synthesis and supplies peptides for presentation by MHC class I molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starck, Shelley R -- Jiang, Vivian -- Pavon-Eternod, Mariana -- Prasad, Sharanya -- McCarthy, Brian -- Pan, Tao -- Shastri, Nilabh -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1719-23. doi: 10.1126/science.1220270.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen Presentation/*genetics ; Antigen-Presenting Cells/immunology ; COS Cells ; Cercopithecus aethiops ; *Codon, Initiator ; HeLa Cells ; Histocompatibility Antigens Class I/*genetics/*immunology ; Humans ; Hybridomas/immunology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Peptide Chain Initiation, Translational ; Protein Biosynthesis/*genetics ; *RNA, Transfer, Leu ; T-Lymphocytes/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    ISSN: 0888-7543
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 0888-7543
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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