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Bencun M, Britto-Borges T, Eschenbach J, Dieterich C. New Tricks with Old Dogs: Computational Identification and Experimental Validation of New miRNA–mRNA Regulation in hiPSC-CMs. Biomedicines 2022; 10:biomedicines10020391. [PMID: 35203600 PMCID: PMC8962266 DOI: 10.3390/biomedicines10020391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
Cardiovascular disease is still the leading cause of morbidity and mortality worldwide. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become a valuable widespread in vitro model to study cardiac disease. Herein, we employ the hiPSC-CM model to identify novel miRNA–mRNA interaction partners during cardiac differentiation and β-adrenergic stress. Whole transcriptome and small RNA sequencing data were combined to identify novel miRNA–mRNA interactions. Briefly, mRNA and miRNA expression profiles were integrated with miRNA target predictions to identify significant statistical dependencies between a miRNA and its candidate target set. We show by experimental validation that our approach discriminates true from false miRNA target predictions. Thereby, we identified several differentially expressed miRNAs and focused on the two top candidates: miR-99a-5p in the context of cardiac differentiation and miR-212-3p in the context of β-adrenergic stress. We validated some target mRNA candidates by 3′UTR luciferase assays as well as in transfection experiments in the hiPSC-CM model system. Our data show that iPSC-derived cardiomyocytes and computational modeling can be used to uncover new valid miRNA–mRNA interactions beyond current knowledge.
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Affiliation(s)
- Maja Bencun
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (T.B.-B.); (J.E.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Thiago Britto-Borges
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (T.B.-B.); (J.E.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jessica Eschenbach
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (T.B.-B.); (J.E.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (T.B.-B.); (J.E.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-56-36884
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Bencun M, Klinke O, Hotz-Wagenblatt A, Klaus S, Tsai MH, Poirey R, Delecluse HJ. Translational profiling of B cells infected with the Epstein-Barr virus reveals 5' leader ribosome recruitment through upstream open reading frames. Nucleic Acids Res 2019. [PMID: 29529302 PMCID: PMC5887285 DOI: 10.1093/nar/gky129] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Epstein-Barr virus (EBV) genome encodes several hundred transcripts. We have used ribosome profiling to characterize viral translation in infected cells and map new translation initiation sites. We show here that EBV transcripts are translated with highly variable efficiency, owing to variable transcription and translation rates, variable ribosome recruitment to the leader region and coverage by monosomes versus polysomes. Some transcripts were hardly translated, others mainly carried monosomes, showed ribosome accumulation in leader regions and most likely represent non-coding RNAs. A similar process was visible for a subset of lytic genes including the key transactivators BZLF1 and BRLF1 in cells infected with weakly replicating EBV strains. This suggests that ribosome trapping, particularly in the leader region, represents a new checkpoint for the repression of lytic replication. We could identify 25 upstream open reading frames (uORFs) located upstream of coding transcripts that displayed 5′ leader ribosome trapping, six of which were located in the leader region shared by many latent transcripts. These uORFs repressed viral translation and are likely to play an important role in the regulation of EBV translation.
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Affiliation(s)
- Maja Bencun
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Klinke
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- German Cancer Research Center (DKFZ), Core Facility Genomics & Proteomics, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Severina Klaus
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Ming-Han Tsai
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Remy Poirey
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Henri-Jacques Delecluse
- German Cancer Research Center (DKFZ), F100, Pathogenesis of Virus Associated Tumors, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
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Delecluse S, Tsai MH, Shumilov A, Bencun M, Arrow S, Beshirova A, Cottignies-Calamarte A, Lasitschka F, Bulut OC, Münz C, Zeier M, Behrends U, Delecluse HJ. Epstein-Barr Virus Induces Expression of the LPAM-1 Integrin in B Cells In Vitro and In Vivo. J Virol 2019; 93:e01618-18. [PMID: 30541846 PMCID: PMC6384065 DOI: 10.1128/jvi.01618-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infects the oropharynx but, surprisingly, frequently induces B cell proliferation in the gut of immunosuppressed individuals. We found that EBV infection in vitro induces the expression of the LPAM-1 integrin on tonsillar B cells and increases it on peripheral blood cells. Similarly, LPAM-1 was induced in the tonsils of patients undergoing primary infectious mononucleosis. EBV-induced LPAM-1 bound to the MAdCAM-1 addressin, which allows B cell homing to the gastrointestinal mucosa-associated lymphoid tissue (GALT). Thus, we hypothesized that EBV-induced LPAM-1 could induce relocation of infected B cells from the tonsil to the GALT. In situ hybridization with an EBER-specific probe revealed the frequent presence of EBV-infected cells in the pericolic lymph nodes of healthy individuals. Relocation of infected B cells into the GALT would expand the EBV reservoir, possibly protecting it from T cells primed in the oropharynx, and explain why EBV induces lymphoid tumors in the gut.IMPORTANCE EBV causes tumors in multiple organs, particularly in the oro- and nasopharyngeal area but also in the digestive system. This virus enters the body in the oropharynx and establishes a chronic infection in this area. The observation that the virus causes tumors in the digestive system implies that the infected cells can move to this organ. We found that EBV infection induces the expression of integrin beta 7 (ITGB7), an integrin that associates with integrin alpha 4 to form the LPAM-1 dimer. LPAM-1 is key for homing of B cells to the gastrointestinal tract, suggesting that induction of this molecule is the mechanism through which EBV-infected cells enter this organ. In favor of this hypothesis, we could also detect EBV-infected cells in the lymph nodes adjacent to the colon and in the appendix.
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Affiliation(s)
- Susanne Delecluse
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Nierenzentrum Heidelberg, Heidelberg, Germany
| | - Ming-Han Tsai
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anatoliy Shumilov
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Maja Bencun
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Sebastian Arrow
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Aisha Beshirova
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Andréa Cottignies-Calamarte
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Olcay Cem Bulut
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | | | - Uta Behrends
- Children's Hospital Schwabing, Technische Universitaet Muenchen, Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Munich, Germany
| | - Henri-Jacques Delecluse
- German Cancer Research Centre (DKFZ), Unit F100, Heidelberg, Germany
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unit U1074, Heidelberg, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
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Feederle R, Linnstaedt SD, Bannert H, Lips H, Bencun M, Cullen BR, Delecluse HJ. A viral microRNA cluster strongly potentiates the transforming properties of a human herpesvirus. PLoS Pathog 2011; 7:e1001294. [PMID: 21379335 PMCID: PMC3040666 DOI: 10.1371/journal.ppat.1001294] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 01/14/2011] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus (EBV), an oncogenic human herpesvirus, induces cell proliferation after infection of resting B lymphocytes, its reservoir in vivo. The viral latent proteins are necessary for permanent B cell growth, but it is unknown whether they are sufficient. EBV was recently found to encode microRNAs (miRNAs) that are expressed in infected B cells and in some EBV-associated lymphomas. EBV miRNAs are grouped into two clusters located either adjacent to the BHRF1 gene or in introns contained within the viral BART transcripts. To understand the role of the BHRF1 miRNA cluster, we have constructed a virus mutant that lacks all its three members (Δ123) and a revertant virus. Here we show that the B cell transforming capacity of the Δ123 EBV mutant is reduced by more than 20-fold, relative to wild type or revertant viruses. B cells exposed to the knock-out virus displayed slower growth, and exhibited a two-fold reduction in the percentage of cells entering the cell cycle S phase. Furthermore, they displayed higher latent gene expression levels and latent protein production than their wild type counterparts. Therefore, the BHRF1 miRNAs accelerate B cell expansion at lower latent gene expression levels. Thus, this miRNA cluster simultaneously enhances expansion of the virus reservoir and reduces the viral antigenic load, two features that have the potential to facilitate persistence of the virus in the infected host. Thus, the EBV BHRF1 miRNAs may represent new therapeutic targets for the treatment of some EBV-associated lymphomas.
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Affiliation(s)
- Regina Feederle
- Department of Virus Associated Tumours, German Cancer Research Center, Heidelberg, Germany
| | - Sarah D. Linnstaedt
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Helmut Bannert
- Department of Virus Associated Tumours, German Cancer Research Center, Heidelberg, Germany
| | - Helge Lips
- Department of Virus Associated Tumours, German Cancer Research Center, Heidelberg, Germany
| | - Maja Bencun
- Department of Virus Associated Tumours, German Cancer Research Center, Heidelberg, Germany
| | - Bryan R. Cullen
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Henri-Jacques Delecluse
- Department of Virus Associated Tumours, German Cancer Research Center, Heidelberg, Germany
- * E-mail:
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