1
|
Marquez-Pedroza J, Hernández-Preciado MR, Valdivia-Tangarife ER, Alvarez-Padilla FJ, Mireles-Ramírez MA, Torres-Mendoza BM. Pregnant Women with Multiple Sclerosis: An Overview of Gene Expression and Molecular Interaction Using Bioinformatics Analysis. Int J Mol Sci 2024; 25:6741. [PMID: 38928446 PMCID: PMC11203715 DOI: 10.3390/ijms25126741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Multiple sclerosis (MS) is a common disease in young women of reproductive age, characterized by demyelination of the central nervous system (CNS). Understanding how genes related to MS are expressed during pregnancy can provide insights into the potential mechanisms by which pregnancy affects the course of this disease. This review article presents evidence-based studies on these patients' gene expression patterns. In addition, it constructs interaction networks using bioinformatics tools, such as STRING and KEGG pathways, to understand the molecular role of each of these genes. Bioinformatics research identified 25 genes and 21 signaling pathways, which allows us to understand pregnancy patients' genetic and biological phenomena and formulate new questions about MS during pregnancy.
Collapse
Affiliation(s)
- Jazmin Marquez-Pedroza
- Neurosciences Division, Western Biomedical Research Center, Mexican Institute of Social Security, Guadalajara 44340, Mexico;
| | - Martha Rocio Hernández-Preciado
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | | | - Francisco J. Alvarez-Padilla
- Translational Bioengineering Department, University Center of Exact Sciences and Engineering, University of Guadalajara, Guadalajara 44430, Mexico;
| | - Mario Alberto Mireles-Ramírez
- High Specialty Medical Unit, Western National Medical Center, Mexican Institute of Social Security, Guadalajara 44340, Mexico;
| | - Blanca Miriam Torres-Mendoza
- Neurosciences Division, Western Biomedical Research Center, Mexican Institute of Social Security, Guadalajara 44340, Mexico;
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico;
| |
Collapse
|
2
|
Snyder BL, Huang R, Burkholder AB, Donahue DR, Mahler BW, Bortner CD, Lai WS, Blackshear PJ. Synergistic roles of tristetraprolin family members in myeloid cells in the control of inflammation. Life Sci Alliance 2024; 7:e202302222. [PMID: 37903626 PMCID: PMC10616675 DOI: 10.26508/lsa.202302222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
Members of the tristetraprolin (TTP) family of RNA-binding proteins can bind to and promote the decay of specific transcripts containing AU-rich motifs. ZFP36 (TTP) is best known for regulating pro-inflammatory cytokine expression in myeloid cells; however, its mammalian paralogues ZFP36L1 and ZFP36L2 have not been viewed as important in controlling inflammation. We knocked out these genes in myeloid cells in mice, singly and together. Single-gene myeloid-specific knockouts resulted in almost no spontaneous phenotypes. In contrast, mice with myeloid cell deficiency of all three genes developed severe inflammation, with a median survival of 8 wk. Macrophages from these mice expressed many more stabilized transcripts than cells from myeloid-specific TTP knockout mice; many of these encoded pro-inflammatory cytokines and chemokines. The failure of weight gain, arthritis, and early death could be prevented completely by two normal alleles of any of the three paralogues, and even one normal allele of Zfp36 or Zfp36l2 was enough to prevent the inflammatory phenotype. Our findings emphasize the importance of all three family members, acting in concert, in myeloid cell function.
Collapse
Affiliation(s)
- Brittany L Snyder
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Rui Huang
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Adam B Burkholder
- https://ror.org/01cwqze88 Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Danielle R Donahue
- NIH Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Beth W Mahler
- Experimental Pathology Laboratories, Inc., Research Triangle Park, Durham, NC, USA
| | - Carl D Bortner
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Wi S Lai
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Perry J Blackshear
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
3
|
Wulf S, Mizko L, Herrmann KH, Sánchez-Carbonell M, Urbach A, Lemke C, Berndt A, Loeffler I, Wolf G. Targeted Disruption of the MORG1 Gene in Mice Causes Embryonic Resorption in Early Phase of Development. Biomolecules 2023; 13:1037. [PMID: 37509073 PMCID: PMC10377003 DOI: 10.3390/biom13071037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The mitogen-activated protein kinase organizer 1 (MORG1) is a scaffold molecule for the ERK signaling pathway, but also binds to prolyl-hydroxylase 3 and modulates HIFα expression. To obtain further insight into the role of MORG1, knockout-mice were generated by homologous recombination. While Morg1+/- mice developed normally without any apparent phenotype, there were no live-born Morg1-/- knockout offspring, indicating embryonic lethality. The intrauterine death of Morg1-/- embryos is caused by a severe failure to develop brain and other neuronal structures such as the spinal cord and a failure of chorioallantoic fusion. On E8.5, Morg1-/- embryos showed severe underdevelopment and proliferative arrest as indicated by absence of Ki67 expression, impaired placental vascularization and altered phenotype of trophoblast giant cells. On E9.5, the malformed Morg1-/- embryos showed defective turning into the final fetal position and widespread apoptosis in many structures. In the subsequent days, apoptosis and decomposition of embryonic tissue progressed, accompanied by a massive infiltration of inflammatory cells. Developmental aberrancies were accompanied by altered expression of HIF-1/2α and VEGF-A and caspase-3 activation in embryos and extraembryonic tissues. In conclusion, the results suggest a multifactorial process that causes embryonic death in homozygous Morg1 mutant mice, described here, to the best of our knowledge, for the first time.
Collapse
Affiliation(s)
- Sophie Wulf
- Department of Internal Medicine III, Jena University Hospital, 07747 Jena, Germany
| | - Luisa Mizko
- Department of Internal Medicine III, Jena University Hospital, 07747 Jena, Germany
| | - Karl-Heinz Herrmann
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, 07747 Jena, Germany
| | | | - Anja Urbach
- Department of Neurology, Jena University Hospital, 07747 Jena, Germany
| | - Cornelius Lemke
- Institute for Anatomy I, Jena University Hospital, 07743 Jena, Germany
| | - Alexander Berndt
- Institute of Forensic Medicine, Section Pathology, Jena University Hospital, 07743 Jena, Germany
| | - Ivonne Loeffler
- Department of Internal Medicine III, Jena University Hospital, 07747 Jena, Germany
| | - Gunter Wolf
- Department of Internal Medicine III, Jena University Hospital, 07747 Jena, Germany
| |
Collapse
|
4
|
Chen J, Patial S, Saini Y. Silencing of RNA binding protein, ZFP36L1, promotes epithelial-mesenchymal transition in liver cancer cells by regulating transcription factor ZEB2. Cell Signal 2022; 100:110462. [PMID: 36100056 DOI: 10.1016/j.cellsig.2022.110462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/13/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022]
Abstract
RNA binding proteins (RBPs) of the zinc finger protein 36 family including zinc finger protein 36 like 1 (ZFP36L1) are implicated in cancer, however, the underlying molecular mechanisms have remained unclear. These proteins function by regulating post-transcriptional gene expression upon binding to the AU-rich elements (ARE's) within the 3'untranslated regions (3'UTRs) of specific mRNAs and increasing their mRNA turnover. Here, we tested the role of ZFP36L1 in hepatocellular carcinoma (HCC) cell lines. ZFP36L1 was under-expressed among the three RBPs in a majority of the HCC cell lines. Silencing of ZFP36L1 in two of the seven HCC cell lines resulted in epithelial-mesenchymal transition (EMT) like morphological changes, which were characterized by the transition of epithelial morphology to elongated mesenchymal morphology and increased migration and invasion potential. Conversely, overexpression of ZFP36L1 abolished these changes. RNA-seq analysis of ZFP36L1-depleted HCC cells revealed a significant upregulation of an EMT-inducing transcription factor, ZEB2 (zinc-finger E-box-binding homeobox 2), and enrichment of pathways associated with mesenchymal cell development and differentiation. ZEB2 mRNA contains AREs within its 3'UTR and its stability was increased following ZFP36L1 knockdown. Conversely, ZEB2 was significantly downregulated following ZFP36L1 overexpression and ZEB2 3'UTR was regulated by ZFP36L1 in luciferase reporter assays. These data identify ZEB2 mRNA as a ZFP36L1 target in HCC cells and demonstrate that ZFP36L1 regulates EMT possibly through direct regulation of ZEB2 mRNA. In summary, our results demonstrate that ZFP36L1 suppresses EMT inliver cancer cells by down-regulating the expression of EMT-inducing transcription factor, ZEB2. These data suggest an important role of ZFP36L1 in the development, progression, and metastasis of hepatocellular cancer.
Collapse
Affiliation(s)
- Jian Chen
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Sonika Patial
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States of America.
| | - Yogesh Saini
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, United States of America.
| |
Collapse
|
5
|
Smith MR, Costa G. RNA-binding proteins and translation control in angiogenesis. FEBS J 2022; 289:7788-7809. [PMID: 34796614 DOI: 10.1111/febs.16286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023]
Abstract
Tissue vascularization through the process of angiogenesis ensures adequate oxygen and nutrient supply during development and regeneration. The complex morphogenetic events involved in new blood vessel formation are orchestrated by a tightly regulated crosstalk between extra and intracellular factors. In this context, RNA-binding protein (RBP) activity and protein translation play fundamental roles during the cellular responses triggered by particular environmental cues. A solid body of work has demonstrated that key RBPs (such as HuR, TIS11 proteins, hnRNPs, NF90, QKIs and YB1) are implicated in both physiological and pathological angiogenesis. These RBPs are critical for the metabolism of messenger (m)RNAs encoding angiogenic modulators and, importantly, strong evidence suggests that RBP-mRNA interactions can be altered in disease. Lesser known, but not less important, the mechanistic aspects of protein synthesis can also regulate the generation of new vessels. In this review, we outline the key findings demonstrating the implications of RBP-mediated RNA regulation and translation control in angiogenesis. Furthermore, we highlight how these mechanisms of post-transcriptional control of gene expression have led to promising therapeutic strategies aimed at targeting undesired blood vessel formation.
Collapse
Affiliation(s)
- Madeleine R Smith
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| | - Guilherme Costa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| |
Collapse
|
6
|
Snyder BL, Blackshear PJ. Clinical implications of tristetraprolin (TTP) modulation in the treatment of inflammatory diseases. Pharmacol Ther 2022; 239:108198. [PMID: 35525391 PMCID: PMC9636069 DOI: 10.1016/j.pharmthera.2022.108198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022]
Abstract
Abnormal regulation of pro-inflammatory cytokine and chemokine mediators can contribute to the excess inflammation characteristic of many autoimmune diseases, such as rheumatoid arthritis, psoriasis, Crohn's disease, type 1 diabetes, and many others. The tristetraprolin (TTP) family consists of a small group of related RNA-binding proteins that bind to preferred AU-rich binding sites within the 3'-untranslated regions of specific mRNAs to promote mRNA deadenylation and decay. TTP deficient mice develop a severe systemic inflammatory syndrome consisting of arthritis, myeloid hyperplasia, dermatitis, autoimmunity and cachexia, due at least in part to the excess accumulation of proinflammatory chemokine and cytokine mRNAs and their encoded proteins. To investigate the possibility that increased TTP expression or activity might have a beneficial effect on inflammatory diseases, at least two mouse models have been developed that provide proof of principle that increasing TTP activity can promote the decay of pro-inflammatory and other relevant transcripts, and decrease the severity of mouse models of inflammatory disease. Animal studies of this type are summarized here, and we briefly review the prospects for harnessing these insights for the development of TTP-based anti-inflammatory treatments in humans.
Collapse
Affiliation(s)
- Brittany L Snyder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States of America; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States of America; Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States of America.
| |
Collapse
|
7
|
Cook ME, Bradstreet TR, Webber AM, Kim J, Santeford A, Harris KM, Murphy MK, Tran J, Abdalla NM, Schwarzkopf EA, Greco SC, Halabi CM, Apte RS, Blackshear PJ, Edelson BT. The ZFP36 family of RNA binding proteins regulates homeostatic and autoreactive T cell responses. Sci Immunol 2022; 7:eabo0981. [PMID: 36269839 PMCID: PMC9832469 DOI: 10.1126/sciimmunol.abo0981] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA binding proteins are important regulators of T cell activation, proliferation, and cytokine production. The zinc finger protein 36 (ZFP36) family genes (Zfp36, Zfp36l1, and Zfp36l2) encode RNA binding proteins that promote the degradation of transcripts containing AU-rich elements. Numerous studies have demonstrated both individual and shared functions of the ZFP36 family in immune cells, but their collective function in T cells remains unclear. Here, we found a redundant and critical role for the ZFP36 proteins in regulating T cell quiescence. T cell-specific deletion of all three ZFP36 family members in mice resulted in early lethality, immune cell activation, and multiorgan pathology characterized by inflammation of the eyes, central nervous system, kidneys, and liver. Mice with T cell-specific deletion of any two Zfp36 genes were protected from this spontaneous syndrome. Triply deficient T cells overproduced proinflammatory cytokines, including IFN-γ, TNF, and GM-CSF, due to increased mRNA stability of these transcripts. Unexpectedly, T cell-specific deletion of both Zfp36l1 and Zfp36l2 rendered mice resistant to experimental autoimmune encephalomyelitits due to failed priming of antigen-specific CD4+ T cells. ZFP36L1 and ZFP36L2 double-deficient CD4+ T cells had poor proliferation during in vitro T helper cell polarization. Thus, the ZFP36 family redundantly regulates T cell quiescence at homeostasis, but ZFP36L1 and ZFP36L2 are specifically required for antigen-specific T cell clonal expansion.
Collapse
Affiliation(s)
- Melissa E. Cook
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Tara R. Bradstreet
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Ashlee M. Webber
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jongshin Kim
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine; St. Louis, MO, USA
- Current address: Medical Science and Engineering Program, School of Convergence Science and Technology, Pohang University of Science and Technology; Pohang, Korea
| | - Andrea Santeford
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine; St. Louis, MO, USA
| | - Kevin M. Harris
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Maegan K. Murphy
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jennifer Tran
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine; St. Louis, MO, USA
| | - Nada M. Abdalla
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Elizabeth A. Schwarzkopf
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
- Current address: Wugen, Inc.; St. Louis, MO, USA
| | - Suellen C. Greco
- Division of Comparative Medicine, Washington University School of Medicine; St. Louis, MO, USA
| | - Carmen M. Halabi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rajendra S. Apte
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine; St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine; St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine; St. Louis, MO, USA
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health; Research Triangle Park, NC, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center; Durham, NC, USA
| | - Brian T. Edelson
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| |
Collapse
|
8
|
Krueger A, Łyszkiewicz M, Heissmeyer V. Post-transcriptional control of T-cell development in the thymus. Immunol Lett 2022; 247:1-12. [DOI: 10.1016/j.imlet.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
|
9
|
Kouzu H, Tatekoshi Y, Chang HC, Shapiro JS, McGee WA, De Jesus A, Ben-Sahra I, Arany Z, Leor J, Chen C, Blackshear PJ, Ardehali H. ZFP36L2 suppresses mTORc1 through a P53-dependent pathway to prevent peripartum cardiomyopathy in mice. J Clin Invest 2022; 132:e154491. [PMID: 35316214 PMCID: PMC9106345 DOI: 10.1172/jci154491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Pregnancy is associated with substantial physiological changes of the heart, and disruptions in these processes can lead to peripartum cardiomyopathy (PPCM). The molecular processes that cause physiological and pathological changes in the heart during pregnancy are not well characterized. Here, we show that mTORc1 was activated in pregnancy to facilitate cardiac enlargement that was reversed after delivery in mice. mTORc1 activation in pregnancy was negatively regulated by the mRNA-destabilizing protein ZFP36L2 through its degradation of Mdm2 mRNA and P53 stabilization, leading to increased SESN2 and REDD1 expression. This pathway impeded uncontrolled cardiomyocyte hypertrophy during pregnancy, and mice with cardiac-specific Zfp36l2 deletion developed rapid cardiac dysfunction after delivery, while prenatal treatment of these mice with rapamycin improved postpartum cardiac function. Collectively, these data provide what we believe to be a novel pathway for the regulation of mTORc1 through mRNA stabilization of a P53 ubiquitin ligase. This pathway was critical for normal cardiac growth during pregnancy, and its reduction led to PPCM-like adverse remodeling in mice.
Collapse
Affiliation(s)
- Hidemichi Kouzu
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Yuki Tatekoshi
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Hsiang-Chun Chang
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Jason S. Shapiro
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Warren A. McGee
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Adam De Jesus
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Issam Ben-Sahra
- Department of Biochemistry, Northwestern University, Chicago, Illinois, USA
| | - Zoltan Arany
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan Leor
- Cardiovascular Research Institute, Tel Aviv University and Sheba Medical Center, Tel Aviv, Israel
| | - Chunlei Chen
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Hossein Ardehali
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Feinberg Cardiovascular and Renal Research Institute and
| |
Collapse
|
10
|
Dong X, Guo R, Ji T, Zhang J, Xu J, Li Y, Sheng Y, Wang Y, Fang K, Wen Y, Liu B, Hu G, Deng H, Yao H. YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency. Nucleic Acids Res 2022; 50:12019-12038. [PMID: 35425987 PMCID: PMC9756953 DOI: 10.1093/nar/gkac230] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 12/24/2022] Open
Abstract
Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structures. Yy1 depletion in EPSCs disrupts the enhancer-promoter (EP) interactions of EPSC-specific genes, including Dnmt3l. Yy1 loss results in DNA hypomethylation and dramatically reduces the enrichment of H3K4me3 and H3K27ac on the promoters of EPSC-specific genes by upregulating the expression of Kdm5c and Hdac6 through facilitating the formation of CCCTC-binding factor (CTCF)-mediated EP interactions surrounding their loci. Furthermore, single-cell RNA sequencing (scRNA-seq) experiments revealed that YY1 is required for the derivation of extraembryonic endoderm (XEN)-like cells from EPSCs in vitro. Together, this study reveals that YY1 functions as a key regulator of multidimensional epigenetic crosstalk associated with extended pluripotency.
Collapse
Affiliation(s)
| | | | - Tianrong Ji
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xu
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yaoyi Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingliang Sheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuxiang Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Fang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Wen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Bei Liu
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongkui Deng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hongjie Yao
- To whom correspondence should be addressed. Tel: +86 20 32015279;
| |
Collapse
|
11
|
Hicks SN, Venters RA, Blackshear PJ. Backbone and sidechain 1H, 15N and 13C resonance assignments of the free and RNA-bound tandem zinc finger domain of the tristetraprolin family member from Selaginella moellendorffii. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:153-158. [PMID: 35279790 PMCID: PMC9196822 DOI: 10.1007/s12104-022-10073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Members of the tristetraprolin (TTP) family of RNA binding proteins (RBPs) regulate the metabolism of a variety of mRNA targets. In mammals, these proteins modulate many physiological processes, including immune cell activation, hematopoiesis, and embryonic development. Regulation of mRNA stability by these proteins requires that the tandem zinc finger (TZF) domain binds initially and directly to target mRNAs, ultimately leading to their deadenylation and decay. Proteins of this type throughout eukarya possess a highly conserved TZF domain, suggesting that they are all capable of high-affinity RNA binding. However, the mechanism of TTP-mediated mRNA decay is largely undefined. Given the vital role that these TTP family proteins play in maintaining RNA homeostasis throughout eukaryotes, we focused here on the first, key step in this process: recognition and binding of the TZF domain to target RNA. For these studies, we chose a primitive plant, the spikemoss Selaginella moellendorffii, which last shared a common ancestor with humans more than a billion years ago. Here we report the near complete backbone and side chain resonance assignments of the spikemoss TZF domain, including: (1) the assignment of the RNA-TZF domain complex, representing one of only two data sets currently available for the entire TTP family of proteins; and (2) the first NMR resonance assignments of the entire TZF domain, in the RNA-free form. This work will serve as the basis for further NMR structural investigations aimed at gaining insights into the process of RNA recognition and the mechanisms of TTP-mediated mRNA decay.
Collapse
Affiliation(s)
- Stephanie N Hicks
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - Ronald A Venters
- Duke University NMR Center, Duke University, Durham, NC, 27710, USA
- Department of Radiology, Duke University, Durham, NC, 27710, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| |
Collapse
|
12
|
Yuan S, Zhai Y, Tao T, Zhang X, Bashir G, Li G, Wang G, Wu S. Conflicting Roles of ZFP36L1 in Regulating the Progression of Muscle Invasive Bladder Cancer. Front Mol Biosci 2022; 9:687786. [PMID: 35359594 PMCID: PMC8962643 DOI: 10.3389/fmolb.2022.687786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
As the most common carcinoma of the human urinary system, bladder cancer (BC) is characterized by high recurrence, and poor prognosis after metastasis. In the past decade, genome-wide expression and sequencing studies had identified key genes and pathways related to BC, and pictured the comprehensive molecular features of the disease. Our previous study indicated that the coding gene of zinc finger protein 36 like 1 (ZFP36L1) mutated frequently in bladder tumor tissues and may be a potential suppressor for BC. The present study aimed to further investigate the role of ZFP36L1 in BC, and the survival analysis based on TCGA dataset revealed that high expressing level of ZFP36L1 associated with poorer prognosis of the patients with muscle invasive bladder cancer (MIBC). The associations of ZFP36L1 expression to the clinicopathological and molecular biological features also implicated the high level of ZFP36L1 may related to worse outcomes of patients. Also, GSEA indicated that high expression of ZFP36L1 significantly associated with enhanced activity of cancer metastasis related pathways. Functions of ZFP36L1 in MIBC were investigated further, and it was found that while ZFP36L1 suppressed the self-renewal of bladder cancer cells, it promoted the invasiveness of the cells markedly. Taken together, these results led to the conflicting roles of ZFP36L1 in regulating the progression of MIBC, and revealed further researches are needed to clarify the functions of the gene in tumor initiation and recurrence.
Collapse
Affiliation(s)
- Simin Yuan
- Department of Anesthesiology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
| | - Yujia Zhai
- Department of Anesthesiology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Tao Tao
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Xiaolong Zhang
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ghassan Bashir
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
- Medical College, Shenzhen University, Shenzhen, China
| | - Guangzhi Li
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Gang Wang
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
| | - Song Wu
- Shenzhen Following Precision Medicine Research Institute (Luohu Hospital Group), Shenzhen, China
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Medical College, Shenzhen University, Shenzhen, China
- *Correspondence: Song Wu,
| |
Collapse
|
13
|
Bathula CS, Chen J, Kumar R, Blackshear PJ, Saini Y, Patial S. ZFP36L1 Regulates Fgf21 mRNA Turnover and Modulates Alcoholic Hepatic Steatosis and Inflammation in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:208-225. [PMID: 34774847 PMCID: PMC8908057 DOI: 10.1016/j.ajpath.2021.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 02/03/2023]
Abstract
Zinc finger protein 36 like 1 (ZFP36L1) enhances the turnover of mRNAs containing AU-rich elements (AREs) in their 3'-untranslated regions (3'UTR). The physiological and pathological functions of ZFP36L1 in liver, however, remain largely unknown. Liver-specific ZFP36L1-deficient (Zfp36l1flox/flox/Cre+; L1LKO) mice were generated to investigate the role of ZFP36L1 in liver physiology and pathology. Under normal conditions, the L1LKO mice and their littermate controls (Zfp36l1flox/flox/Cre-; L1FLX) appeared normal. When fed a Lieber-DeCarli liquid diet containing alcohol, L1LKO mice were significantly protected from developing alcohol-induced hepatic steatosis, injury, and inflammation compared with L1FLX mice. Most importantly, fibroblast growth factor 21 (Fgf21) mRNA was significantly increased in the livers of alcohol diet-fed L1LKO mice compared with the alcohol diet-fed L1FLX group. The Fgf21 mRNA contains three AREs in its 3'UTR, and Fgf21 3'UTR was directly regulated by ZFP36L1 in luciferase reporter assays. Steady-state levels of Fgf21 mRNA were significantly decreased by wild-type ZFP36L1, but not by a non-binding zinc finger ZFP36L1 mutant. Finally, wild-type ZFP36L1, but not the ZFP36L1 mutant, bound to the Fgf21 3'UTR ARE RNA probe. These results demonstrate that ZFP36L1 inactivation protects against alcohol-induced hepatic steatosis and liver injury and inflammation, possibly by stabilizing Fgf21 mRNA. These findings suggest that the modulation of ZFP36L1 may be beneficial in the prevention or treatment of human alcoholic liver disease.
Collapse
Affiliation(s)
- Chandra S. Bathula
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Jian Chen
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Rahul Kumar
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Yogesh Saini
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Sonika Patial
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana,Address correspondence to Sonika Patial, D.V.M., Ph.D., D.A.C.V.P., Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803.
| |
Collapse
|
14
|
Elmore SA, Cochran RZ, Bolon B, Lubeck B, Mahler B, Sabio D, Ward JM. Histology Atlas of the Developing Mouse Placenta. Toxicol Pathol 2021; 50:60-117. [PMID: 34872401 PMCID: PMC8678285 DOI: 10.1177/01926233211042270] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of the mouse as a model organism is common in translational research. This mouse-human similarity holds true for placental development as well. Proper formation of the placenta is vital for development and survival of the maturing embryo. Placentation involves sequential steps with both embryonic and maternal cell lineages playing important roles. The first step in placental development is formation of the blastocyst wall (approximate embryonic days [E] 3.0-3.5). After implantation (∼E4.5), extraembryonic endoderm progressively lines the inner surface of the blastocyst wall (∼E4.5-5.0), forming the yolk sac that provides histiotrophic support to the embryo; subsequently, formation of the umbilical vessels (∼E8.5) supports transition to the chorioallantoic placenta and hemotrophic nutrition. The fully mature ("definitive") placenta is established by ∼E12.5. Abnormal placental development often leads to embryonic mortality, with the timing of death depending on when placental insufficiency takes place and which cells are involved. This comprehensive macroscopic and microscopic atlas highlights the key features of normal and abnormal mouse placental development from E4.5 to E18.5. This in-depth overview of a transient (and thus seldom-analyzed) developmental tissue should serve as a useful reference to aid researchers in identifying and describing mouse placental changes in engineered, induced, and spontaneous disease models.
Collapse
Affiliation(s)
- Susan A Elmore
- National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Robert Z Cochran
- National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Beth Lubeck
- National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Beth Mahler
- Experimental Pathology Laboratories, Inc., Research Triangle Park, NC, USA
| | - David Sabio
- Experimental Pathology Laboratories, Inc., Research Triangle Park, NC, USA
| | - Jerrold M Ward
- Global Vet Pathology, Montgomery Village, MD, USA *Co-first authors
| |
Collapse
|
15
|
Zinc finger protein ZFP36L1 inhibits flavivirus infection by both 5'-3' XRN1 and 3'-5' RNA-exosome RNA decay pathways. J Virol 2021; 96:e0166521. [PMID: 34643435 DOI: 10.1128/jvi.01665-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zinc-finger protein 36, CCCH type-like 1 (ZFP36L1), containing tandem CCCH-type zinc-finger motifs with an RNA-binding property, plays an important role in cellular RNA metabolism mainly via RNA decay pathways. Recently, we demonstrated that human ZFP36L1 has potent antiviral activity against influenza A virus infection. However, its role in the host defense response against flaviviruses has not been addressed. Here, we demonstrate that ZFP36L1 functions as a host innate defender against flaviviruses, including Japanese encephalitis virus (JEV) and dengue virus (DENV). Overexpression of ZFP36L1 reduced JEV and DENV infection, and ZFP36L1 knockdown enhanced viral replication. ZFP36L1 destabilized the JEV genome by targeting and degrading viral RNA mediated by both 5'-3' XRN1 and 3'-5' RNA-exosome RNA decay pathways. Mutation in both zinc-finger motifs of ZFP36L1 disrupted RNA-binding and antiviral activity. Furthermore, the viral RNA sequences specifically recognized by ZFP36L1 were mapped to the 3'-untranslated region of the JEV genome with the AU-rich element (AUUUA) motif. We extend the function of ZFP36L1 to host antiviral defense by directly binding and destabilizing the viral genome via recruiting cellular mRNA decay machineries. Importance Cellular RNA-binding proteins are among the first lines of defense against various viruses, particularly RNA viruses. ZFP36L1 belongs to the CCCH-type zinc-finger protein family and has RNA-binding activity; it has been reported to directly bind to the AU-rich elements (AREs) of a subset of cellular mRNAs and then lead to mRNA decay by recruiting mRNA degrading enzymes. However, the antiviral potential of ZFP36L1 against flaviviruses has not yet been fully demonstrated. Here, we reveal the antiviral potential of human ZFP36L1 against Japanese encephalitis virus (JEV) and dengue virus (DENV). ZFP36L1 specifically targeted the ARE motif within viral RNA and triggered the degradation of viral RNA transcripts via cellular degrading enzymes, 5'-3' XRN1 and 3'-5' RNA exosome. These findings provide mechanistic insights into how human ZFP36L1 serves as a host antiviral factor to restrict flavivirus replication.
Collapse
|
16
|
Kovarik P, Bestehorn A, Fesselet J. Conceptual Advances in Control of Inflammation by the RNA-Binding Protein Tristetraprolin. Front Immunol 2021; 12:751313. [PMID: 34603339 PMCID: PMC8484758 DOI: 10.3389/fimmu.2021.751313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Regulated changes in mRNA stability are critical drivers of gene expression adaptations to immunological cues. mRNA stability is controlled mainly by RNA-binding proteins (RBPs) which can directly cleave mRNA but more often act as adaptors for the recruitment of the RNA-degradation machinery. One of the most prominent RBPs with regulatory roles in the immune system is tristetraprolin (TTP). TTP targets mainly inflammation-associated mRNAs for degradation and is indispensable for the resolution of inflammation as well as the maintenance of immune homeostasis. Recent advances in the transcriptome-wide knowledge of mRNA expression and decay rates together with TTP binding sites in the target mRNAs revealed important limitations in our understanding of molecular mechanisms of TTP action. Such orthogonal analyses lead to the discovery that TTP binding destabilizes some bound mRNAs but not others in the same cell. Moreover, comparisons of various immune cells indicated that an mRNA can be destabilized by TTP in one cell type while it remains stable in a different cell linage despite the presence of TTP. The action of TTP extends from mRNA destabilization to inhibition of translation in a subset of targets. This article will discuss these unexpected context-dependent functions and their implications for the regulation of immune responses. Attention will be also payed to new insights into the role of TTP in physiology and tissue homeostasis.
Collapse
Affiliation(s)
- Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | | | | |
Collapse
|
17
|
RNA binding motif 47 (RBM47): emerging roles in vertebrate development, RNA editing and cancer. Mol Cell Biochem 2021; 476:4493-4505. [PMID: 34499322 DOI: 10.1007/s11010-021-04256-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
RNA-binding proteins (RBPs) are critical players in the post-transcriptional regulation of gene expression and are associated with each event in RNA metabolism. The term 'RNA-binding motif' (RBM) is assigned to novel RBPs with one or more RNA recognition motif (RRM) domains that are mainly involved in the nuclear processing of RNAs. RBM47 is a novel RBP conserved in vertebrates with three RRM domains whose contributions to various aspects of cellular functions are as yet emerging. Loss of RBM47 function affects head morphogenesis in zebrafish embryos and leads to perinatal lethality in mouse embryos, thereby assigning it to be an essential gene in early development of vertebrates. Its function as an essential cofactor for APOBEC1 in C to U RNA editing of several targets through substitution for A1CF in the A1CF-APOBEC1 editosome, established a new paradigm in the field. Recent advances in the understanding of its involvement in cancer progression assigned RBM47 to be a tumor suppressor that acts by inhibiting EMT and Wnt/[Formula: see text]-catenin signaling through post-transcriptional regulation. RBM47 is also required to maintain immune homeostasis, which adds another facet to its regulatory role in cellular functions. Here, we review the emerging roles of RBM47 in various biological contexts and discuss the current gaps in our knowledge alongside future perspectives for the field.
Collapse
|
18
|
The oncogenic role of HIF-1α/miR-182-5p/ZFP36L1 signaling pathway in nasopharyngeal carcinoma. Cancer Cell Int 2021; 21:462. [PMID: 34465330 PMCID: PMC8406720 DOI: 10.1186/s12935-021-02177-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Accumulating evidence indicates that dysregulation of miR-182-5p can serve as diagnostic and prognostic biomarkers for some cancers, whereas the role of miR-182-5p has not been explored in nasopharyngeal carcinoma (NPC). Our study aims to elucidate the biological function of miR-182-5p in NPC and the potential molecular mechanism involved. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to determine miR-182-5p expression in NPC primary tissues and cell lines. Immunohistochemistry (IHC) for ZFP36L1 was conducted in NPC samples. Western blot was used to evaluate protein expression in cell lines. A series of functional assays were carried out to evaluate the roles of miR-182-5p and ZFP36L1 in tumor development and progression of NPC. Bioinformatics tools and luciferase reporter assays were utilized to identify the potential mechanisms of action. Moreover, rescue experiments were applied to explore whether ZFP36L1 mediated the effects of miR-182-5p in NPC. Results Up-regulation of miR-182-5p was significantly associated with tumor development and poor prognosis in patients with NPC. Functional study demonstrated that miR-182-5p overexpression enhanced, whereas suppression of miR-182-5p impeded NPC cell proliferation, migration, tumorigenesis and metastasis. Mechanistically, miR-182-5p interacted with ZFP36L1 at two sites in its 3′ un-translated region (UTR) and repressed ZFP36L1 expression in NPC. Consistently, an inverse correlation was observed between the expression levels of miR-182-5p and ZFP36L1 using clinical NPC tissues, and down-regulation of ZFP36L1 in NPC predicts poor survival. Furthermore, overexpression of miR-182-5p in NPC was partly attributable to the transcriptional activation effect induced by hypoxia-inducible factor 1α (HIF-1α). Conclusions Our data suggests that miR-182-5p facilitates cell proliferation and migration in NPC through its ability to down-regulate ZFP36L1 expression, and that the HIF-1α/miR-182-5p/ZFP36L1 axis may serve as a novel therapeutic target in the management of NPC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02177-3.
Collapse
|
19
|
Albano F, Tucci V, Blackshear PJ, Reale C, Roberto L, Russo F, Marotta P, Porreca I, Colella M, Mallardo M, de Felice M, Ambrosino C. ZFP36L2 Role in Thyroid Functionality. Int J Mol Sci 2021; 22:9379. [PMID: 34502288 PMCID: PMC8431063 DOI: 10.3390/ijms22179379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Thyroid hormone levels are usually genetically determined. Thyrocytes produce a unique set of enzymes that are dedicated to thyroid hormone synthesis. While thyroid transcriptional regulation is well-characterized, post-transcriptional mechanisms have been less investigated. Here, we describe the involvement of ZFP36L2, a protein that stimulates degradation of target mRNAs, in thyroid development and function, by in vivo and in vitro gene targeting in thyrocytes. Thyroid-specific Zfp36l2-/- females were hypothyroid, with reduced levels of circulating free Thyroxine (cfT4) and Triiodothyronine (cfT3). Their hypothyroidism was due to dyshormonogenesis, already evident one week after weaning, while thyroid development appeared normal. We observed decreases in several thyroid-specific transcripts and proteins, such as Nis and its transcriptional regulators (Pax8 and Nkx2.1), and increased apoptosis in Zfp36l2-/- thyroids. Nis, Pax8, and Nkx2.1 mRNAs were also reduced in Zfp36l2 knock-out thyrocytes in vitro (L2KO), in which we confirmed the increased apoptosis. Finally, in L2KO cells, we showed an altered response to TSH stimulation regarding both thyroid-specific gene expression and cell proliferation and survival. This result was supported by increases in P21/WAF1 and p-P38MAPK levels. Mechanistically, we confirmed Notch1 as a target of ZFP36L2 in the thyroid since its levels were increased in both in vitro and in vivo models. In both models, the levels of Id4 mRNA, a potential inhibitor of Pax8 activity, were increased. Overall, the data indicate that the regulation of mRNA stability by ZFP36L2 is a mechanism that controls the function and survival of thyrocytes.
Collapse
Affiliation(s)
- Francesco Albano
- IEOS-CNR, 80131 Naples, Italy;
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
| | - Valeria Tucci
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Carla Reale
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
| | - Luca Roberto
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
| | - Filomena Russo
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
| | - Pina Marotta
- Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy;
| | - Immacolata Porreca
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
| | - Marco Colella
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Mario de Felice
- IEOS-CNR, 80131 Naples, Italy;
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Concetta Ambrosino
- Biogem, Istituto di Biologia e Genetica Molecolare, 83031 Ariano Irpino, Italy; (V.T.); (C.R.); (L.R.); (F.R.); (I.P.); (M.C.)
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| |
Collapse
|
20
|
Matsuura Y, Noguchi A, Sakai S, Yokota N, Kawahara H. Nuclear accumulation of ZFP36L1 is cell cycle-dependent and determined by a C-terminal serine-rich cluster. J Biochem 2021; 168:477-489. [PMID: 32687160 DOI: 10.1093/jb/mvaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/26/2020] [Indexed: 11/14/2022] Open
Abstract
ZFP36L1 is an RNA-binding protein responsible for mRNA decay in the cytoplasm. ZFP36L1 has also been suggested as a nuclear-cytoplasmic shuttling protein because it contains a potential nuclear localization signal and a nuclear export signal. However, it remains unclear how the nuclear localization of ZFP36L1 is controlled. In this study, we provide evidence that the nuclear accumulation of ZFP36L1 protein is modulated in a cell cycle-dependent manner. ZFP36L1 protein accumulation in fractionated nuclei was particularly prominent in cells arrested at G1-/S-phase boundary, while it was downregulated in S-phase cells, and eventually disappeared in G2-phase nuclei. Moreover, forced nuclear targeting of ZFP36L1 revealed marked downregulation of this protein in S- and G2-phase cells, suggesting that ZFP36L1 can be eliminated in the nucleus. The C-terminal serine-rich cluster of ZFP36L1 is critical for the regulation of its nuclear accumulation because truncation of this probable disordered region enhanced the nuclear localization of ZFP36L1, increased its stability and abolished its cell cycle-dependent fluctuations. These findings provide the first hints to the question of how ZFP36L1 nuclear accumulation is controlled during the course of the cell cycle.
Collapse
Affiliation(s)
- Yuki Matsuura
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Aya Noguchi
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Shunsuke Sakai
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Naoto Yokota
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Hiroyuki Kawahara
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| |
Collapse
|
21
|
Understanding the epigenetic landscape and cellular architecture of childhood brain tumors. Neurochem Int 2020; 144:104940. [PMID: 33333210 DOI: 10.1016/j.neuint.2020.104940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/12/2020] [Indexed: 11/22/2022]
Abstract
Pediatric brain tumors are the leading cancer-related cause of death in children and adolescents in the United States, affecting on average 1 in 2000 children per year. Recent advances in cancer genomics have led to profound discoveries about the underlying molecular biology and ontogeny of these tumors. In particular, these studies have revealed epigenetic dysregulation to be one of the main hallmarks of pediatric brain tumorigenesis. In this review, we will highlight a number of important recent findings about the nature of this dysregulation in different types of pediatric brain tumors as well as examine their implications for preclinical research and clinical practice. Specifically, we discuss the emergence of methylation signatures as tools for tumor stratification/classification while also highlighting the importance of mutations that directly affect the epigenome and clarifying their impact on risk stratification and pediatric brain tumor biology. We then incorporate recent advances in our understanding of pediatric brain tumor cellular architecture and emphasize the link between epigenetic dysregulation and the "stalled" development seen in many of these malignant neoplasms. Lastly, we explore recentwork investigating the use of these mutated epigenomic regulators as therapeutic targets and extrapolate their utility in overcoming this "stalling" to halt tumor growth.
Collapse
|
22
|
Guo X, Piao H, Zhang Y, Sun P, Yao B. Overexpression of microRNA-129-5p in glioblastoma inhibits cell proliferation, migration, and colony-forming ability by targeting ZFP36L1. Bosn J Basic Med Sci 2020; 20:459-470. [PMID: 31999936 PMCID: PMC7664791 DOI: 10.17305/bjbms.2019.4503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/24/2019] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a highly invasive cancer with a high recurrence rate. The prognosis of GBM patients remains poor, even after standard surgical resection combined with chemoradiotherapy. Thus, there is an urgent need for new therapeutic targets in GBM. In recent years, microRNAs have received considerable attention due to their important role in tumor development and progression. In this study, we investigated the role of miR-129-5p and miR-129-5p/ZFP36L1 axis in GBM tumorigenesis. Analysis of GSE103228 microarray data from the GEO database showed that miR-129-5p was significantly downregulated in GBM vs. normal brain tissues. Quantitative reverse transcription PCR analysis of miR-129-5p expression in seven GBM cell lines (LN229, A172, U87, T98G, U251, H4, and LN118) vs. normal human astrocytes (NHA) showed miR-129-5p was significantly downregulated in GBM cells. Overexpression of miR-129-5p in LN229 and A172 cells significantly suppressed cell proliferation, migration, invasion, and colony-forming ability. Target Scan analysis identified ZFP36L1 as the target of miR-129-5p. UALCAN dataset analysis found that ZFP36L1 was significantly upregulated in GBM vs. normal brain tissues, and high ZFP36L1 expression was positively associated with poor survival of GBM patients. Western blot analysis demonstrated that ZFP36L1 was significantly upregulated in seven GBM cell lines vs. NHA. Overexpression of miR-129-5p in LN229 and A172 cells significantly inhibited ZFP36L1 mRNA and protein expression, while overexpression of ZFP36L1 in LN229 and A172 cells reversed miR-129-5p-mediated inhibition on GBM tumorigenesis. Our results revealed an important role of miR-129-5p in the negative regulation of ZFP36L1 expression in GBM, suggesting new candidates for targeted therapy in GBM patients.
Collapse
Affiliation(s)
- Xu Guo
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Haozhe Piao
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Ye Zhang
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Peixin Sun
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Bing Yao
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| |
Collapse
|
23
|
Sneezum L, Eislmayr K, Dworak H, Sedlyarov V, Le Heron A, Ebner F, Fischer I, Iwakura Y, Kovarik P. Context-Dependent IL-1 mRNA-Destabilization by TTP Prevents Dysregulation of Immune Homeostasis Under Steady State Conditions. Front Immunol 2020; 11:1398. [PMID: 32733464 PMCID: PMC7358311 DOI: 10.3389/fimmu.2020.01398] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022] Open
Abstract
The bioavailability of the major pro-inflammatory cytokines IL-1α and IL-1β is tightly controlled by transcription and post-translational processing to prevent hyperinflammation. The role of mRNA decay in maintenance of physiological IL-1 amounts remained unknown. Here we show that the down-regulation of Il1a and Il1b mRNA by the mRNA-destabilizing protein TTP (gene Zfp36) is required for immune homeostasis. The TTP deficiency syndrome, a multi organ inflammation in TTP-/- mice, was significantly ameliorated upon deletion of the IL-1 receptor. Il1a and Il1b played non-redundant roles in triggering the pathological IL-1 signaling in TTP-/- mice. Accordingly, tissues from TTP-/- animals contained increased amounts of Il1b mRNA. Unexpectedly, TTP destabilized Il1b mRNA in cell type-specific ways as evident from RNA-Seq and mRNA stability assays. These results demonstrate that TTP-driven mRNA destabilization depends on the cellular context. Moreover, such context-defined mRNA decay is essential for keeping steady state IL-1 levels in the physiological range.
Collapse
Affiliation(s)
- Lucy Sneezum
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Kevin Eislmayr
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Helene Dworak
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Vitaly Sedlyarov
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Anita Le Heron
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Florian Ebner
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Irmgard Fischer
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Tokyo, Japan
| | - Pavel Kovarik
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| |
Collapse
|
24
|
Makita S, Takatori H, Iwata A, Tanaka S, Furuta S, Ikeda K, Suto A, Suzuki K, Ramos SBV, Nakajima H. RNA-Binding Protein ZFP36L2 Downregulates Helios Expression and Suppresses the Function of Regulatory T Cells. Front Immunol 2020; 11:1291. [PMID: 32655569 PMCID: PMC7324482 DOI: 10.3389/fimmu.2020.01291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
The zinc finger protein 36-like 2, ZFP36L2, is a member of a small family of RNA-binding proteins composed by ZFP36 (also known as tristetraprolin, TTP), ZFP36L1 and ZFP36L2 in humans, with corresponding murine orthologs. These proteins bind to adenine uridine-rich element (ARE) in the 3′untranslated region of target messenger RNA and stimulate target degradation. ZFP36 functions as an anti-inflammatory modulator in murine models of inflammatory diseases by down-regulating the production of inflammatory cytokines such as tumor necrosis factor-α. However, how ZFP36L1 and ZFP36L2 alter the function of CD4+ T cells is not completely understood. We addressed this issue by searching for the target genes of ZFP36L2 by comprehensive transcriptome analysis. We observed that ZFP36L2 is highly expressed in naïve CD4+ T cells; however, when CD4+ T cells are stimulated through their T cell receptors, ZFP36L2 expression is rapidly reduced in both humans and mice. Among CD4+ T cell populations, the expression levels of ZFP36L2 in regulatory T cells (Tregs) were significantly lower than those in naïve or effector CD4+ T cells. RNA-sequence analysis revealed that the forced expression of ZFP36L2 decreased Ikzf2 (encoding Helios) expression in Foxp3+ Tregs and inhibited the ability of induced Tregs (iTregs). ZFP36L2 directly bound to and destabilized the 3′untranslated region of Ikzf2 mRNA, which contains AU-rich elements. These results indicate that ZFP36L2 reduces the expression of Ikzf2 and suppresses iTreg function, raising the interesting possibility that the inhibition of ZFP36L2 in iTregs could be a therapeutic strategy for autoimmune diseases.
Collapse
Affiliation(s)
- Sohei Makita
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Takatori
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Rheumatology, Hamamatsu Medical Center, Shizuoka, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shunsuke Furuta
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kei Ikeda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| |
Collapse
|
25
|
The Tristetraprolin Family of RNA-Binding Proteins in Cancer: Progress and Future Prospects. Cancers (Basel) 2020; 12:cancers12061539. [PMID: 32545247 PMCID: PMC7352335 DOI: 10.3390/cancers12061539] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a key role in cellular proliferation, differentiation, migration, and apoptosis. Increasing evidence suggests dysregulated post-transcriptional gene expression as an important mechanism in the pathogenesis of cancer. The tristetraprolin family of RNA-binding proteins (RBPs), which include Zinc Finger Protein 36 (ZFP36; commonly referred to as tristetraprolin (TTP)), Zinc Finger Protein 36 like 1 (ZFP36L1), and Zinc Finger Protein 36 like 2 (ZFP36L2), play key roles in the post-transcriptional regulation of gene expression. Mechanistically, these proteins function by binding to the AU-rich elements within the 3′-untranslated regions of their target mRNAs and, in turn, increasing mRNA turnover. The TTP family RBPs are emerging as key regulators of multiple biological processes relevant to cancer and are aberrantly expressed in numerous human cancers. The TTP family RBPs have tumor-suppressive properties and are also associated with cancer prognosis, metastasis, and resistance to chemotherapy. Herein, we summarize the various hallmark molecular traits of cancers that are reported to be regulated by the TTP family RBPs. We emphasize the role of the TTP family RBPs in the regulation of trait-associated mRNA targets in relevant cancer types/cell lines. Finally, we highlight the potential of the TTP family RBPs as prognostic indicators and discuss the possibility of targeting these TTP family RBPs for therapeutic benefits.
Collapse
|
26
|
3' UTRs Regulate Protein Functions by Providing a Nurturing Niche during Protein Synthesis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:95-104. [PMID: 31900325 DOI: 10.1101/sqb.2019.84.039206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Messenger RNAs (mRNAs) are the templates for protein synthesis as the coding region is translated into the amino acid sequence. mRNAs also contain 3' untranslated regions (3' UTRs) that harbor additional elements for the regulation of protein function. If the amino acid sequence of a protein is necessary and sufficient for its function, we call it 3' UTR-independent. In contrast, functions that are accomplished by protein complexes whose formation requires the presence of a specific 3' UTR are 3' UTR-dependent protein functions. We showed that 3' UTRs can regulate protein activity without affecting protein abundance, and alternative 3' UTRs can diversify protein functions. We currently think that the regulation of protein function by 3' UTRs is facilitated by the local environment at the site of protein synthesis, which we call the nurturing niche for nascent proteins. This niche is composed of the mRNA and the bound proteins that consist of RNA-binding proteins and recruited proteins. It enables the formation of specific protein complexes, as was shown for TIS granules, a recently discovered cytoplasmic membraneless organelle. This finding suggests that changing the niche for nascent proteins will alter protein activity and function, implying that cytoplasmic membraneless organelles can regulate protein function in a manner that is independent of protein abundance.
Collapse
|
27
|
Uchida Y, Chiba T, Kurimoto R, Asahara H. Post-transcriptional regulation of inflammation by RNA-binding proteins via cis-elements of mRNAs. J Biochem 2019; 166:375-382. [PMID: 31511872 DOI: 10.1093/jb/mvz067] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/26/2019] [Indexed: 12/18/2022] Open
Abstract
In human genome, there are approximately 1,500 RNA-binding proteins (RBPs). They can regulate mRNA stability or translational efficiency via ribosomes and these processes are known as 'post-transcriptional regulation'. Accumulating evidences indicate that post-transcriptional regulation is the determinant of the accurate levels of cytokines mRNAs. While transcriptional regulation of cytokines mRNAs has been well studied and found to be important for the rapid induction of mRNA and regulation of the acute phase of inflammation, post-transcriptional regulation by RBPs is essential for resolving inflammation in the later phase, and their dysfunction may lead to severe autoimmune diseases such as rheumatoid arthritis or systemic lupus erythematosus. For post-transcriptional regulation, RBPs recognize and directly bind to cis-regulatory elements in 3' untranslated region of mRNAs such as AU-rich or constitutive decay elements and play various roles. In this review, we summarize the recent findings regarding the role of RBPs in the regulation of inflammation.
Collapse
Affiliation(s)
- Yutaro Uchida
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryota Kurimoto
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
28
|
Liu S, Fang L, Zhou Y, Santos DJA, Xiang R, Daetwyler HD, Chamberlain AJ, Cole JB, Li CJ, Yu Y, Ma L, Zhang S, Liu GE. Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle. BMC Genomics 2019; 20:888. [PMID: 31752687 PMCID: PMC6873545 DOI: 10.1186/s12864-019-6228-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10 kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. Conclusion In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.
Collapse
Affiliation(s)
- Shuli Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Daniel J A Santos
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia
| | - John B Cole
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Cong-Jun Li
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - George E Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
| |
Collapse
|
29
|
Menelaou K, Prater M, Tunster S, Blake G, Geary Joo C, Cross JC, Hamilton R, Watson E. Blastocyst transfer in mice alters the placental transcriptome and growth. Reproduction 2019; 159:115-132. [PMID: 31751309 PMCID: PMC6993209 DOI: 10.1530/rep-19-0293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022]
Abstract
Assisted reproduction technologies (ART) are becoming increasingly common. Therefore, how these procedures influence gene regulation and feto-placental development are important to explore. Here, we assess the effects of blastocyst transfer on mouse placental growth and transcriptome. C57Bl/6 blastocysts were transferred into uteri of B6D2F1 pseudopregnant females and dissected at embryonic day 10.5 for analysis. Compared to non-transferred controls, placentas from transferred conceptuses weighed less even though the embryos were larger on average. This suggested a compensatory increase in placental efficiency. RNA-sequencing of whole male placentas revealed 543 differentially expressed genes (DEGs) after blastocyst transfer: 188 and 355 genes were down-regulated and up-regulated, respectively. DEGs were independently validated in male and female placentas. Bioinformatic analyses revealed that DEGs represented expression in all major placental cell types and included genes that are critical for placenta development and/or function. Furthermore, the direction of transcriptional change in response to blastocyst transfer implied an adaptive response to improve placental function to maintain fetal growth. Our analysis revealed that CpG methylation at regulatory regions of two DEGs was unchanged in female transferred placentas and that DEGs had fewer gene-associated CpG islands (within ~20 kb region) compared to the larger genome. These data suggested that altered methylation at proximal promoter regions might not lead to transcriptional disruption in transferred placentas. Genomic clustering of some DEGs warrants further investigation of long-range, cis-acting epigenetic mechanisms including histone modifications together with DNA methylation. We conclude that embryo transfer, a protocol required for ART, significantly impacts the placental transcriptome and growth.
Collapse
Affiliation(s)
- Katerina Menelaou
- K Menelaou, Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Malwina Prater
- M Prater, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Simon Tunster
- S Tunster, Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Georgina Blake
- G Blake, Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Colleen Geary Joo
- C Geary Joo, Clara Christie Centre for Mouse Genomics, University of Calgary, Calgary, Canada
| | - James C Cross
- J Cross, Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Russell Hamilton
- R Hamilton, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Erica Watson
- E Watson, Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
30
|
Loh XY, Sun QY, Ding LW, Mayakonda A, Venkatachalam N, Yeo MS, Silva TC, Xiao JF, Doan NB, Said JW, Ran XB, Zhou SQ, Dakle P, Shyamsunder P, Koh APF, Huang RYJ, Berman BP, Tan SY, Yang H, Lin DC, Koeffler HP. RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling. Cancer Res 2019; 80:219-233. [PMID: 31551365 DOI: 10.1158/0008-5472.can-18-2796] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/28/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022]
Abstract
ZFP36L1 is a tandem zinc-finger RNA-binding protein that recognizes conserved adenylate-uridylate-rich elements (ARE) located in 3'untranslated regions (UTR) to mediate mRNA decay. We hypothesized that ZFP36L1 is a negative regulator of a posttranscriptional hub involved in mRNA half-life regulation of cancer-related transcripts. Analysis of in silico data revealed that ZFP36L1 was significantly mutated, epigenetically silenced, and downregulated in a variety of cancers. Forced expression of ZFP36L1 in cancer cells markedly reduced cell proliferation in vitro and in vivo, whereas silencing of ZFP36L1 enhanced tumor cell growth. To identify direct downstream targets of ZFP36L1, systematic screening using RNA pull-down of wild-type and mutant ZFP36L1 as well as whole transcriptome sequencing of bladder cancer cells {plus minus} tet-on ZFP36L1 was performed. A network of 1,410 genes was identified as potential direct targets of ZFP36L1. These targets included a number of key oncogenic transcripts such as HIF1A, CCND1, and E2F1. ZFP36L1 specifically bound to the 3'UTRs of these targets for mRNA degradation, thus suppressing their expression. Dual luciferase reporter assays and RNA electrophoretic mobility shift assays showed that wild-type, but not zinc-finger mutant ZFP36L1, bound to HIF1A 3'UTR and mediated HIF1A mRNA degradation, leading to reduced expression of HIF1A and its downstream targets. Collectively, our findings reveal an indispensable role of ZFP36L1 as a posttranscriptional safeguard against aberrant hypoxic signaling and abnormal cell-cycle progression. SIGNIFICANCE: RNA-binding protein ZFP36L1 functions as a tumor suppressor by regulating the mRNA stability of a number of mRNAs involved in hypoxia and cell-cycle signaling.
Collapse
Affiliation(s)
- Xin-Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Mei-Shi Yeo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tiago C Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ngan B Doan
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Jonathan W Said
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Xue-Bin Ran
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Si-Qin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Angele Pei-Fern Koh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.,National University Cancer Institute of Singapore, National University Hospital, Singapore
| |
Collapse
|
31
|
Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
Collapse
Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
| |
Collapse
|
32
|
RNA-binding proteins in hematopoiesis and hematological malignancy. Blood 2019; 133:2365-2373. [PMID: 30967369 PMCID: PMC6716123 DOI: 10.1182/blood-2018-10-839985] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/07/2019] [Indexed: 02/02/2023] Open
Abstract
RNA-binding proteins (RBPs) regulate fundamental processes, such as differentiation and self-renewal, by enabling the dynamic control of protein abundance or isoforms or through the regulation of noncoding RNA. RBPs are increasingly appreciated as being essential for normal hematopoiesis, and they are understood to play fundamental roles in hematological malignancies by acting as oncogenes or tumor suppressors. Alternative splicing has been shown to play roles in the development of specific hematopoietic lineages, and sequence-specific mutations in RBPs lead to dysregulated splicing in myeloid and lymphoid leukemias. RBPs that regulate translation contribute to the development and function of hematological lineages, act as nodes for the action of multiple signaling pathways, and contribute to hematological malignancies. These insights broaden our mechanistic understanding of the molecular regulation of hematopoiesis and offer opportunities to develop disease biomarkers and new therapeutic modalities.
Collapse
|
33
|
Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis. Cell Stem Cell 2019; 24:707-723.e8. [PMID: 30982771 DOI: 10.1016/j.stem.2019.03.006] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/30/2018] [Accepted: 03/05/2019] [Indexed: 11/20/2022]
Abstract
The identity and degree of heterogeneity of glial progenitors and their contributions to brain tumor malignancy remain elusive. By applying lineage-targeted single-cell transcriptomics, we uncover an unanticipated diversity of glial progenitor pools with unique molecular identities in developing brain. Our analysis identifies distinct transitional intermediate states and their divergent developmental trajectories in astroglial and oligodendroglial lineages. Moreover, intersectional analysis uncovers analogous intermediate progenitors during brain tumorigenesis, wherein oligodendrocyte-progenitor intermediates are abundant, hyper-proliferative, and progressively reprogrammed toward a stem-like state susceptible to further malignant transformation. Similar actively cycling intermediate progenitors are prominent components in human gliomas with distinct driver mutations. We further unveil lineage-driving networks underlying glial fate specification and identify Zfp36l1 as necessary for oligodendrocyte-astrocyte lineage transition and glioma growth. Together, our results resolve the dynamic repertoire of common and divergent glial progenitors during development and tumorigenesis and highlight Zfp36l1 as a molecular nexus for balancing glial cell-fate decision and controlling gliomagenesis.
Collapse
|
34
|
Lai WS, Wells ML, Perera L, Blackshear PJ. The tandem zinc finger RNA binding domain of members of the tristetraprolin protein family. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1531. [PMID: 30864256 DOI: 10.1002/wrna.1531] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/12/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022]
Abstract
Tristetraprolin (TTP), the prototype member of the protein family of the same name, was originally discovered as the product of a rapidly inducible gene in mouse cells. Development of a knockout (KO) mouse established that absence of the protein led to a severe inflammatory syndrome, due in part to elevated levels of tumor necrosis factor (TNF). TTP was found to bind directly and with high affinity to specific AU-rich sequences in the 3'-untranslated region of the TNF mRNA. This initial binding led to promotion of TNF mRNA decay and inhibition of its translation. Many additional TTP target mRNAs have since been identified, some of which are cytokines and chemokines involved in the inflammatory response. There are three other proteins in the mouse with similar activities and domain structures, but whose KO phenotypes are remarkably different. Moreover, proteins with similar domain structures and activities have been found throughout eukaryotes, demonstrating that this protein family arose from an ancient ancestor. The defining characteristic of this protein family is the tandem zinc finger (TZF) domain, a 64 amino acid sequence with many conserved residues that is responsible for the direct RNA binding. We discuss here many aspects of this protein domain that have been elucidated since the original discovery of TTP, including its sequence conservation throughout eukarya; its apparent continued evolution in some lineages; its functional dependence on many key conserved residues; its "interchangeability" among evolutionarily distant species; and the evidence that RNA binding is required for the physiological functions of the proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Wi S Lai
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina.,Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina
| |
Collapse
|
35
|
Son YO, Kim HE, Choi WS, Chun CH, Chun JS. RNA-binding protein ZFP36L1 regulates osteoarthritis by modulating members of the heat shock protein 70 family. Nat Commun 2019; 10:77. [PMID: 30622281 PMCID: PMC6325149 DOI: 10.1038/s41467-018-08035-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Osteoarthritis (OA) is a whole-joint disease characterized by cartilage destruction and other whole-joint pathological changes. There is currently no effective disease-modifying therapy. Here we investigate the post-transcriptional mRNA regulation of OA-modulating proteins in chondrocytes and show that the ZFP36 family member, ZFP36L1, is specifically upregulated in OA chondrocytes and OA cartilage of humans and mice. Adenovirus-mediated overexpression of ZFP36L1 alone in mouse knee-joint tissue does not modulate OA pathogenesis. However, genetic ablation or silencing of Zfp36l1 significantly abrogates experimental OA in mice. Knockdown of Zfp36l1 increases the mRNA expression of two heat shock protein 70 (HSP70) family members, which act as its direct targets. Furthermore, overexpression of HSPA1A in joint tissues protects mice against experimental OA by inhibiting chondrocyte apoptosis. Our results indicate that the RNA-binding protein, ZFP36L1, regulates HSP70 family members that appear to protect against OA pathogenesis by inhibiting chondrocyte apoptosis. Osteoarthritis is characterised by degeneration of joint cartilage. Here the authors show that the RNA-binding protein ZFP36L1 is upregulated in chondrocytes of humans and mice with osteoarthritis, and that its knockdown in mouse joints protects chondrocytes against apoptosis by modulating the function of heat shock proteins.
Collapse
Affiliation(s)
- Young-Ok Son
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Hyo-Eun Kim
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Wan-Su Choi
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Churl-Hong Chun
- Department of Orthopedic Surgery, Wonkwang University School of Medicine, Iksan, 54538, Republic of Korea
| | - Jang-Soo Chun
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
36
|
The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly in myogenesis. Skelet Muscle 2018; 8:37. [PMID: 30526691 PMCID: PMC6286576 DOI: 10.1186/s13395-018-0183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/22/2018] [Indexed: 01/07/2023] Open
Abstract
Background Members of the ZFP36 family of RNA-binding proteins regulate gene expression post-transcriptionally by binding to AU-rich elements in the 3’UTR of mRNA and stimulating mRNA degradation. The proteins within this family target different transcripts in different tissues. In particular, ZFP36 targets myogenic transcripts and may have a role in adult muscle stem cell quiescence. Our study examined the requirement of ZFP36L1 and ZFP36L2 in adult muscle cell fate regulation. Methods We generated single and double conditional knockout mice in which Zfp36l1 and/or Zfp36l2 were deleted in Pax7-expressing cells. Immunostained muscle sections were used to analyse resting skeletal muscle, and a cardiotoxin-induced injury model was used to determine the regenerative capacity of muscle. Results We show that ZFP36L1 and ZFP36L2 proteins are expressed in satellite cells. Mice lacking the two proteins in Pax7-expressing cells have reduced body weight and have reduced skeletal muscle mass. Furthermore, the number of satellite cells is reduced in adult skeletal muscle and the capacity of this muscle to regenerate following muscle injury is diminished. Conclusion ZFP36L1 and ZFP36L2 act redundantly in myogenesis. These findings add further intricacy to the regulation of the cell fate of Pax7-expressing cells in skeletal muscle by RNA-binding proteins. Electronic supplementary material The online version of this article (10.1186/s13395-018-0183-9) contains supplementary material, which is available to authorized users.
Collapse
|
37
|
Rytkönen KT, Erkenbrack EM, Poutanen M, Elo LL, Pavlicev M, Wagner GP. Decidualization of Human Endometrial Stromal Fibroblasts is a Multiphasic Process Involving Distinct Transcriptional Programs. Reprod Sci 2018; 26:323-336. [PMID: 30309298 DOI: 10.1177/1933719118802056] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Decidual stromal cells differentiate from endometrial stromal fibroblasts (ESFs) under the influence of progesterone and cyclic adenosine monophosphate (cAMP) and are essential for implantation and the maintenance of pregnancy. They evolved in the stem lineage of placental (eutherian) mammals coincidental with the evolution of implantation. Here we use the well-established in vitro decidualization protocol to compare early (3 days) and late (8 days) gene transcription patterns in immortalized human ESF. We document extensive, dynamic changes in the early and late decidual cell transcriptomes. The data suggest the existence of an early signal transducer and activator of transcription (STAT) pathway dominated state and a later nuclear factor κB (NFKB) pathway regulated state. Transcription factor expression in both phases is characterized by putative or known progesterone receptor ( PGR) target genes, suggesting that both phases are under progesterone control. Decidualization leads to proliferative quiescence, which is reversible by progesterone withdrawal after 3 days but to a lesser extent after 8 days of decidualization. In contrast, progesterone withdrawal induces cell death at comparable levels after short or long exposure to progestins and cAMP. We conclude that decidualization is characterized by a biphasic gene expression dynamic that likely corresponds to different phases in the establishment of the fetal-maternal interface.
Collapse
Affiliation(s)
- Kalle T Rytkönen
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,3 Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu, Finland.,4 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Eric M Erkenbrack
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Matti Poutanen
- 3 Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu, Finland
| | - Laura L Elo
- 4 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mihaela Pavlicev
- 5 Cincinnati Children's Hospital and Medical Center, Cincinnati, OH, USA
| | - Günter P Wagner
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,6 Department of Obstetrics, Yale Medical School, New Haven, CT, USA.,7 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| |
Collapse
|
38
|
Camm EJ, Botting KJ, Sferruzzi-Perri AN. Near to One's Heart: The Intimate Relationship Between the Placenta and Fetal Heart. Front Physiol 2018; 9:629. [PMID: 29997513 PMCID: PMC6029139 DOI: 10.3389/fphys.2018.00629] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2018] [Indexed: 01/19/2023] Open
Abstract
The development of the fetal heart is exquisitely controlled by a multitude of factors, ranging from humoral to mechanical forces. The gatekeeper regulating many of these factors is the placenta, an external fetal organ. As such, resistance within the placental vascular bed has a direct influence on the fetal circulation and therefore, the developing heart. In addition, the placenta serves as the interface between the mother and fetus, controlling substrate exchange and release of hormones into both circulations. The intricate relationship between the placenta and fetal heart is appreciated in instances of clinical placental pathology. Abnormal umbilical cord insertion is associated with congenital heart defects. Likewise, twin-to-twin transfusion syndrome, where monochorionic twins have unequal sharing of their placenta due to inter-twin vascular anastomoses, can result in cardiac remodeling and dysfunction in both fetuses. Moreover, epidemiological studies have suggested a link between placental phenotypic traits and increased risk of cardiovascular disease in adult life. To date, the mechanistic basis of the relationships between the placenta, fetal heart development and later risk of cardiac dysfunction have not been fully elucidated. However, studies using environmental exposures and gene manipulations in experimental animals are providing insights into the pathways involved. Likewise, surgical instrumentation of the maternal and fetal circulations in large animal species has enabled the manipulation of specific humoral and mechanical factors to investigate their roles in fetal cardiac development. This review will focus on such studies and what is known to date about the link between the placenta and heart development.
Collapse
Affiliation(s)
- Emily J Camm
- Department of Physiology, Development and Neuroscience and Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Kimberley J Botting
- Department of Physiology, Development and Neuroscience and Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Amanda N Sferruzzi-Perri
- Department of Physiology, Development and Neuroscience and Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
39
|
Noguchi A, Adachi S, Yokota N, Hatta T, Natsume T, Kawahara H. ZFP36L2 is a cell cycle-regulated CCCH protein necessary for DNA lesion-induced S-phase arrest. Biol Open 2018; 7:bio.031575. [PMID: 29449217 PMCID: PMC5898266 DOI: 10.1242/bio.031575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
ZFP36L2 promotes the destruction of AU-rich element-containing transcripts, while its regulation and functional significance in cell cycle control are scarcely identified. We show that ZFP36L2 is a cell cycle-regulated CCCH protein, the abundance of which is regulated post-translationally at the respective stages of the cell cycle. Indeed, ZFP36L2 protein was eliminated after release from M phase, and ZYG11B-based E3 ligase plays a role in its polyubiquitination in interphase. Although ZFP36L2 is dispensable for normal cell cycle progression, we found that endogenous ZFP36L2 played a key role in cisplatin-induced S-phase arrest, a process in which the suppression of G1/S cyclins is necessary. The accumulation of ZFP36L2 was stimulated under DNA replication stresses and altered interactions with a subset of RNA-binding proteins. Notably, silencing endogenous ZFP36L2 led to impaired cell viability in the presence of cisplatin-induced DNA lesions. Thus, we propose that ZFP36L2 is a key protein that controls S-phase progression in the case of genome instability. Summary: ZFP36L2 is a cell cycle-regulated RNA-binding protein, the abundance of which is regulated post-translationally. This protein is especially accumulated in and critical for the survival of DNA-damaged cells.
Collapse
Affiliation(s)
- Aya Noguchi
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Naoto Yokota
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Hiroyuki Kawahara
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| |
Collapse
|
40
|
A Knock-In Tristetraprolin (TTP) Zinc Finger Point Mutation in Mice: Comparison with Complete TTP Deficiency. Mol Cell Biol 2018; 38:MCB.00488-17. [PMID: 29203639 DOI: 10.1128/mcb.00488-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/25/2017] [Indexed: 01/09/2023] Open
Abstract
Tristetraprolin (TTP) is a tandem CCCH zinc finger protein that can bind to AU-rich element-containing mRNAs and promote their decay. TTP knockout mice develop a severe inflammatory syndrome, largely due to excess tumor necrosis factor (TNF), whose mRNA is a direct target of TTP binding and destabilization. TTP's RNA binding activity and its ability to promote mRNA decay are lost when one of the zinc-coordinating residues of either zinc finger is mutated. To address several long-standing questions about TTP activity in intact animals, we developed a knock-in mouse with a cysteine-to-arginine mutation within the first zinc finger. Homozygous knock-in mice developed a severe inflammatory syndrome that was essentially identical to that of complete TTP deficiency, suggesting that TTP's critical anti-inflammatory role in mammalian physiology is secondary to its ability to bind RNA. In addition, there was no evidence for a "dominant-negative" effect of the mutant allele in heterozygotes, as suggested by previous experiments. Finally, mRNA decay experiments in mutant macrophages demonstrated that TTP can regulate the stability of its own mRNA, albeit to a minor extent. These studies suggest that RNA binding is an essential first step in the physiological activities of members of this protein family.
Collapse
|
41
|
Yang X, Wang J, Zhou Z, Jiang R, Huang J, Chen L, Cao Z, Chu H, Han B, Cheng Y, Chao J. Silica-induced initiation of circular ZC3H4 RNA/ZC3H4 pathway promotes the pulmonary macrophage activation. FASEB J 2018; 32:3264-3277. [PMID: 29401612 DOI: 10.1096/fj.201701118r] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phagocytosis of silicon dioxide (SiO2) into lung cells causes an inflammatory cascade that results in fibroblast proliferation and migration, followed by fibrosis. Circular RNAs (circRNAs) are a subclass of noncoding RNAs that are present within mammalian cells; however, researchers have not determined whether circRNAs are involved in the pathophysiologic process of silicosis. To elucidate the role of these RNAs in SiO2-induced inflammation in pulmonary macrophages, we investigated the upstream molecular mechanisms and functional effects of circRNAs on cell apoptosis, proliferation, and migration. Primary cultures of alveolar macrophages from healthy donors and from patients and the RAW264.7 macrophage cell line were used to explore the functions of circZC3H4 RNA in macrophage activation. The experimental results indicated the following: 1) SiO2 concomitantly increased circZC3H4 RNA expression and increased ZC3H4 protein levels; 2) circular ZC3H4 (circZC3H4) RNA and ZC3H4 protein participated in SiO2-induced macrophage activation; and 3) SiO2-activated macrophages promoted fibroblast proliferation and migration via the circZC3H4 RNA/ZC3H4 pathway. The up-regulation of the ZC3H4 protein was confirmed in tissue samples from patients with silicosis. Our study elucidates a link between SiO2-induced macrophage activation and the circZC3H4 RNA/ZC3H4 pathway, thereby providing novel insight into the potential use of ZC3H4 to develop novel therapeutic strategies for silicosis.-Yang, X., Wang, J., Zhou, Z., Jiang, R., Huang, J., Chen, L., Cao, Z., Chu, H., Han, B., Cheng, Y., Chao, J. Silica-induced initiation of circular ZC3H4 RNA/ZC3H4 pathway promotes the pulmonary macrophage activation.
Collapse
Affiliation(s)
- Xiyue Yang
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Department of Respiration, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China.,Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Jing Wang
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China
| | - Zewei Zhou
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Department of Respiration, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China.,Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Rong Jiang
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Department of Respiration, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Jie Huang
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China
| | - Lulu Chen
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Zhouli Cao
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China
| | - Han Chu
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Bing Han
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yusi Cheng
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China
| | - Jie Chao
- Department of Physiology, Southeast University, Nanjing, Jiangsu, China.,Department of Respiration, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China.,Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| |
Collapse
|
42
|
Tseng KY, Chen YH, Lin S. Zinc finger protein ZFP36L1 promotes osteoblastic differentiation but represses adipogenic differentiation of mouse multipotent cells. Oncotarget 2017; 8:20588-20601. [PMID: 28206953 PMCID: PMC5400528 DOI: 10.18632/oncotarget.15246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/09/2016] [Indexed: 12/21/2022] Open
Abstract
Zinc finger protein 36, C3H type-like 1 (ZFP36L1) is a member of the tristetraprolin (TTP) family and its role in the aging-related bone loss is currently unknown. We present evidence that ZFP36L1 expression in rat femurs and bone marrow mesenchymal stem cells (bmMSCs) was down-regulated with aging. ZFP36L1 knockdown decreased osteoblastic differentiation of MC3T3-E1 and C3H10T1/2 cells, and increased adipogenic differentiation of 3T3-L1 and C3H10T1/2 cells, whereas ZFP36L1 overexpression did the opposite. The finding that ZFP36L1 overexpression enhanced osteoblastic and repressed adipogenic differentiation was also corroborated by ex vivo experiments. Troglitazone prevented ZFP36L1 from inhibiting adipogenic differentiation, suggesting the significance of PPAR?2 repression in ZFP36L1s inhibitory effect on adipogenic differentiation. ZFP36L1 overexpression repressed the expression of Ppar?2 mRNA, but not the PPAR? promoter activity. Biotin pull-down and electrophoretic mobility-shift assays suggested that ZFP36L1 might interact with endogenous Ppar?2 mRNA by binding to its 3UTR. The ZFP36L1-containing ribonucleoprotein complexes of ZFP36L1-overexpressing cells contained less Ppar?2 mRNA than those of control cells. In a luciferase reporter construct, replacement of the SV40 poly(A) fragment by the 3UTR of Ppar?2 mRNA reduced the expression of luciferase transcripts in ZFP36L1-overexpressing cells. Examination of the kinetic expression of Ppar?2 mRNA after transcriptional blockage showed that ZFP36L1 might enhance the degradation of the transcripts. Together, these data imply that ZFP36L1 overexpression might repress adipogenesis at least by down-regulating PPAR?2 expression through post-transcriptional mechanisms. Thus, our findings support the notion that decrease of ZFP36L1 expression in bmMSCs with aging might contribute to the aging-related bone loss.
Collapse
Affiliation(s)
- Kuo-Yun Tseng
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan Town, Miaoli, Taiwan, Republic of China
| | - Yi-Hsuan Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan Town, Miaoli, Taiwan, Republic of China
| | - Shankung Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan Town, Miaoli, Taiwan, Republic of China.,Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan, Republic of China
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
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.
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Saltel F, Giese A, Azzi L, Elatmani H, Costet P, Ezzoukhry Z, Dugot-Senant N, Miquerol L, Boussadia O, Wodrich H, Dubus P, Jacquemin-Sablon H. Unr defines a novel class of nucleoplasmic reticulum involved in mRNA translation. J Cell Sci 2017; 130:1796-1808. [PMID: 28386023 DOI: 10.1242/jcs.198697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/31/2017] [Indexed: 12/23/2022] Open
Abstract
Unr (officially known as CSDE1) is a cytoplasmic RNA-binding protein with roles in the regulation of mRNA stability and translation. In this study, we identified a novel function for Unr, which acts as a positive regulator of placental development. Unr expression studies in the developing placenta revealed the presence of Unr-rich foci that are apparently located in the nuclei of trophoblast giant cells (TGCs). We determined that what we initially thought to be foci, were actually cross sections of a network of double-wall nuclear membrane invaginations that contain a cytoplasmic core related to the nucleoplasmic reticulum (NR). We named them, accordingly, Unr-NRs. Unr-NRs constitute a novel type of NR because they contain high levels of poly(A) RNA and translation factors, and are sites of active translation. In murine tissues, Unr-NRs are only found in two polyploid cell types, in TGCs and hepatocytes. In vitro, their formation is linked to stress and polyploidy because, in three cancer cell lines, cytotoxic drugs that are known to promote polyploidization induce their formation. Finally, we show that Unr is required in vivo for the formation of Unr-containing NRs because these structures are absent in Unr-null TGCs.
Collapse
Affiliation(s)
- Frédéric Saltel
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France .,University of Bordeaux, F-33000 Bordeaux, France
| | - Alban Giese
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | - Lamia Azzi
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France.,Department of Tumor Biology, CHU, F-33000 Bordeaux, France
| | - Habiba Elatmani
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | - Pierre Costet
- Laboratoire de Transgenèse, Université Bordeaux, F-33000 Bordeaux, France
| | - Zakaria Ezzoukhry
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France
| | | | - Lucile Miquerol
- Aix-Marseille University, CNRS, IBDM UMR 7288, Marseille, France
| | | | - Harald Wodrich
- University of Bordeaux, F-33000 Bordeaux, France.,MFP CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, F-33000 Bordeaux, France
| | - Pierre Dubus
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France.,University of Bordeaux, F-33000 Bordeaux, France.,Department of Tumor Biology, CHU, F-33000 Bordeaux, France
| | - Hélène Jacquemin-Sablon
- INSERM UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, F-33000 Bordeaux, France .,University of Bordeaux, F-33000 Bordeaux, France
| |
Collapse
|
48
|
Xie HM, Werner P, Stambolian D, Bailey-Wilson JE, Hakonarson H, White PS, Taylor DM, Goldmuntz E. Rare copy number variants in patients with congenital conotruncal heart defects. Birth Defects Res 2017; 109:271-295. [PMID: 28398664 PMCID: PMC5407323 DOI: 10.1002/bdra.23609] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Previous studies using different cardiac phenotypes, technologies and designs suggest a burden of large, rare or de novo copy number variants (CNVs) in subjects with congenital heart defects. We sought to identify disease-related CNVs, candidate genes, and functional pathways in a large number of cases with conotruncal and related defects that carried no known genetic syndrome. METHODS Cases and control samples were divided into two cohorts and genotyped to assess each subject's CNV content. Analyses were performed to ascertain differences in overall CNV prevalence and to identify enrichment of specific genes and functional pathways in conotruncal cases relative to healthy controls. RESULTS Only findings present in both cohorts are presented. From 973 total conotruncal cases, a burden of rare CNVs was detected in both cohorts. Candidate genes from rare CNVs found in both cohorts were identified based on their association with cardiac development or disease, and/or their reported disruption in published studies. Functional and pathway analyses revealed significant enrichment of terms involved in either heart or early embryonic development. CONCLUSION Our study tested one of the largest cohorts specifically with cardiac conotruncal and related defects. These results confirm and extend previous findings that CNVs contribute to disease risk for congenital heart defects in general and conotruncal defects in particular. As disease heterogeneity renders identification of single recurrent genes or loci difficult, functional pathway and gene regulation network analyses appear to be more informative. Birth Defects Research 109:271-295, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hongbo M Xie
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Petra Werner
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Dwight Stambolian
- Department of Ophthalmology and Human Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joan E Bailey-Wilson
- Statistical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Hakon Hakonarson
- The Center for Applied Genomics, Department of Pediatrics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S White
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio
| | - Deanne M Taylor
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| |
Collapse
|
49
|
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.
Collapse
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.
| |
Collapse
|
50
|
Desroches-Castan A, Feige JJ, Cherradi N. ACTH Action on Messenger RNA Stability Mechanisms. Front Endocrinol (Lausanne) 2017; 8:3. [PMID: 28163695 PMCID: PMC5247459 DOI: 10.3389/fendo.2017.00003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/05/2017] [Indexed: 01/30/2023] Open
Abstract
The regulation of mRNA stability has emerged as a critical control step in dynamic gene expression. This process occurs in response to modifications of the cellular environment, including hormonal variations, and regulates the expression of subsets of proteins whose levels need to be rapidly adjusted. Modulation of messenger RNA stability is usually mediated by stabilizing or destabilizing RNA-binding proteins (RNA-BP) that bind to the 3'-untranslated region regulatory motifs, such as AU-rich elements (AREs). Destabilizing ARE-binding proteins enhance the decay of their target transcripts by recruiting the mRNA decay machineries. Failure of such mechanisms, in particular misexpression of RNA-BP, has been linked to several human diseases. In the adrenal cortex, the expression and activity of mRNA stability regulatory proteins are still understudied. However, ACTH- or cAMP-elicited changes in the expression/phosphorylation status of the major mRNA-destabilizing protein TIS11b/BRF1 or in the subcellular localization of the stabilizing protein Human antigen R have been reported. They suggest that this level of regulation of gene expression is also important in endocrinology.
Collapse
Affiliation(s)
- Agnès Desroches-Castan
- Institut National de la Santé et de la Recherche Médicale, INSERM U1036, Grenoble, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Biologie du Cancer et de l’Infection, Grenoble, France
- Université Grenoble Alpes, Unité Mixte de Recherche-S1036, Grenoble, France
| | - Jean-Jacques Feige
- Institut National de la Santé et de la Recherche Médicale, INSERM U1036, Grenoble, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Biologie du Cancer et de l’Infection, Grenoble, France
- Université Grenoble Alpes, Unité Mixte de Recherche-S1036, Grenoble, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, INSERM U1036, Grenoble, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Biologie du Cancer et de l’Infection, Grenoble, France
- Université Grenoble Alpes, Unité Mixte de Recherche-S1036, Grenoble, France
- *Correspondence: Nadia Cherradi,
| |
Collapse
|