101
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Tarling EJ, Clifford BL, Cheng J, Morand P, Cheng A, Lester E, Sallam T, Turner M, de Aguiar Vallim TQ. RNA-binding protein ZFP36L1 maintains posttranscriptional regulation of bile acid metabolism. J Clin Invest 2017; 127:3741-3754. [PMID: 28891815 DOI: 10.1172/jci94029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 12/15/2022] Open
Abstract
Bile acids function not only as detergents that facilitate lipid absorption but also as signaling molecules that activate the nuclear receptor farnesoid X receptor (FXR). FXR agonists are currently being evaluated as therapeutic agents for a number of hepatic diseases due to their lipid-lowering and antiinflammatory properties. FXR is also essential for maintaining bile acid homeostasis and prevents the accumulation of bile acids. Elevated bile acids activate FXR, which in turn switches off bile acid synthesis by reducing the mRNA levels of bile acid synthesis genes, including cholesterol 7α-hydroxylase (Cyp7a1). Here, we show that FXR activation triggers a rapid posttranscriptional mechanism to degrade Cyp7a1 mRNA. We identified the RNA-binding protein Zfp36l1 as an FXR target gene and determined that gain and loss of function of ZFP36L1 reciprocally regulate Cyp7a1 mRNA and bile acid levels in vivo. Moreover, we found that mice lacking hepatic ZFP36L1 were protected from diet-induced obesity and steatosis. The reduced adiposity and antisteatotic effects observed in ZFP36L1-deficient mice were accompanied by impaired lipid absorption that was consistent with altered bile acid metabolism. Thus, the ZFP36L1-dependent regulation of bile acid metabolism is an important metabolic contributor to obesity and hepatosteatosis.
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Affiliation(s)
- Elizabeth J Tarling
- Department of Medicine, Division of Cardiology, and.,Molecular Biology Institute (MBI), UCLA, Los Angeles, California, USA.,UCLA Johnson Comprehensive Cancer Center (JCCC), Los Angeles, California, USA
| | | | - Joan Cheng
- Department of Medicine, Division of Cardiology, and
| | | | - Angela Cheng
- Department of Medicine, Division of Cardiology, and
| | - Ellen Lester
- Department of Medicine, Division of Cardiology, and
| | - Tamer Sallam
- Department of Medicine, Division of Cardiology, and
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Thomas Q de Aguiar Vallim
- Department of Medicine, Division of Cardiology, and.,Molecular Biology Institute (MBI), UCLA, Los Angeles, California, USA.,UCLA Johnson Comprehensive Cancer Center (JCCC), Los Angeles, California, USA.,Department of Biological Chemistry, UCLA, Los Angeles, California, USA
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102
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Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet 2017; 49. [PMID: 28671688 PMCID: PMC5535770 DOI: 10.1038/ng.3909 10.1182/ng.3909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Genetic alterations that activate NOTCH1 signaling and T cell transcription factors, coupled with inactivation of the INK4/ARF tumor suppressors, are hallmarks of T-lineage acute lymphoblastic leukemia (T-ALL), but detailed genome-wide sequencing of large T-ALL cohorts has not been carried out. Using integrated genomic analysis of 264 T-ALL cases, we identified 106 putative driver genes, half of which had not previously been described in childhood T-ALL (for example, CCND3, CTCF, MYB, SMARCA4, ZFP36L2 and MYCN). We describe new mechanisms of coding and noncoding alteration and identify ten recurrently altered pathways, with associations between mutated genes and pathways, and stage or subtype of T-ALL. For example, NRAS/FLT3 mutations were associated with immature T-ALL, JAK3/STAT5B mutations in HOXA1 deregulated ALL, PTPN2 mutations in TLX1 deregulated T-ALL, and PIK3R1/PTEN mutations in TAL1 deregulated ALL, which suggests that different signaling pathways have distinct roles according to maturational stage. This genomic landscape provides a logical framework for the development of faithful genetic models and new therapeutic approaches.
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Affiliation(s)
- Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States,Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Jamie Maciaszek
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Mark R. Wilkinson
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Kelly McCastlain
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Stanley B. Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Lei Shi
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, United States
| | - Jaime Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland United States
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland United States
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Naomi J. Winick
- University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Nyla A. Heerema
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Elizabeth Raetz
- Department of Pediatrics, Huntsman Cancer Institute and Primary Children’s Hospital, University of Utah, Salt Lake City, Utah, United States
| | - Meenakshi Devidas
- Department of Biostatistics, Colleges of Medicine, Public Health & Health Profession, University of Florida, Gainesville, Florida, United States
| | - Cheryl L. Willman
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Richard C. Harvey
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - William L. Carroll
- Department of Pediatrics, Perlmutter Cancer Center, New York University Medical Center, New York, New York, United States
| | - Kimberly P. Dunsmore
- Health Sciences Center, University of Virginia, Charlottesville, Virginia, United States
| | - Stuart S. Winter
- Department of Pediatrics, University of New Mexico, Albuquerque, New Mexico, United States
| | - Brent L Wood
- Seattle Cancer Care Alliance, Seattle, Washington, United States
| | - Brian P. Sorrentino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - James R. Downing
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital, University of California at San Francisco, San Francisco, California, United States
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States,Address for correspondence: Stephen P. Hunger, Children’s Hospital of Philadelphia, CTRB #3060, 3501 Civic Center Boulevard, Philadelphia, PA 19104, ; Jinghui Zhang, St. Jude Children’s Research Hospital, Department of Computational Biology, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN 38105, T: 1-901-595- 6829, ; Charles G. Mullighan, St. Jude Children’s Research Hospital, Department of Pathology, Mail Stop 342, 262 Danny Thomas Place, Memphis, TN 38105, T: 1-901-595-3387, F: 1-901-595-5947,
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States,Address for correspondence: Stephen P. Hunger, Children’s Hospital of Philadelphia, CTRB #3060, 3501 Civic Center Boulevard, Philadelphia, PA 19104, ; Jinghui Zhang, St. Jude Children’s Research Hospital, Department of Computational Biology, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN 38105, T: 1-901-595- 6829, ; Charles G. Mullighan, St. Jude Children’s Research Hospital, Department of Pathology, Mail Stop 342, 262 Danny Thomas Place, Memphis, TN 38105, T: 1-901-595-3387, F: 1-901-595-5947,
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States,Address for correspondence: Stephen P. Hunger, Children’s Hospital of Philadelphia, CTRB #3060, 3501 Civic Center Boulevard, Philadelphia, PA 19104, ; Jinghui Zhang, St. Jude Children’s Research Hospital, Department of Computational Biology, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN 38105, T: 1-901-595- 6829, ; Charles G. Mullighan, St. Jude Children’s Research Hospital, Department of Pathology, Mail Stop 342, 262 Danny Thomas Place, Memphis, TN 38105, T: 1-901-595-3387, F: 1-901-595-5947,
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103
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Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet 2017; 49:1211-1218. [PMID: 28671688 PMCID: PMC5535770 DOI: 10.1038/ng.3909] [Citation(s) in RCA: 612] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 06/09/2017] [Indexed: 12/11/2022]
Abstract
Genetic alterations that activate NOTCH1 signaling and T cell transcription factors, coupled with inactivation of the INK4/ARF tumor suppressors, are hallmarks of T-lineage acute lymphoblastic leukemia (T-ALL), but detailed genome-wide sequencing of large T-ALL cohorts has not been carried out. Using integrated genomic analysis of 264 T-ALL cases, we identified 106 putative driver genes, half of which had not previously been described in childhood T-ALL (for example, CCND3, CTCF, MYB, SMARCA4, ZFP36L2 and MYCN). We describe new mechanisms of coding and noncoding alteration and identify ten recurrently altered pathways, with associations between mutated genes and pathways, and stage or subtype of T-ALL. For example, NRAS/FLT3 mutations were associated with immature T-ALL, JAK3/STAT5B mutations in HOXA1 deregulated ALL, PTPN2 mutations in TLX1 deregulated T-ALL, and PIK3R1/PTEN mutations in TAL1 deregulated ALL, which suggests that different signaling pathways have distinct roles according to maturational stage. This genomic landscape provides a logical framework for the development of faithful genetic models and new therapeutic approaches.
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Affiliation(s)
- Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Jamie Maciaszek
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Mark R. Wilkinson
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Kelly McCastlain
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Stanley B. Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Lei Shi
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, United States
| | - Jaime Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland United States
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland United States
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Naomi J. Winick
- University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Nyla A. Heerema
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Elizabeth Raetz
- Department of Pediatrics, Huntsman Cancer Institute and Primary Children’s Hospital, University of Utah, Salt Lake City, Utah, United States
| | - Meenakshi Devidas
- Department of Biostatistics, Colleges of Medicine, Public Health & Health Profession, University of Florida, Gainesville, Florida, United States
| | - Cheryl L. Willman
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Richard C. Harvey
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - William L. Carroll
- Department of Pediatrics, Perlmutter Cancer Center, New York University Medical Center, New York, New York, United States
| | - Kimberly P. Dunsmore
- Health Sciences Center, University of Virginia, Charlottesville, Virginia, United States
| | - Stuart S. Winter
- Department of Pediatrics, University of New Mexico, Albuquerque, New Mexico, United States
| | - Brent L Wood
- Seattle Cancer Care Alliance, Seattle, Washington, United States
| | - Brian P. Sorrentino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - James R. Downing
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital, University of California at San Francisco, San Francisco, California, United States
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
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104
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The control of inflammation via the phosphorylation and dephosphorylation of tristetraprolin: a tale of two phosphatases. Biochem Soc Trans 2017; 44:1321-1337. [PMID: 27911715 PMCID: PMC5095909 DOI: 10.1042/bst20160166] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022]
Abstract
Twenty years ago, the first description of a tristetraprolin (TTP) knockout mouse highlighted the fundamental role of TTP in the restraint of inflammation. Since then, work from several groups has generated a detailed picture of the expression and function of TTP. It is a sequence-specific RNA-binding protein that orchestrates the deadenylation and degradation of several mRNAs encoding inflammatory mediators. It is very extensively post-translationally modified, with more than 30 phosphorylations that are supported by at least two independent lines of evidence. The phosphorylation of two particular residues, serines 52 and 178 of mouse TTP (serines 60 and 186 of the human orthologue), has profound effects on the expression, function and localisation of TTP. Here, we discuss the control of TTP biology via its phosphorylation and dephosphorylation, with a particular focus on recent advances and on questions that remain unanswered.
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105
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Newman R, Ahlfors H, Saveliev A, Galloway A, Hodson DJ, Williams R, Besra GS, Cook CN, Cunningham AF, Bell SE, Turner M. Maintenance of the marginal-zone B cell compartment specifically requires the RNA-binding protein ZFP36L1. Nat Immunol 2017; 18:683-693. [PMID: 28394372 PMCID: PMC5438597 DOI: 10.1038/ni.3724] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/09/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins of the ZFP36 family are best known for inhibiting the expression of cytokines through binding to AU-rich elements in the 3' untranslated region and promoting mRNA decay. Here we identified an indispensable role for ZFP36L1 as the regulator of a post-transcriptional hub that determined the identity of marginal-zone B cells by promoting their proper localization and survival. ZFP36L1 controlled a gene-expression program related to signaling, cell adhesion and locomotion; it achieved this in part by limiting expression of the transcription factors KLF2 and IRF8, which are known to enforce the follicular B cell phenotype. These mechanisms emphasize the importance of integrating transcriptional and post-transcriptional processes by RNA-binding proteins for maintaining cellular identity among closely related cell types.
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Affiliation(s)
- Rebecca Newman
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
- Immune Receptor Activation Laboratory, The Francis Crick Institute,
1 Midland Road, London, NW1 1AT, United Kingdom
| | - Helena Ahlfors
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Alexander Saveliev
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Alison Galloway
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Daniel J Hodson
- Department of Haematology, University of Cambridge, The Clifford
Allbutt Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0AH,
United Kingdom
| | - Robert Williams
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Birmingham, B15
2TT, United Kingdom
| | - Charlotte N Cook
- MRC Centre for Immune Regulation, School of Immunity and Infection,
University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Adam F Cunningham
- MRC Centre for Immune Regulation, School of Immunity and Infection,
University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Sarah E Bell
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham
Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
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106
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Thandapani P, Aranda-Orgilles B, Aifantis I. RNA-binding proteins, the guardians of the marginal zone. Nat Immunol 2017; 18:595-597. [PMID: 28518167 DOI: 10.1038/ni.3752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Palaniraja Thandapani
- Department of Pathology; Laura &Isaac Perlmutter Cancer Center, and Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Beatriz Aranda-Orgilles
- Department of Pathology; Laura &Isaac Perlmutter Cancer Center, and Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Iannis Aifantis
- Department of Pathology; Laura &Isaac Perlmutter Cancer Center, and Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York, USA
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107
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McClelland L, Jasper H, Biteau B. Tis11 mediated mRNA decay promotes the reacquisition of Drosophila intestinal stem cell quiescence. Dev Biol 2017; 426:8-16. [PMID: 28445691 DOI: 10.1016/j.ydbio.2017.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/05/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
Adult stem cell proliferation rates are precisely regulated to maintain long-term tissue homeostasis. Defects in the mechanisms controlling stem cell proliferation result in impaired regeneration and hyperproliferative diseases. Many stem cell populations increase proliferation in response to tissue damage and reacquire basal proliferation rates after tissue repair is completed. Although proliferative signals have been extensively studied, much less is known about the molecular mechanisms that restore stem cell quiescence. Here we show that Tis11, an Adenine-uridine Rich Element (ARE) binding protein that promotes mRNA degradation, is required to re-establish basal proliferation rates of adult Drosophila intestinal stem cells (ISC) after a regenerative episode. We find that Tis11 limits ISC proliferation specifically after proliferation has been stimulated in response to heat stress or infection, and show that Tis11 expression and activity are increased in ISCs during tissue repair. Based on stem cell transcriptome analysis and RNA immunoprecipitation, we propose that Tis11 activation represents an integral part of a negative feedback mechanism that limits the expression of key components of several signaling pathways that control ISC function and proliferation. Our results identify Tis11 mediated mRNA decay as an evolutionarily conserved mechanism of re-establishing basal proliferation rates of stem cells in regenerating tissues.
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Affiliation(s)
- Lindy McClelland
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA; The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Heinrich Jasper
- The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Benoît Biteau
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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108
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Khalaj K, Miller JE, Fenn CR, Ahn S, Luna RL, Symons L, Monsanto SP, Koti M, Tayade C. RNA-Binding Proteins in Female Reproductive Pathologies. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:1200-1210. [PMID: 28408123 DOI: 10.1016/j.ajpath.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 01/26/2017] [Indexed: 12/14/2022]
Abstract
RNA-binding proteins are key regulatory molecules involved primarily in post-transcriptional gene regulation of RNAs. Post-transcriptional gene regulation is critical for adequate cellular growth and survival. Recent reports have shown key interactions between these RNA-binding proteins and other regulatory elements, such as miRNAs and long noncoding RNAs, either enhancing or diminishing their response to RNA stabilization. Many RNA-binding proteins have been reported to play a functional role in mediation of cytokines involved in inflammation and immune dysfunction, and some have been classified as global post-transcriptional regulators of inflammation. The ubiquitous expression of RNA-binding proteins in a wide variety of cell types and their unique mechanisms of degradative action provide evidence that they are involved in reproductive tract pathologies. Aberrant inflammation and immune dysfunction are major contributors to the pathogenesis and disease pathophysiology of many reproductive pathologies, including ovarian and endometrial cancers in the female reproductive tract. Herein, we discuss various RNA-binding proteins and their unique contributions to female reproductive pathologies with a focus on those mediated by aberrant inflammation and immune dysfunction.
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Affiliation(s)
- Kasra Khalaj
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Jessica E Miller
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Christian R Fenn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - SooHyun Ahn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Rayana L Luna
- Ultrastructure Laboratory, Aggeu Magalhães Research Center of the Oswaldo Cruz Foundation, Recife, Brazil
| | - Lindsey Symons
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Stephany P Monsanto
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Madhuri Koti
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Chandrakant Tayade
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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109
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Galloway A, Turner M. Cell cycle RNA regulons coordinating early lymphocyte development. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28231639 PMCID: PMC5574005 DOI: 10.1002/wrna.1419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/19/2023]
Abstract
Lymphocytes undergo dynamic changes in gene expression as they develop from progenitor cells lacking antigen receptors, to mature cells that are prepared to mount immune responses. While transcription factors have established roles in lymphocyte development, they act in concert with post-transcriptional and post-translational regulators to determine the proteome. Furthermore, the post-transcriptional regulation of RNA regulons consisting of mRNAs whose protein products act cooperatively allows RNA binding proteins to exert their effects at multiple points in a pathway. Here, we review recent evidence demonstrating the importance of RNA binding proteins that control the cell cycle in lymphocyte development and discuss the implications for tumorigenesis. WIREs RNA 2017, 8:e1419. doi: 10.1002/wrna.1419 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
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110
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RAF, Drexler HG. Identification of a tumor suppressor network in T-cell leukemia. Leuk Lymphoma 2017; 58:2196–2207. [PMID: 28142295 DOI: 10.1080/10428194.2017.1283029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines. Moreover, reduced expression of these genes was also observed in about 7% of T-ALL patients, showing their clinical relevance in this malignancy. Bioinformatic analyses revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, experiments demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1. Taken together, we identified novel TS genes forming a regulatory network in T-cell development and leukemogenesis.
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Affiliation(s)
- Stefan Nagel
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Claudia Pommerenke
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Corinna Meyer
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Maren Kaufmann
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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111
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Wells ML, Perera L, Blackshear PJ. An Ancient Family of RNA-Binding Proteins: Still Important! Trends Biochem Sci 2017; 42:285-296. [PMID: 28096055 DOI: 10.1016/j.tibs.2016.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
RNA-binding proteins are important modulators of mRNA stability, a crucial process that determines the ultimate cellular levels of mRNAs and their encoded proteins. The tristetraprolin (TTP) family of RNA-binding proteins appeared early in the evolution of eukaryotes, and has persisted in modern eukaryotes. The domain structures and biochemical functions of family members from widely divergent lineages are remarkably similar, but their mRNA 'targets' can be very different, even in closely related species. Recent gene knockout studies in species as distantly related as plants, flies, yeasts, and mice have demonstrated crucial roles for these proteins in a wide variety of physiological processes. Inflammatory and hematopoietic phenotypes in mice have suggested potential therapeutic approaches for analogous human disorders.
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Affiliation(s)
- Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Departments of Biochemistry and Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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112
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Yonemori K, Seki N, Kurahara H, Osako Y, Idichi T, Arai T, Koshizuka K, Kita Y, Maemura K, Natsugoe S. ZFP36L2 promotes cancer cell aggressiveness and is regulated by antitumor microRNA-375 in pancreatic ductal adenocarcinoma. Cancer Sci 2017; 108:124-135. [PMID: 27862697 PMCID: PMC5276842 DOI: 10.1111/cas.13119] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/04/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
Due to its aggressive nature, pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and hard-to-treat malignancies. Recently developed targeted molecular strategies have contributed to remarkable improvements in the treatment of several cancers. However, such therapies have not been applied to PDAC. Therefore, new treatment options are needed for PDAC based on current genomic approaches. Expression of microRNA-375 (miR-375) was significantly reduced in miRNA expression signatures of several types of cancers, including PDAC. The aim of the present study was to investigate the functional roles of miR-375 in PDAC cells and to identify miR-375-regulated molecular networks involved in PDAC aggressiveness. The expression levels of miR-375 were markedly downregulated in PDAC clinical specimens and cell lines (PANC-1 and SW1990). Ectopic expression of miR-375 significantly suppressed cancer cell proliferation, migration and invasion. Our in silico and gene expression analyses and luciferase reporter assay showed that zinc finger protein 36 ring finger protein-like 2 (ZFP36L2) was a direct target of miR-375 in PDAC cells. Silencing ZFP36L2 inhibited cancer cell aggressiveness in PDAC cell lines, and overexpression of ZFP36L2 was confirmed in PDAC clinical specimens. Interestingly, Kaplan-Meier survival curves showed that high expression of ZFP36L2 predicted shorter survival in patients with PDAC. Moreover, we investigated the downstream molecular networks of the miR-375/ZFP36L2 axis in PDAC cells. Elucidation of tumor-suppressive miR-375-mediated PDAC molecular networks may provide new insights into the potential mechanisms of PDAC pathogenesis.
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Affiliation(s)
- Keiichi Yonemori
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Naohiko Seki
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Yusaku Osako
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Takayuki Arai
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Keiichi Koshizuka
- Department of Functional GenomicsChiba University Graduate School of MedicineChibaJapan
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Kosei Maemura
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
| | - Shoji Natsugoe
- Department of Digestive Surgery, Breast and Thyroid SurgeryGraduate School of Medical SciencesKagoshima UniversityKagoshimaJapan
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113
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Vlasova-St Louis I, Bohjanen PR. Post-transcriptional regulation of cytokine and growth factor signaling in cancer. Cytokine Growth Factor Rev 2016; 33:83-93. [PMID: 27956133 DOI: 10.1016/j.cytogfr.2016.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022]
Abstract
Cytokines and growth factors regulate cell proliferation, differentiation, migration and apoptosis, and play important roles in coordinating growth signal responses during development. The expression of cytokine genes and the signals transmitted through cytokine receptors are tightly regulated at several levels, including transcriptional and post-transcriptional levels. A majority of cytokine mRNAs, including growth factor transcripts, contain AU-rich elements (AREs) in their 3' untranslated regions that control gene expression by regulating mRNA degradation and changing translational rates. In addition, numerous proteins involved in transmitting signals downstream of cytokine receptors are regulated at the level of mRNA degradation by GU-rich elements (GREs) found in their 3' untranslated regions. Abnormal stabilization and overexpression of ARE or GRE-containing transcripts had been observed in many malignancies, which is a consequence of the malfunction of RNA-binding proteins. In this review, we briefly summarize the role of AREs and GREs in regulating mRNA turnover to coordinate cytokine and growth factor expression, and we describe how dysregulation of mRNA degradation mechanisms contributes to the development and progression of cancer.
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Affiliation(s)
| | - Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Roy S, Dutta S, Datta K, Opavsky R. Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma. PLoS Genet 2016; 12:e1006334. [PMID: 27690235 PMCID: PMC5045215 DOI: 10.1371/journal.pgen.1006334] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/31/2016] [Indexed: 12/29/2022] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is an enzyme involved in DNA methylation that is frequently mutated in human hematologic malignancies. We have previously shown that inactivation of Dnmt3a in hematopoietic cells results in chronic lymphocytic leukemia in mice. Here we show that 12% of Dnmt3a-deficient mice develop CD8+ mature peripheral T cell lymphomas (PTCL) and 29% of mice are affected by both diseases. 10% of Dnmt3a+/- mice develop lymphomas, suggesting that Dnmt3a is a haploinsufficient tumor suppressor in PTCL. DNA methylation was deregulated genome-wide with 10-fold more hypo- than hypermethylated promoters and enhancers, demonstrating that hypomethylation is a major event in the development of PTCL. Hypomethylated promoters were enriched for binding sites of transcription factors AML1, NF-κB and OCT1, implying the transcription factors potential involvement in Dnmt3a-associated methylation. Whereas 71 hypomethylated genes showed an increased expression in PTCL, only 3 hypermethylated genes were silenced, suggesting that cancer-specific hypomethylation has broader effects on the transcriptome of cancer cells than hypermethylation. Interestingly, transcriptomes of Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas were largely conserved and significantly overlapped with those of human tumors. Importantly, we observed downregulation of tumor suppressor p53 in Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas as well as in pre-tumor thymocytes from 9 months old but not 6 weeks old Dnmt3a+/- tumor-free mice, suggesting that p53 downregulation is chronologically an intermediate event in tumorigenesis. Decrease in p53 is likely an important event in tumorigenesis because its overexpression inhibited proliferation in mouse PTCL cell lines, suggesting that low levels of p53 are important for tumor maintenance. Altogether, our data link the haploinsufficient tumor suppressor function of Dnmt3a in the prevention of mouse mature CD8+ PTCL indirectly to a bona fide tumor suppressor of T cell malignancies p53. Global deregulation of cytosine methylation is an epigenetic hallmark of hematologic malignancies that may promote tumorigenesis by silencing tumor suppressor genes, upregulating oncogenes, and inducing genomic instability. DNA methyltransferase 3a (DNMT3A) is one of the three catalytically active enzymes responsible for cytosine methylation and one of the most frequently mutated genes in myeloid and T cell malignancies. Its role in malignant hematopoiesis, however, remains poorly understood. Here we show that Dnmt3a is a haploinsufficient tumor suppressor in the prevention of peripheral T cell lymphomas in mice. Our molecular studies identified a large number of genes deregulated in the absence of Dnmt3a that may be putative drivers of oncogenesis. We also show that downregulation of the tumor suppressor p53 is an important event in the development of mouse T cell lymphomas. Thus, this study establishes a novel mouse model to elucidate how epigenetic deregulation of transcription contributes to the pathogenesis of T cell lymphomas.
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Affiliation(s)
- Staci L. Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - G. Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sohini Roy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Samikshan Dutta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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115
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Vogel KU, Bell LS, Galloway A, Ahlfors H, Turner M. The RNA-Binding Proteins Zfp36l1 and Zfp36l2 Enforce the Thymic β-Selection Checkpoint by Limiting DNA Damage Response Signaling and Cell Cycle Progression. THE JOURNAL OF IMMUNOLOGY 2016; 197:2673-2685. [PMID: 27566829 DOI: 10.4049/jimmunol.1600854] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022]
Abstract
The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly to enforce the β-selection checkpoint during thymopoiesis, yet their molecular targets remain largely unknown. In this study, we identify these targets on a genome-wide scale in primary mouse thymocytes and show that Zfp36l1/l2 regulate DNA damage response and cell cycle transcripts to ensure proper β-selection. Double-negative 3 thymocytes lacking Zfp36l1/l2 share a gene expression profile with postselected double-negative 3b cells despite the absence of intracellular TCRβ and reduced IL-7 signaling. Our findings show that in addition to controlling the timing of proliferation at β-selection, posttranscriptional control by Zfp36l1/l2 limits DNA damage responses, which are known to promote thymocyte differentiation. Zfp36l1/l2 therefore act as posttranscriptional safeguards against chromosomal instability and replication stress by integrating pre-TCR and IL-7 signaling with DNA damage and cell cycle control.
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Affiliation(s)
| | - Lewis S Bell
- Dept. of Medicine, University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Science, University of Dundee, Dundee DD1 5EH, UK
| | - Helena Ahlfors
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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116
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Abstract
T cell acute lymphoblastic leukaemia (T-ALL) is an aggressive haematological malignancy derived from early T cell progenitors. In recent years genomic and transcriptomic studies have uncovered major oncogenic and tumour suppressor pathways involved in T-ALL transformation and identified distinct biological groups associated with prognosis. An increased understanding of T-ALL biology has already translated into new prognostic biomarkers and improved animal models of leukaemia and has opened opportunities for the development of targeted therapies for the treatment of this disease. In this Review we examine our current understanding of the molecular mechanisms of T-ALL and recent developments in the translation of these results to the clinic.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pathology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
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117
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Khabar KSA. Hallmarks of cancer and AU-rich elements. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27251431 PMCID: PMC5215528 DOI: 10.1002/wrna.1368] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/05/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Post‐transcriptional control of gene expression is aberrant in cancer cells. Sustained stabilization and enhanced translation of specific mRNAs are features of tumor cells. AU‐rich elements (AREs), cis‐acting mRNA decay determinants, play a major role in the posttranscriptional regulation of many genes involved in cancer processes. This review discusses the role of aberrant ARE‐mediated posttranscriptional processes in each of the hallmarks of cancer, including sustained cellular growth, resistance to apoptosis, angiogenesis, invasion, and metastasis. WIREs RNA 2017, 8:e1368. doi: 10.1002/wrna.1368 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Khalid S A Khabar
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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118
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Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, Kovarik P. Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. Mol Syst Biol 2016; 12:868. [PMID: 27178967 PMCID: PMC4988506 DOI: 10.15252/msb.20156628] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Precise regulation of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. However, a global model integrating regulation and functional consequences of inflammation‐associated mRNA decay remains to be established. Using time‐resolved high‐resolution RNA binding analysis of the mRNA‐destabilizing protein tristetraprolin (TTP), an inflammation‐limiting factor, we qualitatively and quantitatively characterize TTP binding positions in the transcriptome of immunostimulated macrophages. We identify pervasive destabilizing and non‐destabilizing TTP binding, including a robust intronic binding, showing that TTP binding is not sufficient for mRNA destabilization. A low degree of flanking RNA structuredness distinguishes occupied from silent binding motifs. By functionally relating TTP binding sites to mRNA stability and levels, we identify a TTP‐controlled switch for the transition from inflammatory into the resolution phase of the macrophage immune response. Mapping of binding positions of the mRNA‐stabilizing protein HuR reveals little target and functional overlap with TTP, implying a limited co‐regulation of inflammatory mRNA decay by these proteins. Our study establishes a functionally annotated and navigable transcriptome‐wide atlas (http://ttp-atlas.univie.ac.at) of cis‐acting elements controlling mRNA decay in inflammation.
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Affiliation(s)
- Vitaly Sedlyarov
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jörg Fallmann
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Florian Ebner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jakob Huemer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Lucy Sneezum
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Masa Ivin
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Kristina Kreiner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Andrea Tanzer
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark
| | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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119
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Galloway A, Saveliev A, Łukasiak S, Hodson DJ, Bolland D, Balmanno K, Ahlfors H, Monzón-Casanova E, Mannurita SC, Bell LS, Andrews S, Díaz-Muñoz MD, Cook SJ, Corcoran A, Turner M. RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence. Science 2016; 352:453-9. [PMID: 27102483 DOI: 10.1126/science.aad5978] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/26/2016] [Indexed: 12/12/2022]
Abstract
Progression through the stages of lymphocyte development requires coordination of the cell cycle. Such coordination ensures genomic integrity while cells somatically rearrange their antigen receptor genes [in a process called variable-diversity-joining (VDJ) recombination] and, upon successful rearrangement, expands the pools of progenitor lymphocytes. Here we show that in developing B lymphocytes, the RNA-binding proteins (RBPs) ZFP36L1 and ZFP36L2 are critical for maintaining quiescence before precursor B cell receptor (pre-BCR) expression and for reestablishing quiescence after pre-BCR-induced expansion. These RBPs suppress an evolutionarily conserved posttranscriptional regulon consisting of messenger RNAs whose protein products cooperatively promote transition into the S phase of the cell cycle. This mechanism promotes VDJ recombination and effective selection of cells expressing immunoglobulin-μ at the pre-BCR checkpoint.
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Affiliation(s)
- Alison Galloway
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Alexander Saveliev
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Sebastian Łukasiak
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Daniel J Hodson
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK. Department of Haematology, University of Cambridge, The Clifford Allbutt Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, UK
| | - Daniel Bolland
- Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kathryn Balmanno
- Laboratory of Signalling, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Helena Ahlfors
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK. Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Sara Ciullini Mannurita
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Lewis S Bell
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Manuel D Díaz-Muñoz
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon J Cook
- Laboratory of Signalling, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Anne Corcoran
- Laboratory of Nuclear Dynamics, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
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120
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Ganguly K, Giddaluru J, August A, Khan N. Post-transcriptional Regulation of Immunological Responses through Riboclustering. Front Immunol 2016; 7:161. [PMID: 27199986 PMCID: PMC4850162 DOI: 10.3389/fimmu.2016.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
Immunological programing of immune cells varies in response to changing environmental signals. This process is facilitated by modifiers that regulate the translational fate of mRNAs encoding various immune mediators, including cytokines and chemokines, which in turn determine the rapid activation, tolerance, and plasticity of the immune system. RNA-binding proteins (RBPs) recruited by the specific sequence elements in mRNA transcripts are one such modifiers. These RBPs form RBP-RNA complexes known as "riboclusters." These riboclusters serve as RNA sorting machinery, where depending upon the composition of the ribocluster, translation, degradation, or storage of mRNA is controlled. Recent findings suggest that this regulation of mRNA homeostasis is critical for controlling the immune response. Here, we present the current knowledge of the ribocluster-mediated post-transcriptional regulation of immune mediators and highlight recent findings regarding their implications for the pathogenesis of acute or chronic inflammatory diseases.
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Affiliation(s)
- Koelina Ganguly
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| | - Jeevan Giddaluru
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University , New York, NY , USA
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
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121
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Fu R, Olsen MT, Webb K, Bennett EJ, Lykke-Andersen J. Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements. RNA (NEW YORK, N.Y.) 2016; 22:373-382. [PMID: 26763119 PMCID: PMC4748815 DOI: 10.1261/rna.054833.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The zinc finger protein tristetraprolin (TTP) promotes translation repression and degradation of mRNAs containing AU-rich elements (AREs). Although much attention has been directed toward understanding the decay process and machinery involved, the translation repression role of TTP has remained poorly understood. Here we identify the cap-binding translation repression 4EHP-GYF2 complex as a cofactor of TTP. Immunoprecipitation and in vitro pull-down assays demonstrate that TTP associates with the 4EHP-GYF2 complex via direct interaction with GYF2, and mutational analyses show that this interaction occurs via conserved tetraproline motifs of TTP. Mutant TTP with diminished 4EHP-GYF2 binding is impaired in its ability to repress a luciferase reporter ARE-mRNA. 4EHP knockout mouse embryonic fibroblasts (MEFs) display increased induction and slower turnover of TTP-target mRNAs as compared to wild-type MEFs. Our work highlights the function of the conserved tetraproline motifs of TTP and identifies 4EHP-GYF2 as a cofactor in translational repression and mRNA decay by TTP.
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Affiliation(s)
- Rui Fu
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Myanna T Olsen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Kristofor Webb
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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122
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Zhu JG, Yuan DB, Chen WH, Han ZD, Liang YX, Chen G, Fu X, Liang YK, Chen GX, Sun ZL, Liu ZZ, Chen JH, Jiang FN, Zhong WD. Prognostic value of ZFP36 and SOCS3 expressions in human prostate cancer. Clin Transl Oncol 2015; 18:782-91. [PMID: 26563146 DOI: 10.1007/s12094-015-1432-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/13/2015] [Indexed: 11/25/2022]
Abstract
PURPOSE ZFP36 ring finger protein (ZFP36) and the suppressor of cytokine signaling 3 (SOCS3) have been reported to, respectively, regulate NF-κB and STAT3 signaling pathways. To better understand the correlation of NF-κB and STAT3 negative regulates pathway, we have investigated the involvement of ZFP36 and SOCS3 expressions in human prostate cancer (PCa). METHODS In the present study, paired patient tissue microarrays were analyzed by immunohistochemistry, and the ZFP36 protein expression was quantitated as immunoreactive scores in patients with PCa. Associations between ZFP36/SOCS3 expression and various clinicopathological features and prognosis of PCa patients were statistically analyzed based on the Taylor database. Then, the functions of ZFP36 and SOCS3 in cancerous inflammation were determined using qPCR and immunohistochemistry in vitro and in vivo. RESULTS ZFP36 protein expression in PCa tissues was significantly lower than those in non-cancerous prostate tissues (P < 0.05). In mRNA level, ZFP36 and SOCS3 had a close correlation with each other (P < 0.01, Pearson r = 0.848), and its upregulation was both significantly associated with low Gleason score (P < 0.001 and P < 0.001, respectively), negative metastasis (P < 0.001 and P < 0.001, respectively), favorable overall survival (P < 0.001 and P < 0.05, respectively), and negative biochemical recurrence (P < 0.001 and P < 0.001, respectively). Functionally, LPS treatment could lead to the overexpression of ZFP36 and SOCS3 in vitro and vivo. CONCLUSIONS Our data offer the convincing evidence for the first time that the aberrant expressions of ZFP36 and SOCS3 may be involved into the progression and patients' prognosis of PCa, implying their potentials as candidate markers of this cancer.
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Affiliation(s)
- J-G Zhu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, 550002, China
| | - D-B Yuan
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, 550002, China
| | - W-H Chen
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, 550002, China
| | - Z-D Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Y-X Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - G Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - X Fu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Y-K Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - G-X Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Z-L Sun
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, 550002, China
| | - Z-Z Liu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - J-H Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - F-N Jiang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China.
| | - W-D Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China.
- Guangdong Provincial Institute of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Urology, Huadu District People's Hospital, Southern Medical University, Guangzhou, 510800, China.
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510230, China.
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123
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Chen MT, Dong L, Zhang XH, Yin XL, Ning HM, Shen C, Su R, Li F, Song L, Ma YN, Wang F, Zhao HL, Yu J, Zhang JW. ZFP36L1 promotes monocyte/macrophage differentiation by repressing CDK6. Sci Rep 2015; 5:16229. [PMID: 26542173 PMCID: PMC4635361 DOI: 10.1038/srep16229] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
RNA binding proteins (RBPs)-mediated post-transcriptional control has been implicated in influencing various aspects of RNA metabolism and playing important roles in mammalian development and pathological diseases. However, the functions of specific RBPs and the molecular mechanisms through which they act in monocyte/macrophage differentiation remain to be determined. In this study, through bioinformatics analysis and experimental validation, we identify that ZFP36L1, a member of ZFP36 zinc finger protein family, exhibits significant decrease in acute myeloid leukemia (AML) patients compared with normal controls and remarkable time-course increase during monocyte/macrophage differentiation of PMA-induced THP-1 and HL-60 cells as well as induction culture of CD34+ hematopoietic stem/progenitor cells (HSPCs). Lentivirus-mediated gain and loss of function assays demonstrate that ZFP36L1 acts as a positive regulator to participate in monocyte/macrophage differentiation. Mechanistic investigation further reveals that ZFP36L1 binds to the CDK6 mRNA 3′untranslated region bearing adenine-uridine rich elements and negatively regulates the expression of CDK6 which is subsequently demonstrated to impede the in vitro monocyte/macrophage differentiation of CD34+ HSPCs. Collectively, our work unravels a ZFP36L1-mediated regulatory circuit through repressing CDK6 expression during monocyte/macrophage differentiation, which may also provide a therapeutic target for AML therapy.
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Affiliation(s)
- Ming-Tai Chen
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Lei Dong
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xin-Hua Zhang
- Haematology Department, the 303 Hospital, Nanning, China
| | - Xiao-Lin Yin
- Haematology Department, the 303 Hospital, Nanning, China
| | - Hong-Mei Ning
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital to Academy of Military Medical Science, Beijing, China
| | - Chao Shen
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Rui Su
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Feng Li
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Li Song
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yan-Ni Ma
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Fang Wang
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Hua-Lu Zhao
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jun-Wu Zhang
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
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124
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Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga JI, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nat Genet 2015; 47:1304-15. [PMID: 26437031 DOI: 10.1038/ng.3415] [Citation(s) in RCA: 577] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/09/2015] [Indexed: 12/11/2022]
Abstract
Adult T cell leukemia/lymphoma (ATL) is a peripheral T cell neoplasm of largely unknown genetic basis, associated with human T cell leukemia virus type-1 (HTLV-1) infection. Here we describe an integrated molecular study in which we performed whole-genome, exome, transcriptome and targeted resequencing, as well as array-based copy number and methylation analyses, in a total of 426 ATL cases. The identified alterations overlap significantly with the HTLV-1 Tax interactome and are highly enriched for T cell receptor-NF-κB signaling, T cell trafficking and other T cell-related pathways as well as immunosurveillance. Other notable features include a predominance of activating mutations (in PLCG1, PRKCB, CARD11, VAV1, IRF4, FYN, CCR4 and CCR7) and gene fusions (CTLA4-CD28 and ICOS-CD28). We also discovered frequent intragenic deletions involving IKZF2, CARD11 and TP73 and mutations in GATA3, HNRNPA2B1, GPR183, CSNK2A1, CSNK2B and CSNK1A1. Our findings not only provide unique insights into key molecules in T cell signaling but will also guide the development of new diagnostics and therapeutics in this intractable tumor.
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Affiliation(s)
- Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Kitanaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Center for Neurological Disease and Cancer, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Jun-Ichirou Yasunaga
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satsuki Muto
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Kotani
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosaku Watatani
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - June Takeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masako Iwanaga
- Department of Frontier Life Science, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Guangyong Ma
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Kisato Nosaka
- Department of Hematology, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidehiro Itonaga
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Wataru Munakata
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | | | | | - Ken Sasai
- KAN Research Institute, Inc., Kobe, Japan
| | | | - Marina Penova
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kotaro Shide
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoko Kubuki
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tomonori Hidaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takuro Kameda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tsuyoshi Nakamaki
- Division of Hematology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Ken Ishiyama
- Department of Hematology and Oncology, Kanazawa University Hospital, Kanazawa, Japan
| | - Shuichi Miyawaki
- Division of Hematology, Department of Internal Medicine, Tokyo Metropolitan Ohtsuka Hospital, Tokyo, Japan
| | - Sung-Soo Yoon
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kensei Tobinai
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Toshiki Watanabe
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuya Shimoda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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125
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Newman R, McHugh J, Turner M. RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol 2015. [PMID: 26201441 DOI: 10.1111/cei.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific RNA binding proteins (RBP) are important regulators of the immune response. RBP modulate gene expression by regulating splicing, polyadenylation, localization, translation and decay of target mRNAs. Increasing evidence suggests that RBP play critical roles in the development, activation and function of lymphocyte populations in the immune system. This review will discuss the post-transcriptional regulation of gene expression by RBP during lymphocyte development, with particular focus on the Tristetraprolin family of RBP.
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Affiliation(s)
- R Newman
- Babraham Institute, Cambridge, UK
| | - J McHugh
- Babraham Institute, Cambridge, UK
| | - M Turner
- Babraham Institute, Cambridge, UK
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126
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Lubeck BA, Lapinski PE, Oliver JA, Ksionda O, Parada LF, Zhu Y, Maillard I, Chiang M, Roose J, King PD. Cutting Edge: Codeletion of the Ras GTPase-Activating Proteins (RasGAPs) Neurofibromin 1 and p120 RasGAP in T Cells Results in the Development of T Cell Acute Lymphoblastic Leukemia. THE JOURNAL OF IMMUNOLOGY 2015; 195:31-5. [PMID: 26002977 DOI: 10.4049/jimmunol.1402639] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 04/28/2015] [Indexed: 12/11/2022]
Abstract
Ras GTPase-activating proteins (RasGAPs) inhibit signal transduction initiated through the Ras small GTP-binding protein. However, which members of the RasGAP family act as negative regulators of T cell responses is not completely understood. In this study, we investigated potential roles for the RasGAPs RASA1 and neurofibromin 1 (NF1) in T cells through the generation and analysis of T cell-specific RASA1 and NF1 double-deficient mice. In contrast to mice lacking either RasGAP alone in T cells, double-deficient mice developed T cell acute lymphoblastic leukemia/lymphoma, which originated at an early point in T cell development and was dependent on activating mutations in the Notch1 gene. These findings highlight RASA1 and NF1 as cotumor suppressors in the T cell lineage.
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Affiliation(s)
- Beth A Lubeck
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Philip E Lapinski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Jennifer A Oliver
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Olga Ksionda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143
| | - Luis F Parada
- Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Yuan Zhu
- Division of Molecular Medicine and Genetics, University of Michigan Medical School, Ann Arbor, MI 48109; and
| | - Ivan Maillard
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Mark Chiang
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Jeroen Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143
| | - Philip D King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109;
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127
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Minuesa G, Antczak C, Shum D, Radu C, Bhinder B, Li Y, Djaballah H, Kharas MG. A 1536-well fluorescence polarization assay to screen for modulators of the MUSASHI family of RNA-binding proteins. Comb Chem High Throughput Screen 2015; 17:596-609. [PMID: 24912481 DOI: 10.2174/1386207317666140609122714] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/31/2014] [Accepted: 06/09/2014] [Indexed: 11/22/2022]
Abstract
RNA-binding proteins (RBPs) can act as stem cell modulators and oncogenic drivers, but have been largely ignored by the pharmaceutical industry as potential therapeutic targets for cancer. The MUSASHI (MSI) family has recently been demonstrated to be an attractive clinical target in the most aggressive cancers. Therefore, the discovery and development of small molecule inhibitors could provide a novel therapeutic strategy. In order to find novel compounds with MSI RNA binding inhibitory activity, we have developed a fluorescence polarization (FP) assay and optimized it for high throughput screening (HTS) in a 1536-well microtiter plate format. Using a chemical library of 6,208 compounds, we performed pilot screens, against both MSI1 and MSI2, leading to the identification of 7 molecules for MSI1, 15 for MSI2 and 5 that inhibited both. A secondary FP dose-response screen validated 3 MSI inhibitors with IC50 below 10 μM. Out of the 25 compounds retested in the secondary screen only 8 demonstrated optical interference due to high fluorescence. Utilizing a SYBR-based RNA electrophoresis mobility shift assay (EMSA), we further verified MSI inhibition of the top 3 compounds. Surprisingly, even though several aminoglycosides were present in the library, they failed to demonstrate MSI inhibitor activity challenging the concept that these compounds are pan-active against RBPs. In summary, we have developed an in vitro strategy to identify MSI specific inhibitors using an FP HTS platform, which will facilitate novel drug discovery for this class of RBPs.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael G Kharas
- (Michael G. Kharas) Molecular Pharmacology & Chemistry Program, MSKCC, New York, USA.
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128
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RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation. Proc Natl Acad Sci U S A 2015; 112:E1888-97. [PMID: 25825742 DOI: 10.1073/pnas.1422490112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Posttranscriptional regulation is a major mechanism to rewire transcriptomes during differentiation. Heterogeneous nuclear RNA-binding protein LL (hnRNPLL) is specifically induced in terminally differentiated lymphocytes, including effector T cells and plasma cells. To study the molecular functions of hnRNPLL at a genome-wide level, we identified hnRNPLL RNA targets and binding sites in plasma cells through integrated Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) and RNA sequencing. hnRNPLL preferentially recognizes CA dinucleotide-containing sequences in introns and 3' untranslated regions (UTRs), promotes exon inclusion or exclusion in a context-dependent manner, and stabilizes mRNA when associated with 3' UTRs. During differentiation of primary B cells to plasma cells, hnRNPLL mediates a genome-wide switch of RNA processing, resulting in loss of B-cell lymphoma 6 (Bcl6) expression and increased Ig production--both hallmarks of plasma-cell maturation. Our data identify previously unknown functions of hnRNPLL in B-cell to plasma-cell differentiation and demonstrate that the RNA-binding protein hnRNPLL has a critical role in tuning transcriptomes of terminally differentiating B lymphocytes.
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129
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Morgan BR, Deveau LM, Massi F. Probing the structural and dynamical effects of the charged residues of the TZF domain of TIS11d. Biophys J 2015; 108:1503-1515. [PMID: 25809263 DOI: 10.1016/j.bpj.2015.01.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/25/2022] Open
Abstract
A member of the TTP family of proteins, TIS11d binds RNA with high specificity using a pair of CCCH-type tandem zinc fingers separated by a 18 residue long linker. Our previous work showed that the formation of hydrogen bonds between the C-terminal residue E220 and the residues of the linker region stabilized a compact structure of TIS11d in the absence of RNA. To investigate the role of the C-terminal residues in the structure of unbound TIS11d, the E220A mutant and the truncation mutant lacking the last two residues (D219/E220) were studied using molecular dynamics, NMR spectroscopy, and biochemical methods. This study confirmed the importance of the charged residues D219 and E220 in maintaining structural stability in unbound TIS11d and elucidated the underlying physical mechanisms. We observed a greater structural heterogeneity for the residues of the linker in the molecular dynamics trajectories of both mutant proteins relative to the wild-type. This heterogeneity was more pronounced in the D219/E220 deletion mutant than in the E220A mutant, indicating that a greater reduction of the charge of the C-terminus results in greater flexibility. In agreement with the increased flexibility and the reduced number of negatively charged residues of the D219/E220 deletion mutant, we measured more unfavorable entropic and a more favorable enthalpic contribution to the free energy of RNA binding in the mutant than in the wild-type protein. The relative orientation of the zinc fingers was stabilized by the electrostatic interaction between E220 and positively charged residues of the linker in TIS11d. In the E220A mutant, the relative orientation of the zinc fingers was less constrained, whereas in the D219/E220 deletion mutant, little orientational preference was observed. We posit that favorable electrostatic interactions provide a mechanism to promote preferential orientation of separate domains without imposing structural rigidity.
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Affiliation(s)
- Brittany R Morgan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts
| | - Laura M Deveau
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts.
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130
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Raine T, Liu JZ, Anderson CA, Parkes M, Kaser A. Generation of primary human intestinal T cell transcriptomes reveals differential expression at genetic risk loci for immune-mediated disease. Gut 2015; 64:250-9. [PMID: 24799394 PMCID: PMC4316924 DOI: 10.1136/gutjnl-2013-306657] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWAS) have identified genetic variants within multiple risk loci as predisposing to intestinal inflammatory diseases, including Crohn's disease, ulcerative colitis and coeliac disease. Most risk variants affect regulation of transcription, but a critical challenge is to identify which genes and which cell types these variants affect. We aimed to characterise whole transcriptomes for each common T lymphocyte subset resident within the gut mucosa, and use these to infer biological insights and highlight candidate genes of interest within GWAS risk loci. DESIGN We isolated the four major intestinal T cell populations from pinch biopsies from healthy subjects and generated transcriptomes for each. We computationally integrated these transcriptomes with GWAS data from immune-related diseases. RESULTS Robust, high quality transcriptomic data were generated from 1 ng of RNA from precisely sorted cell subsets. Gene expression patterns clearly differentiated intestinal T cells from counterparts in peripheral blood and revealed distinct signalling pathways for each intestinal T cell subset. Intestinal-specific T cell transcripts were enriched in GWAS risk loci for Crohn's disease, ulcerative colitis and coeliac disease, but also specific extraintestinal immune-mediated diseases, allowing prediction of novel candidate genes. CONCLUSIONS This is the first report of transcriptomes for minimally manipulated intestinal T lymphocyte subsets in humans. We have demonstrated that careful processing of mucosal biopsies allows the generation of transcriptomes from as few as 1000 highly purified cells with minimal interindividual variation. Bioinformatic integration of transcriptomic data with recent GWAS data identified specific candidate genes and cell types for inflammatory pathologies.
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Affiliation(s)
- Tim Raine
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jimmy Z Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Miles Parkes
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Arthur Kaser
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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The Role of p110δ in the Development and Activation of B Lymphocytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 850:119-35. [DOI: 10.1007/978-3-319-15774-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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132
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Hyatt LD, Wasserman GA, Rah YJ, Matsuura KY, Coleman FT, Hilliard KL, Pepper-Cunningham ZA, Ieong M, Stumpo DJ, Blackshear PJ, Quinton LJ, Mizgerd JP, Jones MR. Myeloid ZFP36L1 does not regulate inflammation or host defense in mouse models of acute bacterial infection. PLoS One 2014; 9:e109072. [PMID: 25299049 PMCID: PMC4192124 DOI: 10.1371/journal.pone.0109072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Zinc finger protein 36, C3H type-like 1 (ZFP36L1) is one of several Zinc Finger Protein 36 (Zfp36) family members, which bind AU rich elements within 3' untranslated regions (UTRs) to negatively regulate the post-transcriptional expression of targeted mRNAs. The prototypical member of the family, Tristetraprolin (TTP or ZFP36), has been well-studied in the context of inflammation and plays an important role in repressing pro-inflammatory transcripts such as TNF-α. Much less is known about the other family members, and none have been studied in the context of infection. Using macrophage cell lines and primary alveolar macrophages we demonstrated that, like ZFP36, ZFP36L1 is prominently induced by infection. To test our hypothesis that macrophage production of ZFP36L1 is necessary for regulation of the inflammatory response of the lung during pneumonia, we generated mice with a myeloid-specific deficiency of ZFP36L1. Surprisingly, we found that myeloid deficiency of ZFP36L1 did not result in alteration of lung cytokine production after infection, altered clearance of bacteria, or increased inflammatory lung injury. Although alveolar macrophages are critical components of the innate defense against respiratory pathogens, we concluded that myeloid ZFP36L1 is not essential for appropriate responses to bacteria in the lungs. Based on studies conducted with myeloid-deficient ZFP36 mice, our data indicate that, of the Zfp36 family, ZFP36 is the predominant negative regulator of cytokine expression in macrophages. In conclusion, these results imply that myeloid ZFP36 may fully compensate for loss of ZFP36L1 or that Zfp36l1-dependent mRNA expression does not play an integral role in the host defense against bacterial pneumonia.
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Affiliation(s)
- Lynnae D. Hyatt
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Gregory A. Wasserman
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Yoon J. Rah
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kori Y. Matsuura
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Fadie T. Coleman
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kristie L. Hilliard
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | | | - Michael Ieong
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Deborah J. Stumpo
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lee J. Quinton
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Joseph P. Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Matthew R. Jones
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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133
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Kafasla P, Skliris A, Kontoyiannis DL. Post-transcriptional coordination of immunological responses by RNA-binding proteins. Nat Immunol 2014; 15:492-502. [PMID: 24840980 DOI: 10.1038/ni.2884] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 12/22/2022]
Abstract
Immunological reactions are propelled by ever-changing signals that alter the translational ability of the RNA in the cells involved. Such alterations are considered to be consequential modifications in the transcriptomic decoding of the genetic blueprint. The identification of RNA-binding protein (RBP) assemblies engaged in the coordinative regulation of state-specific RNAs indicates alternative and exclusive means for determining the activation, plasticity and tolerance of cells of the immune system. Here we review current knowledge about RBP-regulated post-transcriptional events involved in the reactivity of cells of the immune system and the importance of their alteration during chronic inflammatory pathology and autoimmunity.
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Affiliation(s)
- Panagiota Kafasla
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Antonis Skliris
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
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134
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Turner M, Galloway A, Vigorito E. Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol 2014; 15:484-91. [PMID: 24840979 DOI: 10.1038/ni.2887] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/01/2014] [Indexed: 12/11/2022]
Abstract
The rapid changes in gene expression that accompany developmental transitions, stress responses and proliferation are controlled by signal-mediated coordination of transcriptional and post-transcriptional mechanisms. In recent years, understanding of the mechanics of these processes and the contexts in which they are employed during hematopoiesis and immune challenge has increased. An important aspect of this progress is recognition of the importance of RNA-binding proteins and noncoding RNAs. These have roles in the development and function of the immune system and in pathogen life cycles, and they represent an important aspect of intracellular immunity.
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Affiliation(s)
- Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Alison Galloway
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Elena Vigorito
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
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135
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Zekavati A, Nasir A, Alcaraz A, Aldrovandi M, Marsh P, Norton JD, Murphy JJ. Post-transcriptional regulation of BCL2 mRNA by the RNA-binding protein ZFP36L1 in malignant B cells. PLoS One 2014; 9:e102625. [PMID: 25014217 PMCID: PMC4094554 DOI: 10.1371/journal.pone.0102625] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 06/22/2014] [Indexed: 12/25/2022] Open
Abstract
The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3' untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the 'maximum information coefficient' (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experiments revealed that ZFP36L1 interacted with the BCL2 adenine uridine rich element. In murine BCL1 leukemia cells stably transduced with a ZFP36L1 ShRNA lentiviral construct, BCL2 mRNA degradation was significantly delayed compared to control lentiviral expressing cells and ZFP36L1 knockdown in different cell types (BCL1, ACHN, Ramos), resulted in increased levels of BCL2 mRNA levels compared to control cells. 3' untranslated region luciferase reporter assays in HEK293T cells showed that wild type but not zinc finger mutant ZFP36L1 protein was able to downregulate a BCL2 construct containing the BCL2 adenine uridine rich element and removal of the adenine uridine rich core from the BCL2 3' untranslated region in the reporter construct significantly reduced the ability of ZFP36L1 to mediate this effect. Taken together, our data are consistent with ZFP36L1 interacting with and mediating degradation of BCL2 mRNA as an important target through which ZFP36L1 mediates its pro-apoptotic effects in malignant B-cells.
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Affiliation(s)
- Anna Zekavati
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Asghar Nasir
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Amor Alcaraz
- Department of Biomedical Sciences, University of Westminster, London, United Kingdom
| | - Maceler Aldrovandi
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Phil Marsh
- Division of Endocrinology, King's College London, London, United Kingdom
| | - John D. Norton
- School of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom
| | - John J. Murphy
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
- Department of Biomedical Sciences, University of Westminster, London, United Kingdom
- * E-mail:
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136
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hnRNP F complexes with tristetraprolin and stimulates ARE-mRNA decay. PLoS One 2014; 9:e100992. [PMID: 24978456 PMCID: PMC4076271 DOI: 10.1371/journal.pone.0100992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/01/2014] [Indexed: 01/12/2023] Open
Abstract
The tristetraprolin (TTP) family of zinc-finger proteins, TTP, BRF1 and BRF2, regulate the stability of a subset of mRNAs containing 3′UTR AU-rich elements (AREs), including mRNAs coding for cytokines, transcription factors, and proto-oncogenes. To better understand the mechanism by which TTP-family proteins control mRNA stability in mammalian cells, we aimed to identify TTP- and BRF1-interacting proteins as potential TTP-family co-factors. This revealed hnRNP F as a prominent interactor of TTP and BRF1. While TTP, BRF1 and hnRNP F are all RNA binding proteins (RBPs), the interaction of hnRNP F with TTP and BRF1 is independent of RNA. Depletion of hnRNP F impairs the decay of a subset of TTP-substrate ARE-mRNAs by a mechanism independent of the extent of hnRNP F binding to the mRNA. Taken together, these findings implicate hnRNP F as a co-factor in a subset of TTP/BRF-mediated mRNA decay and highlight the importance of RBP cooperativity in mRNA regulation.
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137
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Coeliac disease-associated polymorphisms influence thymic gene expression. Genes Immun 2014; 15:355-60. [PMID: 24871462 DOI: 10.1038/gene.2014.26] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/21/2014] [Accepted: 04/22/2014] [Indexed: 01/17/2023]
Abstract
Significant associations between coeliac disease (CD) and single nucleotide polymorphisms (SNPs) distributed over 40 genetic regions have been established. The majority of these SNPs are non-coding and 20 SNPs were, by expression quantitative trait loci (eQTL) analysis, found to harbour cis regulatory potential in peripheral blood mononuclear cells (PBMC). Almost all regions contain genes with an immunological relevant function, of which many act in the same biological pathways. One such pathway is T-cell development in the thymus, a pathway previously not explored in CD pathogenesis. The aim of our study was to explore the regulatory potential of the CD-associated SNPs (n=50) by eQTL analysis in thymic tissue from 42 subjects. In total, 43 nominal significant (P<0.05) eQTLs were found within 24 CD-associated chromosomal regions, corresponding to 27 expression-altering SNPs (eSNPs) and 40 probes (eProbes) that represents 39 unique genes (eGenes). Nine significant probe-SNP pairs (corresponding to 8 eSNPs and 7 eGenes) overlapped with previous findings in PBMC (rs12727642-PARK7, rs296547-DDX59, rs917997-IL18RAP, rs842647-AHSA2, rs13003464-AHSA2, rs6974491-ELMO1, rs2074404-NSF (two independent probes) and rs2298428-UBE2L3). When compared across more tissues, we found that 14 eQTLs could represent potentially novel thymus-specific eQTLs. This implies that CD risk polymorphisms could affect gene regulation in thymus.
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138
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Ball CB, Rodriguez KF, Stumpo DJ, Ribeiro-Neto F, Korach KS, Blackshear PJ, Birnbaumer L, Ramos SBV. The RNA-binding protein, ZFP36L2, influences ovulation and oocyte maturation. PLoS One 2014; 9:e97324. [PMID: 24830504 PMCID: PMC4022657 DOI: 10.1371/journal.pone.0097324] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/17/2014] [Indexed: 02/01/2023] Open
Abstract
ZFP36L2 protein destabilizes AU-rich element-containing transcripts and has been implicated in female fertility. In the C57BL/6NTac mouse, a mutation in Zfp36l2 that results in the decreased expression of a form of ZFP36L2 in which the 29 N-terminal amino acid residues have been deleted, ΔN-ZFP36L2, leads to fertilized eggs that arrest at the two-cell stage. Interestingly, homozygous ΔN-Zfp36l2 females in the C57BL/6NTac strain release 40% fewer eggs than the WT littermates (Ramos et al., 2004), suggesting an additional defect in ovulation and/or oocyte maturation. Curiously, the same ΔN-Zfp36l2 mutation into the SV129 strain resulted in anovulation, prompting us to investigate a potential problem in ovulation and oocyte maturation. Remarkably, only 20% of ΔN-Zfp36l2 oocytes in the 129S6/SvEvTac strain matured ex vivo, suggesting a defect on the oocyte meiotic maturation process. Treatment of ΔN-Zfp36l2 oocytes with a PKA inhibitor partially rescued the meiotic arrested oocytes. Furthermore, cAMP levels were increased in ΔN-Zfp36l2 oocytes, linking the cAMP/PKA pathway and ΔN-Zfp36l2 with meiotic arrest. Since ovulation and oocyte maturation are both triggered by LHR signaling, the downstream pathway was investigated. Adenylyl cyclase activity was increased in ΔN-Zfp36l2 ovaries only upon LH stimulation. Moreover, we discovered that ZFP36L2 interacts with the 3′UTR of LHR mRNA and that decreased expression levels of Zfp36l2 correlates with higher levels of LHR mRNA in synchronized ovaries. Furthermore, overexpression of ZFP36L2 decreases the endogenous expression of LHR mRNA in a cell line. Therefore, we propose that lack of the physiological down regulation of LHR mRNA levels by ZFP36L2 in the ovaries is associated with anovulation and oocyte meiotic arrest.
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Affiliation(s)
- Christopher B. Ball
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Karina F. Rodriguez
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Deborah J. Stumpo
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Fernando Ribeiro-Neto
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Kenneth S. Korach
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- Medicine and Biochemistry Departments, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lutz Birnbaumer
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Silvia B. V. Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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139
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Brf1 posttranscriptionally regulates pluripotency and differentiation responses downstream of Erk MAP kinase. Proc Natl Acad Sci U S A 2014; 111:E1740-8. [PMID: 24733888 DOI: 10.1073/pnas.1320873111] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AU-rich element mRNA-binding proteins (AUBPs) are key regulators of development, but how they are controlled and what functional roles they play depends on cellular context. Here, we show that Brf1 (zfp36l1), an AUBP from the Zfp36 protein family, operates downstream of FGF/Erk MAP kinase signaling to regulate pluripotency and cell fate decision making in mouse embryonic stem cells (mESCs). FGF/Erk MAP kinase signaling up-regulates Brf1, which disrupts the expression of core pluripotency-associated genes and attenuates mESC self-renewal without inducing differentiation. These regulatory effects are mediated by rapid and direct destabilization of Brf1 targets, such as Nanog mRNA. Enhancing Brf1 expression does not compromise mESC pluripotency but does preferentially regulate mesendoderm commitment during differentiation, accelerating the expression of primitive streak markers. Together, these studies demonstrate that FGF signals use targeted mRNA degradation by Brf1 to enable rapid posttranscriptional control of gene expression in mESCs.
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140
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Cosson A, Chapiro E, Belhouachi N, Cung HA, Keren B, Damm F, Algrin C, Lefebvre C, Fert-Ferrer S, Luquet I, Gachard N, Mugneret F, Terre C, Collonge-Rame MA, Michaux L, Rafdord-Weiss I, Talmant P, Veronese L, Nadal N, Struski S, Barin C, Helias C, Lafage M, Lippert E, Auger N, Eclache V, Roos-Weil D, Leblond V, Settegrana C, Maloum K, Davi F, Merle-Beral H, Lesty C, Nguyen-Khac F. 14q deletions are associated with trisomy 12, NOTCH1 mutations and unmutated IGHV genes in chronic lymphocytic leukemia and small lymphocytic lymphoma. Genes Chromosomes Cancer 2014; 53:657-66. [PMID: 24729385 DOI: 10.1002/gcc.22176] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/01/2014] [Indexed: 01/21/2023] Open
Abstract
Deletions of the long arm of chromosome 14 [del(14q)] are rare but recurrently observed in mature B-cell neoplasms, particularly in chronic lymphocytic leukemia (CLL). To further characterize this aberration, we studied 81 cases with del(14q): 54 of CLL and 27 of small lymphocytic lymphoma (SLL), the largest reported series to date. Using karyotype and fluorescence in situ hybridization (FISH), the most frequent additional abnormality was trisomy 12 (tri12), observed in 28/79 (35%) cases, followed by del13q14 (12/79, 15%), delTP53 (11/80, 14%) delATM (5/79, 6%), and del6q21 (3/76, 4%). IGHV genes were unmutated in 41/53 (77%) patients, with a high frequency of IGHV1-69 (21/52, 40%). NOTCH1 gene was mutated in 14/45 (31%) patients. There was no significant difference in cytogenetic and molecular abnormalities between CLL and SLL. Investigations using FISH and SNP-array demonstrated the heterogeneous size of the 14q deletions. However, a group with the same del(14)(q24.1q32.33) was identified in 48% of cases. In this group, tri12 (P = 0.004) and NOTCH1 mutations (P = 0.02) were significantly more frequent than in the other patients. In CLL patients with del(14q), median treatment-free survival (TFS) was 27 months. In conclusion, del(14q) is associated with tri12 and with pejorative prognostic factors: unmutated IGHV genes (with over-representation of the IGHV1-69 repertoire), NOTCH1 mutations, and a short TFS.
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Affiliation(s)
- Adrien Cosson
- INSERM U872, Centre de Recherche des Cordeliers, Paris 6, France
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141
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Minagawa K, Wakahashi K, Kawano H, Nishikawa S, Fukui C, Kawano Y, Asada N, Sato M, Sada A, Katayama Y, Matsui T. Posttranscriptional modulation of cytokine production in T cells for the regulation of excessive inflammation by TFL. THE JOURNAL OF IMMUNOLOGY 2014; 192:1512-24. [PMID: 24415781 DOI: 10.4049/jimmunol.1301619] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Posttranscriptional machinery regulates inflammation and is associated with autoimmunity as well as tumorigenesis in collaboration with transcription factors. We previously identified the tumor suppressor gene transformed follicular lymphoma (TFL) on 6q25 in a patient with follicular lymphoma, which transformed into diffuse large B cell lymphoma. TFL families have a common RNase domain that governs macrophage-mediated inflammation. In human peripheral blood, TFL is dominantly expressed at the glycine- and tryptophan-rich cytoplasmic processing bodies of T lymphocytes, and it is persistently upregulated in activated T cells. To address its physiological role, we established TFL(-/-) mice in which TFL(-/-) lymphocytes proliferated more rapidly than TFL(+/+) upon stimulation with inappropriate cytokine secretion, including IL-2, IL-6, and IL-10. Moreover, TFL inhibited the synthesis of cytokines such as IL-2, IL-6, IL-10, TNF-α, and IL-17a by 3' untranslated region RNA degradation. Experimental autoimmune encephalitis induced in TFL(-/-) mice demonstrated persistent severe paralysis. CNS-infiltrated CD4(+) T cells in TFL(-/-) mice contained a higher proportion of Th17 cells than did those in TFL(+/+) mice during the resolution phase, and IL-17a mRNA levels were markedly increased in TFL(-/-) cells. These results suggest that TFL may play an important role in attenuating local inflammation by suppressing the infiltration of Th17 cells in the CNS during the resolution phase of experimental autoimmune encephalitis. TFL is a novel gradual and persistent posttranscriptional regulator, and the TFL-driven attenuation of excessive inflammation could contribute to recovery from T cell-mediated autoimmune diseases.
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Affiliation(s)
- Kentaro Minagawa
- Division of Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
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Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol 2014; 15:R12. [PMID: 24401661 PMCID: PMC4053807 DOI: 10.1186/gb-2014-15-1-r12] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 01/08/2013] [Indexed: 02/05/2023] Open
Abstract
Background ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embryonic kidney cells, and examined the combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Results Targets bound and negatively regulated by ZFP36 include transcripts encoding proteins necessary for immune function and cancer, and transcripts encoding other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance upon ZFP36 overexpression independent of effects from confounding features. Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes, and found that ZFP36 degrades transcripts through specific AU-rich sequences, representing a subset of the U-rich sequences ELAVL1 interacts with to stabilize transcripts. Conclusions ZFP36-RNA target specificities in vivo are quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to unravel in vivo combinatorial regulation by RNA-binding proteins.
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143
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Storling J, Brorsson CA. Candidate genes expressed in human islets and their role in the pathogenesis of type 1 diabetes. Curr Diab Rep 2013; 13:633-41. [PMID: 23925433 DOI: 10.1007/s11892-013-0408-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In type 1 diabetes (T1D), the insulin-producing β cells are destroyed by an immune-mediated process leading to complete insulin deficiency. There is a strong genetic component in T1D. Genes located in the human leukocyte antigen (HLA) region are the most important genetic determinants of disease, but more than 40 additional loci are known to significantly affect T1D risk. Since most of the currently known genetic candidates have annotated immune cell functions, it is generally considered that most of the genetic susceptibility in T1D is caused by variation in genes affecting immune cell function. Recent studies, however, indicate that most T1D candidate genes are expressed in human islets suggesting that the functions of the genes are not restricted to immune cells, but also play roles in the islets and possibly the β cells. Several candidates change expression levels within the islets following exposure to proinflammatory cytokines highlighting that these genes may be involved in the response of β cells to immune attack. In this review, the compiling evidence that many of the candidate genes are expressed in islets and β cells will be presented. Further, we perform the first systematic human islet expression analysis of all genes located in 50 T1D-associated GWAS loci using a published RNA sequencing dataset. We find that 336 out of 857 genes are expressed in human islets and that many of these interact in protein networks. Finally, the potential pathogenetic roles of some candidate genes will be discussed.
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Affiliation(s)
- Joachim Storling
- Copenhagen Diabetes Research Center, Department of Paediatrics, Herlev University Hospital, Herlev Ringvej, DK-2730, Herlev, Denmark,
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144
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Yuan J, Muljo SA. Exploring the RNA world in hematopoietic cells through the lens of RNA-binding proteins. Immunol Rev 2013; 253:290-303. [PMID: 23550653 DOI: 10.1111/imr.12048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The discovery of microRNAs has renewed interest in posttranscriptional modes of regulation, fueling an emerging view of a rich RNA world within our cells that deserves further exploration. Much work has gone into elucidating genetic regulatory networks that orchestrate gene expression programs and direct cell fate decisions in the hematopoietic system. However, the focus has been to elucidate signaling pathways and transcriptional programs. To bring us one step closer to reverse engineering the molecular logic of cellular differentiation, it will be necessary to map posttranscriptional circuits as well and integrate them in the context of existing network models. In this regard, RNA-binding proteins (RBPs) may rival transcription factors as important regulators of cell fates and represent a tractable opportunity to connect the RNA world to the proteome. ChIP-seq has greatly facilitated genome-wide localization of DNA-binding proteins, helping us to understand genomic regulation at a systems level. Similarly, technological advances such as CLIP-seq allow transcriptome-wide mapping of RBP binding sites, aiding us to unravel posttranscriptional networks. Here, we review RBP-mediated posttranscriptional regulation, paying special attention to findings relevant to the immune system. As a prime example, we highlight the RBP Lin28B, which acts as a heterochronic switch between fetal and adult lymphopoiesis.
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Affiliation(s)
- Joan Yuan
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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145
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Goris A, Pauwels I, Dubois B. Progress in multiple sclerosis genetics. Curr Genomics 2013; 13:646-63. [PMID: 23730204 PMCID: PMC3492804 DOI: 10.2174/138920212803759695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 01/06/2023] Open
Abstract
A genetic component in the susceptibility to multiple sclerosis (MS) has long been known, and the first and major genetic risk factor, the HLA region, was identified in the 1970’s. However, only with the advent of genome-wide association studies in the past five years did the list of risk factors for MS grow from 1 to over 50. In this review, we summarize the search for MS risk genes and the latest results. Comparison with data from other autoimmune and neurological diseases and from animal models indicates parallels and differences between diseases. We discuss how these translate into an improved understanding of disease mechanisms, and address current challenges such as genotype-phenotype correlations, functional mechanisms of risk variants and the missing heritability.
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Affiliation(s)
- An Goris
- Laboratory for Neuroimmunology, Section of Experimental Neurology, KU Leuven, Leuven, Belgium
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146
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Ciais D, Cherradi N, Feige JJ. Multiple functions of tristetraprolin/TIS11 RNA-binding proteins in the regulation of mRNA biogenesis and degradation. Cell Mol Life Sci 2013; 70:2031-44. [PMID: 22968342 PMCID: PMC11113850 DOI: 10.1007/s00018-012-1150-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 02/06/2023]
Abstract
Members of the tristetraprolin (TTP/TIS11) family are important RNA-binding proteins initially characterized as mediators of mRNA degradation. They act via their interaction with AU-rich elements present in the 3'UTR of regulated transcripts. However, it is progressively appearing that the different steps of mRNA processing and fate including transcription, splicing, polyadenylation, translation, and degradation are coordinately regulated by multifunctional integrator proteins that possess a larger panel of functions than originally anticipated. Tristetraprolin and related proteins are very good examples of such integrators. This review gathers the present knowledge on the functions of this family of RNA-binding proteins, including their role in AU-rich element-mediated mRNA decay and focuses on recent advances that support the concept of their broader involvement in distinct steps of mRNA biogenesis and degradation.
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Affiliation(s)
- Delphine Ciais
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
| | - Jean-Jacques Feige
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
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147
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Tréguer K, Faucheux C, Veschambre P, Fédou S, Thézé N, Thiébaud P. Comparative functional analysis of ZFP36 genes during Xenopus development. PLoS One 2013; 8:e54550. [PMID: 23342169 PMCID: PMC3546996 DOI: 10.1371/journal.pone.0054550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 12/14/2012] [Indexed: 01/12/2023] Open
Abstract
ZFP36 constitutes a small family of RNA binding proteins (formerly known as the TIS11 family) that target mRNA and promote their degradation. In mammals, ZFP36 proteins are encoded by four genes and, although they show similar activities in a cellular RNA destabilization assay, there is still a limited knowledge of their mRNA targets and it is not known whether or not they have redundant functions. In the present work, we have used the Xenopus embryo, a model system allowing gain- and loss-of-function studies, to investigate, whether individual ZFP36 proteins had distinct or redundant functions. We show that overexpression of individual amphibian zfp36 proteins leads to embryos having the same defects, with alteration in somites segmentation and pronephros formation. In these embryos, members of the Notch signalling pathway such as hairy2a or esr5 mRNA are down-regulated, suggesting common targets for the different proteins. We also show that mouse Zfp36 protein overexpression gives the same phenotype, indicating an evolutionary conserved property among ZFP36 vertebrate proteins. Morpholino oligonucleotide-induced loss-of-function leads to defects in pronephros formation, reduction in tubule size and duct coiling alterations for both zfp36 and zfp36l1, indicating no functional redundancy between these two genes. Given the conservation in gene structure and function between the amphibian and mammalian proteins and the conserved mechanisms for pronephros development, our study highlights a potential and hitherto unreported role of ZFP36 gene in kidney morphogenesis.
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148
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ZFP36L1 negatively regulates plasmacytoid differentiation of BCL1 cells by targeting BLIMP1 mRNA. PLoS One 2012; 7:e52187. [PMID: 23284928 PMCID: PMC3527407 DOI: 10.1371/journal.pone.0052187] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 11/09/2012] [Indexed: 12/03/2022] Open
Abstract
The ZFP36/Tis11 family of zinc-finger proteins regulate cellular processes by binding to adenine uridine rich elements in the 3′ untranslated regions of various mRNAs and promoting their degradation. We show here that ZFP36L1 expression is largely extinguished during the transition from B cells to plasma cells, in a reciprocal pattern to that of ZFP36 and the plasma cell transcription factor, BLIMP1. Enforced expression of ZFP36L1 in the mouse BCL1 cell line blocked cytokine-induced differentiation while shRNA-mediated knock-down enhanced differentiation. Reconstruction of regulatory networks from microarray gene expression data using the ARACNe algorithm identified candidate mRNA targets for ZFP36L1 including BLIMP1. Genes that displayed down-regulation in plasma cells were significantly over-represented (P = <0.0001) in a set of previously validated ZFP36 targets suggesting that ZFP36L1 and ZFP36 target distinct sets of mRNAs during plasmacytoid differentiation. ShRNA-mediated knock-down of ZFP36L1 in BCL1 cells led to an increase in levels of BLIMP1 mRNA and protein, but not for mRNAs of other transcription factors that regulate plasmacytoid differentiation (xbp1, irf4, bcl6). Finally, ZFP36L1 significantly reduced the activity of a BLIMP1 3′ untranslated region-driven luciferase reporter. Taken together, these findings suggest that ZFP36L1 negatively regulates plasmacytoid differentiation, at least in part, by targeting the expression of BLIMP1.
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149
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Nucleic acid-sensing Toll-like receptors are essential for the control of endogenous retrovirus viremia and ERV-induced tumors. Immunity 2012; 37:867-79. [PMID: 23142781 DOI: 10.1016/j.immuni.2012.07.018] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/17/2012] [Indexed: 01/12/2023]
Abstract
The genome of vertebrates contains endogenous retroviruses (ERVs) that are largely nonfunctional relicts of ancestral germline infection by exogenous retroviruses. However, in some mouse strains ERVs are actively involved in disease. Here we report that nucleic acid-recognizing Toll-like receptors 3, 7, and 9 (TLR 3, TLR7, and TLR9) are essential for the control of ERVs. Loss of TLR7 function caused spontaneous retroviral viremia that coincided with the absence of ERV-specific antibodies. Importantly, additional TLR3 and TLR9 deficiency led to acute T cell lymphoblastic leukemia, underscoring a prominent role for TLR3 and TLR9 in surveillance of ERV-induced tumors. Experimental ERV infection induced a TLR3-, TLR7-, and TLR9-dependent group of "acute-phase" genes previously described in HIV and SIV infections. Our study suggests that in addition to their role in innate immunity against exogenous pathogens, nucleic acid-recognizing TLRs contribute to the immune control of activated ERVs and ERV-induced tumors.
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150
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Rounbehler RJ, Fallahi M, Yang C, Steeves MA, Li W, Doherty JR, Schaub FX, Sanduja S, Dixon DA, Blackshear PJ, Cleveland JL. Tristetraprolin impairs myc-induced lymphoma and abolishes the malignant state. Cell 2012; 150:563-74. [PMID: 22863009 DOI: 10.1016/j.cell.2012.06.033] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 10/10/2011] [Accepted: 06/14/2012] [Indexed: 12/27/2022]
Abstract
Myc oncoproteins directly regulate transcription by binding to target genes, yet this only explains a fraction of the genes affected by Myc. mRNA turnover is controlled via AU-binding proteins (AUBPs) that recognize AU-rich elements (AREs) found within many transcripts. Analyses of precancerous and malignant Myc-expressing B cells revealed that Myc regulates hundreds of ARE-containing (ARED) genes and select AUBPs. Notably, Myc directly suppresses transcription of Tristetraprolin (TTP/ZFP36), an mRNA-destabilizing AUBP, and this circuit is also operational during B lymphopoiesis and IL7 signaling. Importantly, TTP suppression is a hallmark of cancers with MYC involvement, and restoring TTP impairs Myc-induced lymphomagenesis and abolishes maintenance of the malignant state. Further, there is a selection for TTP loss in malignancy; thus, TTP functions as a tumor suppressor. Finally, Myc/TTP-directed control of select cancer-associated ARED genes is disabled during lymphomagenesis. Thus, Myc targets AUBPs to regulate ARED genes that control tumorigenesis.
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Affiliation(s)
- Robert J Rounbehler
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
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