1
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Zhang X, Ng YE, Chini LCS, Heeren AA, White TA, Li H, Huang H, Doolittle ML, Khosla S, LeBrasseur NK. Senescent skeletal muscle fibroadipogenic progenitors recruit and promote M2 polarization of macrophages. Aging Cell 2024; 23:e14069. [PMID: 38115574 PMCID: PMC10928562 DOI: 10.1111/acel.14069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
Senescent cells compromise tissue structure and function in older organisms. We recently identified senescent fibroadipogenic progenitors (FAPs) with activated chemokine signaling pathways in the skeletal muscle of old mice, and hypothesized these cells may contribute to the age-associated accumulation of immune cells in skeletal muscle. In this study, through cell-cell communication analysis of skeletal muscle single-cell RNA-sequencing data, we identified unique interactions between senescent FAPs and macrophages, including those mediated by Ccl2 and Spp1. Using mouse primary FAPs in vitro, we verified increased expression of Ccl2 and Spp1 and secretion of their respective proteins in the context of both irradiation- and etoposide-induced senescence. Compared to non-senescent FAPs, the medium of senescent FAPs markedly increased the recruitment of macrophages in an in vitro migration assay, an effect that was mitigated by preincubation with antibodies to either CCL2 or osteopontin (encoded by Spp1). Further studies demonstrated that the secretome of senescent FAPs promotes polarization of macrophages toward an M2 subtype. These data suggest the unique secretome of senescent FAPs may compromise skeletal muscle homeostasis by recruiting and directing the behavior of macrophages.
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Affiliation(s)
- Xu Zhang
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
- Paul F. Glenn Center for Biology of Aging Research at Mayo ClinicRochesterMinnesotaUSA
| | - Yan Er Ng
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Lucas C. S. Chini
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Amanda A. Heeren
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Thomas A. White
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Hao Li
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | - Haojie Huang
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | - Madison L. Doolittle
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Sundeep Khosla
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Nathan K. LeBrasseur
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Paul F. Glenn Center for Biology of Aging Research at Mayo ClinicRochesterMinnesotaUSA
- Department of Physical Medicine and RehabilitationMayo ClinicRochesterMinnesotaUSA
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2
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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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3
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Schutt WR, Conde JN, Mladinich MC, Himmler GE, Mackow ER. ZIKV induction of tristetraprolin in endothelial and Sertoli cells post-transcriptionally inhibits IFNβ/λ expression and promotes ZIKV persistence. mBio 2023; 14:e0174223. [PMID: 37707056 PMCID: PMC10653947 DOI: 10.1128/mbio.01742-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE Our findings define a novel role for ZIKV-induced TTP expression in regulating IFNβ/IFNλ production in primary hBMECs and Sertoli cells. These cells comprise key physiological barriers subverted by ZIKV to access brain and testicular compartments and serve as reservoirs for persistent replication and dissemination. We demonstrate for the first time that the ARE-binding protein TTP is virally induced and post-transcriptionally regulates IFNβ/IFNλ secretion. In ZIKV-infected hBMEC and Sertoli cells, TTP knockout increased IFNβ/IFNλ secretion, while TTP expression blocked IFNβ/IFNλ secretion. The TTP-directed blockade of IFN secretion permits ZIKV spread and persistence in hBMECs and Sertoli cells and may similarly augment ZIKV spread across IFNλ-protected placental barriers. Our work highlights the importance of post-transcriptional ZIKV regulation of IFN expression and secretion in cells that regulate viral access to protected compartments and defines a novel mechanism of ZIKV-regulated IFN responses which may facilitate neurovirulence and sexual transmission.
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Affiliation(s)
- William R. Schutt
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Jonas N. Conde
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Megan C. Mladinich
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Grace E. Himmler
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Erich R. Mackow
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
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4
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Liberti A, Pollastro C, Pinto G, Illiano A, Marino R, Amoresano A, Spagnuolo A, Sordino P. Transcriptional and proteomic analysis of the innate immune response to microbial stimuli in a model invertebrate chordate. Front Immunol 2023; 14:1217077. [PMID: 37600818 PMCID: PMC10433773 DOI: 10.3389/fimmu.2023.1217077] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Inflammatory response triggered by innate immunity can act to protect against microorganisms that behave as pathogens, with the aim to restore the homeostatic state between host and beneficial microbes. As a filter-feeder organism, the ascidian Ciona robusta is continuously exposed to external microbes that may be harmful under some conditions. In this work, we used transcriptional and proteomic approaches to investigate the inflammatory response induced by stimuli of bacterial (lipopolysaccharide -LPS- and diacylated lipopeptide - Pam2CSK4) and fungal (zymosan) origin, in Ciona juveniles at stage 4 of metamorphosis. We focused on receptors, co-interactors, transcription factors and cytokines belonging to the TLR and Dectin-1 pathways and on immune factors identified by homology approach (i.e. immunoglobulin (Ig) or C-type lectin domain containing molecules). While LPS did not induce a significant response in juvenile ascidians, Pam2CSK4 and zymosan exposure triggered the activation of specific inflammatory mechanisms. In particular, Pam2CSK4-induced inflammation was characterized by modulation of TLR and Dectin-1 pathway molecules, including receptors, transcription factors, and cytokines, while immune response to zymosan primarily involved C-type lectin receptors, co-interactors, Ig-containing molecules, and cytokines. A targeted proteomic analysis enabled to confirm transcriptional data, also highlighting a temporal delay between transcriptional induction and protein level changes. Finally, a protein-protein interaction network of Ciona immune molecules was rendered to provide a wide visualization and analysis platform of innate immunity. The in vivo inflammatory model described here reveals interconnections of innate immune pathways in specific responses to selected microbial stimuli. It also represents the starting point for studying ontogeny and regulation of inflammatory disorders in different physiological conditions.
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Affiliation(s)
- Assunta Liberti
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Carla Pollastro
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
| | - Anna Illiano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
| | - Rita Marino
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
| | - Antonietta Spagnuolo
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
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5
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Alessio N, Acar MB, Squillaro T, Aprile D, Ayaz‐Güner Ş, Di Bernardo G, Peluso G, Özcan S, Galderisi U. Progression of irradiated mesenchymal stromal cells from early to late senescence: Changes in SASP composition and anti-tumour properties. Cell Prolif 2023; 56:e13401. [PMID: 36949664 PMCID: PMC10280137 DOI: 10.1111/cpr.v56.6 10.1111/cpr.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 09/30/2023] Open
Abstract
Genotoxic injuries converge on senescence-executive program that promotes production of a senescence-specific secretome (SASP). The study of SASP is particularly intriguing, since through it a senescence process, triggered in a few cells, can spread to many other cells and produce either beneficial or negative consequences for health. We analysed the SASP of quiescent mesenchymal stromal cells (MSCs) following stress induced premature senescence (SIPS) by ionizing radiation exposure. We performed a proteome analysis of SASP content obtained from early and late senescent cells. The bioinformatics studies evidenced that early and late SASPs, besides some common ontologies and signalling pathways, contain specific factors. In spite of these differences, we evidenced that SASPs can block in vitro proliferation of cancer cells and promote senescence/apoptosis. It is possible to imagine that SASP always contains core components that have an anti-tumour activity, the progression from early to late senescence enriches the SASP of factors that may promote SASP tumorigenic activity only by interacting and instructing cells of the immune system. Our results on Caco-2 cancer cells incubated with late SASP in presence of peripheral white blood cells strongly support this hypothesis. We evidenced that quiescent MSCs following SIPS produced SASP that, while progressively changed its composition, preserved the capacity to block cancer growth by inducing senescence and/or apoptosis only in an autonomous manner.
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Affiliation(s)
- Nicola Alessio
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | | | - Tiziana Squillaro
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | - Domenico Aprile
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | - Şerife Ayaz‐Güner
- Department of Molecular Biology and Genetics, Faculty of Life and Natural ScienceAbdullah Gül UniversityKayseriTurkey
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
| | - Giovanni Di Bernardo
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
- The Interuniversity Consortium “Istituto Nazionale Biostrutture e Biosistemi” (INBB – Biostructures and Biosystems National Institute)RomeItaly
| | | | - Servet Özcan
- Genome and Stem Cell Center (GENKÖK) Erciyes UniversityKayseriTurkey
- Department of Biology, Faculty of ScienceErciyes UniversityKayseriTurkey
| | - Umberto Galderisi
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
- Genome and Stem Cell Center (GENKÖK) Erciyes UniversityKayseriTurkey
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for BiotechnologyTemple UniversityPhiladelphiaPennsylvaniaUSA
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6
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Alessio N, Acar MB, Squillaro T, Aprile D, Ayaz‐Güner Ş, Di Bernardo G, Peluso G, Özcan S, Galderisi U. Progression of irradiated mesenchymal stromal cells from early to late senescence: Changes in SASP composition and anti-tumour properties. Cell Prolif 2023; 56:e13401. [PMID: 36949664 PMCID: PMC10280137 DOI: 10.1111/cpr.v56.6+10.1111/cpr.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2024] Open
Abstract
Genotoxic injuries converge on senescence-executive program that promotes production of a senescence-specific secretome (SASP). The study of SASP is particularly intriguing, since through it a senescence process, triggered in a few cells, can spread to many other cells and produce either beneficial or negative consequences for health. We analysed the SASP of quiescent mesenchymal stromal cells (MSCs) following stress induced premature senescence (SIPS) by ionizing radiation exposure. We performed a proteome analysis of SASP content obtained from early and late senescent cells. The bioinformatics studies evidenced that early and late SASPs, besides some common ontologies and signalling pathways, contain specific factors. In spite of these differences, we evidenced that SASPs can block in vitro proliferation of cancer cells and promote senescence/apoptosis. It is possible to imagine that SASP always contains core components that have an anti-tumour activity, the progression from early to late senescence enriches the SASP of factors that may promote SASP tumorigenic activity only by interacting and instructing cells of the immune system. Our results on Caco-2 cancer cells incubated with late SASP in presence of peripheral white blood cells strongly support this hypothesis. We evidenced that quiescent MSCs following SIPS produced SASP that, while progressively changed its composition, preserved the capacity to block cancer growth by inducing senescence and/or apoptosis only in an autonomous manner.
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Affiliation(s)
- Nicola Alessio
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | | | - Tiziana Squillaro
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | - Domenico Aprile
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
| | - Şerife Ayaz‐Güner
- Department of Molecular Biology and Genetics, Faculty of Life and Natural ScienceAbdullah Gül UniversityKayseriTurkey
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
| | - Giovanni Di Bernardo
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
- The Interuniversity Consortium “Istituto Nazionale Biostrutture e Biosistemi” (INBB – Biostructures and Biosystems National Institute)RomeItaly
| | | | - Servet Özcan
- Genome and Stem Cell Center (GENKÖK) Erciyes UniversityKayseriTurkey
- Department of Biology, Faculty of ScienceErciyes UniversityKayseriTurkey
| | - Umberto Galderisi
- Department of Experimental MedicineLuigi Vanvitelli Campania UniversityNaplesItaly
- Genome and Stem Cell Center (GENKÖK) Erciyes UniversityKayseriTurkey
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for BiotechnologyTemple UniversityPhiladelphiaPennsylvaniaUSA
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7
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Scinicariello S, Soderholm A, Schäfer M, Shulkina A, Schwartz I, Hacker K, Gogova R, Kalis R, Froussios K, Budroni V, Bestehorn A, Clausen T, Kovarik P, Zuber J, Versteeg GA. HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation. eLife 2023; 12:e83159. [PMID: 36961408 PMCID: PMC10038661 DOI: 10.7554/elife.83159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/26/2023] [Indexed: 03/25/2023] Open
Abstract
Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.
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Affiliation(s)
- Sara Scinicariello
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Adrian Soderholm
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Markus Schäfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Alexandra Shulkina
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Irene Schwartz
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Kathrin Hacker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Rebeca Gogova
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Robert Kalis
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Kimon Froussios
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Annika Bestehorn
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Pavel Kovarik
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
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8
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Liu Q, Novak MK, Pepin RM, Maschhoff KR, Hu W. Different congenital hydrocephalus-associated mutations in Trim71 impair stem cell differentiation via distinct gain-of-function mechanisms. PLoS Biol 2023; 21:e3001947. [PMID: 36757932 PMCID: PMC9910693 DOI: 10.1371/journal.pbio.3001947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/06/2022] [Indexed: 02/10/2023] Open
Abstract
Congenital hydrocephalus (CH) is a common neurological disorder affecting many newborns. Imbalanced neurogenesis is a major cause of CH. Multiple CH-associated mutations are within the RNA-binding domain of Trim71, a conserved, stem cell-specific RNA-binding protein. How these mutations alter stem cell fate is unclear. Here, we show that the CH-associated mutations R595H and R783H in Trim71 accelerate differentiation and enhance neural lineage commitment in mouse embryonic stem cells (mESCs), and reduce binding to mRNAs targeted by wild-type Trim71, consistent with previous reports. Unexpectedly, however, each mutant binds an ectopic and distinct repertoire of target mRNAs. R595H-Trim71, but not R783H-Trim71 nor wild-type Trim71, binds the mRNA encoding β-catenin and represses its translation. Increasing β-catenin by overexpression or treatment with a Wnt agonist specifically restores differentiation of R595H-Trim71 mESCs. These results suggest that Trim71 mutations give rise to unique gain-of-function pathological mechanisms in CH. Further, our studies suggest that disruption of the Wnt/β-catenin signaling pathway can be used to stratify disease etiology and develop precision medicine approaches for CH.
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Affiliation(s)
- Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mariah K. Novak
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rachel M. Pepin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Katharine R. Maschhoff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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9
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Liu Q, Novak MK, Pepin RM, Maschhoff KR, Worner K, Chen X, Zhang S, Hu W. A congenital hydrocephalus-causing mutation in Trim71 induces stem cell defects via inhibiting Lsd1 mRNA translation. EMBO Rep 2023; 24:e55843. [PMID: 36573342 PMCID: PMC9900330 DOI: 10.15252/embr.202255843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Congenital hydrocephalus (CH) is a major cause of childhood morbidity. Mono-allelic mutations in Trim71, a conserved stem-cell-specific RNA-binding protein, cause CH; however, the molecular basis for pathogenesis mediated by these mutations remains unknown. Here, using mouse embryonic stem cells as a model, we reveal that the mouse R783H mutation (R796H in human) alters Trim71's mRNA substrate specificity and leads to accelerated stem-cell differentiation and neural lineage commitment. Mutant Trim71, but not wild-type Trim71, binds Lsd1 (Kdm1a) mRNA and represses its translation. Specific inhibition of this repression or a slight increase of Lsd1 in the mutant cells alleviates the defects in stem cell differentiation and neural lineage commitment. These results determine a functionally relevant target of the CH-causing Trim71 mutant that can potentially be a therapeutic target and provide molecular mechanistic insights into the pathogenesis of this disease.
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Affiliation(s)
- Qiuying Liu
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMNUSA
| | - Mariah K Novak
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMNUSA
| | - Rachel M Pepin
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMNUSA
| | | | - Kailey Worner
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMNUSA
| | - Xiaoli Chen
- Department of Computer ScienceUniversity of Central FloridaOrlandoFLUSA
| | - Shaojie Zhang
- Department of Computer ScienceUniversity of Central FloridaOrlandoFLUSA
| | - Wenqian Hu
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMNUSA
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10
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Malekos E, Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization. Trends Immunol 2022; 43:741-756. [PMID: 35965152 PMCID: PMC10118063 DOI: 10.1016/j.it.2022.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.
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Affiliation(s)
- Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Susan Carpenter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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11
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Aloufi N, Alluli A, Eidelman DH, Baglole CJ. Aberrant Post-Transcriptional Regulation of Protein Expression in the Development of Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2021; 22:ijms222111963. [PMID: 34769392 PMCID: PMC8584689 DOI: 10.3390/ijms222111963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is an incurable and prevalent respiratory disorder that is characterized by chronic inflammation and emphysema. COPD is primarily caused by cigarette smoke (CS). CS alters numerous cellular processes, including the post-transcriptional regulation of mRNAs. The identification of RNA-binding proteins (RBPs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as main factors engaged in the regulation of RNA biology opens the door to understanding their role in coordinating physiological cellular processes. Dysregulation of post-transcriptional regulation by foreign particles in CS may lead to the development of diseases such as COPD. Here we review current knowledge about post-transcriptional events that may be involved in the pathogenesis of COPD.
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Affiliation(s)
- Noof Aloufi
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medical Laboratory Technology, Applied Medical Science, Taibah University, Universities Road, Medina P.O. Box 344, Saudi Arabia
| | - Aeshah Alluli
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
| | - David H. Eidelman
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Carolyn J. Baglole
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
- Correspondence:
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12
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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.
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Affiliation(s)
- Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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13
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Tristetraprolin, Inflammation, and Metabolic Syndrome in Arab Adults: A Case Control Study. BIOLOGY 2021; 10:biology10060550. [PMID: 34207463 PMCID: PMC8235193 DOI: 10.3390/biology10060550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 01/06/2023]
Abstract
Simple Summary Metabolic syndrome (MetS) is a common disorder characterized as a low-grade chronic inflammatory state. The association of tristetraprolin (TTP), a novel anti-inflammatory protein, and MetS remains to be explored. We evaluated circulating TTP in a group of adult males and females with and without MetS. Serum levels of TTP were higher in the MetS group than in controls. In all subjects, serum TTP was also correlated with MetS components (e.g., glucose, lipids, and obesity indices). These findings suggest that TTP may be a promising biomarker for MetS. Abstract Tristetraprolin (TTP) is an mRNA binding protein suggested to have a substantial role in regulating the mRNA expression of numerous inflammatory factors, but data on TTP and its association with metabolic syndrome (MetS), a chronic low-grade inflammatory disorder, are scarce. We hypothesize that TTP may modulate MetS and its components. A total of 200 Saudi adults (aged 38.6 ± 8.3 years) were included in this cross-sectional study. Anthropometrics data were collected and fasting blood glucose taken for the assessment of glycemic, lipids and inflammatory markers using commercially available assays. The National Cholesterol Education Program Adult Treatment Panel (NCEP ATP III) criteria were used to define MetS. Results showed significantly higher levels of TTP in the MetS group than in controls [288.1 pg/mL vs. 150.9 pg/mL, p < 0.001]. Circulating TTP was significantly associated with tumor necrosis factor alpha [TNF-α, R = 0.30, p < 0.05], interleukin 1β [IL-1β, R = 0.41, p < 0.01] and C-reactive protein [CRP, R = 0.36, p < 0.01], adiponectin [R = 0.36, p < 0.05], insulin [R = 0.37, p < 0.05], and insulin resistance [HOMA-IR, R = 0.40, p < 0.05]. Receiver operating characteristics (ROC) suggest a potential use of TTP as diagnostic biomarker for MetS [AUC = 0.819, p < 0.001]. The findings suggest that TTP is associated with inflammation and glycemia, which may influence MetS. TTP is a promising diagnostic biomarker for MetS which can be confirmed in larger cohorts.
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14
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Assabban A, Dubois-Vedrenne I, Van Maele L, Salcedo R, Snyder BL, Zhou L, Azouz A, de Toeuf B, Lapouge G, La C, Melchior M, Nguyen M, Thomas S, Wu SF, Hu W, Kruys V, Blanpain C, Trinchieri G, Gueydan C, Blackshear PJ, Goriely S. Tristetraprolin expression by keratinocytes protects against skin carcinogenesis. JCI Insight 2021; 6:140669. [PMID: 33497366 PMCID: PMC8021119 DOI: 10.1172/jci.insight.140669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/20/2021] [Indexed: 01/27/2023] Open
Abstract
Cancer is caused primarily by genomic alterations resulting in deregulation of gene regulatory circuits in key growth, apoptosis, or DNA repair pathways. Multiple genes associated with the initiation and development of tumors are also regulated at the level of mRNA decay, through the recruitment of RNA-binding proteins to AU-rich elements (AREs) located in their 3'-untranslated regions. One of these ARE-binding proteins, tristetraprolin (TTP; encoded by Zfp36), is consistently dysregulated in many human malignancies. Herein, using regulated overexpression or conditional ablation in the context of cutaneous chemical carcinogenesis, we show that TTP represents a critical regulator of skin tumorigenesis. We provide evidence that TTP controlled both tumor-associated inflammation and key oncogenic pathways in neoplastic epidermal cells. We identify Areg as a direct target of TTP in keratinocytes and show that EGFR signaling potentially contributed to exacerbated tumor formation. Finally, single-cell RNA-Seq analysis indicated that ZFP36 was downregulated in human malignant keratinocytes. We conclude that TTP expression by epidermal cells played a major role in the control of skin tumorigenesis.
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Affiliation(s)
- Assiya Assabban
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ingrid Dubois-Vedrenne
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Laurye Van Maele
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Rosalba Salcedo
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - Lecong Zhou
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Abdulkader Azouz
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Bérengère de Toeuf
- Laboratoire de Biologie Moléculaire du Gène, ULB Center for Research in Immunology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Gaëlle Lapouge
- Laboratory of Stem Cells and Cancer, WELBIO, and ULB Cancer Research Center, Université Libre de Bruxelles, Brussels, Belgium
| | - Caroline La
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Maxime Melchior
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Muriel Nguyen
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Séverine Thomas
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
| | - Si Fan Wu
- Laboratoire de Biologie Moléculaire du Gène, ULB Center for Research in Immunology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, New York, USA
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, ULB Center for Research in Immunology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, WELBIO, and ULB Cancer Research Center, Université Libre de Bruxelles, Brussels, Belgium
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, ULB Center for Research in Immunology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Perry J. Blackshear
- Signal Transduction Laboratory and
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Stanislas Goriely
- Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium
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15
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Liu Q, Chen X, Novak MK, Zhang S, Hu W. Repressing Ago2 mRNA translation by Trim71 maintains pluripotency through inhibiting let-7 microRNAs. eLife 2021; 10:66288. [PMID: 33599613 PMCID: PMC7906602 DOI: 10.7554/elife.66288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
The regulation of stem cell fate is poorly understood. Genetic studies in Caenorhabditis elegans lead to the hypothesis that a conserved cytoplasmic double-negative feedback loop consisting of the RNA-binding protein Trim71 and the let-7 microRNA controls the pluripotency and differentiation of stem cells. Although let-7-microRNA-mediated inhibition of Trim71 promotes differentiation, whether and how Trim71 regulates pluripotency and inhibits the let-7 microRNA are still unknown. Here, we show that Trim71 represses Ago2 mRNA translation in mouse embryonic stem cells. Blocking this repression leads to a specific post-transcriptional increase of mature let-7 microRNAs, resulting in let-7-dependent stemness defects and accelerated differentiation in the stem cells. These results not only support the Trim71-let-7-microRNA bi-stable switch model in controlling stem cell fate, but also reveal that repressing the conserved pro-differentiation let-7 microRNAs at the mature microRNA level by Ago2 availability is critical to maintaining pluripotency.
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Affiliation(s)
- Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, United States
| | - Mariah K Novak
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, United States
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
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16
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Rappl P, Brüne B, Schmid T. Role of Tristetraprolin in the Resolution of Inflammation. BIOLOGY 2021; 10:biology10010066. [PMID: 33477783 PMCID: PMC7832405 DOI: 10.3390/biology10010066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/18/2022]
Abstract
Simple Summary Chronic inflammatory diseases account for up to 60% of deaths worldwide and, thus, are considered a great threat for human health by the World Health Organization. Nevertheless, acute inflammatory reactions are an integral part of the host defense against invading pathogens or injuries. To avoid excessive damage due to the persistence of a highly reactive environment, inflammations need to resolve in a coordinate and timely manner, ensuring for the immunological normalization of the affected tissues. Since post-transcriptional regulatory mechanisms are essential for effective resolution, the present review discusses the key role of the RNA-binding and post-transcriptional regulatory protein tristetraprolin in establishing resolution of inflammation. Abstract Inflammation is a crucial part of immune responses towards invading pathogens or tissue damage. While inflammatory reactions are aimed at removing the triggering stimulus, it is important that these processes are terminated in a coordinate manner to prevent excessive tissue damage due to the highly reactive inflammatory environment. Initiation of inflammatory responses was proposed to be regulated predominantly at a transcriptional level, whereas post-transcriptional modes of regulation appear to be crucial for resolution of inflammation. The RNA-binding protein tristetraprolin (TTP) interacts with AU-rich elements in the 3′ untranslated region of mRNAs, recruits deadenylase complexes and thereby facilitates degradation of its targets. As TTP regulates the mRNA stability of numerous inflammatory mediators, it was put forward as a crucial post-transcriptional regulator of inflammation. Here, we summarize the current understanding of the function of TTP with a specific focus on its role in adding to resolution of inflammation.
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Affiliation(s)
- Peter Rappl
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (P.R.); (B.B.)
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (P.R.); (B.B.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt, Germany
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular and Applied Ecology, 60596 Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (P.R.); (B.B.)
- Correspondence:
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17
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The RNA-binding protein tristetraprolin regulates RALDH2 expression by intestinal dendritic cells and controls local Treg homeostasis. Mucosal Immunol 2021; 14:80-91. [PMID: 32467605 PMCID: PMC9386908 DOI: 10.1038/s41385-020-0302-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 02/04/2023]
Abstract
AU-rich element (ARE)-mediated mRNA decay represents a key mechanism to avoid excessive production of inflammatory cytokines. Tristetraprolin (TTP, encoded by Zfp36) is a major ARE-binding protein, since Zfp36-/- mice develop a complex multiorgan inflammatory syndrome that shares many features with spondyloarthritis. The role of TTP in intestinal homeostasis is not known. Herein, we show that Zfp36-/- mice do not develop any histological signs of gut pathology. However, they display a clear increase in intestinal inflammatory markers and discrete alterations in microbiota composition. Importantly, oral antibiotic treatment reduced both local and systemic joint and skin inflammation. We further show that absence of overt intestinal pathology is associated with local expansion of regulatory T cells. We demonstrate that this is related to increased vitamin A metabolism by gut dendritic cells, and identify RALDH2 as a direct target of TTP. In conclusion, these data bring insights into the interplay between microbiota-dependent gut and systemic inflammation during immune-mediated disorders, such as spondyloarthritis.
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18
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Covarrubias S, Vollmers AC, Capili A, Boettcher M, Shulkin A, Correa MR, Halasz H, Robinson EK, O'Briain L, Vollmers C, Blau J, Katzman S, McManus MT, Carpenter S. High-Throughput CRISPR Screening Identifies Genes Involved in Macrophage Viability and Inflammatory Pathways. Cell Rep 2020; 33:108541. [PMID: 33378675 PMCID: PMC7901356 DOI: 10.1016/j.celrep.2020.108541] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/08/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Macrophages are critical effector cells of the immune system, and understanding genes involved in their viability and function is essential for gaining insights into immune system dysregulation during disease. We use a high-throughput, pooled-based CRISPR-Cas screening approach to identify essential genes required for macrophage viability. In addition, we target 3' UTRs to gain insights into previously unidentified cis-regulatory regions that control these essential genes. Next, using our recently generated nuclear factor κB (NF-κB) reporter line, we perform a fluorescence-activated cell sorting (FACS)-based high-throughput genetic screen and discover a number of previously unidentified positive and negative regulators of the NF-κB pathway. We unravel complexities of the TNF signaling cascade, showing that it can function in an autocrine manner in macrophages to negatively regulate the pathway. Utilizing a single complex library design, we are capable of interrogating various aspects of macrophage biology, thus generating a resource for future studies.
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Affiliation(s)
- Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Apple Cortez Vollmers
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Allyson Capili
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael Boettcher
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; W.M. Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA, USA; Institute for Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Aaron Shulkin
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michele Ramos Correa
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Laura O'Briain
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - James Blau
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; W.M. Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; W.M. Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
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19
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Gharib E, Nazemalhosseini-Mojarad E, Baghdar K, Nayeri Z, Sadeghi H, Rezasoltani S, Jamshidi-Fard A, Larki P, Sadeghi A, Hashemi M, Asadzadeh Aghdaei H. Identification of a stool long non-coding RNAs panel as a potential biomarker for early detection of colorectal cancer. J Clin Lab Anal 2020; 35:e23601. [PMID: 33094859 PMCID: PMC7891513 DOI: 10.1002/jcla.23601] [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: 05/22/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background The feces of colorectal cancer (CRC) patients contain tumor colonocytes, which constantly shed into the lumen area. Therefore, stool evaluation can be considered as a rapid and low‐risk way to directly determine the colon and rectum status. As long non‐coding RNAs (lncRNAs) alterations are important in cancer cells fate regulation, we aimed to assess the level of a panel of cancer‐related lncRNAs in fecal colonocytes. Methods The population study consisted of 150 subjects, including a training set, a validation set, and a group of 30 colon polyps. The expression levels of lncRNAs were evaluated by quantitative real‐time PCR (qRT‐PCR). The NPInetr and EnrichR tools were used to identify the interactions and functions of lncRNAs. Results A total of 10 significantly dysregulated lncRNAs, including CCAT1, CCAT2, H19, HOTAIR, HULC, MALAT1, PCAT1, MEG3, PTENP1, and TUSC7, were chosen for designing a predictive panel. The diagnostic performance of the panel in distinguishing CRCs from the healthy group was AUC: 0.8554 in the training set and 0.8465 in the validation set. The AUC for early CRCs (I‐II TNM stages) was 0.8554 in the training set and 0.8465 in the validation set, and for advanced CRCs (III‐IV TNM stages) were 0.9281 in the training set and 0.9236 in the validation set. The corresponding AUC for CRCs vs polyps were 0.9228 (I‐IV TNM stages), 0.9042 (I‐II TNM stages), and 0.9362 (III‐IV TNM stages). Conclusions These data represented the application of analysis of fecal colonocytes lncRNAs in early detection of CRC.
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Affiliation(s)
- Ehsan Gharib
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghdar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Nayeri
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Sadeghi
- Molecular Genetics Department, Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sama Rezasoltani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arezo Jamshidi-Fard
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pegah Larki
- Molecular Genetics Department, Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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20
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Besic V, Habibolahi F, Noël B, Rupp S, Genovesio A, Lebreton A. Coordination of transcriptional and translational regulations in human epithelial cells infected by Listeria monocytogenes. RNA Biol 2020; 17:1492-1507. [PMID: 32584699 PMCID: PMC7549700 DOI: 10.1080/15476286.2020.1777380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
The invasion of mammalian cells by intracellular bacterial pathogens reshuffles their gene expression and functions; however, we lack dynamic insight into the distinct control levels that shape the host response. Here, we have addressed the respective contribution of transcriptional and translational regulations during a time-course of infection of human intestinal epithelial cells by an epidemic strain of Listeria monocytogenes, using transcriptome analysis paralleled with ribosome profiling. Upregulations were dominated by early transcriptional activation of pro-inflammatory genes, whereas translation inhibition appeared as the major driver of downregulations. Instead of a widespread but transient shutoff, translation inhibition affected specifically and durably transcripts encoding components of the translation machinery harbouring a 5'-terminal oligopyrimidine motif. Pre-silencing the most repressed target gene (PABPC1) slowed down the intracellular multiplication of Listeria monocytogenes, suggesting that the infected host cell can benefit from the repression of genes involved in protein synthesis and thereby better control infection.
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Affiliation(s)
- Vinko Besic
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fatemeh Habibolahi
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benoît Noël
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sebastian Rupp
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Auguste Genovesio
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alice Lebreton
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, IBENS, Paris, France
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21
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Translational profiling of macrophages infected with Leishmania donovani identifies mTOR- and eIF4A-sensitive immune-related transcripts. PLoS Pathog 2020; 16:e1008291. [PMID: 32479529 PMCID: PMC7310862 DOI: 10.1371/journal.ppat.1008291] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/23/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022] Open
Abstract
The protozoan parasite Leishmania donovani (L. donovani) causes visceral leishmaniasis, a chronic infection which is fatal when untreated. Herein, we investigated whether in addition to altering transcription, L. donovani modulates host mRNA translation to establish a successful infection. Polysome-profiling revealed that one third of protein-coding mRNAs expressed in primary mouse macrophages are differentially translated upon infection with L. donovani promastigotes or amastigotes. Gene ontology analysis identified key biological processes enriched for translationally regulated mRNAs and were predicted to be either activated (e.g. chromatin remodeling and RNA metabolism) or inhibited (e.g. intracellular trafficking and antigen presentation) upon infection. Mechanistic in silico and biochemical analyses showed selective activation mTOR- and eIF4A-dependent mRNA translation, including transcripts encoding central regulators of mRNA turnover and inflammation (i.e. PABPC1, EIF2AK2, and TGF-β). L. donovani survival within macrophages was favored under mTOR inhibition but was dampened by pharmacological blockade of eIF4A. Overall, this study uncovers a vast yet selective reprogramming of the host cell translational landscape early during L. donovani infection, and suggests that some of these changes are involved in host defense mechanisms while others are part of parasite-driven survival strategies. Further in vitro and in vivo investigation will shed light on the contribution of mTOR- and eIF4A-dependent translational programs to the outcome of visceral leishmaniasis.
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22
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Lai WS, Stumpo DJ, Wells ML, Gruzdev A, Hicks SN, Nicholson CO, Yang Z, Faccio R, Webster MW, Passmore LA, Blackshear PJ. Importance of the Conserved Carboxyl-Terminal CNOT1 Binding Domain to Tristetraprolin Activity In Vivo. Mol Cell Biol 2019; 39:e00029-19. [PMID: 31036567 PMCID: PMC6580703 DOI: 10.1128/mcb.00029-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/12/2019] [Accepted: 04/19/2019] [Indexed: 01/19/2023] Open
Abstract
Tristetraprolin (TTP) is an anti-inflammatory protein that modulates the stability of certain cytokine/chemokine mRNAs. After initial high-affinity binding to AU-rich elements in 3' untranslated regions of target mRNAs, mediated through its tandem zinc finger (TZF) domain, TTP promotes the deadenylation and ultimate decay of target transcripts. These transcripts and their encoded proteins accumulate abnormally in TTP knockout (KO) mice, leading to a severe inflammatory syndrome. To assess the importance of the highly conserved C-terminal CNOT1 binding domain (CNBD) of TTP to the TTP deficiency phenotype in mice, we created a mouse model in which TTP lacked its CNBD. CNBD deletion mice exhibited a less severe phenotype than the complete TTP KO mice. In macrophages, the stabilization of target transcripts seen in KO mice was partially normalized in the CNBD deletion mice. In cell-free experiments, recombinant TTP lacking its CNBD could still activate target mRNA deadenylation by purified recombinant Schizosaccharomyces pombe CCR4/NOT complexes, although to a lesser extent than full-length TTP. Thus, TTP lacking its CNBD can still act to promote target mRNA instability in vitro and in vivo These data have implications for TTP family members throughout the eukarya, since species from all four kingdoms contain proteins with linked TZF and CNOT1 binding domains.
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Affiliation(s)
- Wi S Lai
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Deborah J Stumpo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Artiom Gruzdev
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stephanie N Hicks
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Cindo O Nicholson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Zhengfeng Yang
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
- Shriners Hospitals for Children, St. Louis, Missouri, USA
| | - Roberta Faccio
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
- Shriners Hospitals for Children, St. Louis, Missouri, USA
| | | | - Lori A Passmore
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
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23
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Zhao Y, Ding L, Wang D, Ye Z, He Y, Ma L, Zhu R, Pan Y, Wu Q, Pang K, Hou X, Weroha SJ, Han C, Coleman R, Coleman I, Karnes RJ, Zhang J, Nelson PS, Wang L, Huang H. EZH2 cooperates with gain-of-function p53 mutants to promote cancer growth and metastasis. EMBO J 2019; 38:e99599. [PMID: 30723117 PMCID: PMC6396169 DOI: 10.15252/embj.201899599] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
In light of the increasing number of identified cancer-driven gain-of-function (GOF) mutants of p53, it is important to define a common mechanism to systematically target several mutants, rather than developing strategies tailored to inhibit each mutant individually. Here, using RNA immunoprecipitation-sequencing (RIP-seq), we identified the Polycomb-group histone methyltransferase EZH2 as a p53 mRNA-binding protein. EZH2 bound to an internal ribosome entry site (IRES) in the 5'UTR of p53 mRNA and enhanced p53 protein translation in a methyltransferase-independent manner. EZH2 augmented p53 GOF mutant-mediated cancer growth and metastasis by increasing protein levels of mutant p53. EZH2 overexpression was associated with worsened outcome selectively in patients with p53-mutated cancer. Depletion of EZH2 by antisense oligonucleotides inhibited p53 GOF mutant-mediated cancer growth. Our findings reveal a non-methyltransferase function of EZH2 that controls protein translation of p53 GOF mutants, inhibition of which causes synthetic lethality in cancer cells expressing p53 GOF mutants.
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Affiliation(s)
- Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Liya Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dejie Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Zhenqing Ye
- Division of Medical Informatics and Statistics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yundong He
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Linlin Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Runzhi Zhu
- Center for Cell Therapy, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yunqian Pan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Qiang Wu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kun Pang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Urology, Xuzhou Central Hospital and Medical College affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaonan Hou
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Saravut J Weroha
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Conghui Han
- Department of Urology, Xuzhou Central Hospital and Medical College affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Roger Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - R Jeffery Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Liguo Wang
- Division of Medical Informatics and Statistics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN, USA
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24
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Chen X, Castro SA, Liu Q, Hu W, Zhang S. Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. Methods 2019; 155:49-57. [PMID: 30527764 PMCID: PMC6387833 DOI: 10.1016/j.ymeth.2018.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022] Open
Abstract
RNA-binding proteins are important players in post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. Identifying and characterizing the RNA substrates is a critical step in deciphering the function and molecular mechanisms of the target RNA-binding proteins. High-throughput sequencing of the RNA fragments isolated by crosslinking immunoprecipitation (CLIP-seq) is one of the standard techniques to identify the in vivo transcriptome-wide binding sites of the target RNA-binding protein. This method is widely used in functional and mechanistic characterizations of RNA-binding proteins. In this review, we provide several practical considerations on performing and analyzing CLIP-seq experiments. Particularly, we focus on how to perform CLIP-seq experiments on endogenous RNA-binding proteins. In addition, we provide a practical summary on how to choose and use computational pipelines from an increasing number of computational methods and packages that are available for analyzing the sequencing datasets from the CLIP-seq experiments. We hope these practical considerations will facilitate experimental biologists in performing and analyzing CLIP-seq experiment to obtain biologically relevant mechanistic insights.
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Affiliation(s)
- Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Sarah A Castro
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
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Ramos-Alonso L, Romero AM, Polaina J, Puig S, Martínez-Pastor MT. Dissecting mRNA decay and translation inhibition during iron deficiency. Curr Genet 2018; 65:139-145. [PMID: 30128746 DOI: 10.1007/s00294-018-0880-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
Iron participates as a vital cofactor in multiple metabolic pathways. Despite its abundance, iron bioavailability is highly restricted in aerobic and alkaline environments. Therefore, living organisms have evolved multiple adaptive mechanisms to respond to iron scarcity. These strategies include a global remodeling of iron metabolism directed to optimize iron utilization. In the baker's yeast Saccharomyces cerevisiae, this metabolic reorganization is accomplished to a large extent by an mRNA-binding protein called Cth2. Yeast Cth2 belongs to a conserved family of tandem zinc finger containing proteins that specifically bind to transcripts with AU-rich elements and promote their turnover. A recent study has revealed that Cth2 also inhibits the translation of its target mRNAs (Ramos-Alonso et al., PLoS Genet 14:e1007476, https://doi.org/10.1371/journal.pgen.1007476 , 2018). Interestingly, the mammalian Cth2 ortholog known as tristetraprolin (aka TTP/TIS11/ZFP36), which is also implicated in controlling iron metabolism, promotes the decay and prevents the translation of its regulated transcripts. These observations open the possibility to study the relative contribution of altering mRNA stability and translation to the physiological adaptation to iron deficiency, the function played by the different domains within the mRNA-binding protein, and the potential factors implicated in coordinating both post-transcriptional events.
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Affiliation(s)
- Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Julio Polaina
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Ave. Doctor Moliner 50, Burjassot, 46100, Valencia, Spain.
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26
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Kontoyiannis DL. An RNA checkpoint that keeps immunological memory at bay. Nat Immunol 2018; 19:795-797. [PMID: 29988088 DOI: 10.1038/s41590-018-0168-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dimitris L Kontoyiannis
- Aristotle University of Thessaloniki, School of Biology, Department of Genetics, Development & Molecular Biology, Thessaloniki, Greece. .,Biomedical Sciences Research Centre 'Alexander Fleming', Division of Immunology, Vari, Greece.
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27
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Ramos-Alonso L, Romero AM, Soler MÀ, Perea-García A, Alepuz P, Puig S, Martínez-Pastor MT. Yeast Cth2 protein represses the translation of ARE-containing mRNAs in response to iron deficiency. PLoS Genet 2018; 14:e1007476. [PMID: 29912874 PMCID: PMC6023232 DOI: 10.1371/journal.pgen.1007476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/28/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022] Open
Abstract
In response to iron deficiency, the budding yeast Saccharomyces cerevisiae undergoes a metabolic remodeling in order to optimize iron utilization. The tandem zinc finger (TZF)-containing protein Cth2 plays a critical role in this adaptation by binding and promoting the degradation of multiple mRNAs that contain AU-rich elements (AREs). Here, we demonstrate that Cth2 also functions as a translational repressor of its target mRNAs. By complementary approaches, we demonstrate that Cth2 protein inhibits the translation of SDH4, which encodes a subunit of succinate dehydrogenase, and CTH2 mRNAs in response to iron depletion. Both the AREs within SDH4 and CTH2 transcripts, and the Cth2 TZF are essential for translational repression. We show that the role played by Cth2 as a negative translational regulator extends to other mRNA targets such as WTM1, CCP1 and HEM15. A structure-function analysis of Cth2 protein suggests that the Cth2 amino-terminal domain (NTD) is important for both mRNA turnover and translation inhibition, while its carboxy-terminal domain (CTD) only participates in the regulation of translation, but is dispensable for mRNA degradation. Finally, we demonstrate that the Cth2 CTD is physiologically relevant for adaptation to iron deficiency. Iron is essential for eukaryotes because it is required for many fundamental processes such as DNA replication, protein translation or respiration, but it is very insoluble and can, therefore, easily go scarce. For this reason, eukaryotic cells have developed adaptive responses to iron deficiency. Under iron limitation conditions, the yeast Saccharomyces cerevisiae induces the expression of Cth2, a protein with tandem zinc fingers that binds to adenine and uracil-rich sequences in the 3’-UTR of specific mRNAs related to iron metabolism, promoting their degradation. Here we show that Cth2 inhibits the translation of ARE-containing mRNAs, including SDH4, WTM1, HEM15 and CCP1, which encode proteins that contain iron or participate in iron-dependent pathways, and CTH2 itself, which is subjected to an autoregulatory loop that controls its expression. We also dissected different domains of Cth2 that are differentially involved in mRNA decay and translational inhibition. The involvement of Cth2 in translational control reinforces the importance of this ARE-binding protein as a post-transcriptional regulator of the iron response in yeast. By acting at different steps in the life of specific mRNA targets, Cth2 action ensures yeast cells a proper distribution of iron by optimizing its utilization in essential processes.
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Affiliation(s)
- Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Maria Àngel Soler
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Ana Perea-García
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
- ERI Biotecmed, Universitat de València, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- * E-mail: (MTMP); (SP)
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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.
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29
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Dassi E. Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins. Front Mol Biosci 2017; 4:67. [PMID: 29034245 PMCID: PMC5626838 DOI: 10.3389/fmolb.2017.00067] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/20/2017] [Indexed: 12/31/2022] Open
Abstract
What drives the flow of signals controlling the outcome of post-transcriptional regulation of gene expression? This regulatory layer, presiding to processes ranging from splicing to mRNA stability and localization, is a key determinant of protein levels and thus cell phenotypes. RNA-binding proteins (RBPs) form a remarkable army of post-transcriptional regulators, strong of more than 1,500 genes implementing this expression fine-tuning plan and implicated in both cell physiology and pathology. RBPs can bind and control a wide array of RNA targets. This sheer amount of interactions form complex regulatory networks (PTRNs) where the action of individual RBPs cannot be easily untangled from each other. While past studies have mostly focused on the action of individual RBPs on their targets, we are now observing an increasing amount of evidence describing the occurrence of interactions between RBPs, defining how common target RNAs are regulated. This suggests that the flow of signals in PTRNs is driven by the intertwined contribution of multiple RBPs, concurrently acting on each of their targets. Understanding how RBPs cooperate and compete is thus of paramount importance to chart the wiring of PTRNs and their impact on cell phenotypes. Here we review the current knowledge about patterns of RBP interaction and attempt at describing their general principles. We also discuss future directions which should be taken to reach a comprehensive understanding of this fundamental aspect of gene expression regulation.
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Affiliation(s)
- Erik Dassi
- Centre for Integrative Biology, University of Trento, Trento, Italy
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