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Perl AJ, Liu H, Hass M, Adhikari N, Chaturvedi P, Hu YC, Jiang R, Liu Y, Kopan R. Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. J Am Soc Nephrol 2024; 35:566-577. [PMID: 38447671 PMCID: PMC11149036 DOI: 10.1681/asn.0000000000000324] [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: 02/03/2023] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Key Points Aberrant enhancer–promoter interactions detected by Hi-C drive ectopic expression of Six3 in the Six2TGCtg line. Disruption of Six3 in the Six2TGCtg line restores nephron number, implicating SIX3 interference with SIX2 function in nephron progenitor cell renewal. Background Lifelong kidney function relies on the complement of nephrons generated during mammalian development from a mesenchymal nephron progenitor cell population. Low nephron endowment confers increased susceptibility to CKD. Reduced nephron numbers in the popular Six2TGC transgenic mouse line may be due to disruption of a regulatory gene at the integration site and/or ectopic expression of a gene(s) contained within the transgene. Methods Targeted locus amplification was performed to identify the integration site of the Six2TGC transgene. Genome-wide chromatin conformation capture (Hi-C) datasets were generated from nephron progenitor cells isolated from the Six2TGC +/tg mice, the Cited1 CreERT2/+ control mice, and the Six2TGC +/tg ; Tsc1 +/Flox mice that exhibited restored nephron number compared with Six2TGC +/tg mice. Modified transgenic mice lacking the C-terminal domain of Six3 were used to evaluate the mechanism of nephron number reduction in the Six2TGC +/tg mouse line. Results Targeted locus amplification revealed integration of the Six2TGC transgene within an intron of Cntnap5a on chr1, and Hi-C analysis mapped the precise integration of Six2TGC and Cited1 CreERT2 transgenes to chr1 and chr14, respectively. No changes in topology, accessibility, or expression were observed within the 50-megabase region centered on Cntnap5a in Six2TGC +/tg mice compared with control mice. By contrast, we identified an aberrant regulatory interaction between a Six2 distal enhancer and the Six3 promoter contained within the transgene. Increasing the Six2TGC tg to Six2 locus ratio or removing one Six2 allele in Six2TGC +/tg mice caused severe renal hypoplasia. Furthermore, clustered regularly interspaced short palindromic repeats disruption of Six3 within the transgene (Six2TGC ∆Six3CT ) restored nephron endowment to wild-type levels and abolished the stoichiometric effect. Conclusions These findings broadly demonstrate the utility of Hi-C data in mapping transgene integration sites and architecture. Data from genetic and biochemical studies together suggest that in Six2TGC kidneys, SIX3 interferes with SIX2 function in nephron progenitor cell renewal through its C-terminal domain.
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Affiliation(s)
- Alison J. Perl
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Han Liu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Matthew Hass
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Nirpesh Adhikari
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Praneet Chaturvedi
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rulang Jiang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yaping Liu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Raphael Kopan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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Sharma G, Paganin M, Lauria F, Perenthaler E, Viero G. The SMN-ribosome interplay: a new opportunity for Spinal Muscular Atrophy therapies. Biochem Soc Trans 2024; 52:465-479. [PMID: 38391004 PMCID: PMC10903476 DOI: 10.1042/bst20231116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The underlying cause of Spinal Muscular Atrophy (SMA) is in the reduction of survival motor neuron (SMN) protein levels due to mutations in the SMN1 gene. The specific effects of SMN protein loss and the resulting pathological alterations are not fully understood. Given the crucial roles of the SMN protein in snRNP biogenesis and its interactions with ribosomes and translation-related proteins and mRNAs, a decrease in SMN levels below a specific threshold in SMA is expected to affect translational control of gene expression. This review covers both direct and indirect SMN interactions across various translation-related cellular compartments and processes, spanning from ribosome biogenesis to local translation and beyond. Additionally, it aims to outline deficiencies and alterations in translation observed in SMA models and patients, while also discussing the implications of the relationship between SMN protein and the translation machinery within the context of current and future therapies.
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Hansel-Frose AFF, Allmer J, Friedrichs M, dos Santos HG, Dallagiovanna B, Spangenberg L. Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs. Front Mol Biosci 2024; 11:1336336. [PMID: 38380430 PMCID: PMC10877728 DOI: 10.3389/fmolb.2024.1336336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
Alternative polyadenylation (APA) increases transcript diversity through the generation of isoforms with varying 3' untranslated region (3' UTR) lengths. As the 3' UTR harbors regulatory element target sites, such as miRNAs or RNA-binding proteins, changes in this region can impact post-transcriptional regulation and translation. Moreover, the APA landscape can change based on the cell type, cell state, or condition. Given that APA events can impact protein expression, investigating translational control is crucial for comprehending the overall cellular regulation process. Revisiting data from polysome profiling followed by RNA sequencing, we investigated the cardiomyogenic differentiation of pluripotent stem cells by identifying the transcripts that show dynamic 3' UTR lengthening or shortening, which are being actively recruited to ribosome complexes. Our findings indicate that dynamic 3' UTR lengthening is not exclusively associated with differential expression during cardiomyogenesis but rather with recruitment to polysomes. We confirm that the differentiated state of cardiomyocytes shows a preference for shorter 3' UTR in comparison to the pluripotent stage although preferences vary during the days of the differentiation process. The most distinct regulatory changes are seen in day 4 of differentiation, which is the mesoderm commitment time point of cardiomyogenesis. After identifying the miRNAs that would target specifically the alternative 3' UTR region of the isoforms, we constructed a gene regulatory network for the cardiomyogenesis process, in which genes related to the cell cycle were identified. Altogether, our work sheds light on the regulation and dynamic 3' UTR changes of polysome-recruited transcripts that take place during the cardiomyogenic differentiation of pluripotent stem cells.
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Affiliation(s)
- Aruana F. F. Hansel-Frose
- Laboratory of Basic Stem Cell Biology, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil
| | - Jens Allmer
- Department of Medical Informatics and Bioinformatics, University of Applied Sciences Ruhr West, Mülheim, Germany
| | - Marcel Friedrichs
- Bioinformatics and Medical Informatics Department, University of Bielefeld, Bielefeld, Germany
| | | | - Bruno Dallagiovanna
- Laboratory of Basic Stem Cell Biology, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil
| | - Lucía Spangenberg
- Bioinformatics Unit, Pasteur Institute of Montevideo, Montevideo, Uruguay
- Departamento Basico de Medicina, Hospital de Clinicas, Universidad de la República (Udelar), Montevideo, Uruguay
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Kuntschar S, Cardamone G, Klann K, Bauer R, Meyer SP, Raue R, Rappl P, Münch C, Brüne B, Schmid T. Mmp12 Is Translationally Regulated in Macrophages during the Course of Inflammation. Int J Mol Sci 2023; 24:16981. [PMID: 38069304 PMCID: PMC10707645 DOI: 10.3390/ijms242316981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Despite the importance of rapid adaptive responses in the course of inflammation and the notion that post-transcriptional regulation plays an important role herein, relevant translational alterations, especially during the resolution phase, remain largely elusive. In the present study, we analyzed translational changes in inflammatory bone marrow-derived macrophages upon resolution-promoting efferocytosis. Total RNA-sequencing confirmed that apoptotic cell phagocytosis induced a pro-resolution signature in LPS/IFNγ-stimulated macrophages (Mϕ). While inflammation-dependent transcriptional changes were relatively small between efferocytic and non-efferocytic Mϕ; considerable differences were observed at the level of de novo synthesized proteins. Interestingly, translationally regulated targets in response to inflammatory stimuli were mostly downregulated, with only minimal impact of efferocytosis. Amongst these targets, pro-resolving matrix metallopeptidase 12 (Mmp12) was identified as a translationally repressed candidate during early inflammation that recovered during the resolution phase. Functionally, reduced MMP12 production enhanced matrix-dependent migration of Mϕ. Conclusively, translational control of MMP12 emerged as an efficient strategy to alter the migratory properties of Mϕ throughout the inflammatory response, enabling Mϕ migration within the early inflammatory phase while restricting migration during the resolution phase.
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Affiliation(s)
- Silvia Kuntschar
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Giulia Cardamone
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Rebekka Bauer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Sofie Patrizia Meyer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Rebecca Raue
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Peter Rappl
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Bhattacharyya S, Wang J, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations. Mol Autism 2023; 14:39. [PMID: 37880800 PMCID: PMC10601155 DOI: 10.1186/s13229-023-00572-3] [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: 05/16/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND.
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Affiliation(s)
- Inci S Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Pauline Martin
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Francis Robert
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Nicholas E Redmond
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Srirupa Bhattacharyya
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Jennifer Wang
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Roberta L Beauchamp
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences,, Birkbeck, University of London, London, WC1E 7HX, UK
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden.
| | - Vijaya Ramesh
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA.
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Perl AJ, Liu H, Hass M, Adhikari N, Chaturvedi P, Hu YC, Jiang R, Liu Y, Kopan R. Reduced nephron endowment in the common Six2-TGC tg mouse line is due to Six3 misexpression by aberrant enhancer-promoter interactions in the transgene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561202. [PMID: 37873415 PMCID: PMC10592608 DOI: 10.1101/2023.10.06.561202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Lifelong kidney function relies on the complement of nephrons generated during mammalian development from a mesenchymal nephron progenitor cell (NPC) population. Low nephron endowment confers increased susceptibility to chronic kidney disease. We asked whether reduced nephron numbers in the popular Six2TGC transgenic mouse line 1 was due to disruption of a regulatory gene at the integration site or to ectopic expression of a gene(s) contained within the transgene. Targeted locus amplification identified integration of the Six2TGC transgene within an intron of Cntnap5a on chr1. We generated Hi-C datasets from NPCs isolated from the Six2TGC tg/+ mice, the Cited1 CreERT2/+ control mice, and the Six2TGC tg/+ ; Tsc1 +/Flox,2 mice that exhibited restored nephron number compared with Six2TGC tg/+ mice, and mapped the precise integration of Six2TGC and Cited1 CreERT2 transgenes to chr1 and chr14, respectively. No changes in topology, accessibility, or expression were observed within the 50-megabase region centered on Cntnap5a in Six2TGC tg/+ mice compared with control mice. By contrast, we identified an aberrant regulatory interaction between a Six2 distal enhancer and the Six3 promoter contained within the transgene. Increasing the Six2TGC tg to Six2 locus ratio or removing one Six2 allele in Six2TGC tg/+ mice, caused severe renal hypoplasia. Furthermore, CRISPR disruption of Six3 within the transgene ( Six2TGC Δ Six3CT ) restored nephron endowment to wildtype levels and abolished the stoichiometric effect. Data from genetic and biochemical studies together suggest that in Six2TGC, SIX3 interferes with SIX2 function in NPC renewal through its C-terminal domain. Significance Using high-resolution chromatin conformation and accessibility datasets we mapped the integration site of two popular transgenes used in studies of nephron progenitor cells and kidney development. Aberrant enhancer-promoter interactions drive ectopic expression of Six3 in the Six2TGC tg line which was correlated with disruption of nephrogenesis. Disruption of Six3 within the transgene restored nephron numbers to control levels; further genetic and biochemical studies suggest that Six3 interferes with Six2 -mediated regulation of NPC renewal.
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Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D'Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff JH, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. NATURE CANCER 2023; 4:1102-1121. [PMID: 37460872 DOI: 10.1038/s43018-023-00594-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/13/2023] [Indexed: 08/25/2023]
Abstract
Cancer is highly infiltrated by myeloid-derived suppressor cells (MDSCs). Currently available immunotherapies do not completely eradicate MDSCs. Through a genome-wide analysis of the translatome of prostate cancers driven by different genetic alterations, we demonstrate that prostate cancer rewires its secretome at the translational level to recruit MDSCs. Among different secreted proteins released by prostate tumor cells, we identified Hgf, Spp1 and Bgn as the key factors that regulate MDSC migration. Mechanistically, we found that the coordinated loss of Pdcd4 and activation of the MNK/eIF4E pathways regulate the mRNAs translation of Hgf, Spp1 and Bgn. MDSC infiltration and tumor growth were dampened in prostate cancer treated with the MNK1/2 inhibitor eFT508 and/or the AKT inhibitor ipatasertib, either alone or in combination with a clinically available MDSC-targeting immunotherapy. This work provides a therapeutic strategy that combines translation inhibition with available immunotherapies to restore immune surveillance in prostate cancer.
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Affiliation(s)
- Daniela Brina
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adele Ponzoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Ima Biotech, Lille, France
| | - Martina Troiani
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Bianca Calì
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simone Mosole
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Michela Mirenda
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Evotec, Toulouse, France
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Imperial College London, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Ilaria Guccini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ajinkya Revandkar
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Abdullah Alajati
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Department of Urology, Universitätklinikum Bonn, Bonn, Germany
| | - Toma Tebaldi
- Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Nahjme Parhizgari
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Biosun Pharmed, Kordan, Iran
| | - Aurora Valdata
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Martino Maddalena
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Arianna Calcinotto
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Marco Bolis
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, Milano, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simon Barry
- IMED Oncology AstraZeneca, Li Ka Shing Centre, Cambridge, UK
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Semini Sumanasuriya
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mateus Crespo
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mathew Grinu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Alexandra Boyle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Cynthia Miller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Lloyd Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Matteo Fassan
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Johann de Bono
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
- The Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Department of Medicine, Venetian Institute of Molecular Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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Gutierrez Guarnizo SA, Tikhonova EB, Karamyshev AL, Muskus CE, Karamysheva ZN. Translational reprogramming as a driver of antimony-drug resistance in Leishmania. Nat Commun 2023; 14:2605. [PMID: 37147291 PMCID: PMC10163012 DOI: 10.1038/s41467-023-38221-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Leishmania is a unicellular protozoan that has a limited transcriptional control and mostly uses post-transcriptional regulation of gene expression, although the molecular mechanisms of the process are still poorly understood. Treatments of leishmaniasis, pathologies associated with Leishmania infections, are limited due to drug resistance. Here, we report dramatic differences in mRNA translation in antimony drug-resistant and sensitive strains at the full translatome level. The major differences (2431 differentially translated transcripts) were demonstrated in the absence of the drug pressure supporting that complex preemptive adaptations are needed to efficiently compensate for the loss of biological fitness once they are exposed to the antimony. In contrast, drug-resistant parasites exposed to antimony activated a highly selective translation of only 156 transcripts. This selective mRNA translation is associated with surface protein rearrangement, optimized energy metabolism, amastins upregulation, and improved antioxidant response. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania.
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Affiliation(s)
- Sneider Alexander Gutierrez Guarnizo
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
- Programa de Estudio y Control de Enfermedades Tropicales, Universidad de Antioquia. Medellín, Medellín, 050010, Colombia
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
| | - Carlos E Muskus
- Programa de Estudio y Control de Enfermedades Tropicales, Universidad de Antioquia. Medellín, Medellín, 050010, Colombia.
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9
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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of Tuberous Sclerosis Complex-1 patient-derived neural progenitor cells reveal rapamycin-dependent and independent alterations. RESEARCH SQUARE 2023:rs.3.rs-2702044. [PMID: 37034588 PMCID: PMC10081384 DOI: 10.21203/rs.3.rs-2702044/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD). The hamartin-tuberin (TSC1-TSC2) protein complex inactivates mechanistic target of rapamycin complex 1 (mTORC1) signaling, leading to increased protein synthesis via inactivation of translational repressor eIF4E-binding proteins (4E-BPs). In TSC1-null neural progenitor cells (NPCs), we previously reported early ND phenotypic changes, including increased proliferation/altered neurite outgrowth, which were unaffected by mTORC1-inhibitor rapamycin. Here, using polysome-profiling to quantify translational efficiencies at a transcriptome-wide level, we observed numerous TSC1-dependent alterations in NPCs, largely recapitulated in post-mortem brains from ASD donors. Although rapamycin partially reversed TSC1-associated alterations, most neural activity/synaptic- or ASD-related genes remained insensitive but were inhibited by third-generation bi-steric, mTORC1-selective inhibitor RMC-6272, which also reversed altered ND phenotypes. Together these data reveal potential implications for treatment of TAND.
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Affiliation(s)
- Inci S. Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
- These authors contributed equally to this work
| | - Pauline Martin
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
- These authors contributed equally to this work
| | - Francis Robert
- Department of Biochem. and Goodman Cancer Res. Ctr., McGill Univ., Montreal, QC, Canada
- These authors contributed equally to this work
| | - Krzysztof J. Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
- These authors contributed equally to this work
| | - Nicholas E. Redmond
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Roberta L. Beauchamp
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
| | - Irene Nobeli
- Department of Biol. Sciences, Inst. of Structural and Mol. Biology, Birkbeck, Univ. of London, London, United Kingdom
| | - Jerry Pelletier
- Department of Biochem. and Goodman Cancer Res. Ctr., McGill Univ., Montreal, QC, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Vijaya Ramesh
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
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10
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Whitworth GB, Watson FL. Translating Ribosome Affinity Purification (TRAP) and Bioinformatic RNA-Seq Analysis in Post-metamorphic Xenopus laevis. Methods Mol Biol 2023; 2636:279-310. [PMID: 36881307 DOI: 10.1007/978-1-0716-3012-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Recent technical advances provide the ability to isolate and purify mRNAs from genetically distinct cell types so as to provide a broader view of gene expression as they relate to gene networks. These tools allow the genome of organisms undergoing different developmental or diseased states and environmental or behavioral conditions to be compared. Translating ribosome affinity purification (TRAP), a method using transgenic animals expressing a ribosomal affinity tag (ribotag) that targets ribosome-bound mRNAs, allows for the rapid isolation of genetically distinct populations of cells. In this chapter, we provide stepwise methods for carrying out an updated protocol for using the TRAP method in the South African clawed frog Xenopus laevis. A discussion of the experimental design and necessary controls and their rationale, along with a description of the bioinformatic steps involved in analyzing the Xenopus laevis translatome using TRAP and RNA-Seq, is also provided.
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Affiliation(s)
- Gregg B Whitworth
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - Fiona L Watson
- Department of Biology, Washington and Lee University, Lexington, VA, USA.
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11
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A Label-Free Quantitative Analysis for the Search of Proteomic Differences between Goat Breeds. Animals (Basel) 2022; 12:ani12233336. [PMID: 36496858 PMCID: PMC9740416 DOI: 10.3390/ani12233336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The intensification and standardization of livestock farming are causing a decline in the number of animal breeds in many species, such as the goat. The availability of more studies on the potentiality of goat breeds could raise awareness of their importance, conservation and productive possibilities. Label-free quantitative analysis was applied in this study to investigate the proteomic differences between the autochthon Teramana and Saanen goats that could be useful for defining peculiar features of these breeds. A total of 2093 proteins were characterized in the muscle exudate proteome of the Teramana and Saanen breeds. A total of 41 proteins clearly separated the two breeds. Eukaryotic initiation factor proteins and aldehyde-dehydrogenase 7 family-member A1 were up-regulated in the autochthon breed and associated with its resilience, whereas catalase was down-regulated and associated with lower muscular mass. This study is the most detailed report of goat muscle proteome. Several differentially regulated proteins between the two breeds were identified, providing insights into functional pathways that define this organism and its biology.
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12
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Matheson LS, Petkau G, Sáenz-Narciso B, D'Angeli V, McHugh J, Newman R, Munford H, West J, Chakraborty K, Roberts J, Łukasiak S, Díaz-Muñoz MD, Bell SE, Dimeloe S, Turner M. Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4 + T cell. Sci Rep 2022; 12:19657. [PMID: 36385275 PMCID: PMC9669047 DOI: 10.1038/s41598-022-24132-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.
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Affiliation(s)
- Louise S Matheson
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Georg Petkau
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Beatriz Sáenz-Narciso
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Vanessa D'Angeli
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: IONTAS, The Works, Unity Campus, Cambridge, CB22 3EF, UK
| | - Jessica McHugh
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Nature Reviews Rheumatology, The Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Rebecca Newman
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Immunology Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Haydn Munford
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Krishnendu Chakraborty
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Bioanalysis, Immunogenicity and Biomarkers (BIB), IVIVT, GSK, Stevenage, SG1 2NY, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Sebastian Łukasiak
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, BP3028, 31024, Toulouse, France
| | - Sarah E Bell
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Sarah Dimeloe
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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13
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Hoffmann G, Mahboubi A, Bente H, Garcia D, Hanson J, Hafrén A. Arabidopsis RNA processing body components LSM1 and DCP5 aid in the evasion of translational repression during Cauliflower mosaic virus infection. THE PLANT CELL 2022; 34:3128-3147. [PMID: 35511183 PMCID: PMC9338796 DOI: 10.1093/plcell/koac132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
- Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Amir Mahboubi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Heinrich Bente
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
- Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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14
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Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
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Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Haruka Aoyama
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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15
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Morin C, Moyret-Lalle C, Mertani HC, Diaz JJ, Marcel V. Heterogeneity and dynamic of EMT through the plasticity of ribosome and mRNA translation. Biochim Biophys Acta Rev Cancer 2022; 1877:188718. [PMID: 35304296 DOI: 10.1016/j.bbcan.2022.188718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence exposes translation and its translational machinery as key players in establishing and maintaining physiological and pathological biological processes. Examining translation may not only provide new biological insight but also identify novel innovative therapeutic targets in several fields of biology, including that of epithelial-to-mesenchymal transition (EMT). EMT is currently considered as a dynamic and reversible transdifferentiation process sustaining the transition from an epithelial to mesenchymal phenotype, known to be mainly driven by transcriptional reprogramming. However, it seems that the characterization of EMT plasticity is challenging, relying exclusively on transcriptomic and epigenetic approaches. Indeed, heterogeneity in EMT programs was reported to depend on the biological context. Here, by reviewing the involvement of translational control, translational machinery and ribosome biogenesis characterizing the different types of EMT, from embryonic and adult physiological to pathological contexts, we discuss the added value of integrating translational control and its machinery to depict the heterogeneity and dynamics of EMT programs.
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Affiliation(s)
- Chloé Morin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Caroline Moyret-Lalle
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France.
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16
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Incoming new IUPAB Councilor 2021-Gabriella Viero. Biophys Rev 2022; 13:845-847. [PMID: 35059004 DOI: 10.1007/s12551-021-00861-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022] Open
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17
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Licata NV, Cristofani R, Salomonsson S, Wilson KM, Kempthorne L, Vaizoglu D, D’Agostino VG, Pollini D, Loffredo R, Pancher M, Adami V, Bellosta P, Ratti A, Viero G, Quattrone A, Isaacs AM, Poletti A, Provenzani A. C9orf72 ALS/FTD dipeptide repeat protein levels are reduced by small molecules that inhibit PKA or enhance protein degradation. EMBO J 2022; 41:e105026. [PMID: 34791698 PMCID: PMC8724771 DOI: 10.15252/embj.2020105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Intronic GGGGCC (G4C2) hexanucleotide repeat expansion within the human C9orf72 gene represents the most common cause of familial forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9ALS/FTD). Repeat-associated non-AUG (RAN) translation of repeat-containing C9orf72 RNA results in the production of neurotoxic dipeptide-repeat proteins (DPRs). Here, we developed a high-throughput drug screen for the identification of positive and negative modulators of DPR levels. We found that HSP90 inhibitor geldanamycin and aldosterone antagonist spironolactone reduced DPR levels by promoting protein degradation via the proteasome and autophagy pathways respectively. Surprisingly, cAMP-elevating compounds boosting protein kinase A (PKA) activity increased DPR levels. Inhibition of PKA activity, by both pharmacological and genetic approaches, reduced DPR levels in cells and rescued pathological phenotypes in a Drosophila model of C9ALS/FTD. Moreover, knockdown of PKA-catalytic subunits correlated with reduced translation efficiency of DPRs, while the PKA inhibitor H89 reduced endogenous DPR levels in C9ALS/FTD patient-derived iPSC motor neurons. Together, our results suggest new and druggable pathways modulating DPR levels in C9ALS/FTD.
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Affiliation(s)
- Nausicaa V Licata
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Sally Salomonsson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Katherine M Wilson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Liam Kempthorne
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Deniz Vaizoglu
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Vito G D’Agostino
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Pollini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michael Pancher
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Valentina Adami
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
- Department of MedicineNYU at Grossman School of MedicineNYUSA
| | - Antonia Ratti
- Department of NeurologyStroke Unit and Laboratory of NeuroscienceIstituto Auxologico Italiano, IRCCSMilanItaly
- Dipartimento di Biotecnologie Mediche e Medicina TraslazionaleUniversità degli Studi di MilanoMilanItaly
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Adrian M Isaacs
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
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18
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Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics. mSphere 2021; 6:e0036621. [PMID: 34468164 PMCID: PMC8550152 DOI: 10.1128/msphere.00366-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Trypanosoma cruzi is the etiological agent for Chagas disease, a neglected parasitic disease in Latin America. Gene transcription control governs the eukaryotic cell replication but is absent in trypanosomatids; thus, it must be replaced by posttranscriptional regulatory events. We investigated the entrance into the T. cruzi replicative cycle using ribosome profiling and proteomics on G1/S epimastigote cultures synchronized with hydroxyurea. We identified 1,784 translationally regulated genes (change > 2, false-discovery rate [FDR] < 0.05) and 653 differentially expressed proteins (change > 1.5, FDR < 0.05), respectively. A major translational remodeling accompanied by an extensive proteome change is found, while the transcriptome remains largely unperturbed at the replicative entrance of the cell cycle. The differentially expressed genes comprise specific cell cycle processes, confirming previous findings while revealing candidate cell cycle regulators that undergo previously unnoticed translational regulation. Clusters of genes showing a coordinated regulation at translation and protein abundance share related biological functions such as cytoskeleton organization and mitochondrial metabolism; thus, they may represent posttranscriptional regulons. The translatome and proteome of the coregulated clusters change in both coupled and uncoupled directions, suggesting that complex cross talk between the two processes is required to achieve adequate protein levels of different regulons. This is the first simultaneous assessment of the transcriptome, translatome, and proteome of trypanosomatids, which represent a paradigm for the absence of transcriptional control. The findings suggest that gene expression chronology along the T. cruzi cell cycle is controlled mainly by translatome and proteome changes coordinated using different mechanisms for specific gene groups. IMPORTANCE Trypanosoma cruzi is an ancient eukaryotic unicellular parasite causing Chagas disease, a potentially life-threatening illness that affects 6 to 7 million people, mostly in Latin America. The antiparasitic treatments for the disease have incomplete efficacy and adverse reactions; thus, improved drugs are needed. We study the mechanisms governing the replication of the parasite, aiming to find differences with the human host, valuable for the development of parasite-specific antiproliferative drugs. Transcriptional regulation is essential for replication in most eukaryotes, but in trypanosomatids, it must be replaced by subsequent gene regulation steps since they lack transcription initiation control. We identified the genome-wide remodeling of mRNA translation and protein abundance during the entrance to the replicative phase of the cell cycle. We found that translation is strongly regulated, causing variation in protein levels of specific cell cycle processes, representing the first simultaneous study of the translatome and proteome in trypanosomatids.
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19
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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20
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Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection. Int J Mol Sci 2021; 22:ijms22073392. [PMID: 33806254 PMCID: PMC8036502 DOI: 10.3390/ijms22073392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, allowing tight control over potent host responses by both the host and the invading virus. Here, we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors (JUN, ZBTB20, ATF3, HIVEP2 and EGR1) as well as select antiviral cytokine genes, namely IFNB1, IFNL1,2 and 3, IL-6 and CCL5, that are restricted at the post-transcriptional level by SARS-CoV-2 infection and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection.
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21
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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22
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Boussaid I, Le Goff S, Floquet C, Gautier EF, Raimbault A, Viailly PJ, Al Dulaimi D, Burroni B, Dusanter-Fourt I, Hatin I, Mayeux P, Cosson B, Fontenay M. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells. Haematologica 2021; 106:746-758. [PMID: 32327500 PMCID: PMC7927886 DOI: 10.3324/haematol.2019.239970] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
In ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syndrome, ribosomal protein (RP) genes are affected by mutation or deletion, resulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content regulates translation at the expense of the master erythroid transcription factor GATA1. In RPS14-deficient cells mimicking 5q- syndrome erythroid defects, we show that the transcript length, codon bias of the coding sequence (CDS) and 3’UTR (untranslated region) structure are the key determinants of translation. In these cells, short transcripts with a structured 3’UTR and high codon adaptation index (CAI) showed a decreased translation efficiency. Quantitative analysis of the whole proteome confirmed that the post-transcriptional changes depended on the transcript characteristics that governed the translation efficiency in conditions of low ribosome availability. In addition, proteins involved in normal erythroid differentiation share most determinants of translation selectivity. Our findings thus indicate that impaired erythroid maturation due to 5q- syndrome may proceed from a translational selectivity at the expense of the erythroid differentiation program, and suggest that an interplay between the CDS and UTR may regulate mRNA translation.
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Affiliation(s)
- Ismael Boussaid
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Salomé Le Goff
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris
| | - Célia Floquet
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Emilie-Fleur Gautier
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Anna Raimbault
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Pierre-Julien Viailly
- Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen
| | - Dina Al Dulaimi
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Barbara Burroni
- Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris - Cochin, Service de Pathologie, Paris
| | | | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université de Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex
| | - Patrick Mayeux
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Bertrand Cosson
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR 7216, Paris
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France.,Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen,Assistance Publique- Hôpitaux de Paris, Centre-Université de Paris - Hôpital Cochin, Service d’Hématologie Biologique, Paris, France
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23
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Subedi P, Gomolka M, Moertl S, Dietz A. Ionizing Radiation Protein Biomarkers in Normal Tissue and Their Correlation to Radiosensitivity: A Systematic Review. J Pers Med 2021; 11:jpm11020140. [PMID: 33669522 PMCID: PMC7922485 DOI: 10.3390/jpm11020140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/14/2021] [Indexed: 12/16/2022] Open
Abstract
Background and objectives: Exposure to ionizing radiation (IR) has increased immensely over the past years, owing to diagnostic and therapeutic reasons. However, certain radiosensitive individuals show toxic enhanced reaction to IR, and it is necessary to specifically protect them from unwanted exposure. Although predicting radiosensitivity is the way forward in the field of personalised medicine, there is limited information on the potential biomarkers. The aim of this systematic review is to identify evidence from a range of literature in order to present the status quo of our knowledge of IR-induced changes in protein expression in normal tissues, which can be correlated to radiosensitivity. Methods: Studies were searched in NCBI Pubmed and in ISI Web of Science databases and field experts were consulted for relevant studies. Primary peer-reviewed studies in English language within the time-frame of 2011 to 2020 were considered. Human non-tumour tissues and human-derived non-tumour model systems that have been exposed to IR were considered if they reported changes in protein levels, which could be correlated to radiosensitivity. At least two reviewers screened the titles, keywords, and abstracts of the studies against the eligibility criteria at the first phase and full texts of potential studies at the second phase. Similarly, at least two reviewers manually extracted the data and accessed the risk of bias (National Toxicology Program/Office for Health Assessment and Translation—NTP/OHAT) for the included studies. Finally, the data were synthesised narratively in accordance to synthesis without meta analyses (SWiM) method. Results: In total, 28 studies were included in this review. Most of the records (16) demonstrated increased residual DNA damage in radiosensitive individuals compared to normo-sensitive individuals based on γH2AX and TP53BP1. Overall, 15 studies included proteins other than DNA repair foci, of which five proteins were selected, Vascular endothelial growth factor (VEGF), Caspase 3, p16INK4A (Cyclin-dependent kinase inhibitor 2A, CDKN2A), Interleukin-6, and Interleukin-1β, that were connected to radiosensitivity in normal tissue and were reported at least in two independent studies. Conclusions and implication of key findings: A majority of studies used repair foci as a tool to predict radiosensitivity. However, its correlation to outcome parameters such as repair deficient cell lines and patients, as well as an association to moderate and severe clinical radiation reactions, still remain contradictory. When IR-induced proteins reported in at least two studies were considered, a protein network was discovered, which provides a direction for further studies to elucidate the mechanisms of radiosensitivity. Although the identification of only a few of the commonly reported proteins might raise a concern, this could be because (i) our eligibility criteria were strict and (ii) radiosensitivity is influenced by multiple factors. Registration: PROSPERO (CRD42020220064).
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24
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A Binary Cre Transgenic Approach Dissects Microglia and CNS Border-Associated Macrophages. Immunity 2020; 54:176-190.e7. [PMID: 33333014 DOI: 10.1016/j.immuni.2020.11.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023]
Abstract
The developmental and molecular heterogeneity of tissue macrophages is unravelling, as are their diverse contributions to physiology and pathophysiology. Moreover, also given tissues harbor macrophages in discrete anatomic locations. Functional contributions of specific cell populations can in mice be dissected using Cre recombinase-mediated mutagenesis. However, single promoter-based Cre models show limited specificity for cell types. Focusing on macrophages in the brain, we establish here a binary transgenic system involving complementation-competent NCre and CCre fragments whose expression is driven by distinct promoters: Sall1ncre: Cx3cr1ccre mice specifically target parenchymal microglia and compound transgenic Lyve1ncre: Cx3cr1ccre animals target vasculature-associated macrophages, in the brain, as well as other tissues. We imaged the respective cell populations and retrieved their specific translatomes using the RiboTag in order to define them and analyze their differential responses to a challenge. Collectively, we establish the value of binary transgenesis to dissect tissue macrophage compartments and their functions.
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25
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Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:1016-1024. [PMID: 33294289 PMCID: PMC7689039 DOI: 10.1016/j.omtn.2020.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/18/2020] [Indexed: 01/09/2023]
Abstract
Adult cardiac hypoxia as a crucial pathogenesis factor can induce detrimental effects on cardiac injury and dysfunction. The global transcriptome and translatome reflecting the cellular response to hypoxia have not yet been extensively studied in myocardium. In this study, we conducted RNA sequencing (RNA-seq) and ribosome profiling technique (polyribo-seq) in rat heart tissues and H9C2 cells exposed to different periods of hypoxia stress in vivo and in vitro. The temporal gene-expression profiling displayed the distinction of transcriptome and translatome, which were mainly concentrated in cell apoptosis, autophagy, DNA repair, angiogenesis, vascular process, and cardiac cell proliferation and differentiation. A large number of genes such as GNAI3, SEPT4, FANCL, BNIP3, TBX3, ESR2, PTGS2, KLF4, and ADRB2, whose transcript and translation levels are closely correlated, were identified to own a common RNA motif “5′-GAAGCUGCC-3′” in 5′ UTR. NCBP3 was further determined to recognize this RNA motif and facilitate translational process in myocardium under hypoxia stress. Taken together, our data show the close connection between alterations of transcriptome and translatome after hypoxia exposure, emphasizing the significance of translational regulation in related studies. The profiled molecular responses in current study may be valuable resources for advanced understanding of the mechanisms underlying hypoxia-induced effect on heart diseases.
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26
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Iosub IA, Marchioretto M, van Nues RW, McKellar S, Viero G, Granneman S. The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli. RNA Biol 2020; 18:914-931. [PMID: 33043783 PMCID: PMC8081044 DOI: 10.1080/15476286.2020.1827784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous high-throughput studies in Gram-negative bacteria identified a large number of 3ʹUTR fragments that potentially function as sRNAs. Here we extensively characterize the MalH sRNA. We show that MalH is a stable degradation intermediate derived from the 3ʹ end of malG, which is part of the maltose uptake operon transcript malEFG. Unlike the majority of bacterial sRNAs, MalH is transiently expressed during the transition from the exponential to the stationary growth phase, suggesting that it contributes to adaptation to changes in nutrient availability. Over-expression of MalH reduces expression of general outer membrane porins and MicA, a repressor of the high-affinity maltose/maltodextrin transporter LamB. Disrupting MalH production and function significantly reduces lamB accumulation when maltose is the only available carbon source, presumably due to the accumulation of the MicA repressor. We propose that MalH is part of a regulatory network that, during the transition phase, directly or indirectly promotes accumulation of high-affinity maltose transporters in the outer membrane by dampening competing pathways.
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Affiliation(s)
- Ira A Iosub
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
| | | | - Rob W van Nues
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Stuart McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
| | | | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
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27
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Lauria F, Bernabò P, Tebaldi T, Groen EJN, Perenthaler E, Maniscalco F, Rossi A, Donzel D, Clamer M, Marchioretto M, Omersa N, Orri J, Dalla Serra M, Anderluh G, Quattrone A, Inga A, Gillingwater TH, Viero G. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat Cell Biol 2020; 22:1239-1251. [PMID: 32958857 PMCID: PMC7610479 DOI: 10.1038/s41556-020-00577-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
The contribution of ribosome heterogeneity and ribosome-associated proteins to the molecular control of proteomes in health and disease remains unclear. Here, we demonstrate that survival motor neuron (SMN) protein-the loss of which causes the neuromuscular disease spinal muscular atrophy (SMA)-binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are preferentially positioned within the first five codons of a set of mRNAs that are enriched for translational enhancer sequences in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence. These SMN-specific mRNAs are associated with neurogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation. Loss of SMN induces ribosome depletion, especially at the beginning of the coding sequence of SMN-specific mRNAs, leading to impairment of proteins that are involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs encoding proteins that are relevant to SMA pathogenesis.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Toma Tebaldi
- Department CIBIO, University of Trento, Trento, Italy
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ewout Joan Nicolaas Groen
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Federica Maniscalco
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | | | | | - Neža Omersa
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Julia Orri
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- La Fundació Jesuïtes Educació, Barcelona, Spain
| | | | | | | | - Alberto Inga
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Henry Gillingwater
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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28
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Hoang HD, Graber TE, Jia JJ, Vaidya N, Gilchrist VH, Xiang X, Li W, Cowan KN, Gkogkas CG, Jaramillo M, Jafarnejad SM, Alain T. Induction of an Alternative mRNA 5' Leader Enhances Translation of the Ciliopathy Gene Inpp5e and Resistance to Oncolytic Virus Infection. Cell Rep 2020; 29:4010-4023.e5. [PMID: 31851930 DOI: 10.1016/j.celrep.2019.11.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/16/2019] [Accepted: 11/15/2019] [Indexed: 01/10/2023] Open
Abstract
Residual cell-intrinsic innate immunity in cancer cells hampers infection with oncolytic viruses. Translational control of mRNA is an important feature of innate immunity, yet the identity of translationally regulated mRNAs functioning in host defense remains ill-defined. We report the translatomes of resistant murine "4T1" breast cancer cells infected with three of the most clinically advanced oncolytic viruses: herpes simplex virus 1, reovirus, and vaccinia virus. Common among all three infections are translationally de-repressed mRNAs, including Inpp5e, encoding an inositol 5-phosphatase that modifies lipid second messenger signaling. We find that viral infection induces the expression of an Inpp5e mRNA variant that lacks repressive upstream open reading frames (uORFs) within its 5' leader and is efficiently translated. Furthermore, we show that INPP5E contributes to antiviral immunity by altering virus attachment. These findings uncover a role for translational control through alternative 5' leader expression and assign an antiviral function to the ciliopathy gene Inpp5e.
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Affiliation(s)
- Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jian-Jun Jia
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Nasana Vaidya
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Victoria H Gilchrist
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Xiao Xiang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Wencheng Li
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | - Kyle N Cowan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Surgery, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Christos G Gkogkas
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Maritza Jaramillo
- INRS Institut Armand-Frappier Research Centre, Laval, QC H7V 1B7, Canada
| | - Seyed Mehdi Jafarnejad
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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29
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Burgenson D, Linton J, Ge X, Kostov Y, Tolosa L, Szeto GL, Rao G. A Cell-Free Protein Expression System Derived from Human Primary Peripheral Blood Mononuclear Cells. ACS Synth Biol 2020; 9:2188-2196. [PMID: 32698572 DOI: 10.1021/acssynbio.0c00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Historically, some of the first cell-free protein expression systems studied in vitro translation in various human blood cells. However, because of limited knowledge of eukaryotic translation and the advancement of cell line development, interest in these systems decreased. Eukaryotic translation is a complex system of factors that contribute to the overall translation of mRNA to produce proteins. The intracellular translateome of a cell can be modified by various factors and disease states, but it is impossible to individually measure all factors involved when there is no comprehensive understanding of eukaryotic translation. The present work outlines the use of a coupled transcription and translation cell-free protein expression system to produce recombinant proteins derived from human donor peripheral blood mononuclear cells (PBMCs) activated with phytohemagglutinin-M (PHA-M). The methods outlined here could result in tools to aid immunology, gene therapy, cell therapy, and synthetic biology research and provide a convenient and holistic method to study and assess the intracellular translation environment of primary immune cells.
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Affiliation(s)
- David Burgenson
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Jonathan Linton
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Xudong Ge
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Leah Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Gregory L. Szeto
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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30
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Bernabò P, Viero G, Lencioni V. A long noncoding RNA acts as a post-transcriptional regulator of heat shock protein (HSP70) synthesis in the cold hardy Diamesa tonsa under heat shock. PLoS One 2020; 15:e0227172. [PMID: 32240200 PMCID: PMC7117718 DOI: 10.1371/journal.pone.0227172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/28/2020] [Indexed: 12/24/2022] Open
Abstract
Cold stenothermal insects living in glacier-fed streams are stressed by temperature variations resulting from glacial retreat during global warming. The molecular aspects of insect response to environmental stresses remain largely unexplored. The aim of this study was to expand our knowledge of how a cold stenothermal organism controls gene expression at the transcriptional, translational, and protein level under warming conditions. Using the chironomid Diamesa tonsa as target species and a combination of RACE, qPCR, polysomal profiling, western blotting, and bioinformatics techniques, we discovered a new molecular pathway leading to previously overlooked adaptive strategies to stress. We obtained and characterized the complete cDNA sequences of three heat shock inducible 70 (hsp70) and two members of heat-shock cognate 70 (hsc70). Strikingly, we showed that a novel pseudo-hsp70 gene encoding a putative long noncoding RNA (lncRNA) which is transcribed during thermal stress, acting as a ribosome sponge to provide post-transcriptional control of HSP70 protein levels. The expression of the pseudo-hsp70 gene and its function suggest the existence of a new and unexpected mechanism to cope with thermal stress: lowering the pace of protein production to save energy and optimize resources for recovery.
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Affiliation(s)
- Paola Bernabò
- Department of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
- Institute of Biophysics-CNR Trento Unit, Povo, Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics-CNR Trento Unit, Povo, Trento, Italy
| | - Valeria Lencioni
- Department of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
- * E-mail:
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31
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The translational landscape of ground state pluripotency. Nat Commun 2020; 11:1617. [PMID: 32238817 PMCID: PMC7113317 DOI: 10.1038/s41467-020-15449-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/09/2020] [Indexed: 12/30/2022] Open
Abstract
Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. Here, we used genome-wide approaches combined with time-course analysis to measure the mRNA-abundance, mRNA-translation rate and protein expression during the transition of naïve-to-primed mouse embryonic stem cells (ESCs). We find that the ground state ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. This set of mRNAs undergo strong translational buffering to maintain stable protein expression levels in 2iL-ESCs. Importantly, we show that the global alteration of cellular proteome during the transition of naïve-to-primed pluripotency is largely accompanied by transcriptional rewiring. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression in different states of ESCs and dissect the relative contributions of mRNA-transcription, translation and regulation of protein stability in controlling protein abundance. Translational control of gene expression can lead to significant divergence between mRNA and protein abundance. Here, the authors describe transcriptional rewiring and translational buffering during transition from naïve to primed pluripotency through quantitation of mRNA-abundance, translation rate and protein expression.
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32
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Choe HK, Cho J. Comprehensive Genome-Wide Approaches to Activity-Dependent Translational Control in Neurons. Int J Mol Sci 2020; 21:ijms21051592. [PMID: 32111062 PMCID: PMC7084349 DOI: 10.3390/ijms21051592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Activity-dependent regulation of gene expression is critical in experience-mediated changes in the brain. Although less appreciated than transcriptional control, translational control is a crucial regulatory step of activity-mediated gene expression in physiological and pathological conditions. In the first part of this review, we overview evidence demonstrating the importance of translational controls under the context of synaptic plasticity as well as learning and memory. Then, molecular mechanisms underlying the translational control, including post-translational modifications of translation factors, mTOR signaling pathway, and local translation, are explored. We also summarize how activity-dependent translational regulation is associated with neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and depression. In the second part, we highlight how recent application of high-throughput sequencing techniques has added insight into genome-wide studies on translational regulation of neuronal genes. Sequencing-based strategies to identify molecular signatures of the active neuronal population responding to a specific stimulus are discussed. Overall, this review aims to highlight the implication of translational control for neuronal gene regulation and functions of the brain and to suggest prospects provided by the leading-edge techniques to study yet-unappreciated translational regulation in the nervous system.
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Affiliation(s)
- Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (H.K.C.); (J.C.)
| | - Jun Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Correspondence: (H.K.C.); (J.C.)
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33
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Abou-Fadel J, Smith M, Falahati K, Zhang J. Comparative omics of CCM signaling complex (CSC). Chin Neurosurg J 2020; 6:4. [PMID: 32922933 PMCID: PMC7398211 DOI: 10.1186/s41016-019-0183-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cerebral cavernous malformations (CCMs), a major neurosurgical condition, characterized by abnormally dilated intracranial capillaries, result in increased susceptibility to stroke. KRIT1 (CCM1), MGC4607 (CCM2), and PDCD10 (CCM3) have been identified as causes of CCMs in which at least one of them is disrupted in most familial cases. Our goal is to identify potential biomarkers and genetic modifiers of CCMs, using a global comparative omics approach across several in vitro studies and multiple in vivo animal models. We hypothesize that through analysis of the CSC utilizing various omics, we can identify potential biomarkers and genetic modifiers, by systemically evaluating effectors and binding partners of the CSC as well as second layer interactors. METHODS We utilize a comparative omics approach analyzing multiple CCMs deficient animal models across nine independent studies at the genomic, transcriptomic, and proteomic levels to dissect alterations in various signaling cascades. RESULTS Our analysis revealed a large set of genes that were validated across multiple independent studies, suggesting an important role for these identified genes in CCM pathogenesis. CONCLUSION This is currently one of the largest comparative omics analysis of CCM deficiencies across multiple models, allowing us to investigate global alterations among multiple signaling cascades involved in both angiogenic and non-angiogenic events and to also identify potential biomarker candidates of CCMs, which can be used for new therapeutic strategies.
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Affiliation(s)
- Johnathan Abou-Fadel
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Mark Smith
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Kamran Falahati
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Jun Zhang
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
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34
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Pavey S, Pinder A, Fernando W, D'Arcy N, Matigian N, Skalamera D, Lê Cao KA, Loo-Oey D, Hill MM, Stark M, Kimlin M, Burgess A, Cloonan N, Sturm RA, Gabrielli B. Multiple interaction nodes define the postreplication repair response to UV-induced DNA damage that is defective in melanomas and correlated with UV signature mutation load. Mol Oncol 2019; 14:22-41. [PMID: 31733171 PMCID: PMC6944116 DOI: 10.1002/1878-0261.12601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 01/25/2023] Open
Abstract
Ultraviolet radiation‐induced DNA mutations are a primary environmental driver of melanoma. The reason for this very high level of unrepaired DNA lesions leading to these mutations is still poorly understood. The primary DNA repair mechanism for UV‐induced lesions, that is, the nucleotide excision repair pathway, appears intact in most melanomas. We have previously reported a postreplication repair mechanism that is commonly defective in melanoma cell lines. Here we have used a genome‐wide approach to identify the components of this postreplication repair mechanism. We have used differential transcript polysome loading to identify transcripts that are associated with UV response, and then functionally assessed these to identify novel components of this repair and cell cycle checkpoint network. We have identified multiple interaction nodes, including global genomic nucleotide excision repair and homologous recombination repair, and previously unexpected MASTL pathway, as components of the response. Finally, we have used bioinformatics to assess the contribution of dysregulated expression of these pathways to the UV signature mutation load of a large melanoma cohort. We show that dysregulation of the pathway, especially the DNA damage repair components, are significant contributors to UV mutation load, and that dysregulation of the MASTL pathway appears to be a significant contributor to high UV signature mutation load.
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Affiliation(s)
- Sandra Pavey
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Alex Pinder
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Winnie Fernando
- Mater Research, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Nicholas D'Arcy
- Mater Research, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Nicholas Matigian
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia.,QFAB Bioinformatics, The University of Queensland, Brisbane, QLD, Australia
| | - Dubravka Skalamera
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia.,Mater Research, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Kim-Anh Lê Cao
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Dorothy Loo-Oey
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Michelle M Hill
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia.,QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Mitchell Stark
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Michael Kimlin
- University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | | | - Nicole Cloonan
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Richard A Sturm
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia
| | - Brian Gabrielli
- Diamantina Institute, TRI, The University of Queensland, Woolloongabba, QLD, Australia.,Mater Research, TRI, The University of Queensland, Woolloongabba, QLD, Australia
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35
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Abou-Fadel J, Vasquez M, Grajeda B, Ellis C, Zhang J. Systems-wide analysis unravels the new roles of CCM signal complex (CSC). Heliyon 2019; 5:e02899. [PMID: 31872111 PMCID: PMC6909108 DOI: 10.1016/j.heliyon.2019.e02899] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/17/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are characterized by abnormally dilated intracranial capillaries that result in increased susceptibility to stroke. Three genes have been identified as causes of CCMs; KRIT1 (CCM1), MGC4607 (CCM2) and PDCD10 (CCM3); one of them is disrupted in most CCM cases. It was demonstrated that both CCM1 and CCM3 bind to CCM2 to form a CCM signaling complex (CSC) to modulate angiogenesis. In this report, we deployed both RNA-seq and proteomic analysis of perturbed CSC after depletion of one of three CCM genes to generate interactomes for system-wide studies. Our results demonstrated a unique portrait detailing alterations in angiogenesis and vascular integrity. Interestingly, only in-direct overlapped alterations between RNA and protein levels were detected, supporting the existence of multiple layers of regulation in CSC cascades. Notably, this is the first report identifying that both β4 integrin and CAV1 signaling are downstream of CSC, conveying the angiogenic signaling. Our results provide a global view of signal transduction modulated by the CSC, identifies novel regulatory signaling networks and key cellular factors associated with CSC.
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Affiliation(s)
- Johnathan Abou-Fadel
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Mariana Vasquez
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Brian Grajeda
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Cameron Ellis
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Jun Zhang
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
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36
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Lorent J, Kusnadi EP, van Hoef V, Rebello RJ, Leibovitch M, Ristau J, Chen S, Lawrence MG, Szkop KJ, Samreen B, Balanathan P, Rapino F, Close P, Bukczynska P, Scharmann K, Takizawa I, Risbridger GP, Selth LA, Leidel SA, Lin Q, Topisirovic I, Larsson O, Furic L. Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. EMBO J 2019; 38:e101323. [PMID: 31556460 DOI: 10.15252/embj.2018101323] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Estrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as "translational offsetting" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome association, are reduced following ERα depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERα-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.
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Affiliation(s)
- Julie Lorent
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Eric P Kusnadi
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Vincent van Hoef
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Richard J Rebello
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Matthew Leibovitch
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Johannes Ristau
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Shan Chen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Mitchell G Lawrence
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Krzysztof J Szkop
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Baila Samreen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Preetika Balanathan
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Francesca Rapino
- Laboratory of Cancer Signaling, GIGA-Institute, University of Liège, Liège, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA-Institute, University of Liège, Liège, Belgium
| | - Patricia Bukczynska
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, Münster, Germany
| | - Itsuhiro Takizawa
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Gail P Risbridger
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, Münster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, Department of Chemistry, University at Albany, Albany, NY, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Luc Furic
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
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37
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Istomine R, Alvarez F, Almadani Y, Philip A, Piccirillo CA. The Deubiquitinating Enzyme Ubiquitin-Specific Peptidase 11 Potentiates TGF-β Signaling in CD4 + T Cells to Facilitate Foxp3 + Regulatory T and T H17 Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2019; 203:2388-2400. [PMID: 31554694 DOI: 10.4049/jimmunol.1801689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
Foxp3+ regulatory T (TREG) cells are central mediators in the control of peripheral immune responses. Genome-wide transcriptional profiles show canonical signatures for Foxp3+ TREG cells, distinguishing them from Foxp3- effector T (TEFF) cells. We previously uncovered distinct mRNA translational signatures differentiating CD4+ TEFF and TREG cells through parallel measurements of cytosolic (global) and polysome-associated (translationally enhanced) mRNA levels in both subsets. We show that the mRNA encoding for the ubiquitin-specific peptidase 11 (USP11), a known modulator of TGF-β signaling, was preferentially translated in TCR-activated TREG cells compared with conventional, murine CD4+ T cells. TGF-β is a key cytokine driving the induction and maintenance of Foxp3 expression in T cells. We hypothesized that differential translation of USP11 mRNA endows TREG cells with an advantage to respond to TGF-β signals. In an in vivo mouse model promoting TREG cells plasticity, we found that USP11 protein was expressed at elevated levels in stable TREG cells, whereas ectopic USP11 expression enhanced the suppressive capacity and lineage commitment of these cells in vitro and in vivo. USP11 overexpression in TEFF cells enhanced the activation of the TGF-β pathway and promoted TREG or TH17, but not Th1, cell differentiation in vitro and in vivo, an effect abrogated by USP11 gene silencing or the inhibition of enzymatic activity. Thus, USP11 potentiates TGF-β signaling in both TREG and TEFF cells, in turn driving increased suppressive function and lineage commitment in thymic-derived TREG cells and potentiating the TGF-β-dependent differentiation of TEFF cells to peripherally induced TREG and TH17 cells.
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Affiliation(s)
- Roman Istomine
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.,Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Centre of Excellence in Translational Immunology, Montreal, Quebec H4A 3J1, Canada; and
| | - Fernando Alvarez
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.,Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Centre of Excellence in Translational Immunology, Montreal, Quebec H4A 3J1, Canada; and
| | - Yasser Almadani
- Division of Plastic Surgery, Department of Surgery, McGill University, Montreal, Quebec H3G 1A4, Canada; and.,Plastic Surgery Research Laboratory, Research Institute of the McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
| | - Anie Philip
- Division of Plastic Surgery, Department of Surgery, McGill University, Montreal, Quebec H3G 1A4, Canada; and.,Plastic Surgery Research Laboratory, Research Institute of the McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
| | - Ciriaco A Piccirillo
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada; .,Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Centre of Excellence in Translational Immunology, Montreal, Quebec H4A 3J1, Canada; and
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38
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Blevins WR, Tavella T, Moro SG, Blasco-Moreno B, Closa-Mosquera A, Díez J, Carey LB, Albà MM. Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast. Sci Rep 2019; 9:11005. [PMID: 31358845 PMCID: PMC6662803 DOI: 10.1038/s41598-019-47424-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed to directly influence protein abundances. However, the correlation between RNA-Seq and proteomics data is in general quite limited owing to differences in protein stability and translational regulation. Here we perform RNA-Seq, ribosome profiling and proteomics analyses in baker's yeast cells grown in rich media and oxidative stress conditions to examine gene expression regulation at various levels. With the exception of a small set of genes involved in the maintenance of the redox state, which are regulated at the transcriptional level, modulation of protein expression is largely driven by changes in the relative ribosome density across conditions. The majority of shifts in mRNA abundance are compensated by changes in the opposite direction in the number of translating ribosomes and are predicted to result in no net change at the protein level. We also identify a subset of mRNAs which is likely to undergo specific translational repression during stress and which includes cell cycle control genes. The study suggests that post-transcriptional buffering of gene expression may be more common than previously anticipated.
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Affiliation(s)
- William R Blevins
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Teresa Tavella
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Dipartimento di Farmacia e Biotecnologie (FaBiT), Università di Bologna, Bologna, Italy
| | - Simone G Moro
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bernat Blasco-Moreno
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain
| | - Adrià Closa-Mosquera
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain.,John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Juana Díez
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain
| | - Lucas B Carey
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain.,Center for Quantitative Biology and Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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39
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Pereira IT, Spangenberg L, Robert AW, Amorín R, Stimamiglio MA, Naya H, Dallagiovanna B. Cardiomyogenic differentiation is fine-tuned by differential mRNA association with polysomes. BMC Genomics 2019; 20:219. [PMID: 30876407 PMCID: PMC6420765 DOI: 10.1186/s12864-019-5550-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination between transcription and post-transcriptional regulation during the differentiation processes. Here, we took advantage of the polysome profiling technique to isolate and high-throughput sequence ribosome-free and polysome-bound RNAs during cardiomyogenesis. RESULTS We showed that polysome-bound RNAs exhibit the cardiomyogenic commitment gene expression and that mesoderm-to-cardiac progenitor stages are strongly regulated. Additionally, we compared ribosome-free and polysome-bound RNAs and found that the post-transcriptional regulation vastly contributes to cardiac phenotype determination, including RNA recruitment to and dissociation from ribosomes. Moreover, we found that protein synthesis is decreased in cardiomyocytes compared to human embryonic stem-cells (hESCs), possibly due to the down-regulation of translation-related genes. CONCLUSIONS Our data provided a powerful tool to investigate genes potentially controlled by post-transcriptional mechanisms during the cardiac differentiation of hESC. This work could prospect fundamental tools to develop new therapy and research approaches.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Anny Waloski Robert
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Rocío Amorín
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Marco Augusto Stimamiglio
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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40
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Abstract
Stem cells can reside in a state of reversible growth arrest, or quiescence, for prolonged periods of time. Although quiescence has long been viewed as a dormant, low-activity state, increasing evidence suggests that quiescence represents states of poised potential and active restraint, as stem cells "idle" in anticipation of activation, proliferation, and differentiation. Improved understanding of quiescent stem cell dynamics is leading to novel approaches to enhance maintenance and repair of aged or diseased tissues. In this Review, we discuss recent advances in our understanding of stem cell quiescence and techniques enabling more refined analyses of quiescence in vivo.
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Affiliation(s)
- Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
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41
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Abstract
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 1990s, reconstructing the structure of such networks has been a central computational problem in systems biology. While the problem is certainly not solved in its entirety, considerable progress has been made in the last two decades, with mature tools now available. This chapter aims to provide an introduction to the basic concepts underpinning network inference tools, attempting a categorization which highlights commonalities and relative strengths. While the chapter is meant to be self-contained, the material presented should provide a useful background to the later, more specialized chapters of this book.
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Affiliation(s)
- Vân Anh Huynh-Thu
- Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium
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42
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Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs. Sci Data 2018; 5:180287. [PMID: 30512016 PMCID: PMC6278691 DOI: 10.1038/sdata.2018.287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
The regulation of gene expression acts at numerous complementary levels to control and refine protein abundance. The analysis of mRNAs associated with polysomes, called polysome profiling, has been used to investigate the post-transcriptional mechanisms that are involved in different biological processes. Pluripotent stem cells are able to differentiate into a variety of cell lineages, and the cell commitment progression is carefully orchestrated. Genome-wide expression profiling has provided the possibility to investigate transcriptional changes during cardiomyogenesis; however, a more accurate study regarding post-transcriptional regulation is required. In the present work, we isolated and high-throughput sequenced ribosome-free and polysome-bound RNAs from NKX2-5eGFP/w HES3 undifferentiated pluripotent stem cells at the subsequent differentiation stages of cardiomyogenesis: embryoid body aggregation, mesoderm, cardiac progenitor and cardiomyocyte. The expression of developmental markers was followed by flow cytometry, and quality analyses were performed as technical controls to ensure high quality data. Our dataset provides valuable information about hESC cardiac differentiation and can be used to investigate genes potentially controlled by post-transcriptional mechanisms.
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43
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Kakegawa T, Yoshida LS, Takada M, Noguchi M, Yasukawa K, Takano-Ohmuro H. Comparison of the effects of pachymic acid, moronic acid and hydrocortisone on the polysome loading of RNAs in lipopolysaccharide-treated THP-1 macrophages. J Nat Med 2018; 73:190-201. [PMID: 30414015 DOI: 10.1007/s11418-018-1260-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/17/2018] [Indexed: 11/25/2022]
Abstract
We have proposed that analysis of ribosome-loaded mRNAs (i.e., the translatome) is useful for elucidation of pharmacological effects of phytocompounds in immune cells, regarding the involvement of post-transcriptional regulation mechanisms. In the present study, we compared the effects of pachymic acid from Poria cocos fungus and moronic acid from propolis with those of hydrocortisone on the translatomes of THP-1 macrophages exposed to bacterial lipopolysaccharide (LPS) to find clues to their biological effects. Polysome-associated RNAs collected from cells treated for 3 h with LPS plus each of the compounds were analyzed by DNA microarray followed by analyses of pathways/gene ontologies (GO). Upregulated mRNAs in enriched pathways that were found to contain AUUUA (AU)-rich motifs were checked by real-time PCR, and expression of candidate RNA-binding proteins stabilizing/destabilizing such AU-rich mRNAs was checked by Western blotting. The numbers of upregulated and downregulated genes (fold-changes ± 2.0 versus vehicle-control) were, respectively, 209 and 125 for moronic acid, 23 and 2 for pachymic acid, and 214 and 59 for hydrocortisone treatment. Overlapping with hydrocortisone treatment for upregulation were 158 genes in moronic acid and 17 in pachymic acid treatment; of these, 16 overlapped within all treatments (C-X-C motif chemokine ligands, interferon-induced protein with tetratricopeptide repeats, etc.). Pathway analyses showed GO enrichments such as 'immune response', 'receptor binding', 'extracellular space' etc. The pachymic acid-upregulated mRNAs (highly overlapped with the other 2 treatments) showed the presence of signal peptides and AU-rich motifs, suggesting regulation by AU-rich element (ARE)-binding proteins. The expression of ARE-binding protein HuR/ELAV-1 was increased by the 3 compounds, and AUF1/hnRNP D was decreased by pachymic acid. These results suggested that pachymic acid and moronic acid effects may involve as yet unknown post-transcriptional modulation via ARE-binding proteins resembling that of glucocorticoids.
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Affiliation(s)
- Tomohito Kakegawa
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, 283-8555, Japan.
| | - Lucia Satiko Yoshida
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, 202-8585, Japan
| | - Mariko Takada
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, 283-8555, Japan
| | - Mari Noguchi
- Faculty of Pharmaceutical Sciences, Josai International University, 1 Gumyo, Togane, 283-8555, Japan
| | - Ken Yasukawa
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba, 274-8555, Japan
| | - Hiromi Takano-Ohmuro
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo, 202-8585, Japan
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44
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Kubová H, Bendová Z, Moravcová S, Pačesová D, Rocha LL, Mareš P. Neonatal Clonazepam Administration Induces Long-Lasting Changes in Glutamate Receptors. Front Mol Neurosci 2018; 11:382. [PMID: 30364265 PMCID: PMC6193113 DOI: 10.3389/fnmol.2018.00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/24/2018] [Indexed: 11/13/2022] Open
Abstract
γ-aminobutyric acid (GABA) pathways play an important role in neuronal circuitry formation during early postnatal development. Our previous studies revealed an increased risk for adverse neurodevelopmental consequences in animals exposed to benzodiazepines, which enhance GABA inhibition via GABAA receptors. We reported that administration of the benzodiazepine clonazepam (CZP) during postnatal days 7-11 resulted in permanent behavioral alterations. However, the mechanisms underlying these changes are unknown. We hypothesized that early CZP exposure modifies development of glutamatergic receptors and their composition due to the tight developmental link between GABAergic functions and maturation of glutamatergic signaling. These changes may alter excitatory synapses, as well as neuronal connectivity and function of the neural network. We used quantitative real-time PCR and quantitative autoradiography to examine changes in NMDA and AMPA receptor composition and binding in response to CZP (1 mg/kg/day) administration for five consecutive days, beginning on P7. Brains were collected 48 h, 1 week, or 60 days after treatment cessation, and mRNA subunit expression was assessed in the hippocampus and sensorimotor cortex. A separate group of animals was used to determine binding to NMDA in different brain regions. Patterns of CZP-induced alterations in subunit mRNA expression were dependent on brain structure, interval after CZP cessation, and receptor subunit type. In the hippocampus, upregulation of GluN1, GluN3, and GluR2 subunit mRNA was observed at the 48-h interval, and GluN2A and GluR1 mRNA expression levels were higher 1 week after CZP cessation compared to controls, while GluN2B was downregulated. CZP exposure increased GluN3 and GluR2 subunit mRNA expression levels in the sensorimotor cortex 48 h after treatment cessation. GluA3 was higher 1 week after the CZP exposure, and GluN2A and GluA4 mRNA were significantly upregulated 2 months later. Expression of other subunits was not significantly different from that of the controls. NMDA receptor binding increased 1 week after the end of exposure in most hippocampal and cortical areas, including the sensorimotor cortex at the 48-h interval. CZP exposure decreased NMDA receptor binding in most evaluated hippocampal and cortical areas 2 months after the end of administration. Overall, early CZP exposure likely results in long-term glutamatergic receptor modulation that may affect synaptic development and function, potentially causing behavioral impairment.
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Affiliation(s)
- Hana Kubová
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Zdenka Bendová
- Faculty of Science, Charles University, Prague, Czechia.,National Institute of Mental Health, Klecany, Czechia
| | - Simona Moravcová
- Faculty of Science, Charles University, Prague, Czechia.,National Institute of Mental Health, Klecany, Czechia
| | - Dominika Pačesová
- Faculty of Science, Charles University, Prague, Czechia.,National Institute of Mental Health, Klecany, Czechia
| | - Luisa Lilia Rocha
- Pharmacobiology Department, Center of Research and Advanced Studies, Mexico City, Mexico
| | - Pavel Mareš
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czechia
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45
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Active Ribosome Profiling with RiboLace. Cell Rep 2018; 25:1097-1108.e5. [DOI: 10.1016/j.celrep.2018.09.084] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/20/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
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46
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Song KA, Hosono Y, Turner C, Jacob S, Lochmann TL, Murakami Y, Patel NU, Ham J, Hu B, Powell KM, Coon CM, Windle BE, Oya Y, Koblinski JE, Harada H, Leverson JD, Souers AJ, Hata AN, Boikos S, Yatabe Y, Ebi H, Faber AC. Increased Synthesis of MCL-1 Protein Underlies Initial Survival of EGFR-Mutant Lung Cancer to EGFR Inhibitors and Provides a Novel Drug Target. Clin Cancer Res 2018; 24:5658-5672. [PMID: 30087143 DOI: 10.1158/1078-0432.ccr-18-0304] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/29/2018] [Accepted: 08/01/2018] [Indexed: 11/16/2022]
Abstract
Purpose: EGFR inhibitors (EGFRi) are effective against EGFR-mutant lung cancers. The efficacy of these drugs, however, is mitigated by the outgrowth of resistant cells, most often driven by a secondary acquired mutation in EGFR, T790M We recently demonstrated that T790M can arise de novo during treatment; it follows that one potential therapeutic strategy to thwart resistance would be identifying and eliminating these cells [referred to as drug-tolerant cells (DTC)] prior to acquiring secondary mutations like T790M Experimental Design: We have developed DTCs to EGFRi in EGFR-mutant lung cancer cell lines. Subsequent analyses of DTCs included RNA-seq, high-content microscopy, and protein translational assays. Based on these results, we tested the ability of MCL-1 BH3 mimetics to combine with EGFR inhibitors to eliminate DTCs and shrink EGFR-mutant lung cancer tumors in vivo Results: We demonstrate surviving EGFR-mutant lung cancer cells upregulate the antiapoptotic protein MCL-1 in response to short-term EGFRi treatment. Mechanistically, DTCs undergo a protein biosynthesis enrichment resulting in increased mTORC1-mediated mRNA translation of MCL-1, revealing a novel mechanism in which lung cancer cells adapt to short-term pressures of apoptosis-inducing kinase inhibitors. Moreover, MCL-1 is a key molecule governing the emergence of early EGFR-mutant DTCs to EGFRi, and we demonstrate it can be effectively cotargeted with clinically emerging MCL-1 inhibitors both in vitro and in vivo Conclusions: Altogether, these data reveal that this novel therapeutic combination may delay the acquisition of secondary mutations, therefore prolonging therapy efficacy. Clin Cancer Res; 24(22); 5658-72. ©2018 AACR.
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Affiliation(s)
- Kyung-A Song
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yasuyuki Hosono
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Crystal Turner
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Sheeba Jacob
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Timothy L Lochmann
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yoshiko Murakami
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Neha U Patel
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Jungoh Ham
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Bin Hu
- Department of Pathology, VCU School of Medicine, Richmond, Virginia
| | - Krista M Powell
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Colin M Coon
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Brad E Windle
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yuko Oya
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | - Hisashi Harada
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | | | | | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sosipatros Boikos
- Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Massey Cancer Center, Richmond, Virginia
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Precision Medicine Center, Aichi Cancer Center, Nagoya, Japan
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan. .,Precision Medicine Center, Aichi Cancer Center, Nagoya, Japan
| | - Anthony C Faber
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia.
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47
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Negro S, Stazi M, Marchioretto M, Tebaldi T, Rodella U, Duregotti E, Gerke V, Quattrone A, Montecucco C, Rigoni M, Viero G. Hydrogen peroxide is a neuronal alarmin that triggers specific RNAs, local translation of Annexin A2, and cytoskeletal remodeling in Schwann cells. RNA (NEW YORK, N.Y.) 2018; 24:915-925. [PMID: 29643068 PMCID: PMC6004060 DOI: 10.1261/rna.064816.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Schwann cells are key players in neuro-regeneration: They sense "alarm" signals released by degenerating nerve terminals and differentiate toward a proregenerative phenotype, with phagocytosis of nerve debris and nerve guidance. At the murine neuromuscular junction, hydrogen peroxide (H2O2) is a key signal of Schwann cells' activation in response to a variety of nerve injuries. Here we report that Schwann cells exposed to low doses of H2O2 rewire the expression of several RNAs at both transcriptional and translational levels. Among the genes positively regulated at both levels, we identified an enriched cluster involved in cytoskeleton remodeling and cell migration, with the Annexin (Anxa) proteins being the most represented family. We show that both Annexin A2 (Anxa2) transcript and protein accumulate at the tips of long pseudopods that Schwann cells extend upon H2O2 exposure. Interestingly, Schwann cells reply to this signal and to nerve injury by locally translating Anxa2 in pseudopods, and undergo an extensive cytoskeleton remodeling. Our results show that, similarly to neurons, Schwann cells take advantage of local protein synthesis to change shape and move toward damaged axonal terminals to facilitate axonal regeneration.
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Affiliation(s)
- Samuele Negro
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Marco Stazi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | | | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, 38123 Povo, Italy
| | - Umberto Rodella
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Elisa Duregotti
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Volker Gerke
- Institute of Medical Biochemistry, University of Münster, 48149 Münster, Germany
| | | | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
- CNR Institute of Neuroscience, 35131 Padua, Italy
| | - Michela Rigoni
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Italy
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48
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Bernabò P, Tebaldi T, Groen EJN, Lane FM, Perenthaler E, Mattedi F, Newbery HJ, Zhou H, Zuccotti P, Potrich V, Shorrock HK, Muntoni F, Quattrone A, Gillingwater TH, Viero G. In Vivo Translatome Profiling in Spinal Muscular Atrophy Reveals a Role for SMN Protein in Ribosome Biology. Cell Rep 2018; 21:953-965. [PMID: 29069603 PMCID: PMC5668566 DOI: 10.1016/j.celrep.2017.10.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/22/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic alterations impacting ubiquitously expressed proteins involved in RNA metabolism often result in neurodegenerative conditions, with increasing evidence suggesting that translation defects can contribute to disease. Spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of SMN protein, whose role in pathogenesis remains unclear. Here, we identified in vivo and in vitro translation defects that are cell autonomous and SMN dependent. By determining in parallel the in vivo transcriptome and translatome in SMA mice, we observed a robust decrease in translation efficiency arising during early stages of disease. We provide a catalogue of RNAs with altered translation efficiency, identifying ribosome biology and translation as central processes affected by SMN depletion. This was further supported by a decrease in the number of ribosomes in SMA motor neurons in vivo. Overall, our findings suggest ribosome biology as an important, yet largely overlooked, factor in motor neuron degeneration. Polysomal profiling reveals translation defects in SMA mice Translation defects are SMN dependent and cell autonomous Translation efficiency alterations highlight defects in ribosome biology The number of axonal ribosomes is decreased in SMA in vivo
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Affiliation(s)
- Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Ewout J N Groen
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Fiona M Lane
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Francesca Mattedi
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Helen J Newbery
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Haiyan Zhou
- Dubowitz Neuromuscular Centre, Great Ormond Street Institute of Child Health, University College London 30, Guilford Street, WC1N 1EH London, UK
| | - Paola Zuccotti
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Valentina Potrich
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Hannah K Shorrock
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, Great Ormond Street Institute of Child Health, University College London 30, Guilford Street, WC1N 1EH London, UK
| | - Alessandro Quattrone
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy.
| | - Thomas H Gillingwater
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy.
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49
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Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies. Nat Immunol 2018; 19:636-644. [PMID: 29777220 PMCID: PMC5986066 DOI: 10.1038/s41590-018-0110-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 04/05/2018] [Indexed: 12/20/2022]
Abstract
Transcriptome profiling is widely used to infer functional states of specific cell types, as well as their responses to stimuli, to define contributions to physiology and pathophysiology. Focusing on microglia, the brain macrophages, we report here a side-by-side comparison of classical cell sort-based transcriptome sequencing and the ‘RiboTag’ method that avoids cell retrieval from tissue context and yields translatome sequencing information. Conventional whole cell microglia transcriptomes were found to be significantly tainted by artifacts induced by tissue-dissociation, cargo contaminations and transcripts sequestered from ribosomes. Conversely, our data highlight the added value of RiboTag profiling to assess the accuracy of Cre transgenic mice. Collectively, this study indicates method-based biases, reveals observer effects and establishes RiboTag-based translatome profiling as a valuable complement to standard sort-based profiling strategies.
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50
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Tréfier A, Guillou F, Crépieux P. [Investigation methods to explore G protein-coupled receptor-regulated translatome]. C R Biol 2018; 341:65-74. [PMID: 29326051 DOI: 10.1016/j.crvi.2017.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/26/2022]
Abstract
With the advent of next-generation sequencing technologies, identifying the translatome, which includes genome-wide ribosome-associated mRNAs, provides new opportunities to define faithfully the protein repertoire of a cell, as opposed to transcriptomic approaches. In addition, the role that extracellular signals such as hormonal modulations could play on the translatome remains to be deciphered. In particular, the regulation of the translatome by G protein-coupled receptors (GPCR) is still poorly described, albeit the trophic role that many receptors of this family play in their target cells. Here, we provide an overview of the current methods that are used to study the translatome, applied to the GPCR receptor family.
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Affiliation(s)
- Aurélie Tréfier
- Groupe Biologie et bioinformatique des systèmes de signalisation, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France
| | - Florian Guillou
- Plasticité génomique et expression phénotypique, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France
| | - Pascale Crépieux
- Groupe Biologie et bioinformatique des systèmes de signalisation, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France.
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