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Sainz MM, Sotelo-Silveira M, Filippi CV, Zardo S. Legume-rhizobia symbiosis: Translatome analysis. Genet Mol Biol 2024; 47Suppl 1:e20230284. [PMID: 38954532 PMCID: PMC11223499 DOI: 10.1590/1678-4685-gmb-2023-0284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/31/2024] [Indexed: 07/04/2024] Open
Abstract
Leguminous plants can establish endosymbiotic relationships with nitrogen-fixing soil rhizobacteria. Bacterial infection and nodule organogenesis are two independent but highly coordinated genetic programs that are active during this interaction. These genetic programs can be regulated along all the stages of gene expression. Most of the studies, for both eukaryotes and prokaryotes, focused on the transcriptional regulation level determining the abundance of mRNAs. However, it has been demonstrated that mRNA levels only sometimes correlate with the abundance or activity of the coded proteins. For this reason, in the past two decades, interest in the role of translational control of gene expression has increased, since the subset of mRNA being actively translated outperforms the information gained only by the transcriptome. In the case of legume-rhizobia interactions, the study of the translatome still needs to be explored further. Therefore, this review aims to discuss the methodologies for analyzing polysome-associated mRNAs at the genome-scale and their contribution to studying translational control to understand the complexity of this symbiotic interaction. Moreover, the Dual RNA-seq approach is discussed for its relevance in the context of a symbiotic nodule, where intricate multi-species gene expression networks occur.
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Affiliation(s)
- María Martha Sainz
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Mariana Sotelo-Silveira
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Carla V. Filippi
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Sofía Zardo
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
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2
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Godina C, Belting M, Vallon-Christersson J, Isaksson K, Bosch A, Jernström H. Caveolin-1 gene expression provides additional prognostic information combined with PAM50 risk of recurrence (ROR) score in breast cancer. Sci Rep 2024; 14:6675. [PMID: 38509243 PMCID: PMC10954762 DOI: 10.1038/s41598-024-57365-8] [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: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Combining information from the tumor microenvironment (TME) with PAM50 Risk of Recurrence (ROR) score could improve breast cancer prognostication. Caveolin-1 (CAV1) is a marker of an active TME. CAV1 is a membrane protein involved in cell signaling, extracellular matrix organization, and tumor-stroma interactions. We sought to investigate CAV1 gene expression in relation to PAM50 subtypes, ROR score, and their joint prognostic impact. CAV1 expression was compared between PAM50 subtypes and ROR categories in two cohorts (SCAN-B, n = 5326 and METABRIC, n = 1980). CAV1 expression was assessed in relation to clinical outcomes using Cox regression and adjusted for clinicopathological predictors. Effect modifications between CAV1 expression and ROR categories on clinical outcome were investigated using multiplicative and additive two-way interaction analyses. Differential gene expression and gene set enrichment analyses were applied to compare high and low expressing CAV1 tumors. All samples expressed CAV1 with the highest expression in the Normal-like subtype. Gene modules consistent with epithelial-mesenchymal transition (EMT), hypoxia, and stromal activation were associated with high CAV1 expression. CAV1 expression was inversely associated with ROR category. Interactions between CAV1 expression and ROR categories were observed in both cohorts. High expressing CAV1 tumors conferred worse prognosis only within the group classified as ROR high. ROR gave markedly different prognostic information depending on the underlying CAV1 expression. CAV1, a potential mediator between the malignant cells and TME, could be a useful biomarker that enhances and further refines PAM50 ROR risk stratification in patients with ROR high tumors and a potential therapeutic target.
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Affiliation(s)
- Christopher Godina
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden.
| | - Mattias Belting
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Skåne, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
| | - Karolin Isaksson
- Department of Clinical Sciences Lund, Surgery, Lund University and Kristianstad Hospital, Kristianstad, Sweden
| | - Ana Bosch
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Skåne, Sweden
| | - Helena Jernström
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden.
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3
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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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4
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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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5
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Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol 2022; 24:968-980. [PMID: 35697785 DOI: 10.1038/s41556-022-00928-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/27/2022] [Indexed: 12/12/2022]
Abstract
In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocytes or embryos per stage. Ribo-lite can also accommodate single oocytes. Combining PAIso-seq to interrogate poly(A) tail lengths, we found a global switch of translatome that closely parallels changes of poly(A) tails upon meiotic resumption. Translation activation correlates with polyadenylation and is supported by polyadenylation signal proximal cytoplasmic polyadenylation elements (papCPEs) in 3' untranslated regions. By contrast, translation repression parallels global de-adenylation. The latter includes transcripts containing no CPEs or non-papCPEs, which encode many transcription regulators that are preferentially re-activated before zygotic genome activation. CCR4-NOT, the major de-adenylation complex, and its key adaptor protein BTG4 regulate translation downregulation often independent of RNA decay. BTG4 is not essential for global de-adenylation but is required for selective gene de-adenylation and production of very short-tailed transcripts. In sum, our data reveal intimate interplays among translation, RNA stability and poly(A) tail length regulation underlying mammalian OET.
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6
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Dalal H, Dahlgren M, Gladchuk S, Brueffer C, Gruvberger-Saal SK, Saal LH. Clinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors. Sci Rep 2022; 12:4696. [PMID: 35304506 PMCID: PMC8933558 DOI: 10.1038/s41598-022-08210-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/03/2022] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors and is the key biomarker to direct endocrine therapies. On the other hand, much less is known about estrogen receptor beta (ERβ, encoded by ESR2) and its importance in cancer. Previous studies had some disagreement, however most reports suggested a more favorable prognosis for patients with high ESR2 expression. To add further clarity to ESR2 in breast cancer, we interrogated a large population-based cohort of primary breast tumors (n = 3207) from the SCAN-B study. RNA-seq shows ESR2 is expressed at low levels overall with a slight inverse correlation to ESR1 expression (Spearman R = −0.18, p = 2.2e−16), and highest ESR2 expression in the basal- and normal-like PAM50 subtypes. ESR2-high tumors had favorable overall survival (p = 0.006), particularly in subgroups receiving endocrine therapy (p = 0.03) and in triple-negative breast cancer (p = 0.01). These results were generally robust in multivariable analyses accounting for patient age, tumor size, node status, and grade. Gene modules consistent with immune response were associated to ESR2-high tumors. Taken together, our results indicate that ESR2 is generally expressed at low levels in breast cancer but associated with improved overall survival and may be related to immune response modulation.
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Affiliation(s)
- Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Malin Dahlgren
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Sofia K Gruvberger-Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Section for Molecular Diagnostics, Skåne University Hospital, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden. .,Lund University Cancer Center, Medicon Village, Lund, Sweden.
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7
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Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell 2021; 81:4300-4318.e13. [PMID: 34437836 PMCID: PMC8567535 DOI: 10.1016/j.molcel.2021.07.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022]
Abstract
The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
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Affiliation(s)
- Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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8
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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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9
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Seeking a Role for Translational Control by Alternative Polyadenylation in Saccharomyces cerevisiae. Microorganisms 2021; 9:microorganisms9091885. [PMID: 34576779 PMCID: PMC8464734 DOI: 10.3390/microorganisms9091885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Alternative polyadenylation (APA) represents an important mechanism for regulating isoform-specific translation efficiency, stability, and localisation. Though some progress has been made in understanding its consequences in metazoans, the role of APA in the model organism Saccharomyces cerevisiae remains a relative mystery because, despite abundant studies on the translational state of mRNA, none differentiate mRNA isoforms’ alternative 3′-end. This review discusses the implications of alternative polyadenylation in S. cerevisiae using other organisms to draw inferences. Given the foundational role that research in this yeast has played in the discovery of the mechanisms of cleavage and polyadenylation and in the drivers of APA, it is surprising that such an inference is required. However, because advances in ribosome profiling are insensitive to APA, how it impacts translation is still unclear. To bridge the gap between widespread observed APA and the discovery of any functional consequence, we also provide a review of the experimental techniques used to uncover the functional importance of 3′ UTR isoforms on translation.
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10
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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11
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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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12
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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 PMCID: PMC6885737 DOI: 10.15252/embj.2018101323] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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 LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Eric P Kusnadi
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVic.Australia
| | - Vincent van Hoef
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Richard J Rebello
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
| | - Matthew Leibovitch
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental MedicineLady Davis InstituteMcGill UniversityMontrealQCCanada
| | - Johannes Ristau
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Shan Chen
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Mitchell G Lawrence
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVic.Australia
| | - Krzysztof J Szkop
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Baila Samreen
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Preetika Balanathan
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
| | - Francesca Rapino
- Laboratory of Cancer SignalingGIGA‐InstituteUniversity of LiègeLiègeBelgium
| | - Pierre Close
- Laboratory of Cancer SignalingGIGA‐InstituteUniversity of LiègeLiègeBelgium
| | - Patricia Bukczynska
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
| | - Karin Scharmann
- Max Planck Institute for Molecular BiomedicineMünsterGermany
- Cells‐in‐Motion Cluster of ExcellenceUniversity of MünsterMünsterGermany
| | - Itsuhiro Takizawa
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
| | - Gail P Risbridger
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVic.Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's HealthAdelaide Medical SchoolFaculty of Health and Medical SciencesThe University of AdelaideAdelaideSAAustralia
| | - Sebastian A Leidel
- Max Planck Institute for Molecular BiomedicineMünsterGermany
- Cells‐in‐Motion Cluster of ExcellenceUniversity of MünsterMünsterGermany
- Department of Chemistry and BiochemistryUniversity of BernBernSwitzerland
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics ResourceDepartment of ChemistryUniversity at AlbanyAlbanyNYUSA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental MedicineLady Davis InstituteMcGill UniversityMontrealQCCanada
| | - Ola Larsson
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetSolnaSweden
| | - Luc Furic
- Prostate Cancer Translational Research LaboratoryPeter MacCallum Cancer CentreMelbourneVic.Australia
- Cancer ProgramBiomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityClaytonVic.Australia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVic.Australia
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13
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Lupinacci FCS, Ferreira EN, Roffe M, Bellato HM, Carraro DM, Hajj GNM. Effects of tumor biobank storage on polysome stability. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41241-019-0077-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Liu W, Xiang L, Zheng T, Jin J, Zhang G. TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data. Nucleic Acids Res 2019; 46:D206-D212. [PMID: 29106630 PMCID: PMC5753366 DOI: 10.1093/nar/gkx1034] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/17/2017] [Indexed: 01/08/2023] Open
Abstract
Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power.
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Affiliation(s)
- Wanting Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | | | - Tingkai Zheng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China.,Chi-Biotech Co. Ltd., Shenzhen 518000, China
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15
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Sandri BJ, Masvidal L, Murie C, Bartish M, Avdulov S, Higgins L, Markowski T, Peterson M, Bergh J, Yang P, Rolny C, Limper AH, Griffin TJ, Bitterman PB, Wendt CH, Larsson O. Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function. Am J Respir Crit Care Med 2019; 200:348-358. [PMID: 30742544 PMCID: PMC6680296 DOI: 10.1164/rccm.201801-0080oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/08/2019] [Indexed: 12/31/2022] Open
Abstract
Rationale: Chronic obstructive pulmonary disease is an independent risk factor for lung cancer, but the underlying molecular mechanisms are unknown. We hypothesized that lung stromal cells activate pathological gene expression programs that support oncogenesis.Objectives: To identify molecular mechanisms operating in the lung stroma that support the development of lung cancer.Methods: The study included subjects with and without lung cancer across a spectrum of lung-function values. We conducted a multiomics analysis of nonmalignant lung tissue to quantify the transcriptome, translatome, and proteome.Measurements and Main Results: Cancer-associated gene expression changes predominantly manifested as alterations in the efficiency of mRNA translation modulating protein levels in the absence of corresponding changes in mRNA levels. The molecular mechanisms that drove these cancer-associated translation programs differed based on lung function. In subjects with normal to mildly impaired lung function, the mammalian target of rapamycin (mTOR) pathway served as an upstream driver, whereas in subjects with severe airflow obstruction, pathways downstream of pathological extracellular matrix emerged. Consistent with a role during cancer initiation, both the mTOR and extracellular matrix gene expression programs paralleled the activation of previously identified procancer secretomes. Furthermore, an in situ examination of lung tissue showed that stromal fibroblasts expressed cancer-associated proteins from two procancer secretomes: one that included IL-6 (in cases of mild or no airflow obstruction), and one that included BMP1 (in cases of severe airflow obstruction).Conclusions: Two distinct stromal gene expression programs that promote cancer initiation are activated in patients with lung cancer depending on lung function. Our work has implications both for screening strategies and for personalized approaches to cancer treatment.
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Affiliation(s)
- Brian J. Sandri
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Laia Masvidal
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Carl Murie
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Margarita Bartish
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Svetlana Avdulov
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Todd Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Mark Peterson
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Jonas Bergh
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | - Charlotte Rolny
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew H. Limper
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; and
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Peter B. Bitterman
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Chris H. Wendt
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, Veterans Affairs Medical Center, Minneapolis, Minnesota
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
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16
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Ernlund AW, Schneider RJ, Ruggles KV. RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data. BMC Genomics 2018; 19:809. [PMID: 30409155 PMCID: PMC6225633 DOI: 10.1186/s12864-018-5166-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Abstract
Background Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, as well translational efficiency. The increasing popularity of these techniques has resulted in multiple algorithms to detect translational regulation, typically distributed in the form of command line tools that require a basic level of programming ability. Additionally, due to the static nature of current software, dynamic transcriptional and translational comparative analysis cannot be adequately achieved. In order to streamline hypothesis generation, investigators must have the ability to manipulate and interact with their data in real-time. Results To address the lack of integration in current software, we introduce RIVET, Ribosomal Investigation and Visualization to Evaluate Translation, an R shiny based graphical user interface for translatomics data exploration and differential analysis. RIVET can analyze either microarray or RNA sequencing data from polysome profiling and ribosome profiling experiments. RIVET provides multiple choices for statistical analysis as well as integration of transcription, translation, and translational efficiency data analytics and the ability to visualize all results dynamically. Conclusions RIVET is a user-friendly tool designed for bench scientists with little to no programming background. RIVET facilitates the data analysis of translatomics data allowing for dynamic generation of results based on user-defined inputs and publication ready visualization. We expect RIVET will allow for scientists to efficiently make more comprehensive data observations that will lead to more robust hypothesis regarding translational regulation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5166-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanda W Ernlund
- Department of Microbiology, New York University School of Medicine, New York, 10016, USA
| | - Robert J Schneider
- Department of Microbiology, New York University School of Medicine, New York, 10016, USA.
| | - Kelly V Ruggles
- Department of Medicine, Department of Translational Medicine, New York University School of Medicine, New York, 10016, USA.
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17
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Timmons JA, Atherton PJ, Larsson O, Sood S, Blokhin IO, Brogan RJ, Volmar CH, Josse AR, Slentz C, Wahlestedt C, Phillips SM, Phillips BE, Gallagher IJ, Kraus WE. A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. Nucleic Acids Res 2018; 46:7772-7792. [PMID: 29986096 PMCID: PMC6125682 DOI: 10.1093/nar/gky570] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/23/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS), relying on hundreds of thousands of individuals, have revealed >200 genomic loci linked to metabolic disease (MD). Loss of insulin sensitivity (IS) is a key component of MD and we hypothesized that discovery of a robust IS transcriptome would help reveal the underlying genomic structure of MD. Using 1,012 human skeletal muscle samples, detailed physiology and a tissue-optimized approach for the quantification of coding (>18,000) and non-coding (>15,000) RNA (ncRNA), we identified 332 fasting IS-related genes (CORE-IS). Over 200 had a proven role in the biochemistry of insulin and/or metabolism or were located at GWAS MD loci. Over 50% of the CORE-IS genes responded to clinical treatment; 16 quantitatively tracking changes in IS across four independent studies (P = 0.0000053: negatively: AGL, G0S2, KPNA2, PGM2, RND3 and TSPAN9 and positively: ALDH6A1, DHTKD1, ECHDC3, MCCC1, OARD1, PCYT2, PRRX1, SGCG, SLC43A1 and SMIM8). A network of ncRNA positively related to IS and interacted with RNA coding for viral response proteins (P < 1 × 10-48), while reduced amino acid catabolic gene expression occurred without a change in expression of oxidative-phosphorylation genes. We illustrate that combining in-depth physiological phenotyping with robust RNA profiling methods, identifies molecular networks which are highly consistent with the genetics and biochemistry of human metabolic disease.
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Affiliation(s)
- James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, London, UK
- Scion House, Stirling University Innovation Park, Stirling, UK
| | | | - Ola Larsson
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | - Sanjana Sood
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robert J Brogan
- Scion House, Stirling University Innovation Park, Stirling, UK
| | | | | | - Cris Slentz
- Duke University School of Medicine, Durham, USA
| | - Claes Wahlestedt
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | | | | | - Iain J Gallagher
- Scion House, Stirling University Innovation Park, Stirling, UK
- School of Health Sciences and Sport, University of Stirling, Stirling, UK
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18
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Martinez-Nunez RT, Rupani H, Platé M, Niranjan M, Chambers RC, Howarth PH, Sanchez-Elsner T. Genome-Wide Posttranscriptional Dysregulation by MicroRNAs in Human Asthma as Revealed by Frac-seq. THE JOURNAL OF IMMUNOLOGY 2018; 201:251-263. [PMID: 29769273 DOI: 10.4049/jimmunol.1701798] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/17/2018] [Indexed: 12/07/2022]
Abstract
MicroRNAs are small noncoding RNAs that inhibit gene expression posttranscriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing subcellular fractionation and RNA sequencing (Frac-seq) in human primary bronchoepithelium from healthy controls and severe asthmatics. Severe asthma is a chronic inflammatory disease of the airways characterized by poor response to therapy. We found genes (i.e., isoforms of a gene) and mRNA isoforms differentially expressed in asthma, with novel inflammatory and structural pathophysiological mechanisms related to bronchoepithelium disclosed solely by polyribosome-bound mRNAs (e.g., IL1A and LTB genes or ITGA6 and ITGA2 alternatively spliced isoforms). Gene expression (i.e., isoforms of a gene) and mRNA expression analysis revealed different molecular candidates and biological pathways, with differentially expressed polyribosome-bound and total mRNAs also showing little overlap. We reveal a hub of six dysregulated microRNAs accounting for ∼90% of all microRNA targeting, displaying preference for polyribosome-bound mRNAs. Transfection of this hub in bronchial epithelial cells from healthy donors mimicked asthma characteristics. Our work demonstrates extensive posttranscriptional gene dysregulation in human asthma, in which microRNAs play a central role, illustrating the feasibility and importance of assessing posttranscriptional gene expression when investigating human disease.
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Affiliation(s)
- Rocio T Martinez-Nunez
- School of Immunology and Microbial Sciences, Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE19RT, United Kingdom; .,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom
| | - Hitasha Rupani
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom.,Southampton National Institute for Health Research Respiratory Biomedical Research Unit, Southampton Centre for Biomedical Research, University Hospital Southampton National Health Service Foundation Trust, Southampton SO16 6YD, United Kingdom
| | - Manuela Platé
- Centre for Inflammation and Tissue Repair, Department of Respiratory Medicine, Rayne Institute, University College London, London WC1E 6JF, United Kingdom; and
| | - Mahesan Niranjan
- School of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Rachel C Chambers
- Centre for Inflammation and Tissue Repair, Department of Respiratory Medicine, Rayne Institute, University College London, London WC1E 6JF, United Kingdom; and
| | - Peter H Howarth
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom.,Southampton National Institute for Health Research Respiratory Biomedical Research Unit, Southampton Centre for Biomedical Research, University Hospital Southampton National Health Service Foundation Trust, Southampton SO16 6YD, United Kingdom
| | - Tilman Sanchez-Elsner
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom
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19
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Davari K, Lichti J, Friedel CC, Glasmacher E. Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation. J Vis Exp 2018. [PMID: 29578509 PMCID: PMC5931490 DOI: 10.3791/56752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for example, during cellular differentiation, morphogenesis, and functional stimulation (such as activation of immune cells), or after exposure to drugs and other factors from the local environment. Depending on the stimulus and cell type, these changes occur rapidly and at any possible level of gene regulation. Displaying all molecular processes of a responding cell to a certain type of stimulus/drug is one of the hardest tasks in molecular biology. Here, we describe a protocol that enables the simultaneous analysis of multiple layers of gene regulation. We compare, in particular, transcription factor binding (Chromatin-immunoprecipitation-sequencing (ChIP-seq)), de novo transcription (4-thiouridine-sequencing (4sU-seq)), mRNA processing, and turnover as well as translation (ribosome profiling). By combining these methods, it is possible to display a detailed and genome-wide course of action. Sequencing newly transcribed RNA is especially recommended when analyzing rapidly adapting or changing systems, since this depicts the transcriptional activity of all genes during the time of 4sU exposure (irrespective of whether they are up- or downregulated). The combinatorial use of total RNA-seq and ribosome profiling additionally allows the calculation of RNA turnover and translation rates. Bioinformatic analysis of high-throughput sequencing results allows for many means for analysis and interpretation of the data. The generated data also enables tracking co-transcriptional and alternative splicing, just to mention a few possible outcomes. The combined approach described here can be applied for different model organisms or cell types, including primary cells. Furthermore, we provide detailed protocols for each method used, including quality controls, and discuss potential problems and pitfalls.
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Affiliation(s)
- Kathrin Davari
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München
| | - Johannes Lichti
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München
| | | | - Elke Glasmacher
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München; Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg;
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20
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Marcon BH, Holetz FB, Eastman G, Origa-Alves AC, Amorós MA, de Aguiar AM, Rebelatto CK, Brofman PRS, Sotelo-Silveira J, Dallagiovanna B. Downregulation of the protein synthesis machinery is a major regulatory event during early adipogenic differentiation of human adipose-derived stromal cells. Stem Cell Res 2017; 25:191-201. [PMID: 29156375 DOI: 10.1016/j.scr.2017.10.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/11/2017] [Accepted: 10/27/2017] [Indexed: 12/26/2022] Open
Abstract
Commitment of adult stem cells involves the activation of specific gene networks regulated from transcription to protein synthesis. Here, we used ribosome profiling to identify mRNAs regulated at the translational level, through both differential association to polysomes and modulation of their translational rates. We observed that translational regulation during the differentiation of human adipose-derived stromal cells (hASCs, also known as adipose-derived mesenchymal stem cells), a subset of which are stem cells, to adipocytes was a major regulatory event. hASCs showed a significant reduction of whole protein synthesis after adipogenic induction and a downregulation of the expression and translational efficiency of ribosomal proteins. Additionally, focal adhesion and cytoskeletal proteins were downregulated at the translational level. This negative regulation of the essential biological functions of hASCs resulted in a reduction in cell size and the potential of hASCs to migrate. We analyzed whether the inactivation of key translation initiation factors was involved in this observed major repression of translation. We showed that there was an increase in the hypo phosphorylated forms of 4E-BP1, a negative regulator of translation, during early adipogenesis. Our results showed that extensive translational regulation occurred during the early stage of the adipogenic differentiation of hASCs.
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Affiliation(s)
- Bruna H Marcon
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR 81350-010, Brazil
| | - Fabíola B Holetz
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR 81350-010, Brazil
| | - Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, CP 11600 Montevideo, Uruguay
| | - Ana Carolina Origa-Alves
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR 81350-010, Brazil
| | - Mariana Andrea Amorós
- Laboratory of Stem Cells, Institute of Biology and Experimental Medicine - National Council of Scientific and Technical Research (IByME-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Alessandra Melo de Aguiar
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR 81350-010, Brazil
| | - Carmen K Rebelatto
- Núcleo de Tecnologia Celular, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, PR 80215-901, Brazil
| | - Paulo R S Brofman
- Núcleo de Tecnologia Celular, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição, 1155, Curitiba, PR 80215-901, Brazil
| | - Jose Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, CP 11600 Montevideo, Uruguay; Department of Cell and Molecular Biology, School of Sciences, Universidad de la República, Montevideo, Uruguay.
| | - Bruno Dallagiovanna
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR 81350-010, Brazil.
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21
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Chen Q, Hu G. Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev 2017; 46:15-23. [PMID: 28654825 DOI: 10.1016/j.gde.2017.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/17/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
Pluripotency describes the developmental capacity to give rise to all cell types in the adult body. A comprehensive understanding of the molecular mechanisms that regulate pluripotency is important for both basic and translational research. While earlier studies mostly focused on signaling pathways, transcriptional regulation, and epigenetic modifications, recent investigations showed that RNA binding proteins, RNA processing machineries, and regulatory RNA molecules also play essential roles. Here, we provide a concise review on the latest findings and developments in post-transcriptional regulation of the pluripotent state.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
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Davari K, Lichti J, Gallus C, Greulich F, Uhlenhaut NH, Heinig M, Friedel CC, Glasmacher E. Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses. Cell Rep 2017; 19:643-654. [PMID: 28423325 DOI: 10.1016/j.celrep.2017.03.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/17/2017] [Accepted: 03/22/2017] [Indexed: 12/24/2022] Open
Abstract
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNA Pol II carboxy-terminal domain (CTD) and activation of the positive transcription elongation factor (pTEFb). Thus, rapid de novo recruitment of RNA Pol II dictates the course of events during T cell activation, particularly transcription, splicing, and consequently translation.
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Affiliation(s)
- Kathrin Davari
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany; German Center for Diabetes Research (DZD), German Center for Environmental Health GmbH, Munich 85764, Germany
| | - Johannes Lichti
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany; German Center for Diabetes Research (DZD), German Center for Environmental Health GmbH, Munich 85764, Germany
| | - Christian Gallus
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany; German Center for Diabetes Research (DZD), German Center for Environmental Health GmbH, Munich 85764, Germany
| | - Franziska Greulich
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany
| | - Matthias Heinig
- Institute for Computational Biology (ICB), German Center for Environmental Health GmbH, Munich 85764, Germany
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, Munich 80333, Germany.
| | - Elke Glasmacher
- Institute for Diabetes and Obesity (IDO), German Center for Environmental Health GmbH, Munich 85748, Germany; German Center for Diabetes Research (DZD), German Center for Environmental Health GmbH, Munich 85764, Germany.
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23
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Bhargava S, Patil V, Mahalingam K, Somasundaram K. Elucidation of the genetic and epigenetic landscape alterations in RNA binding proteins in glioblastoma. Oncotarget 2017; 8:16650-16668. [PMID: 28035070 PMCID: PMC5369992 DOI: 10.18632/oncotarget.14287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/30/2016] [Indexed: 01/03/2023] Open
Abstract
RNA binding proteins (RBPs) have been implicated in cancer development. An integrated bioinformatics analysis of RBPs (n = 1756) in various datasets (n = 11) revealed several genetic and epigenetically altered events among RBPs in glioblastoma (GBM). We identified 13 mutated and 472 differentially regulated RBPs in GBM samples. Mutations in AHNAK predicted poor prognosis. Copy number variation (CNV), DNA methylation and miRNA targeting contributed to RBP differential regulation. Two sets of differentially regulated RBPs that may be implicated in initial astrocytic transformation and glioma progression were identified. We have also identified a four RBP (NOL3, SUCLG1, HERC5 and AFF3) signature, having a unique expression pattern in glioma stem-like cells (GSCs), to be an independent poor prognostic indicator in GBM. RBP risk score derived from the signature also stratified GBM into low-risk and high-risk groups with significant survival difference. Silencing NOL3, SUCLG1 and HERC5 inhibited GSC maintenance. Gene set enrichment analysis of differentially regulated genes between high-risk and low-risk underscored the importance of inflammation, EMT and hypoxia in high-risk GBM. Thus, we provide a comprehensive overview of genetic and epigenetic regulation of RBPs in glioma development and progression.
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Affiliation(s)
- Shruti Bhargava
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| | - Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore-632014, India
| | - Kulandaivelu Mahalingam
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore-632014, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
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24
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Chassé H, Boulben S, Costache V, Cormier P, Morales J. Analysis of translation using polysome profiling. Nucleic Acids Res 2017; 45:e15. [PMID: 28180329 PMCID: PMC5388431 DOI: 10.1093/nar/gkw907] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 09/07/2016] [Accepted: 09/30/2016] [Indexed: 02/05/2023] Open
Abstract
During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification. We applied this protocol to obtain experimental results on translational regulation of mRNAs following fertilization. Our protocol should prove useful for integrating the study of the role of translational regulation in gene regulatory networks in any biological model. In addition, we demonstrate how to carry out high-throughput processing of polysome gradient fractions, for the simultaneous screening of multiple biological conditions and large-scale preparation of samples for next-generation sequencing.
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Affiliation(s)
- Héloïse Chassé
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Sandrine Boulben
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Vlad Costache
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Patrick Cormier
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Julia Morales
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
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25
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Hücker SM, Simon S, Scherer S, Neuhaus K. Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation. FEMS Microbiol Lett 2016; 364:fnw262. [PMID: 27856567 DOI: 10.1093/femsle/fnw262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 12/24/2022] Open
Abstract
The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5'UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally.
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Affiliation(s)
- Sarah Maria Hücker
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Svenja Simon
- Chair for Data Analysis and Visualization, Department of Computer and Information Science, University of Konstanz, Box 78, 78457 Konstanz, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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26
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Liu L, Liu L, Shi J, Tan M, Xiong J, Li X, Hu Q, Yi Z, Mao D. MicroRNA-34b mediates hippocampal astrocyte apoptosis in a rat model of recurrent seizures. BMC Neurosci 2016; 17:56. [PMID: 27514646 PMCID: PMC4981991 DOI: 10.1186/s12868-016-0291-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Abstract
Background Recurrent convulsions can cause irreversible astrocyte death, impede neuron regeneration, and further aggravate brain damage. MicroRNAs have been revealed as players in the progression of numerous diseases including cancer and Alzheimer’s disease. Particularly, microRNA has been found linked to seizure-induced neuronal death. In this study, a rat model of recurrent convulsions induced by flurothyl treatments was utilised to assess the alterations of microRNA expressions in hippocampus tissues. We also applied an in vitro model in which primary astrocytes were exposed to kainic acid to verify the targets of miR-34b-5p identified in the animal model. Results We discovered that miR-34b-5p, a member of the miR-34 family, increased significantly in flurothyl-treated rat hippocampus tissue. More surprisingly, this upregulation occurred concurrently with accumulating astrocyte apoptosis, indicating the involvement of miR-34b-5p in seizures caused astrocyte apoptosis. Results from the in vitro experiments further demonstrated that miR-34b-5p directly targeted Bcl-2 mRNA, translationally repressed Bcl-2 protein, and thus modulated cell apoptosis by influencing Bcl-2, Bax, and Caspase-3. Conclusion Our findings prove microRNAs play a role in mediating recurrent convulsions-induced astrocyte death and further indicate that miR-34b-5p could acts as a regulator for astrocyte apoptosis induced by recurrent seizures. Electronic supplementary material The online version of this article (doi:10.1186/s12868-016-0291-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liqun Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Lingjuan Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Jiayun Shi
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Menglin Tan
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Jie Xiong
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Xingfang Li
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Qingpeng Hu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Zhuwen Yi
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China
| | - Ding'an Mao
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, 86 Renmin Middle Rd, Changsha, 410011, Hunan, People's Republic of China.
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27
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Weingarten-Gabbay S, Segal E. Toward a systematic understanding of translational regulatory elements in human and viruses. RNA Biol 2016; 13:927-933. [PMID: 27442807 DOI: 10.1080/15476286.2016.1212802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Translational regulation is a critical step in the production of proteins from genomic material in both human and viruses. However, unlike other steps of the central dogma, such as transcriptional regulation, little is known about the cis-regulatory elements involved. In a recent study we devised a high-throughput bicistronic reporter assay for the discovery and the characterization of thousands of novel Internal Ribosome Entry Sites (IRESs) in human and hundreds of viral genomes. Our results provide insights into the landscape of IRES elements in human and viral transcripts and the cis-regulatory sequences underlying their activity. Here, we discuss these results as well as emerging insights from other studies, providing new views about translational regulation in human and viruses. In addition, we highlight recent high-throughput technologies in the field and discuss how combining insights from high- and low-throughput approaches can illuminate yet uncovered mechanisms of translational regulation.
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Affiliation(s)
- Shira Weingarten-Gabbay
- a Department of Computer Science and Applied Mathematics , Weizmann Institute of Science , Rehovot , Israel.,b Department of Molecular Cell Biology , Weizmann Institute of Science , Rehovot , Israel
| | - Eran Segal
- a Department of Computer Science and Applied Mathematics , Weizmann Institute of Science , Rehovot , Israel.,b Department of Molecular Cell Biology , Weizmann Institute of Science , Rehovot , Israel
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28
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Lian X, Guo J, Gu W, Cui Y, Zhong J, Jin J, He QY, Wang T, Zhang G. Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells. PLoS Genet 2016; 12:e1005901. [PMID: 26926465 PMCID: PMC4771717 DOI: 10.1371/journal.pgen.1005901] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By integrating three types of RNA-seq methods, we experimentally and computationally resolved elongation speed, with our proposed elongation velocity index (EVI), a relative measure at individual gene level and under physiological condition in human cells. We successfully distinguished slow-translating genes from the background translatome. We demonstrated that low-EVI genes encoded more stable proteins. We further identified cell-specific slow-translating codons, which might serve as a causal factor of elongation deceleration. As an example for the biological relevance, we showed that the relatively slow-translating genes tended to be associated with the maintenance of malignant phenotypes per pathway analyses. In conclusion, EVI opens a new view to understand why human cells tend to avoid simultaneously speeding up translation initiation and decelerating elongation, and the possible cancer relevance of translating low-EVI genes to gain better protein quality. In protein synthesis, ribosome assembles to mRNA to initiate translation, followed by the process of elongation to read the codons along the mRNA molecule for polypeptide chain production. It is known that slowing down the elongation speed at certain regions of mRNA is critical for the correct folding of numerous proteins—the so-called “pause-to-fold”. However, it has been an open question to evaluate elongation speed under cellular physiological conditions in genome-wide scale. Here, we used three types of next-generation sequencing approaches to experimentally and computationally address this question. With a new relative measure of elongation velocity index (EVI), we successfully distinguished slow-translating genes. Their protein products are more stable than the background genes. We found that different cell types tended to have distinct slow-translating codons, which might be relevant to the cell/tissue specific tRNA composition. Such elongation deceleration is potentially disease-relevant: cancer cells tend to slow down numerous cancer-favorable genes, and vice versa. Furthermore, we justified that translation initiation and elongation are evolutionarily synergistic as no gene with both high initiation efficiency and low elongation speed was observed: that would cause a traffic jam of ribosomes that should be maximally avoided per evolution.
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Affiliation(s)
- Xinlei Lian
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiahui Guo
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Wei Gu
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Yizhi Cui
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiayong Zhong
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jingjie Jin
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Tong Wang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Gong Zhang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
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29
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Abstract
Type-I interferon (IFN)-induced activation of the mammalian target of rapamycin (mTOR) signaling pathway has been implicated in translational control of mRNAs encoding interferon-stimulated genes (ISGs). However, mTOR-sensitive translatomes commonly include mRNAs with a 5’ terminal oligopyrimidine tract (TOP), such as those encoding ribosomal proteins, but not ISGs. Because these translatomes were obtained under conditions when ISG expression is not induced, we examined the mTOR-sensitive translatome in human WISH cells stimulated with IFN β. The mTOR inhibitor Torin1 resulted in a repression of global protein synthesis, including that of ISG products, and translation of all but 3 ISG mRNAs (TLR3, NT5C3A, and RNF19B) was not selectively more sensitive to mTOR inhibition. Detailed studies of NT5C3A revealed an IFN-induced change in transcription start site resulting in a switch from a non-TOP to a TOP-like transcript variant and mTOR sensitive translation. Thus, we show that, in the cell model used, translation of the vast majority of ISG mRNAs is not selectively sensitive to mTOR activity and describe an uncharacterized mechanism wherein the 5’-UTR of an mRNA is altered in response to a cytokine, resulting in a shift from mTOR-insensitive to mTOR-sensitive translation.
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30
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MacNicol MC, Cragle CE, Arumugam K, Fosso B, Pesole G, MacNicol AM. Functional Integration of mRNA Translational Control Programs. Biomolecules 2015. [PMID: 26197342 PMCID: PMC4598765 DOI: 10.3390/biom5031580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Regulated mRNA translation plays a key role in control of cell cycle progression in a variety of physiological and pathological processes, including in the self-renewal and survival of stem cells and cancer stem cells. While targeting mRNA translation presents an attractive strategy for control of aberrant cell cycle progression, mRNA translation is an underdeveloped therapeutic target. Regulated mRNAs are typically controlled through interaction with multiple RNA binding proteins (RBPs) but the mechanisms by which the functions of distinct RBPs bound to a common target mRNA are coordinated are poorly understood. The challenge now is to gain insight into these mechanisms of coordination and to identify the molecular mediators that integrate multiple, often conflicting, inputs. A first step includes the identification of altered mRNA ribonucleoprotein complex components that assemble on mRNAs bound by multiple, distinct RBPs compared to those recruited by individual RBPs. This review builds upon our knowledge of combinatorial control of mRNA translation during the maturation of oocytes from Xenopus laevis, to address molecular strategies that may mediate RBP diplomacy and conflict resolution for coordinated control of mRNA translational output. Continued study of regulated ribonucleoprotein complex dynamics promises valuable new insights into mRNA translational control and may suggest novel therapeutic strategies for the treatment of disease.
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Affiliation(s)
- Melanie C MacNicol
- Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Center for Translational Neuroscience, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Chad E Cragle
- Interdisciplinary BioSciences Graduate Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Karthik Arumugam
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Bruno Fosso
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari 70126, Italy.
| | - Graziano Pesole
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari 70126, Italy.
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70125, Italy.
| | - Angus M MacNicol
- Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Center for Translational Neuroscience, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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31
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Gallo JM, Birtwistle MR. Network pharmacodynamic models for customized cancer therapy. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:243-51. [PMID: 25914386 DOI: 10.1002/wsbm.1300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/27/2022]
Abstract
Pharmacokinetics (PKs) and pharmacodynamics (PDs) have always been integral to the design of rational drug dosing regimens. Early on PK-driven approaches came under the auspices of therapeutic drug monitoring that progressed into population-based PK and PK/PD modeling analyses. As the availability of tissue samples for measurement of drug concentrations is limited in patients, the bulk of such model-based methods relied on plasma drug concentrations to both build models and monitor therapy. The continued advances in systems biology and the spawning of systems pharmacology propelled the creation of enhanced PD (ePD) models. One of the main characteristic of ePD models is that they are derived from mechanistically grounded biochemical reaction networks. These models are commonly represented as systems of coupled ordinary differential equations with the ability to tailor each reaction and protein concentration to an individual's genomic/proteomic profile. As patient genomic analyses become more common, many genetic and protein abnormalities can be represented in the ePD models, and thus offer a path toward personalized anticancer therapies. By linking PK models to ePD models, a full spectrum of pharmacological simulation tools is available to design sophisticated multidrug regimens. However, ePD models are not a panacea and face challenges in model identifiability, scaling and parameter estimation. Nonetheless, as new technologies evolve and are coupled with fresh ideas on model implementation, it is likely that ePD and PK/ePD models will be considered a viable enterprise to customize anticancer drug therapy.
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Affiliation(s)
- James M Gallo
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc R Birtwistle
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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32
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Abstract
Dysregulation of mRNA translation is a frequent feature of neoplasia. Many oncogenes and tumour suppressors affect the translation machinery, making aberrant translation a widespread characteristic of tumour cells, independent of the genetic make-up of the cancer. Therefore, therapeutic agents that target components of the protein synthesis apparatus hold promise as novel anticancer drugs that can overcome intra-tumour heterogeneity. In this Review, we discuss the role of translation in cancer, with a particular focus on the eIF4F (eukaryotic translation initiation factor 4F) complex, and provide an overview of recent efforts aiming to 'translate' these results to the clinic.
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33
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Franks AM, Csárdi G, Drummond DA, Airoldi EM. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. J Am Stat Assoc 2015; 110:27-44. [PMID: 25954056 PMCID: PMC4418505 DOI: 10.1080/01621459.2014.964404] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We consider the problem of quantifying the degree of coordination between transcription and translation, in yeast. Several studies have reported a surprising lack of coordination over the years, in organisms as different as yeast and human, using diverse technologies. However, a close look at this literature suggests that the lack of reported correlation may not reflect the biology of regulation. These reports do not control for between-study biases and structure in the measurement errors, ignore key aspects of how the data connect to the estimand, and systematically underestimate the correlation as a consequence. Here, we design a careful meta-analysis of 27 yeast data sets, supported by a multilevel model, full uncertainty quantification, a suite of sensitivity analyses and novel theory, to produce a more accurate estimate of the correlation between mRNA and protein levels-a proxy for coordination. From a statistical perspective, this problem motivates new theory on the impact of noise, model mis-specifications and non-ignorable missing data on estimates of the correlation between high dimensional responses. We find that the correlation between mRNA and protein levels is quite high under the studied conditions, in yeast, suggesting that post-transcriptional regulation plays a less prominent role than previously thought.
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34
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Translational control of immune responses: from transcripts to translatomes. Nat Immunol 2014; 15:503-11. [DOI: 10.1038/ni.2891] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/08/2014] [Indexed: 12/13/2022]
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35
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Gandin V, Sikström K, Alain T, Morita M, McLaughlan S, Larsson O, Topisirovic I. Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale. J Vis Exp 2014. [PMID: 24893926 PMCID: PMC4189431 DOI: 10.3791/51455] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. Accordingly, dysregulation of mRNA translation is considered to play a major role in a variety of pathological states including cancer. Ribosomes also host chaperones, which facilitate folding of nascent polypeptides, thereby modulating function and stability of newly synthesized polypeptides. In addition, emerging data indicate that ribosomes serve as a platform for a repertoire of signaling molecules, which are implicated in a variety of post-translational modifications of newly synthesized polypeptides as they emerge from the ribosome, and/or components of translational machinery. Herein, a well-established method of ribosome fractionation using sucrose density gradient centrifugation is described. In conjunction with the in-house developed “anota” algorithm this method allows direct determination of differential translation of individual mRNAs on a genome-wide scale. Moreover, this versatile protocol can be used for a variety of biochemical studies aiming to dissect the function of ribosome-associated protein complexes, including those that play a central role in folding and degradation of newly synthesized polypeptides.
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Affiliation(s)
- Valentina Gandin
- Lady Davis Institute and Department of Oncology, McGill University
| | | | - Tommy Alain
- Goodman Cancer Centre and Department of Biochemistry, McGill University
| | - Masahiro Morita
- Goodman Cancer Centre and Department of Biochemistry, McGill University
| | | | - Ola Larsson
- Department of Oncology-Pathology, Karolinska Institutet;
| | - Ivan Topisirovic
- Lady Davis Institute and Department of Oncology, McGill University;
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Parker MW, Rossi D, Peterson M, Smith K, Sikström K, White ES, Connett JE, Henke CA, Larsson O, Bitterman PB. Fibrotic extracellular matrix activates a profibrotic positive feedback loop. J Clin Invest 2014; 124:1622-35. [PMID: 24590289 DOI: 10.1172/jci71386] [Citation(s) in RCA: 398] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 12/27/2013] [Indexed: 12/13/2022] Open
Abstract
Pathological remodeling of the extracellular matrix (ECM) by fibroblasts leads to organ failure. Development of idiopathic pulmonary fibrosis (IPF) is characterized by a progressive fibrotic scarring in the lung that ultimately leads to asphyxiation; however, the cascade of events that promote IPF are not well defined. Here, we examined how the interplay between the ECM and fibroblasts affects both the transcriptome and translatome by culturing primary fibroblasts generated from IPF patient lung tissue or nonfibrotic lung tissue on decellularized lung ECM from either IPF or control patients. Surprisingly, the origin of the ECM had a greater impact on gene expression than did cell origin, and differences in translational control were more prominent than alterations in transcriptional regulation. Strikingly, genes that were translationally activated by IPF-derived ECM were enriched for those encoding ECM proteins detected in IPF tissue. We determined that genes encoding IPF-associated ECM proteins are targets for miR-29, which was downregulated in fibroblasts grown on IPF-derived ECM, and baseline expression of ECM targets could be restored by overexpression of miR-29. Our data support a model in which fibroblasts are activated to pathologically remodel the ECM in IPF via a positive feedback loop between fibroblasts and aberrant ECM. Interrupting this loop may be a strategy for IPF treatment.
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Knudsen BR, Jepsen ML, Ho YP. Quantum dot-based nanosensors for diagnosis via enzyme activity measurement. Expert Rev Mol Diagn 2014; 13:367-75. [DOI: 10.1586/erm.13.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Morfoisse F, Kuchnio A, Frainay C, Gomez-Brouchet A, Delisle MB, Marzi S, Helfer AC, Hantelys F, Pujol F, Guillermet-Guibert J, Bousquet C, Dewerchin M, Pyronnet S, Prats AC, Carmeliet P, Garmy-Susini B. Hypoxia induces VEGF-C expression in metastatic tumor cells via a HIF-1α-independent translation-mediated mechanism. Cell Rep 2014; 6:155-67. [PMID: 24388748 DOI: 10.1016/j.celrep.2013.12.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/28/2013] [Accepted: 12/06/2013] [Indexed: 01/04/2023] Open
Abstract
Various tumors metastasize via lymph vessels and lymph nodes to distant organs. Even though tumors are hypoxic, the mechanisms of how hypoxia regulates lymphangiogenesis remain poorly characterized. Here, we show that hypoxia reduced vascular endothelial growth factor C (VEGF-C) transcription and cap-dependent translation via the upregulation of hypophosphorylated 4E-binding protein 1 (4E-BP1). However, initiation of VEGF-C translation was induced by hypoxia through an internal ribosome entry site (IRES)-dependent mechanism. IRES-dependent VEGF-C translation was independent of hypoxia-inducible factor 1α (HIF-1α) signaling. Notably, the VEGF-C IRES activity was higher in metastasizing tumor cells in lymph nodes than in primary tumors, most likely because lymph vessels in these lymph nodes were severely hypoxic. Overall, this transcription-independent but translation-dependent upregulation of VEGF-C in hypoxia stimulates lymphangiogenesis in tumors and lymph nodes and may contribute to lymphatic metastasis.
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Affiliation(s)
- Florent Morfoisse
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Anna Kuchnio
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Clement Frainay
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Anne Gomez-Brouchet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Marie-Bernadette Delisle
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Stefano Marzi
- UPR 9002 CNRS-ARN, Université De Strasbourg, IBMC, 67084 Strasbourg, France
| | | | - Fransky Hantelys
- Université de Toulouse, UPS, TRADGENE, EA4554, 31432 Toulouse, France
| | - Francoise Pujol
- Université de Toulouse, UPS, TRADGENE, EA4554, 31432 Toulouse, France
| | - Julie Guillermet-Guibert
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Corinne Bousquet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | - Mieke Dewerchin
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Stephane Pyronnet
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France
| | | | - Peter Carmeliet
- Vesalius Research Center, VIB, University of Leuven, 3000 Leuven, Belgium
| | - Barbara Garmy-Susini
- Inserm, U1037, 31432 Toulouse, France; Université de Toulouse, UPS, Cancer Research Center of Toulouse, Equipe Labellisee Ligue Contre le Cancer and Laboratoire d'Excellence Toulouse Cancer, 31432 Toulouse, France.
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Stougaard M, Ho YP. DNA-based nanosensors for next-generation clinical diagnostics via detection of enzyme activity. Expert Rev Mol Diagn 2013; 14:1-3. [PMID: 24308335 DOI: 10.1586/14737159.2014.863151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specific and sensitive detection of DNA-modifying enzymes represents a cornerstone in modern medical diagnostics. Many of the currently prevalent methods are not preferred in the clinics because they rely heavily on pre-amplification or post-separation steps. This editorial highlights the potential of adopting DNA-based nanosensors for the assessment of the activities of DNA-modifying enzymes, with emphasis on the topoisomerase and tyrosyl-DNA phosphodiesterase families. By underlining the existing challenges, we expect that the DNA-nanosensors may soon be promoted to clinical diagnostics via enzyme detection.
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Affiliation(s)
- Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000 Aarhus C, Denmark +45 7846 3672
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Environmental sensing and regulation of gene expression in CD4+ T cell subsets. Curr Opin Immunol 2013; 25:564-70. [DOI: 10.1016/j.coi.2013.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/19/2013] [Accepted: 09/22/2013] [Indexed: 11/19/2022]
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Hershey JWB, Sonenberg N, Mathews MB. Principles of translational control: an overview. Cold Spring Harb Perspect Biol 2012; 4:4/12/a011528. [PMID: 23209153 DOI: 10.1101/cshperspect.a011528] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Translational control plays an essential role in the regulation of gene expression. It is especially important in defining the proteome, maintaining homeostasis, and controlling cell proliferation, growth, and development. Numerous disease states result from aberrant regulation of protein synthesis, so understanding the molecular basis and mechanisms of translational control is critical. Here we outline the pathway of protein synthesis, with special emphasis on the initiation phase, and identify areas needing further clarification. Features of translational control are described together with numerous specific examples, and we discuss prospects for future conceptual advances.
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Affiliation(s)
- John W B Hershey
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95616, USA.
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