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Kim S, Chen J, Ou F, Liu TT, Jo S, Gillanders WE, Murphy TL, Murphy KM. Transcription factor C/EBPα is required for the development of Ly6C hi monocytes but not Ly6C lo monocytes. Proc Natl Acad Sci U S A 2024; 121:e2315659121. [PMID: 38564635 PMCID: PMC11009651 DOI: 10.1073/pnas.2315659121] [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: 09/11/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Monocytes comprise two major subsets, Ly6Chi classical monocytes and Ly6Clo nonclassical monocytes. Notch2 signaling in Ly6Chi monocytes triggers transition to Ly6Clo monocytes, which require Nr4a1, Bcl6, Irf2, and Cebpb. By comparison, less is known about transcriptional requirements for Ly6Chi monocytes. We find transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) is highly expressed in Ly6Chi monocytes, but down-regulated in Ly6Clo monocytes. A few previous studies described the requirement of C/EBPα in the development of neutrophils and eosinophils. However, the role of C/EBPα for in vivo monocyte development has not been understood. We deleted the Cebpa +37 kb enhancer in mice, eliminating hematopoietic expression of C/EBPα, reproducing the expected neutrophil defect. Surprisingly, we also found a severe and selective loss of Ly6Chi monocytes, while preserving Ly6Clo monocytes. We find that BM progenitors from Cebpa +37-/- mice rapidly progress through the monocyte progenitor stage to develop directly into Ly6Clo monocytes even in the absence of Notch2 signaling. These results identify a previously unrecognized role for C/EBPα in maintaining Ly6Chi monocyte identity.
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Affiliation(s)
- Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Jing Chen
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Suin Jo
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - William E. Gillanders
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Theresa L. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Kenneth M. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
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2
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Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nat Commun 2023; 14:6166. [PMID: 37789015 PMCID: PMC10547706 DOI: 10.1038/s41467-023-41799-1] [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: 10/17/2022] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we data-mined human and mouse heart ribosome profiling analyses and identified a double-stranded RNA (dsRNA) structure within the GATA4 uORF that cooperates with the start codon to augment uORF translation and inhibits mORF translation. A trans-acting RNA helicase DDX3X inhibits the GATA4 uORF-dsRNA activity and modulates the translational balance of uORF and mORF. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the broad utility of uORF-dsRNA- or mORF-targeting ASO to regulate mORF translation for other mRNAs. This work demonstrates that the uORF-dsRNA element regulates the translation of multiple mRNAs as a generalizable translational control mechanism. Moreover, we develop a valuable strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon.
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Affiliation(s)
- Omar M Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Eng-Soon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
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3
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Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545153. [PMID: 37397986 PMCID: PMC10312771 DOI: 10.1101/2023.06.15.545153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we identified a double-stranded RNA (dsRNA) structure residing within the GATA4 uORF that augments uORF translation and inhibits mORF translation. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the general utility of uORF-dsRNA- or mORF- targeting ASO to regulate mORF translation for other mRNAs. Our work demonstrates a regulatory paradigm that controls translational efficiency and a useful strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon. Bullet points for discoveries dsRNA within GATA4 uORF activates uORF translation and inhibits mORF translation. ASOs that target the dsRNA can either inhibit or enhance GATA4 mORF translation. ASOs can be used to impede hypertrophy in human cardiomyocytes and mouse hearts.uORF- and mORF-targeting ASOs can be used to control translation of multiple mRNAs.
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Affiliation(s)
- Omar M. Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Kadiam C. Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - EngSoon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
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4
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Maslakova AA, Golyshev SA, Potashnikova DM, Moisenovich AM, Orlovsky IV, Smirnova OV, Rubtsov MA. SERPINA1 long transcripts produce non-secretory alpha1-antitrypsin isoform: In vitro translation in living cells. Int J Biol Macromol 2023; 241:124433. [PMID: 37086761 DOI: 10.1016/j.ijbiomac.2023.124433] [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: 01/21/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
SERPINA1 is a well-studied serpin gene due to its dramatic impact on human health. Translation initiation at the main SERPINA1 start codon produces the only known alpha1-antitrypsin (AAT) isoform intended for secretion. AAT performs essential functions by inhibiting proteases and modulating immunity. However, SERPINA1 expression at the level of translation is not sufficiently studied. Here we hypothesize that the main SERPINA1 ORF can be alternatively translated, producing a non-secretory AAT isoform by either masking or excluding a signal peptide. We defined SERPINA1 long mRNA isoforms specific for prostate (DU145) and liver (HepG2) cell lines and studied their individual expression by in vitro assay. We found that all long transcripts produce both glycosylated secretory AAT-eGFP fusion protein and non-glycosylated intracellular AAT-eGFP (initiated from an alternative AUG-2 start codon), with the proportion regulated by the SERPINA1 5'-UTR. Both fusion proteins localize to distinct cellular compartments: in contrast to a fusion with the secretory AAT accumulating in the ER, the intracellular one exhibits nuclear-cytoplasmic shuttling. We detected putative endogenous AAT isoform enriching the nuclear speckles. CONCLUSION: Alternative translation initiation might be a mechanism through which SERPINA1 expands the biological diversity of its protein products. Our findings open up new prospects for the study of SERPINA1 gene expression.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - S A Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- Research Institute of Molecular and Cellular Medicine, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya, Moscow 117198, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
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5
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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6
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Matherne MG, Phillips ES, Embrey SJ, Burke CM, Machado HL. Emerging functions of C/EBPβ in breast cancer. Front Oncol 2023; 13:1111522. [PMID: 36761942 PMCID: PMC9905667 DOI: 10.3389/fonc.2023.1111522] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Breast tumorigenesis relies on complex interactions between tumor cells and their surrounding microenvironment, orchestrated by tightly regulated transcriptional networks. C/EBPβ is a key transcription factor that regulates the proliferation and differentiation of multiple cell types and modulates a variety of biological processes such as tissue homeostasis and the immune response. In addition, C/EBPβ has well-established roles in mammary gland development, is overexpressed in breast cancer, and has tumor-promoting functions. In this review, we discuss context-specific roles of C/EBPβ during breast tumorigenesis, isoform-specific gene regulation, and regulation of the tumor immune response. We present challenges in C/EBPβ biology and discuss the importance of C/EBPβ isoform-specific gene regulation in devising new therapeutic strategies.
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Affiliation(s)
- Megan G. Matherne
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, United States
| | - Emily S. Phillips
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, United States
| | - Samuel J. Embrey
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, United States
| | - Caitlin M. Burke
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, United States
| | - Heather L. Machado
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, LA, United States,Tulane Cancer Center, Louisiana Cancer Research Consortium, New Orleans, LA, United States,*Correspondence: Heather L. Machado,
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7
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Moshkovits I, Kaminitz A, Reuveni D, Pasmanik‐Chor M, Brazowski E, Mildner A, Leutz A, Zigmond E. Immune cell C/EBPβ deficiency is associated with hepatic mononuclear defects and spontaneous hepatitis but not steatohepatitis induced liver fibrosis. Immun Inflamm Dis 2022; 10:e728. [PMID: 36301029 PMCID: PMC9609438 DOI: 10.1002/iid3.728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND CCAAT/enhancer-binding protein β (C/EBPβ) is a transcription factor known to be involved in macrophage differentiation and function, steatohepatitis and liver fibrosis. METHODS Immune restricted C/EBPβ deficient and control mice were investigated in steady-state and in the CDA-HFD steatohepatitis model. Mice were assessed for weight change, liver biochemical profile, histology and hepatic phagocytes composition. RESULTS Flow cytometry analysis of hepatic nonparenchymal cells revealed reduced numbers of hepatic monocytes and Kupffer cells and an increase in hepatic MHC class II positive myeloid cells in immune cells restricted C/EBPβ deficient mice. Immune-restricted C/EBPβ deficiency resulted in decreased weight gain and appearance of mild spontaneous liver inflammation. Nevertheless, In the CDA-HFD steatohepatitis model, immune restricted C/EBPβ deficient and proficient mice exhibit similar grade of hepatic steatosis, liver enzymes levels and fibrosis stage. CONCLUSIONS Immune-restricted C/EBPβ deficiency leads to significant alteration in hepatic mononuclear phagocytes composition associated with spontaneous mild hepatitis. Steatohepatitis associated fibrosis is not dependent on C/EBPβ expression by immune cells.
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Affiliation(s)
- Itay Moshkovits
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Ayelet Kaminitz
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Debby Reuveni
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Center for Autoimmune Liver DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - Metsada Pasmanik‐Chor
- Bioinformatics Unit, George‐S. Wise Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Eli Brazowski
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Department of PathologyTel Aviv Sourasky Medical CenterTel AvivIsrael
| | | | - Achim Leutz
- Max Delbrück Center for Molecular MedicineBerlinGermany
| | - Ehud Zigmond
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Center for Autoimmune Liver DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael
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8
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Müller C, Zidek LM, Eichwald S, Kortman G, Koster MH, Calkhoven CF. Enhanced C/EBPβ function promotes hypertrophic versus hyperplastic fat tissue growth and prevents steatosis in response to high-fat diet feeding. eLife 2022; 11:62625. [PMID: 35451956 PMCID: PMC9071262 DOI: 10.7554/elife.62625] [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: 09/01/2020] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
Chronic obesity is correlated with severe metabolic and cardiovascular diseases as well as with an increased risk for developing cancers. Obesity is usually characterized by fat accumulation in enlarged – hypertrophic – adipocytes that are a source of inflammatory mediators, which promote the development and progression of metabolic disorders. Yet, in certain healthy obese individuals, fat is stored in metabolically more favorable hyperplastic fat tissue that contains an increased number of smaller adipocytes that are less inflamed. In a previous study, we demonstrated that loss of the inhibitory protein-isoform C/EBPβ-LIP and the resulting augmented function of the transactivating isoform C/EBPβ-LAP promotes fat metabolism under normal feeding conditions and expands health- and lifespan in mice. Here, we show that in mice on a high-fat diet, LIP-deficiency results in adipocyte hyperplasia associated with reduced inflammation and metabolic improvements. Furthermore, fat storage in subcutaneous depots is significantly enhanced specifically in LIP-deficient male mice. Our data identify C/EBPβ as a regulator of adipocyte fate in response to increased fat intake, which has major implications for metabolic health and aging.
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Affiliation(s)
- Christine Müller
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
| | - Laura M Zidek
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Sabrina Eichwald
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Gertrud Kortman
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
| | - Mirjam H Koster
- Department of Pediatrics, University Medical Center Groningen, Groningen, Netherlands
| | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
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9
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C/EBPβ isoform-specific regulation of migration and invasion in triple-negative breast cancer cells. NPJ Breast Cancer 2022; 8:11. [PMID: 35042889 PMCID: PMC8766495 DOI: 10.1038/s41523-021-00372-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
The transcription factor C/EBPβ is a master regulator of mammary gland development and tissue remodelling during lactation. The CEBPB-mRNA is translated into three distinct protein isoforms named C/EBPβ-LAP1, -LAP2 and -LIP that are functionally different. The smaller isoform LIP lacks the N-terminal transactivation domains and is considered to act as an inhibitor of the transactivating LAP1/2 isoforms by competitive binding for the same DNA recognition sequences. Aberrantly high expression of LIP is associated with mammary epithelial proliferation and is found in grade III, estrogen receptor (ER) and progesterone (PR) receptor-negative human breast cancer. Here, we show that reverting the high LIP/LAP ratios in triple-negative breast cancer (TNBC) cell lines into low LIP/LAP ratios by overexpression of LAP reduces migration and matrix invasion of these TNBC cells. In addition, in untransformed MCF10A human mammary epithelial cells overexpression of LIP stimulates migration. Knockout of CEBPB in TNBC cells where LIP expression prevails, resulted in strongly reduced migration that was accompanied by a downregulation of genes involved in cell migration, extracellular matrix production and cytoskeletal remodelling, many of which are epithelial to mesenchymal transition (EMT) marker genes. Together, this study suggests that the LIP/LAP ratio is involved in regulating breast cancer cell migration and invasion. This study together with studies from others shows that understanding the functions the C/EBPβ-isoforms in breast cancer development may reveal new avenues of treatment.
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10
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Metformin inhibits human non-small cell lung cancer by regulating AMPK-CEBPB-PDL1 signaling pathway. Cancer Immunol Immunother 2021; 71:1733-1746. [PMID: 34837101 DOI: 10.1007/s00262-021-03116-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022]
Abstract
Metformin has been found to have inhibitory effects on a variety of tumors. However, its effects on non-small cell lung cancer (NSCLC) remain unclear. We demonstrated that metformin could inhibit the proliferation of A549 and H1299 cells. RNA transcriptome sequencing revealed that PDL1 was significantly downregulated in both cell types following treatment with metformin (P < 0.001). Jaspar analysis and chromatin immunoprecipitation showed that CEBPB could directly bind the promoter region of PDL1. Western blotting showed that protein expression of the isoforms CEBPB-LAP*, CEBPB-LAP, and CEBPB-LIP was significantly upregulated and the LIP/LAP ratio was increased. Gene chip analysis showed that PDL1 was significantly upregulated in A549-CEBPB-LAP cells and significantly downregulated in A549-CEBPB-LIP cells (P < 0.05) compared with CEBPB-NC cells. Dual-luciferase reporter gene assay showed that CEBPB-LAP overexpression could promote transcription of PDL1 and CEBPB-LIP overexpression could inhibit the process. Functional assays showed that the changes in CEBPB isoforms affected the function of NSCLC cells. Western blotting showed that metformin could regulate the function of NSCLC cells via AMPK-CEBPB-PDL1 signaling. Animal experiments showed that tumor growth was significantly inhibited by metformin, and atezolizumab and metformin had a synergistic effect on tumor growth. A total of 1247 patients were retrospectively analyzed, including 166 and 1081 patients in metformin and control groups, respectively. The positive rate of PDL1 was lower than that of the control group (HR = 0.338, 95% CI = 0.235-0.487; P < 0.001). In conclusion, metformin inhibited the proliferation of NSCLC cells and played an anti-tumor role in an AMPK-CEBPB-PDL1 signaling-dependent manner.
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11
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Kurata M, Onishi I, Takahara T, Yamazaki Y, Ishibashi S, Goitsuka R, Kitamura D, Takita J, Hayashi Y, Largaesapda DA, Kitagawa M, Nakamura T. C/EBPβ induces B-cell acute lymphoblastic leukemia and cooperates with BLNK mutations. Cancer Sci 2021; 112:4920-4930. [PMID: 34653294 PMCID: PMC8645713 DOI: 10.1111/cas.15164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022] Open
Abstract
BLNK (BASH/SLP‐65) encodes an adaptor protein that plays an important role in B‐cell receptor (BCR) signaling. Loss‐of‐function mutations in this gene are observed in human pre‐B acute lymphoblastic leukemia (ALL), and a subset of Blnk knock‐out (KO) mice develop pre‐B‐ALL. To understand the molecular mechanism of the Blnk mutation‐associated pre‐B‐ALL development, retroviral tagging was applied to KO mice using the Moloney murine leukemia virus (MoMLV). The Blnk mutation that significantly accelerated the onset of MoMLV‐induced leukemia and increased the incidence of pre‐B‐ALL Cebpb was identified as a frequent site of retroviral integration, suggesting that its upregulation cooperates with Blnk mutations. Transgenic expression of the liver‐enriched activator protein (LAP) isoform of Cebpb reduced the number of mature B‐lymphocytes in the bone marrow and inhibited differentiation at the pre‐BI stage. Furthermore, LAP expression significantly accelerated leukemogenesis in Blnk KO mice and alone acted as a B‐cell oncogene. Furthermore, an inverse relationship between BLNK and C/EBPβ expression was also noted in human pre‐B‐ALL cases, and the high level of CEBPB expression was associated with short survival periods in patients with BLNK‐downregulated pre‐B‐ALL. These results indicate the association between the C/EBPβ transcriptional network and BCR signaling in pre‐B‐ALL development and leukemogenesis. This study gives insight into ALL progression and suggests that the BCR/C/EBPβ pathway can be a therapeutic target.
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Affiliation(s)
- Morito Kurata
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Iichiro Onishi
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoko Takahara
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yukari Yamazaki
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryo Goitsuka
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Junko Takita
- Department of Pediatrics, Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Yasuhide Hayashi
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa, Japan
| | - David A Largaesapda
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuro Nakamura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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12
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Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress. Sci Rep 2021; 11:18808. [PMID: 34552146 PMCID: PMC8458439 DOI: 10.1038/s41598-021-98323-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence of new primate-specific genes is an essential factor in human and primate brain development and functioning. POU2F1/Oct-1 is a transcription regulator in higher eukaryotes which is involved in the regulation of development, differentiation, stress response, and other processes. We have demonstrated that the Tigger2 transposon insertion into the POU2F1 gene which occurred in the primate lineage led to the formation of an additional exon (designated the Z-exon). Z-exon-containing primate-specific Oct-1Z transcript includes a short upstream ORF (uORF) located at its 5’-end and the main ORF encoding the Oct-1Z protein isoform (Pou2F1 isoform 3, P14859-3), which differs from other Oct-1 isoforms by its N-terminal peptide. The Oct-1Z-encoding transcript is expressed mainly in human brain cortex. Under normal conditions, the translation of the ORF coding for the Oct-1Z isoform is repressed by uORF. Under various stress conditions, uORF enables a strong increase in the translation of the Oct-1Z-encoding ORF. Increased Oct-1Z expression levels in differentiating human neuroblasts activate genes controlling stress response, neural cell differentiation, brain formation, and organogenesis. We have shown that the Oct-1Z isoform of the POU2F1/Oct-1 transcription factor is an example of a primate-specific genomic element contributing to brain development and cellular stress defense.
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13
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Jürgens L, Manske F, Hubert E, Kischka T, Flötotto L, Klaas O, Shabardina V, Schliemann C, Makalowski W, Wethmar K. Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer. Biomedicines 2021; 9:biomedicines9060618. [PMID: 34072580 PMCID: PMC8227997 DOI: 10.3390/biomedicines9060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer.
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Affiliation(s)
- Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Felix Manske
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Elvira Hubert
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Tabea Kischka
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Lea Flötotto
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Oliver Klaas
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Victoria Shabardina
- Institute of Evolutionary Biology, CSIC-Unversitat Pompeu Frabra, 08002 Barcelona, Spain;
| | - Christoph Schliemann
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Klaus Wethmar
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
- Correspondence: ; Tel.: +49-251-8347587; Fax: +49-251-8347588
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14
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The transcription factor C/EBPβ orchestrates dendritic cell maturation and functionality under homeostatic and malignant conditions. Proc Natl Acad Sci U S A 2020; 117:26328-26339. [PMID: 33020261 DOI: 10.1073/pnas.2008883117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dendritic cell (DC) maturation is a prerequisite for the induction of adaptive immune responses against pathogens and cancer. Transcription factor (TF) networks control differential aspects of early DC progenitor versus late-stage DC cell fate decisions. Here, we identified the TF C/EBPβ as a key regulator for DC maturation and immunogenic functionality under homeostatic and lymphoma-transformed conditions. Upon cell-specific deletion of C/EBPβ in CD11c+MHCIIhi DCs, gene expression profiles of splenic C/EBPβ-/- DCs showed a down-regulation of E2F cell cycle target genes and associated proliferation signaling pathways, whereas maturation signatures were enriched. Total splenic DC cell numbers were modestly increased but differentiation into cDC1 and cDC2 subsets were unaltered. The splenic CD11c+MHCIIhiCD64+ DC compartment was also increased, suggesting that C/EBPβ deficiency favors the expansion of monocytic-derived DCs. Expression of C/EBPβ could be mimicked in LAP/LAP* isoform knockin DCs, whereas the short isoform LIP supported a differentiation program similar to deletion of the full-length TF. In accordance with E2F1 being a negative regulator of DC maturation, C/EBPβ-/- bone marrow-derived DCs matured much faster enabling them to activate and polarize T cells stronger. In contrast to a homeostatic condition, lymphoma-exposed DCs exhibited an up-regulation of the E2F transcriptional pathways and an impaired maturation. Pharmacological blockade of C/EBPβ/mTOR signaling in human DCs abrogated their protumorigenic function in primary B cell lymphoma cocultures. Thus, C/EBPβ plays a unique role in DC maturation and immunostimulatory functionality and emerges as a key factor of the tumor microenvironment that promotes lymphomagenesis.
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15
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Renz PF, Valdivia-Francia F, Sendoel A. Some like it translated: small ORFs in the 5'UTR. Exp Cell Res 2020; 396:112229. [PMID: 32818479 DOI: 10.1016/j.yexcr.2020.112229] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 01/06/2023]
Abstract
The 5' untranslated region (5'UTR) is critical in determining post-transcriptional control, which is partly mediated by short upstream open reading frames (uORFs) present in half of mammalian transcripts. uORFs are generally considered to provide functionally important repression of the main-ORF by engaging initiating ribosomes, but under specific environmental conditions such as cellular stress, uORFs can become essential to activate the translation of the main coding sequence. In addition, a growing number of uORF-encoded bioactive microproteins have been described, which have the potential to significantly increase cellular protein diversity. Here we review the diverse cellular contexts in which uORFs play a critical role and discuss the molecular mechanisms underlying their function and regulation. The progress over the last decades in dissecting uORF function suggests that the 5'UTR remains an exciting frontier towards understanding how the cellular proteome is shaped in health and disease.
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Affiliation(s)
- Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Switzerland
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland.
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16
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Spike AJ, Rosen JM. C/EBPß Isoform Specific Gene Regulation: It's a Lot more Complicated than you Think! J Mammary Gland Biol Neoplasia 2020; 25:1-12. [PMID: 32078094 PMCID: PMC7694698 DOI: 10.1007/s10911-020-09444-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/06/2020] [Indexed: 11/29/2022] Open
Abstract
It has been almost 30 years since C/EBPß was discovered. Seminal studies have shown that C/EBPß is a master regulator of mammary gland development and has been shown to control and influence proliferation and differentiation through varying mechanisms. The single-exon C/EBPß mRNA yields at least three different protein isoforms which have diverse, specific, context-dependent, and often non-overlapping roles throughout development and breast cancer progression. These roles are dictated by a number of complex factors including: expression levels of other C/EBP family members and their stoichiometry relative to the isoform in question, binding site affinity, post-translational modifications, co-factor expression, and even hormone levels and lactogenic status. Here we summarize the historical work up to the latest findings in the field on C/EBPß in the mammary gland and in breast cancer. With the current emphasis on improving immunotherapy in breast cancer the role of specific C/EBPß isoforms in regulating specific chemokine and cytokine expression and the immune microenvironment will be of increasing interest.
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Affiliation(s)
- Aaron J Spike
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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17
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Jaud M, Philippe C, Di Bella D, Tang W, Pyronnet S, Laurell H, Mazzolini L, Rouault-Pierre K, Touriol C. Translational Regulations in Response to Endoplasmic Reticulum Stress in Cancers. Cells 2020; 9:cells9030540. [PMID: 32111004 PMCID: PMC7140484 DOI: 10.3390/cells9030540] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
During carcinogenesis, almost all the biological processes are modified in one way or another. Among these biological processes affected, anomalies in protein synthesis are common in cancers. Indeed, cancer cells are subjected to a wide range of stresses, which include physical injuries, hypoxia, nutrient starvation, as well as mitotic, oxidative or genotoxic stresses. All of these stresses will cause the accumulation of unfolded proteins in the Endoplasmic Reticulum (ER), which is a major organelle that is involved in protein synthesis, preservation of cellular homeostasis, and adaptation to unfavourable environment. The accumulation of unfolded proteins in the endoplasmic reticulum causes stress triggering an unfolded protein response in order to promote cell survival or to induce apoptosis in case of chronic stress. Transcription and also translational reprogramming are tightly controlled during the unfolded protein response to ensure selective gene expression. The majority of stresses, including ER stress, induce firstly a decrease in global protein synthesis accompanied by the induction of alternative mechanisms for initiating the translation of mRNA, later followed by a translational recovery. After a presentation of ER stress and the UPR response, we will briefly present the different modes of translation initiation, then address the specific translational regulatory mechanisms acting during reticulum stress in cancers and highlight the importance of translational control by ER stress in tumours.
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Affiliation(s)
- Manon Jaud
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Weiwei Tang
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Henrik Laurell
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Inserm UMR1048, I2MC (Institut des Maladies Métaboliques et Cardiovasculaires), BP 84225, CEDEX 04, 31 432 Toulouse, France
| | - Laurent Mazzolini
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Christian Touriol
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Correspondence:
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18
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Salotti J, Johnson PF. Regulation of senescence and the SASP by the transcription factor C/EBPβ. Exp Gerontol 2019; 128:110752. [PMID: 31648009 DOI: 10.1016/j.exger.2019.110752] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022]
Abstract
Oncogene-induced senescence (OIS) serves as an important barrier to tumor progression in cells that have acquired activating mutations in RAS and other oncogenes. Senescent cells also produce a secretome known as the senescence-associated secretory phenotype (SASP) that includes pro-inflammatory cytokines and chemokines. SASP factors reinforce and propagate the senescence program and identify senescent cells to the immune system for clearance. The OIS program is executed by several transcriptional effectors that include p53, RB, NF-κB and C/EBPβ. In this review, we summarize the critical role of C/EBPβ in regulating OIS and the SASP. Post-translational modifications induced by oncogenic RAS signaling control C/EBPβ activity and dimerization, and these alterations switch C/EBPβ to a pro-senescence form during OIS. In addition, C/EBPβ is regulated by a unique 3'UTR-mediated mechanism that restrains its activity in tumor cells to facilitate senescence bypass and suppression of the SASP.
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Affiliation(s)
- Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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19
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Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
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Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
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20
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Li F, Wen J, Shi J, Wang Y, Yang F, Liu C. MicroRNA-191 targets CCAAT/enhanced binding protein β and functions as an oncogenic molecule in human non-small cell lung carcinoma cells. Exp Ther Med 2019; 18:1175-1183. [PMID: 31316611 PMCID: PMC6601399 DOI: 10.3892/etm.2019.7668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 10/26/2018] [Indexed: 12/24/2022] Open
Abstract
The aberrant expression of microRNAs (miRs) may be involved in tumor growth and progression in human non-small cell lung carcinoma (NSCLC). The present study aimed to investigate the potential roles of miR-191 in NSCLC. Western blotting and reverse transcription-quantitative polymerase chain reaction were performed to assess protein and/or mRNA levels. Scratch wound healing and transwell assays were performed to determine the NSCLC cell migration and invasion. A luciferase demonstrated that CCAAT/enhanced binding protein β (C/EBPβ) was a target of miR-191. Previously, miR-191 has been reported to act as an oncogenic player in multiple human cancers. C/EBPβ has been identified as a target gene of miR-191; however, the roles and underlying mechanisms of miR-191 associated with the regulation of tumor invasion in NSCLC remain unknown. In the present study, it was demonstrated that miR-191 expression levels were higher in human NSCLC tumors compared with in normal adjacent tissue and elevated miR-191 expression levels were closely associated with tumor node metastasis stage in patients with NSCLC. Furthermore, transfection with miR-191 mimic inhibited C/EBPβ expression at the mRNA and protein levels and promoted A549 cell migration and invasion. C/EBPβ was reported to be the direct target gene of miR-191 using a dual luciferase reporter assay. Finally, C/EBPβ siRNA can mimic the effects of miR-191. These findings indicated that miR-191 may function as an oncogene in NSCLC, at least partially due to its negative regulatory on C/EBPβ.
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Affiliation(s)
- Fuliang Li
- Department of Pathology, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Jingjing Wen
- Department of Pathology, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
| | - Jinsheng Shi
- Department of Pathology, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
| | - Yun Wang
- Department of Pathology, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Feifei Yang
- Department of Pathology, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Chunying Liu
- Department of B-ultrasound, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
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21
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Dumesic PA, Egan DF, Gut P, Tran MT, Parisi A, Chatterjee N, Jedrychowski M, Paschini M, Kazak L, Wilensky SE, Dou F, Bogoslavski D, Cartier JA, Perrimon N, Kajimura S, Parikh SM, Spiegelman BM. An Evolutionarily Conserved uORF Regulates PGC1α and Oxidative Metabolism in Mice, Flies, and Bluefin Tuna. Cell Metab 2019; 30:190-200.e6. [PMID: 31105043 PMCID: PMC6620024 DOI: 10.1016/j.cmet.2019.04.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/25/2019] [Accepted: 04/21/2019] [Indexed: 12/29/2022]
Abstract
Mitochondrial abundance and function are tightly controlled during metabolic adaptation but dysregulated in pathological states such as diabetes, neurodegeneration, cancer, and kidney disease. We show here that translation of PGC1α, a key governor of mitochondrial biogenesis and oxidative metabolism, is negatively regulated by an upstream open reading frame (uORF) in the 5' untranslated region of its gene (PPARGC1A). We find that uORF-mediated translational repression is a feature of PPARGC1A orthologs from human to fly. Strikingly, whereas multiple inhibitory uORFs are broadly present in fish PPARGC1A orthologs, they are completely absent in the Atlantic bluefin tuna, an animal with exceptionally high mitochondrial content. In mice, an engineered mutation disrupting the PPARGC1A uORF increases PGC1α protein levels and oxidative metabolism and confers protection from acute kidney injury. These studies identify a translational regulatory element governing oxidative metabolism and highlight its potential contribution to the evolution of organismal mitochondrial function.
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Affiliation(s)
- Phillip A Dumesic
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Daniel F Egan
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Philipp Gut
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Mei T Tran
- Division of Nephrology and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Alice Parisi
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Nirmalya Chatterjee
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mark Jedrychowski
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | | | - Lawrence Kazak
- Goodman Cancer Research Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Florence Dou
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | | | - Norbert Perrimon
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Shingo Kajimura
- Diabetes Center and Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | - Samir M Parikh
- Division of Nephrology and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Bruce M Spiegelman
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA.
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22
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Chen HH, Tarn WY. uORF-mediated translational control: recently elucidated mechanisms and implications in cancer. RNA Biol 2019; 16:1327-1338. [PMID: 31234713 DOI: 10.1080/15476286.2019.1632634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is tightly regulated, and its dysregulation can contribute to the pathology of various diseases, including cancer. Increased or selective translation of mRNAs can promote cancer cell proliferation, metastasis and tumor expansion. Translational control is one of the most important means for cells to quickly adapt to environmental stresses. Adaptive translation involves various alternative mechanisms of translation initiation. Upstream open reading frames (uORFs) serve as a major regulator of stress-responsive translational control. Since recent advances in omics technologies including ribo-seq have expanded our knowledge of translation, we discuss emerging mechanisms for uORF-mediated translation regulation and its impact on cancer cell biology. A better understanding of dysregulated translational control of uORFs in cancer would facilitate the development of new strategies for cancer therapy.
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Affiliation(s)
- Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
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23
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Ackermann T, Hartleben G, Müller C, Mastrobuoni G, Groth M, Sterken BA, Zaini MA, Youssef SA, Zuidhof HR, Krauss SR, Kortman G, de Haan G, de Bruin A, Wang ZQ, Platzer M, Kempa S, Calkhoven CF. C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice. Commun Biol 2019; 2:208. [PMID: 31240246 PMCID: PMC6572810 DOI: 10.1038/s42003-019-0461-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
The transcription factors LAP1, LAP2 and LIP are derived from the Cebpb-mRNA through the use of alternative start codons. High LIP expression has been associated with human cancer and increased cancer incidence in mice. However, how LIP contributes to cellular transformation is poorly understood. Here we present that LIP induces aerobic glycolysis and mitochondrial respiration reminiscent of cancer metabolism. We show that LIP-induced metabolic programming is dependent on the RNA-binding protein LIN28B, a translational regulator of glycolytic and mitochondrial enzymes with known oncogenic function. LIP activates LIN28B through repression of the let-7 microRNA family that targets the Lin28b-mRNA. Transgenic mice overexpressing LIP have reduced levels of let-7 and increased LIN28B expression, which is associated with metabolic reprogramming as shown in primary bone marrow cells, and with hyperplasia in the skin. This study establishes LIP as an inducer of cancer-type metabolic reprogramming and as a regulator of the let-7/LIN28B regulatory circuit.
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Affiliation(s)
- Tobias Ackermann
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Götz Hartleben
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Christine Müller
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | | | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Britt A. Sterken
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Mohamad A. Zaini
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Sameh A. Youssef
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, NL-3584 CL Utrecht, the Netherlands
| | - Hidde R. Zuidhof
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Sara R. Krauss
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Gertrud Kortman
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Gerald de Haan
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Alain de Bruin
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, NL-3584 CL Utrecht, the Netherlands
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine, D-13092 Berlin, Germany
| | - Cornelis F. Calkhoven
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, The Netherlands
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24
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Silva J, Fernandes R, Romão L. Translational Regulation by Upstream Open Reading Frames and Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:99-116. [DOI: 10.1007/978-3-030-19966-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Wang W, Do HN, Aupperlee MD, Durairaj S, Flynn EE, Miksicek RJ, Haslam SZ, Schwartz RC. C/EBPβ LIP and c-Jun synergize to regulate expression of the murine progesterone receptor. Mol Cell Endocrinol 2018; 477:57-69. [PMID: 29870755 PMCID: PMC6153074 DOI: 10.1016/j.mce.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/11/2023]
Abstract
CCAAT/enhancer binding protein β (C/EBPβ) is required for murine mammary ductal morphogenesis and alveologenesis. Progesterone is critical for proliferation and alveologenesis in adult mammary glands, and there is a similar requirement for progesterone receptor isoform B (PRB) in alveologenesis. We examined C/EBPβ regulation of PR expression. All three C/EBPβ isoforms, including typically inhibitory LIP, transactivated the PR promoter. LIP, particularly, strongly synergized with c-Jun to drive PR transcription. Endogenous C/EBPβ and c-Jun stimulated a PR promoter-reporter and these two factors showed promoter occupancy on the endogenous PR gene. Additionally, LIP overexpression elevated endogenous PR protein expression. In pregnancy, both PRB and the relative abundance of LIP among C/EBPβ isoforms increase. Consistent with a role in PRB expression, in vivo C/EBPβ and PR isoform A expression showed mutually exclusive localization in mammary epithelium, while C/EBPβ and PRB largely co-localized. We suggest a critical role for C/EBPβ, particularly LIP, in PRB expression.
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Affiliation(s)
- Weizhong Wang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Han Ngoc Do
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Mark D Aupperlee
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA; Breast Cancer and the Environment Research Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Srinivasan Durairaj
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily E Flynn
- Genetics Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard J Miksicek
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Sandra Z Haslam
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA; Breast Cancer and the Environment Research Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard C Schwartz
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA; Breast Cancer and the Environment Research Program, Michigan State University, East Lansing, MI, 48824, USA.
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26
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Müller C, Zidek LM, Ackermann T, de Jong T, Liu P, Kliche V, Zaini MA, Kortman G, Harkema L, Verbeek DS, Tuckermann JP, von Maltzahn J, de Bruin A, Guryev V, Wang ZQ, Calkhoven CF. Reduced expression of C/EBPβ-LIP extends health and lifespan in mice. eLife 2018; 7:34985. [PMID: 29708496 PMCID: PMC5986274 DOI: 10.7554/elife.34985] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Ageing is associated with physical decline and the development of age-related diseases such as metabolic disorders and cancer. Few conditions are known that attenuate the adverse effects of ageing, including calorie restriction (CR) and reduced signalling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. Synthesis of the metabolic transcription factor C/EBPβ-LIP is stimulated by mTORC1, which critically depends on a short upstream open reading frame (uORF) in the Cebpb-mRNA. Here, we describe that reduced C/EBPβ-LIP expression due to genetic ablation of the uORF delays the development of age-associated phenotypes in mice. Moreover, female C/EBPβΔuORF mice display an extended lifespan. Since LIP levels increase upon aging in wild type mice, our data reveal an important role for C/EBPβ in the aging process and suggest that restriction of LIP expression sustains health and fitness. Thus, therapeutic strategies targeting C/EBPβ-LIP may offer new possibilities to treat age-related diseases and to prolong healthspan. The risks of major diseases including type II diabetes, cancer and Alzheimer’s are linked to the biological process of ageing. By finding ways to slow ageing, we can help more people to live longer healthier lives while avoiding these illnesses. Placing some animals on a diet that contains only two-thirds as many calories as they would normally eat can improve their fitness during old age and delay the onset of many age-related problems. It is unrealistic to expect people to control their diet to this extent, yet there may be other ways to bring about the same effects. Calorie restriction affects the activity of many different genes; for example, it causes a gene that produces a protein known as Liver-enriched Inhibitory Protein (LIP for short) to shut down. LIP controls the activity of many genes involved in metabolism, so it could be a key target for drugs to control ageing. Müller, Zidek et al. used mice that are unable to produce LIP to study this protein’s effect on ageing. The life expectancy of female mice lacking LIP increased by up to 20%. These mice were leaner, fitter, more resistant to cancer, had stronger immune systems and controlled their blood sugar levels better than normal mice. Male mice that lacked LIP did not live longer but did experience some ageing-related benefits. Genetic analysis also showed that gene activity particularly of metabolic genes is more robust in old female LIP-deficient mice and thus more similar to young control mice than old control mice. The results presented by Müller, Zidek et al. suggest that targeting the activity of the LIP gene could help to slow the ageing process. It is not yet clear whether shutting off LIP has similar beneficial effects in humans. Further research is also needed to investigate why female mice gain more benefits from a lack of LIP than males do.
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Affiliation(s)
- Christine Müller
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Laura M Zidek
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Tobias Ackermann
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Tristan de Jong
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Peng Liu
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Verena Kliche
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Mohamad Amr Zaini
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Gertrud Kortman
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Liesbeth Harkema
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jan P Tuckermann
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | | | - Alain de Bruin
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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27
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Bégay V, Baumeier C, Zimmermann K, Heuser A, Leutz A. The C/EBPβ LIP isoform rescues loss of C/EBPβ function in the mouse. Sci Rep 2018; 8:8417. [PMID: 29849099 PMCID: PMC5976626 DOI: 10.1038/s41598-018-26579-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/22/2018] [Indexed: 12/26/2022] Open
Abstract
The transcription factor C/EBPβ regulates hematopoiesis, bone, liver, fat, and skin homeostasis, and female reproduction. C/EBPβ protein expression from its single transcript occurs by alternative in-frame translation initiation at consecutive start sites to generate three isoforms, two long (LAP*, LAP) and one truncated (LIP), with the same C-terminal bZip dimerization domain. The long C/EBPβ isoforms are considered gene activators, whereas the LIP isoform reportedly acts as a dominant-negative repressor. Here, we tested the putative repressor functions of the C/EBPβ LIP isoform in mice by comparing monoallelic WT or LIP knockin mice with Cebpb knockout mice, in combination with monoallelic Cebpa mice. The C/EBPβ LIP isoform was sufficient to function in coordination with C/EBPα in murine development, adipose tissue and sebocyte differentiation, and female fertility. Thus, the C/EBPβ LIP isoform likely has more physiological functions than its currently known role as a dominant-negative inhibitor, which are more complex than anticipated.
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Affiliation(s)
- Valérie Bégay
- Tumorigenesis and Cell Differentiation, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany. .,Molecular Physiology of Somatic Sensation, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany.
| | - Christian Baumeier
- Tumorigenesis and Cell Differentiation, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany.,Department of experimental Diabetology (DIAB), German Institute of Human Nutrition Potsdam-Rehbruecke (DifE), 14558, Nuthetal, Germany, German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Karin Zimmermann
- Tumorigenesis and Cell Differentiation, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany
| | - Arnd Heuser
- Pathophysiology Group, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany
| | - Achim Leutz
- Tumorigenesis and Cell Differentiation, Max Delbrueck Center for Molecular Medicine, Berlin, 13125, Berlin, Germany. .,Humboldt-University, Berlin, Institute of Biology, 10115, Berlin, Germany.
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28
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Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
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Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
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29
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Mildner A, Schönheit J, Giladi A, David E, Lara-Astiaso D, Lorenzo-Vivas E, Paul F, Chappell-Maor L, Priller J, Leutz A, Amit I, Jung S. Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C − Cells. Immunity 2017; 46:849-862.e7. [DOI: 10.1016/j.immuni.2017.04.018] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/22/2017] [Accepted: 04/26/2017] [Indexed: 12/11/2022]
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30
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A screening strategy for the discovery of drugs that reduce C/EBPβ-LIP translation with potential calorie restriction mimetic properties. Sci Rep 2017; 7:42603. [PMID: 28198412 PMCID: PMC5309760 DOI: 10.1038/srep42603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
An important part of the beneficial effects of calorie restriction (CR) on healthspan and lifespan is mediated through regulation of protein synthesis that is under control of the mechanistic target of rapamycin complex 1 (mTORC1). As one of its activities, mTORC1 stimulates translation into the metabolic transcription factor CCAAT/Enhancer Binding Protein β (C/EBPβ) isoform Liver-specific Inhibitory Protein (LIP). Regulation of LIP expression strictly depends on a translation re-initiation event that requires a conserved cis-regulatory upstream open reading frame (uORF) in the C/EBPβ-mRNA. We showed before that suppression of LIP in mice, reflecting reduced mTORC1-signaling at the C/EBPβ level, results in CR-type of metabolic improvements. Hence, we aim to find possibilities to pharmacologically down-regulate LIP in order to induce CR-mimetic effects. We engineered a luciferase-based cellular reporter system that acts as a surrogate for C/EBPβ-mRNA translation, emulating uORF-dependent C/EBPβ-LIP expression under different translational conditions. By using the reporter system in a high-throughput screening (HTS) strategy we identified drugs that reduce LIP. The drug Adefovir Dipivoxil passed all counter assays and increases fatty acid β-oxidation in a hepatoma cell line in a LIP-dependent manner. Therefore, these drugs that suppress translation into LIP potentially exhibit CR-mimetic properties.
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31
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Curran JA, Weiss B. What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? Front Genet 2016; 7:156. [PMID: 27630668 PMCID: PMC5005323 DOI: 10.3389/fgene.2016.00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
A major determinant in the efficiency of ribosome loading onto mRNAs is the 5′ TL (transcript leader or 5′ UTR). In addition, elements within this region also impact on start site selection demonstrating that it can modulate the protein readout at both quantitative and qualitative levels. With the increasing wealth of data generated by the mining of the mammalian transcriptome, it has become evident that a genes 5′ TL is not homogeneous but actually exhibits significant heterogeneity. This arises due to the utilization of alternative promoters, and is further compounded by significant variability with regards to the precise transcriptional start sites of each (not to mention alternative splicing). Consequently, the transcript for a protein coding gene is not a unique mRNA, but in-fact a complexed quasi-species of variants whose composition may respond to the changing physiological environment of the cell. Here we examine the potential impact of these events with regards to the protein readout.
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Affiliation(s)
- Joseph A Curran
- Department of Microbiology and Molecular Medicine, Medical School, University of GenevaGeneva, Switzerland; Institute of Genetics and Genomics of Geneva, University of GenevaGeneva, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Medical School, University of Geneva Geneva, Switzerland
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32
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Young SK, Wek RC. Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response. J Biol Chem 2016; 291:16927-35. [PMID: 27358398 DOI: 10.1074/jbc.r116.733899] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translation regulation largely occurs during initiation, which features ribosome assembly onto mRNAs and selection of the translation start site. Short, upstream ORFs (uORFs) located in the 5'-leader of the mRNA can be selected for translation. Multiple transcripts associated with stress amelioration are preferentially translated through uORF-mediated mechanisms during activation of the integrated stress response (ISR) in which phosphorylation of the α subunit of eIF2 results in a coincident global reduction in translation initiation. This review presents key features of uORFs that serve to optimize translational control that is essential for regulation of cell fate in response to environmental stresses.
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Affiliation(s)
- Sara K Young
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Ronald C Wek
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
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33
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Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5'-untranslated regions of eukaryotic mRNAs. Science 2016; 352:1413-6. [PMID: 27313038 DOI: 10.1126/science.aad9868] [Citation(s) in RCA: 651] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eukaryotic 5' untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. The ribosomal initiation complex is assembled on the mRNA via a cap-dependent or cap-independent mechanism. We describe various mechanisms controlling ribosome scanning and initiation codon selection by 5' upstream open reading frames, translation initiation factors, and primary and secondary structures of the 5'UTR, including particular sequence motifs. We also discuss translational control via phosphorylation of eukaryotic initiation factor 2, which is implicated in learning and memory, neurodegenerative diseases, and cancer.
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Affiliation(s)
- Alan G Hinnebusch
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.
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34
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Kowenz-Leutz E, Schuetz A, Liu Q, Knoblich M, Heinemann U, Leutz A. Functional interaction of CCAAT/enhancer-binding-protein-α basic region mutants with E2F transcription factors and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:841-7. [PMID: 27131901 DOI: 10.1016/j.bbagrm.2016.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 11/28/2022]
Abstract
The transcription factor CCAAT/enhancer-binding protein α (C/EBPα) regulates cell cycle arrest and terminal differentiation of neutrophils and adipocytes. Mutations in the basic leucine zipper domain (bZip) of C/EBPα are associated with acute myeloid leukemia. A widely used murine transforming C/EBPα basic region mutant (BRM2) entails two bZip point mutations (I294A/R297A). BRM2 has been discordantly described as defective for DNA binding or defective for interaction with E2F. We have separated the two BRM2 mutations to shed light on the intertwined reciprocity between C/EBPα-E2F-DNA interactions. Both, C/EBPα I294A and R297A retain transactivation capacity and interaction with E2F-DP. The C/EBPα R297A mutation destabilized DNA binding, whereas the C/EBPα I294A mutation enhanced binding to DNA. The C/EBPα R297A mutant, like BRM2, displayed enhanced interaction with E2F-DP but failed to repress E2F-dependent transactivation although both mutants were readily suppressed by E2F1 for transcription through C/EBP cis-regulatory sites. In contrast, the DNA binding enhanced C/EBPα I294A mutant displayed increased repression of E2F-DP mediated transactivation and resisted E2F-DP mediated repression. Thus, the efficient repression of E2F dependent S-phase genes and the activation of differentiation genes reside in the balanced DNA binding capacity of C/EBPα.
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Affiliation(s)
- Elisabeth Kowenz-Leutz
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anja Schuetz
- Protein Sample Production Facility, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Qingbin Liu
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Maria Knoblich
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Udo Heinemann
- Protein Sample Production Facility, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Chemistry and Biochemistry Institute, Freie Universität Berlin, Berlin, Germany
| | - Achim Leutz
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany.
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35
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Abstract
The past several years have seen dramatic leaps in our understanding of how gene expression is rewired at the translation level during tumorigenesis to support the transformed phenotype. This work has been driven by an explosion in technological advances and is revealing previously unimagined regulatory mechanisms that dictate functional expression of the cancer genome. In this Review we discuss emerging trends and exciting new discoveries that reveal how this translational circuitry contributes to specific aspects of tumorigenesis and cancer cell function, with a particular focus on recent insights into the role of translational control in the adaptive response to oncogenic stress conditions.
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Affiliation(s)
- Morgan L Truitt
- Department of Urology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
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In K, Zaini MA, Müller C, Warren AJ, von Lindern M, Calkhoven CF. Shwachman-Bodian-Diamond syndrome (SBDS) protein deficiency impairs translation re-initiation from C/EBPα and C/EBPβ mRNAs. Nucleic Acids Res 2016; 44:4134-46. [PMID: 26762974 PMCID: PMC4872075 DOI: 10.1093/nar/gkw005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/31/2015] [Indexed: 01/24/2023] Open
Abstract
Mutations in the Shwachman–Bodian–Diamond Syndrome (SBDS) gene cause Shwachman–Diamond Syndrome (SDS), a rare congenital disease characterized by bone marrow failure with neutropenia, exocrine pancreatic dysfunction and skeletal abnormalities. The SBDS protein is important for ribosome maturation and therefore SDS belongs to the ribosomopathies. It is unknown, however, if loss of SBDS functionality affects the translation of specific mRNAs and whether this could play a role in the development of the clinical features of SDS. Here, we report that translation of the C/EBPα and -β mRNAs, that are indispensible regulators of granulocytic differentiation, is altered by SBDS mutations or knockdown. We show that SBDS function is specifically required for efficient translation re-initiation into the protein isoforms C/EBPα-p30 and C/EBPβ-LIP, which is controlled by a single cis-regulatory upstream open reading frame (uORF) in the 5′ untranslated regions (5′ UTRs) of both mRNAs. Furthermore, we show that as a consequence of the C/EBPα and -β deregulation the expression of MYC is decreased with associated reduction in proliferation, suggesting that failure of progenitor proliferation contributes to the haematological phenotype of SDS. Therefore, our study provides the first indication that disturbance of specific translation by loss of SBDS function may contribute to the development of the SDS phenotype.
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Affiliation(s)
- Kyungmin In
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Mohamad A Zaini
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany European Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD, Groningen, The Netherlands
| | - Christine Müller
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany European Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD, Groningen, The Netherlands
| | - Alan J Warren
- Cambridge Institute for Medical Research, Wellcome Trust-Medical Research Council Stem Cell Institute, the Department of Haematology, University of Cambridge, CB2 0XY, Cambridge, UK
| | - Marieke von Lindern
- Sanquin Research and Landsteiner Laboratory, Department of Hematopoiesis, 1066 CX Amsterdam, The Netherlands
| | - Cornelis F Calkhoven
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany European Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD, Groningen, The Netherlands
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Dieudonné FX, O'Connor PBF, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J. The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics 2015; 16:986. [PMID: 26589636 PMCID: PMC4654819 DOI: 10.1186/s12864-015-2179-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell's protein composition. Since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. However, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mRNA population (the translatome). This is particularly pertinent for genes using multiple transcriptional start sites (TSS) generating mRNAs with heterogeneous 5' transcript leaders (5'TL). Furthermore, the relative abundance of the TSS gene variants is frequently cell-type specific. Indeed, promoter switches have been reported in pathologies such as cancer. The consequences of this 5'TL heterogeneity within the transcriptome for the translatome remain unresolved. This is not a moot point because the 5'TL plays a key role in regulating mRNA recruitment onto polysomes. RESULTS In this article, we have characterised both the transcriptome and translatome of the MCF7 (tumoural) and MCF10A (non-tumoural) cell lines. We identified ~550 genes exhibiting differential translation efficiency (TE). In itself, this is maybe not surprising. However, by focusing on genes exhibiting TSS heterogeneity we observed distinct differential promoter usage patterns in both the transcriptome and translatome. Only a minor fraction of these genes belonged to those exhibiting differential TE. Nonetheless, reporter assays demonstrated that the TSS variants impacted on the translational readout both quantitatively (the overall amount of protein expressed) and qualitatively (the nature of the proteins expressed). CONCLUSIONS The results point to considerable and distinct cell-specific 5'TL heterogeneity within both the transcriptome and translatome of the two cell lines analysed. This observation is in-line with the ribosome filter hypothesis which posits that the ribosomal machine can selectively filter information from within the transcriptome. As such it cautions against the simple extrapolation transcriptome → proteome. Furthermore, polysomal occupancy of specific gene 5'TL variants may also serve as novel disease biomarkers.
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Affiliation(s)
- Francois-Xavier Dieudonné
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | | | - Pascale Gubler-Jaquier
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Haleh Yasrebi
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Beatrice Conne
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Sergey Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Stylianos Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Joseph Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland. .,The Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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Shi Z, Barna M. Translating the genome in time and space: specialized ribosomes, RNA regulons, and RNA-binding proteins. Annu Rev Cell Dev Biol 2015; 31:31-54. [PMID: 26443190 DOI: 10.1146/annurev-cellbio-100814-125346] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A central question in cell and developmental biology is how the information encoded in the genome is differentially interpreted to generate a diverse array of cell types. A growing body of research on posttranscriptional gene regulation is revealing that both global protein synthesis rates and the translation of specific mRNAs are highly specialized in different cell types. How this exquisite translational regulation is achieved is the focus of this review. Two levels of regulation are discussed: the translation machinery and cis-acting elements within mRNAs. Recent evidence shows that the ribosome itself directs how the genome is translated in time and space and reveals surprising functional specificity in individual components of the core translation machinery. We are also just beginning to appreciate the rich regulatory information embedded in the untranslated regions of mRNAs, which direct the selective translation of transcripts. These hidden RNA regulons may interface with a myriad of RNA-binding proteins and specialized translation machinery to provide an additional layer of regulation to how transcripts are spatiotemporally expressed. Understanding this largely unexplored world of translational codes hardwired in the core translation machinery is an exciting new research frontier fundamental to our understanding of gene regulation, organismal development, and evolution.
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Affiliation(s)
- Zhen Shi
- Department of Developmental Biology and Department of Genetics, Stanford University, Stanford, California 94305;
| | - Maria Barna
- Department of Developmental Biology and Department of Genetics, Stanford University, Stanford, California 94305;
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40
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Legrand N, Jaquier-Gubler P, Curran J. The impact of the phosphomimetic eIF2αS/D on global translation, reinitiation and the integrated stress response is attenuated in N2a cells. Nucleic Acids Res 2015; 43:8392-404. [PMID: 26264663 PMCID: PMC4787802 DOI: 10.1093/nar/gkv827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022] Open
Abstract
A plethora of stresses trigger a rapid downregulation of protein synthesis. However, a fraction of mRNAs continue to be recruited onto polysomes and their protein products play a key role in deciding cell fate. These transcripts are characterized by the presence of uORFs within their 5' TL coupling protein expression to reinitiation. The translational brake arises due to the activation of a family of kinases targeting the α subunit of the trimolecular eIF2(αβγ) initiation factor. Phosphorylation of eIF2αSer51 inhibits ternary complex regeneration reducing the pool of 43S ribosomes. It is popular to mimic this event, and hence the integrated stress response (ISR), by the expression of the phosphomimetic eIF2αS51D. However, we report that whereas the ISR is reproduced by eIF2αS51D expression in human HEK293T cells this is not the case in N2a mouse neuroblastoma cells. With regards to translational downregulation, this arises due to the failure of the phosphomimetic protein to assemble an eIF2 complex with endogenous eIF2β/γ. This can be compensated for by the transient co-expression of all three subunits. Curiously, these conditions do not modulate reinitiation and consequently fail to trigger the ISR. This is the first demonstration that the inhibitory and reinitiation functions of eIF2αS/D can be separated.
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Affiliation(s)
- Noemie Legrand
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland
| | - Pascale Jaquier-Gubler
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland
| | - Joseph Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
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41
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Pulido-Salgado M, Vidal-Taboada JM, Saura J. C/EBPβ and C/EBPδ transcription factors: Basic biology and roles in the CNS. Prog Neurobiol 2015; 132:1-33. [PMID: 26143335 DOI: 10.1016/j.pneurobio.2015.06.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/08/2015] [Accepted: 06/16/2015] [Indexed: 02/01/2023]
Abstract
CCAAT/enhancer binding protein (C/EBP) β and C/EBPδ are transcription factors of the basic-leucine zipper class which share phylogenetic, structural and functional features. In this review we first describe in depth their basic molecular biology which includes fascinating aspects such as the regulated use of alternative initiation codons in the C/EBPβ mRNA. The physical interactions with multiple transcription factors which greatly opens the number of potentially regulated genes or the presence of at least five different types of post-translational modifications are also remarkable molecular mechanisms that modulate C/EBPβ and C/EBPδ function. In the second part, we review the present knowledge on the localization, expression changes and physiological roles of C/EBPβ and C/EBPδ in neurons, astrocytes and microglia. We conclude that C/EBPβ and C/EBPδ share two unique features related to their role in the CNS: whereas in neurons they participate in memory formation and synaptic plasticity, in glial cells they regulate the pro-inflammatory program. Because of their role in neuroinflammation, C/EBPβ and C/EBPδ in microglia are potential targets for treatment of neurodegenerative disorders. Any strategy to reduce C/EBPβ and C/EBPδ activity in neuroinflammation needs to take into account its potential side-effects in neurons. Therefore, cell-specific treatments will be required for the successful application of this strategy.
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Affiliation(s)
- Marta Pulido-Salgado
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain
| | - Jose M Vidal-Taboada
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain
| | - Josep Saura
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain.
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42
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Albert V, Hall MN. Reduced C/EBPβ-LIP translation improves metabolic health. EMBO Rep 2015; 16:881-2. [PMID: 26113367 DOI: 10.15252/embr.201540757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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43
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Zidek LM, Ackermann T, Hartleben G, Eichwald S, Kortman G, Kiehntopf M, Leutz A, Sonenberg N, Wang ZQ, von Maltzahn J, Müller C, Calkhoven CF. Deficiency in mTORC1-controlled C/EBPβ-mRNA translation improves metabolic health in mice. EMBO Rep 2015; 16:1022-36. [PMID: 26113365 PMCID: PMC4552494 DOI: 10.15252/embr.201439837] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/21/2015] [Indexed: 01/17/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is a central regulator of physiological adaptations in response to changes in nutrient supply. Major downstream targets of mTORC1 signalling are the mRNA translation regulators p70 ribosomal protein S6 kinase 1 (S6K1p70) and the 4E-binding proteins (4E-BPs). However, little is known about vertebrate mRNAs that are specifically controlled by mTORC1 signalling and are engaged in regulating mTORC1-associated physiology. Here, we show that translation of the CCAAT/enhancer binding protein beta (C/EBPβ) mRNA into the C/EBPβ-LIP isoform is suppressed in response to mTORC1 inhibition either through pharmacological treatment or through calorie restriction. Our data indicate that the function of 4E-BPs is required for suppression of LIP. Intriguingly, mice lacking the cis-regulatory upstream open reading frame (uORF) in the C/EBPβ-mRNA, which is required for mTORC1-stimulated translation into C/EBPβ-LIP, display an improved metabolic phenotype with features also found under calorie restriction. Thus, our data suggest that translational adjustment of C/EBPβ-isoform expression is one of the key processes that direct metabolic adaptation in response to changes in mTORC1 activity.
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Affiliation(s)
- Laura M Zidek
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Tobias Ackermann
- European Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Götz Hartleben
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany European Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sabrina Eichwald
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Gertrud Kortman
- European Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael Kiehntopf
- Department of Clinical Chemistry and Laboratory Diagnostics, University Hospital Jena, Jena, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nahum Sonenberg
- Department of Biochemistry & Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Zhao-Qi Wang
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Julia von Maltzahn
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Christine Müller
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany European Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cornelis F Calkhoven
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany European Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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44
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de Klerk E, Fokkema IFAC, Thiadens KAMH, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PAC. Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res 2015; 43:4408-28. [PMID: 25873627 PMCID: PMC4482065 DOI: 10.1093/nar/gkv281] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/21/2015] [Indexed: 01/08/2023] Open
Abstract
The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The contribution of regulation of mRNA translation during myogenesis has not been studied so far. We monitored translation during myogenic differentiation of C2C12 myoblasts, using a simplified protocol for ribosome footprint profiling. Comparison of ribosome footprints to total RNA showed that gene expression is mostly regulated at the transcriptional level. However, a subset of transcripts, enriched for mRNAs encoding for ribosomal proteins, was regulated at the level of translation. Enrichment was also found for specific pathways known to regulate muscle biology. We developed a dedicated pipeline to identify translation initiation sites (TISs) and discovered 5333 unannotated TISs, providing a catalog of upstream and alternative open reading frames used during myogenesis. We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE. Also these transcripts were enriched for ribosomal protein genes. This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis. Experimental protocols, analytical workflows, tools and data are available through public repositories (http://lumc.github.io/ribosome-profiling-analysis-framework/).
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Affiliation(s)
- Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Ivo F A C Fokkema
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Klaske A M H Thiadens
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands
| | - Jelle J Goeman
- Biostatistics, Department for Health Evidence, Radboud University Medical Center, Postzone 133, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
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45
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Abstract
Over the past decade, high-throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non-coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein-encoding mRNAs to potentially non-functional peptide-producing RNAs to non-coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela/ELABELA/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts.
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Affiliation(s)
- Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Eivind Valen
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Alexander F. Schier
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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46
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Bégay V, Smink JJ, Loddenkemper C, Zimmermann K, Rudolph C, Scheller M, Steinemann D, Leser U, Schlegelberger B, Stein H, Leutz A. Deregulation of the endogenous C/EBPβ LIP isoform predisposes to tumorigenesis. J Mol Med (Berl) 2014; 93:39-49. [PMID: 25401168 DOI: 10.1007/s00109-014-1215-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/17/2014] [Accepted: 10/17/2014] [Indexed: 12/25/2022]
Abstract
UNLABELLED Two long and one truncated isoforms (termed LAP*, LAP, and LIP, respectively) of the transcription factor CCAAT enhancer binding protein beta (C/EBPβ) are expressed from a single intronless Cebpb gene by alternative translation initiation. Isoform expression is sensitive to mammalian target of rapamycin (mTOR)-mediated activation of the translation initiation machinery and relayed through an upstream open reading frame (uORF) on the C/EBPβ mRNA. The truncated C/EBPβ LIP, initiated by high mTOR activity, has been implied in neoplasia, but it was never shown whether endogenous C/EBPβ LIP may function as an oncogene. In this study, we examined spontaneous tumor formation in C/EBPβ knockin mice that constitutively express only the C/EBPβ LIP isoform from its own locus. Our data show that deregulated C/EBPβ LIP predisposes to oncogenesis in many tissues. Gene expression profiling suggests that C/EBPβ LIP supports a pro-tumorigenic microenvironment, resistance to apoptosis, and alteration of cytokine/chemokine expression. The results imply that enhanced translation reinitiation of C/EBPβ LIP promotes tumorigenesis. Accordingly, pharmacological restriction of mTOR function might be a therapeutic option in tumorigenesis that involves enhanced expression of the truncated C/EBPβ LIP isoform. KEY MESSAGE Elevated C/EBPβ LIP promotes cancer in mice. C/EBPβ LIP is upregulated in B-NHL. Deregulated C/EBPβ LIP alters apoptosis and cytokine/chemokine networks. Deregulated C/EBPβ LIP may support a pro-tumorigenic microenvironment.
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Affiliation(s)
- Valérie Bégay
- Department of Tumorigenesis and Cell Differentiation, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Str.10, 13125, Berlin, Germany
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Perino A, Pols TWH, Nomura M, Stein S, Pellicciari R, Schoonjans K. TGR5 reduces macrophage migration through mTOR-induced C/EBPβ differential translation. J Clin Invest 2014; 124:5424-36. [PMID: 25365223 DOI: 10.1172/jci76289] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/30/2014] [Indexed: 02/06/2023] Open
Abstract
The bile acid-responsive G protein-coupled receptor TGR5 is involved in several metabolic processes, and recent studies suggest that TGR5 activation may promote pathways that are protective against diet-induced diabetes. Here, we investigated the role of macrophage-specific TGR5 signaling in protecting adipose tissue from inflammation and associated insulin resistance. Examination of adipose tissue from obese mice lacking macrophage Tgr5 revealed enhanced inflammation, increased chemokine expression, and higher macrophage numbers compared with control obese animals. Moreover, macrophage-specific deletion of Tgr5 exacerbated insulin resistance in obese animals. Conversely, pharmacological activation of TGR5 markedly decreased LPS-induced chemokine expression in primary macrophages. This reduction was mediated by AKT-dependent activation of mTOR complex 1, which in turn induced the differential translation of the dominant-negative C/EBPβ isoform, liver inhibitory protein (LIP). Overall, these studies reveal a signaling pathway downstream of TGR5 that modulates chemokine expression in response to high-fat diet and suggest that targeting this pathway has the potential to be therapeutically exploited for prevention of chronic inflammatory diseases and type 2 diabetes mellitus.
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Koch A, Gawron D, Steyaert S, Ndah E, Crappé J, De Keulenaer S, De Meester E, Ma M, Shen B, Gevaert K, Van Criekinge W, Van Damme P, Menschaert G. A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. Proteomics 2014; 14:2688-98. [PMID: 25156699 DOI: 10.1002/pmic.201400180] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/28/2014] [Accepted: 08/19/2014] [Indexed: 12/24/2022]
Abstract
Next-generation transcriptome sequencing is increasingly integrated with MS to enhance MS-based protein and peptide identification. Recently, a breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (ribo-seq). This technology is based on the deep sequencing of ribosome-protected mRNA fragments, thereby enabling the direct observation of in vivo protein synthesis at the transcript level. In order to explore the impact of a ribo-seq-derived protein sequence search space on MS/MS spectrum identification, we performed a comprehensive proteome study on a human cancer cell line, using both shotgun and N-terminal proteomics, next to ribosome profiling, which was used to delineate (alternative) translational reading frames. By including protein-level evidence of sample-specific genetic variation and alternative translation, this strategy improved the identification score of 69 proteins and identified 22 new proteins in the shotgun experiment. Furthermore, we discovered 18 new alternative translation start sites in the N-terminal proteomics data and observed a correlation between the quantitative measures of ribo-seq and shotgun proteomics with a Pearson correlation coefficient ranging from 0.483 to 0.664. Overall, this study demonstrated the benefits of ribosome profiling for MS-based protein and peptide identification and we believe this approach could develop into a common practice for next-generation proteomics.
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Affiliation(s)
- Alexander Koch
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Rehm A, Gätjen M, Gerlach K, Scholz F, Mensen A, Gloger M, Heinig K, Lamprecht B, Mathas S, Bégay V, Leutz A, Lipp M, Dörken B, Höpken UE. Dendritic cell-mediated survival signals in Eμ-Myc B-cell lymphoma depend on the transcription factor C/EBPβ. Nat Commun 2014; 5:5057. [PMID: 25266931 DOI: 10.1038/ncomms6057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/21/2014] [Indexed: 01/07/2023] Open
Abstract
The capacity of dendritic cells (DCs) to regulate tumour-specific adaptive immune responses depends on their proper differentiation and homing status. Whereas DC-associated tumour-promoting functions are linked to T-cell tolerance and formation of an inflammatory milieu, DC-mediated direct effects on tumour growth have remained unexplored. Here we show that deletion of DCs substantially delays progression of Myc-driven lymphomas. Lymphoma-exposed DCs upregulate immunomodulatory cytokines, growth factors and the CCAAT/enhancer-binding protein β (C/EBPβ). Moreover, Eμ-Myc lymphomas induce the preferential translation of the LAP/LAP* isoforms of C/EBPβ. C/EBPβ(-/-) DCs are unresponsive to lymphoma-associated cytokine changes and in contrast to wild-type DCs, they are unable to mediate enhanced Eμ-Myc lymphoma cell survival. Antigen-specific T-cell proliferation in lymphoma-bearing mice is impaired; however, this immune suppression is reverted by the DC-restricted deletion of C/EBPβ. Thus, we show that C/EBPβ-controlled DC functions are critical steps for the creation of a lymphoma growth-promoting and -immunosuppressive niche.
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Affiliation(s)
- Armin Rehm
- 1] Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany [2] Department of Hematology and Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Marcel Gätjen
- Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Kerstin Gerlach
- Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Florian Scholz
- Department of Tumor Genetics and Immunogenetics, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Angela Mensen
- 1] Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany [2]
| | - Marleen Gloger
- Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Kristina Heinig
- Department of Tumor Genetics and Immunogenetics, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Björn Lamprecht
- Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Stephan Mathas
- 1] Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany [2] Department of Hematology and Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Valérie Bégay
- Department of Cell Differentiation and Tumorigenesis, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Achim Leutz
- Department of Cell Differentiation and Tumorigenesis, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Martin Lipp
- Department of Tumor Genetics and Immunogenetics, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
| | - Bernd Dörken
- 1] Department of Hematology, Oncology and Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany [2] Department of Hematology and Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Uta E Höpken
- Department of Tumor Genetics and Immunogenetics, Max-Delbrück-Center for Molecular Medicine, MDC, 13125 Berlin, Germany
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Hurtado S, Kim Guisbert KS, Sontheimer EJ. SPO24 is a transcriptionally dynamic, small ORF-encoding locus required for efficient sporulation in Saccharomyces cerevisiae. PLoS One 2014; 9:e105058. [PMID: 25127041 PMCID: PMC4134269 DOI: 10.1371/journal.pone.0105058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 07/20/2014] [Indexed: 01/22/2023] Open
Abstract
In Saccharomyces cerevisiae, meiosis and sporulation are highly regulated responses that are driven in part by changes in RNA expression. Alternative mRNA forms with extended 5′ UTRs are atypical in S. cerevisiae, and 5′ extensions with upstream open reading frames (uORFs) are even more unusual. Here we characterize the gene YPR036W-A, now renamed SPO24, which encodes a very small (67-amino-acid) protein. This gene gives rise to two mRNA forms: a shorter form throughout meiosis and a longer, 5′-extended form in mid-late meiosis. The latter form includes a uORF for a 14-amino-acid peptide (Spo24u14). Deletion of the downstream ORF (dORF) leads to sporulation defects and the appearance of pseudohyphae-like projections. Experiments with luciferase reporters indicate that the uORF does not downregulate dORF translation. The protein encoded by the dORF (Spo24d67) localizes to the prospore membrane and is differentially phosphorylated during meiosis. Transcription of the 5′-extended mRNA in mid-meiosis depends upon the presence of two middle sporulation elements (MSEs). Removal of the MSEs severely inhibits the mid-meiotic appearance of the 5′-extended mRNA and limits the ability of plasmid-borne SPO24 to rescue the sporulation defect of a spo24Δ mutant, suggesting that the 5′-extended mRNA is functionally important. These results reveal Spo24d67 as a sporulation-related factor that is encoded by a transcriptionally dynamic, uORF-containing locus.
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Affiliation(s)
- Sara Hurtado
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Karen S. Kim Guisbert
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik J. Sontheimer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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