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Hofmann C, Aghajani M, Alcock CD, Blackwood EA, Sandmann C, Herzog N, Groß J, Plate L, Wiseman RL, Kaufman RJ, Katus HA, Jakobi T, Völkers M, Glembotski CC, Doroudgar S. ATF6 protects against protein misfolding during cardiac hypertrophy. J Mol Cell Cardiol 2024; 189:12-24. [PMID: 38401179 DOI: 10.1016/j.yjmcc.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Cardiomyocytes activate the unfolded protein response (UPR) transcription factor ATF6 during pressure overload-induced hypertrophic growth. The UPR is thought to increase ER protein folding capacity and maintain proteostasis. ATF6 deficiency during pressure overload leads to heart failure, suggesting that ATF6 protects against myocardial dysfunction by preventing protein misfolding. However, conclusive evidence that ATF6 prevents toxic protein misfolding during cardiac hypertrophy is still pending. Here, we found that activation of the UPR, including ATF6, is a common response to pathological cardiac hypertrophy in mice. ATF6 KO mice failed to induce sufficient levels of UPR target genes in response to chronic isoproterenol infusion or transverse aortic constriction (TAC), resulting in impaired cardiac growth. To investigate the effects of ATF6 on protein folding, the accumulation of poly-ubiquitinated proteins as well as soluble amyloid oligomers were directly quantified in hypertrophied hearts of WT and ATF6 KO mice. Whereas only low levels of protein misfolding was observed in WT hearts after TAC, ATF6 KO mice accumulated increased quantities of misfolded protein, which was associated with impaired myocardial function. Collectively, the data suggest that ATF6 plays a critical adaptive role during cardiac hypertrophy by protecting against protein misfolding.
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Affiliation(s)
- Christoph Hofmann
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany; SDSU Heart Institute and Department of Biology, San Diego State University, San Diego, CA, USA
| | - Marjan Aghajani
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA
| | - Cecily D Alcock
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA
| | - Erik A Blackwood
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA
| | - Clara Sandmann
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Nicole Herzog
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Julia Groß
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Tobias Jakobi
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany; Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christopher C Glembotski
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA
| | - Shirin Doroudgar
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany; Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, USA.
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2
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Jakobi T. State-of-the-Art Circular RNA Analytics Using the Circtools Software Suite. Methods Mol Biol 2024; 2765:23-46. [PMID: 38381332 DOI: 10.1007/978-1-0716-3678-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Circular RNAs (circRNAs) are types of RNA molecules that have been discovered relatively recently and have been found to be widely expressed in eukaryotic cells. Unlike canonical linear RNA molecules, circRNAs form a covalently closed continuous loop structure without a 5' or 3' end. They are generated by a process called back-splicing, in which a downstream splice donor site is joined to an upstream splice acceptor site. CircRNAs have been found to play important roles in various biological processes, including gene regulation, alternative splicing, and protein translation. They can act as sponges for microRNAs or RNA-binding proteins and can also encode peptides or proteins. Additionally, circRNAs have been implicated in several diseases, including cancer, neurological disorders, and cardiovascular diseases.This protocol provides all necessary steps to detect and analyze circRNAs in silico from RNA sequencing data using the circtools circRNA analytics software suite. The protocol starts from raw sequencing data with circRNA detection via back-splice events and includes statistical testing of circRNAs as well as primer design for follow-up wet lab experiments.
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Affiliation(s)
- Tobias Jakobi
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona - College of Medicine - Phoenix, Phoenix, AZ, USA.
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3
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Kmietczyk V, Oelschläger J, Gupta P, Varma E, Hartl S, Furkel J, Konstandin M, Marx A, Loewenthal Z, Kamuf-Schenk V, Jürgensen L, Stroh C, Gorska A, Martin-Garrido A, Heineke J, Jakobi T, Frey N, Völkers M. Ythdf2 regulates cardiac remodeling through its mRNA target transcripts. J Mol Cell Cardiol 2023; 181:57-66. [PMID: 37315764 DOI: 10.1016/j.yjmcc.2023.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
m6A mRNA methylation controls cardiomyocyte function and increased overall m6A levels are a stereotyping finding in heart failure independent of the underlying etiology. However, it is largely unknown how the information is read by m6A reader proteins in heart failure. Here we show that the m6A reader protein Ythdf2 controls cardiac function and identified a novel mechanism how reader proteins control gene expression and cardiac function. Deletion of Ythdf2 in cardiomyocytes in vivo leads to mild cardiac hypertrophy, reduced heart function, and increased fibrosis during pressure overload as well as during aging. Similarly, in vitro the knockdown of Ythdf2 results in cardiomyocyte growth and remodeling. Mechanistically, we identified the eucaryotic elongation factor 2 as post-transcriptionally regulated by Ythdf2 using cell type specific Ribo-seq data. Our study expands our understanding on the regulatory functions of m6A methylation in cardiomyocytes and how cardiac function is controlled by the m6A reader protein Ythdf2.
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Affiliation(s)
- V Kmietczyk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - J Oelschläger
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - P Gupta
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - E Varma
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - S Hartl
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - J Furkel
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - M Konstandin
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - A Marx
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Z Loewenthal
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - V Kamuf-Schenk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - L Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - C Stroh
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - A Gorska
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - A Martin-Garrido
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University
| | - J Heineke
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University
| | - T Jakobi
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona, College of Medicine - Phoenix, Phoenix, USA
| | - N Frey
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - M Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
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Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J, Volders PJ. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat Methods 2023; 20:1159-1169. [PMID: 37443337 PMCID: PMC10870000 DOI: 10.1038/s41592-023-01944-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/12/2023] [Indexed: 07/15/2023]
Abstract
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation.
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Affiliation(s)
- Marieke Vromman
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Zhejiang, China
| | | | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science and of Biochemistry, Stanford University, Stanford, CA, USA
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, University Hospital Heidelberg, German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Xin Dong
- School of Basic Medical Science, Department of Medical Genetics, Wuhan University, Wuhan, China
| | | | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Wanjun Gu
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunjiang He
- School of Basic Medical Science, Department of Medical Genetics, Wuhan University, Wuhan, China
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Michael S Jackson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tobias Jakobi
- Translational Cardiovascular Research Center, University of Arizona - College of Medicine Phoenix, Phoenix, AZ, USA
| | - Eric C Lai
- Sloan Kettering Institute, New York, NY, USA
| | - Justine Nuytens
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julia Salzman
- Department of Biomedical Data Science and of Biochemistry, Stanford University, Stanford, CA, USA
| | | | - Peter Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Olivier Thas
- Data Science Institute, I-Biostat, Hasselt University, Hasselt, Belgium
| | - Eveline Vanden Eynde
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Jakub Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Fudan, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Zhejiang, China
| | - Nurten Yigit
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Guo-Hua Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Pieter-Jan Volders
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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5
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Jakobi T, Groß J, Cyganek L, Doroudgar S. Transcriptional Effects of Candidate COVID-19 Treatments on Cardiac Myocytes. Front Cardiovasc Med 2022; 9:844441. [PMID: 35686037 PMCID: PMC9170897 DOI: 10.3389/fcvm.2022.844441] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/28/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) has emerged as a major cause of morbidity and mortality worldwide, placing unprecedented pressure on healthcare. Cardiomyopathy is described in patients with severe COVID-19 and increasing evidence suggests that cardiovascular involvement portends a high mortality. To facilitate fast development of antiviral interventions, drugs initially developed to treat other diseases are currently being repurposed as COVID-19 treatments. While it has been shown that SARS-CoV-2 invades cells through the angiotensin-converting enzyme 2 receptor (ACE2), the effect of drugs currently repurposed to treat COVID-19 on the heart requires further investigation.MethodsHuman induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs) were treated with five repurposed drugs (remdesivir, lopinavir/ritonavir, lopinavir/ritonavir/interferon beta (INF-β), hydroxychloroquine, and chloroquine) and compared with DMSO controls. Transcriptional profiling was performed to identify global changes in gene expression programs.ResultsRNA sequencing of hiPSC-CMs revealed significant changes in gene programs related to calcium handling and the endoplasmic reticulum stress response, most prominently for lopinavir/ritonavir and lopinavir/ritonavir/interferon-beta. The results of the differential gene expression analysis are available for interactive access at https://covid19drugs.jakobilab.org.ConclusionTranscriptional profiling in hiPSC-CMs treated with COVID-19 drugs identified unfavorable changes with lopinavir/ritonavir and lopinavir/ritonavir/INF-β in key cardiac gene programs that may negatively affect heart function.
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Affiliation(s)
- Tobias Jakobi
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona – College of Medicine – Phoenix, Phoenix, AZ, United States
- *Correspondence: Tobias Jakobi,
| | - Julia Groß
- Department of Cardiology, Angiology, and Pneumology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Department of Cardiology and Pneumology, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - Shirin Doroudgar
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona – College of Medicine – Phoenix, Phoenix, AZ, United States
- Shirin Doroudgar,
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Wagner JUG, Bojkova D, Shumliakivska M, Luxán G, Nicin L, Aslan GS, Milting H, Kandler JD, Dendorfer A, Heumueller AW, Fleming I, Bibli SI, Jakobi T, Dieterich C, Zeiher AM, Ciesek S, Cinatl J, Dimmeler S. Increased susceptibility of human endothelial cells to infections by SARS-CoV-2 variants. Basic Res Cardiol 2021; 116:42. [PMID: 34224022 PMCID: PMC8256413 DOI: 10.1007/s00395-021-00882-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/01/2021] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) spawned a global health crisis in late 2019 and is caused by the novel coronavirus SARS-CoV-2. SARS-CoV-2 infection can lead to elevated markers of endothelial dysfunction associated with higher risk of mortality. It is unclear whether endothelial dysfunction is caused by direct infection of endothelial cells or is mainly secondary to inflammation. Here, we investigate whether different types of endothelial cells are susceptible to SARS-CoV-2. Human endothelial cells from different vascular beds including umbilical vein endothelial cells, coronary artery endothelial cells (HCAEC), cardiac and lung microvascular endothelial cells, or pulmonary arterial cells were inoculated in vitro with SARS-CoV-2. Viral spike protein was only detected in HCAECs after SARS-CoV-2 infection but not in the other endothelial cells tested. Consistently, only HCAEC expressed the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2), required for virus infection. Infection with the SARS-CoV-2 variants B.1.1.7, B.1.351, and P.2 resulted in significantly higher levels of viral spike protein. Despite this, no intracellular double-stranded viral RNA was detected and the supernatant did not contain infectious virus. Analysis of the cellular distribution of the spike protein revealed that it co-localized with endosomal calnexin. SARS-CoV-2 infection did induce the ER stress gene EDEM1, which is responsible for clearance of misfolded proteins from the ER. Whereas the wild type of SARS-CoV-2 did not induce cytotoxic or pro-inflammatory effects, the variant B.1.1.7 reduced the HCAEC cell number. Of the different tested endothelial cells, HCAECs showed highest viral uptake but did not promote virus replication. Effects on cell number were only observed after infection with the variant B.1.1.7, suggesting that endothelial protection may be particularly important in patients infected with this variant.
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Affiliation(s)
- Julian U G Wagner
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
| | - Denisa Bojkova
- Institute of Medical Virology, University Frankfurt, Frankfurt, Germany
| | - Mariana Shumliakivska
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Guillermo Luxán
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
| | - Luka Nicin
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Galip S Aslan
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Hendrik Milting
- Clinic for Thoracic and Cardiovascular Surgery, Bad Oeyenhausen, Germany
| | - Joshua D Kandler
- Institute of Medical Virology, University Frankfurt, Frankfurt, Germany
| | - Andreas Dendorfer
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Walter-Brendel-Centre, Hospital of the Ludwig-Maximilians-University München, Munich, Germany
| | - Andreas W Heumueller
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
| | - Ingrid Fleming
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
| | - Sofia-Iris Bibli
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
| | - Tobias Jakobi
- Department of Internal Medicine and the Center for Translational Cardiovascular Research, University of Arizona, 475 N. 5th Street, Phoenix, AZ, 85004, USA
| | - Christoph Dieterich
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas M Zeiher
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany
- Cardiopulmonary Institute (CPI), Frankfurt, Germany
- Department of Cardiology, University Frankfurt, Frankfurt, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine und Pharmacology, Frankfurt, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, Germany
| | - Jindrich Cinatl
- Institute of Medical Virology, University Frankfurt, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Frankfurt, Germany.
- Cardiopulmonary Institute (CPI), Frankfurt, Germany.
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7
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Kapoor U, Licht K, Amman F, Jakobi T, Martin D, Dieterich C, Jantsch MF. ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Genome Res 2020; 30:1107-1118. [PMID: 32727871 PMCID: PMC7462079 DOI: 10.1101/gr.256933.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 09/09/2019] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
Adenosine-to-inosine RNA editing and pre-mRNA splicing largely occur cotranscriptionally and influence each other. Here, we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA editing on splicing across different tissues. We find that ADAR has a 100× higher impact on splicing than ADARB1, although both enzymes target a similar number of substrates with a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 5′ of differentially spliced regions. Several of these ADARB1-mediated editing events change splice consensus sequences, therefore strongly influencing splicing of some mRNAs. A significant overlap between differentially edited and differentially spliced sites suggests evolutionary selection toward splicing being regulated by editing in a tissue-specific manner.
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Affiliation(s)
- Utkarsh Kapoor
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Konstantin Licht
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Tobias Jakobi
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - David Martin
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christoph Dieterich
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - Michael F Jantsch
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
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8
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Jakobi T, Siede D, Eschenbach J, Heumüller AW, Busch M, Nietsch R, Meder B, Most P, Dimmeler S, Backs J, Katus HA, Dieterich C. Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue. Cells 2020; 9:cells9071616. [PMID: 32635460 PMCID: PMC7407233 DOI: 10.3390/cells9071616] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
For decades, cardiovascular disease (CVD) has been the leading cause of death throughout most developed countries. Several studies relate RNA splicing, and more recently also circular RNAs (circRNAs), to CVD. CircRNAs originate from linear transcripts and have been shown to exhibit tissue-specific expression profiles. Here, we present an in-depth analysis of sequence, structure, modification, and cardiac circRNA interactions. We used human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs), human healthy and diseased (ischemic cardiomyopathy, dilated cardiomyopathy) cardiac tissue, and human umbilical vein endothelial cells (HUVECs) to profile circRNAs. We identified shared circRNAs across all samples, as well as model-specific circRNA signatures. Based on these circRNAs, we identified 63 positionally conserved and expressed circRNAs in human, pig, and mouse hearts. Furthermore, we found that the sequence of circRNAs can deviate from the sequence derived from the genome sequence, an important factor in assessing potential functions. Integration of additional data yielded evidence for m6A-methylation of circRNAs, potentially linked to translation, as well as, circRNAs overlapping with potential Argonaute 2 binding sites, indicating potential association with the RISC complex. Moreover, we describe, for the first time in cardiac model systems, a sub class of circRNAs containing the start codon of their primary transcript (AUG circRNAs) and observe an enrichment for m6A-methylation for AUG circRNAs.
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Affiliation(s)
- Tobias Jakobi
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
- Correspondence: (T.J.); (C.D.)
| | - Dominik Siede
- Institute of Experimental Cardiology, 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;
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
| | - Andreas W. Heumüller
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany; (A.W.H.); (S.D.)
- German Centre for Cardiovascular Research (DZHK)-Partner site Rhine/Main, 60590 Frankfurt, Germany
| | - Martin Busch
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
| | - Rouven Nietsch
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
| | - Benjamin Meder
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
| | - Patrick Most
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany; (A.W.H.); (S.D.)
- German Centre for Cardiovascular Research (DZHK)-Partner site Rhine/Main, 60590 Frankfurt, Germany
| | - Johannes Backs
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
- Institute of Experimental Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Hugo A. Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, 69120 Heidelberg, Germany; (M.B.); (R.N.); (B.M.); (P.M.); (H.A.K.)
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany;
- Correspondence: (T.J.); (C.D.)
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9
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Jakobi T, Uvarovskii A, Dieterich C. circtools-a one-stop software solution for circular RNA research. Bioinformatics 2020; 35:2326-2328. [PMID: 30462173 PMCID: PMC6596886 DOI: 10.1093/bioinformatics/bty948] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 07/19/2018] [Revised: 10/02/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not polyadenylated and have been shown to be highly specific for cell type and developmental stage. CircRNA detection starts from high-throughput sequencing data and is a multi-stage bioinformatics process yielding sets of potential circRNA candidates that require further analyses. While a number of tools for the prediction process already exist, publicly available analysis tools for further characterization are rare. Our work provides researchers with a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights. RESULTS Here, we present circtools, a modular, Python-based framework for computational circRNA analyses. The software includes modules for circRNA detection, internal sequence reconstruction, quality checking, statistical testing, screening for enrichment of RBP binding sites, differential exon RNase R resistance and circRNA-specific primer design. circtools supports researchers with visualization options and data export into commonly used formats. AVAILABILITY AND IMPLEMENTATION circtools is available via https://github.com/dieterich-lab/circtools and http://circ.tools under GPLv3.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tobias Jakobi
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Alexey Uvarovskii
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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10
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Blackwood EA, Thuerauf DJ, Stastna M, Stephens H, Sand Z, Pentoney A, Azizi K, Jakobi T, Van Eyk JE, Katus HA, Glembotski CC, Doroudgar S. Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response. J Mol Cell Cardiol 2020; 143:132-144. [PMID: 32339566 PMCID: PMC8597053 DOI: 10.1016/j.yjmcc.2020.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/25/2022]
Abstract
The effects of ER stress on protein secretion by cardiac myocytes are not well understood. In this study, the ER stressor thapsigargin (TG), which depletes ER calcium, induced death of cultured neonatal rat ventricular myocytes (NRVMs) in high media volume but fostered protection in low media volume. In contrast, another ER stressor, tunicamycin (TM), a protein glycosylation inhibitor, induced NRVM death in all media volumes, suggesting that protective proteins were secreted in response to TG but not TM. Proteomic analyses of TG- and TM-conditioned media showed that the secretion of most proteins was inhibited by TG and TM; however, secretion of several ER-resident proteins, including GRP78 was increased by TG but not TM. Simulated ischemia, which decreases ER/SR calcium also increased secretion of these proteins. Mechanistically, secreted GRP78 was shown to enhance survival of NRVMs by collaborating with a cell-surface protein, CRIPTO, to activate protective AKT signaling and to inhibit death-promoting SMAD2 signaling. Thus, proteins secreted during ER stress mediated by ER calcium depletion can enhance cardiac myocyte viability.
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Affiliation(s)
- Erik A Blackwood
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Donna J Thuerauf
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Miroslava Stastna
- Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| | - Haley Stephens
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Zoe Sand
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Amber Pentoney
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Khalid Azizi
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Tobias Jakobi
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany; Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany
| | - Christopher C Glembotski
- San Diego State University Heart Institute and the Department of Biology, San Diego State University, San Diego, CA, USA
| | - Shirin Doroudgar
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany.
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11
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Blackwood EA, Hofmann C, Santo Domingo M, Bilal AS, Sarakki A, Stauffer W, Arrieta A, Thuerauf DJ, Kolkhorst FW, Müller OJ, Jakobi T, Dieterich C, Katus HA, Doroudgar S, Glembotski CC. ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb. Circ Res 2019; 124:79-93. [PMID: 30582446 DOI: 10.1161/circresaha.118.313854] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Endoplasmic reticulum (ER) stress dysregulates ER proteostasis, which activates the transcription factor, ATF6 (activating transcription factor 6α), an inducer of genes that enhance protein folding and restore ER proteostasis. Because of increased protein synthesis, it is possible that protein folding and ER proteostasis are challenged during cardiac myocyte growth. However, it is not known whether ATF6 is activated, and if so, what its function is during hypertrophic growth of cardiac myocytes. OBJECTIVE To examine the activity and function of ATF6 during cardiac hypertrophy. METHODS AND RESULTS We found that ER stress and ATF6 were activated and ATF6 target genes were induced in mice subjected to an acute model of transverse aortic constriction, or to free-wheel exercise, both of which promote adaptive cardiac myocyte hypertrophy with preserved cardiac function. Cardiac myocyte-specific deletion of Atf6 (ATF6 cKO [conditional knockout]) blunted transverse aortic constriction and exercise-induced cardiac myocyte hypertrophy and impaired cardiac function, demonstrating a role for ATF6 in compensatory myocyte growth. Transcript profiling and chromatin immunoprecipitation identified RHEB (Ras homologue enriched in brain) as an ATF6 target gene in the heart. RHEB is an activator of mTORC1 (mammalian/mechanistic target of rapamycin complex 1), a major inducer of protein synthesis and subsequent cell growth. Both transverse aortic constriction and exercise upregulated RHEB, activated mTORC1, and induced cardiac hypertrophy in wild type mouse hearts but not in ATF6 cKO hearts. Mechanistically, knockdown of ATF6 in neonatal rat ventricular myocytes blocked phenylephrine- and IGF1 (insulin-like growth factor 1)-mediated RHEB induction, mTORC1 activation, and myocyte growth, all of which were restored by ectopic RHEB expression. Moreover, adeno-associated virus 9- RHEB restored cardiac growth to ATF6 cKO mice subjected to transverse aortic constriction. Finally, ATF6 induced RHEB in response to growth factors, but not in response to other activators of ATF6 that do not induce growth, indicating that ATF6 target gene induction is stress specific. CONCLUSIONS Compensatory cardiac hypertrophy activates ER stress and ATF6, which induces RHEB and activates mTORC1. Thus, ATF6 is a previously unrecognized link between growth stimuli and mTORC1-mediated cardiac growth.
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Affiliation(s)
- Erik A Blackwood
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Christoph Hofmann
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.).,Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.)
| | - Michelle Santo Domingo
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Alina S Bilal
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Anup Sarakki
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Winston Stauffer
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Adrian Arrieta
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Donna J Thuerauf
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Fred W Kolkhorst
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
| | - Oliver J Müller
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.).,Department of Internal Medicine III, University of Kiel, Germany, and German Centre for Cardiovascular Research, Partner Site Hamburg/Kiel/Lübeck, Germany (O.J.M.)
| | - Tobias Jakobi
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.).,Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, University Hospital Heidelberg, Germany (T.J., C.D.)
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.).,Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, University Hospital Heidelberg, Germany (T.J., C.D.)
| | - Hugo A Katus
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.)
| | - Shirin Doroudgar
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.H., O.J.M., H.A.K., S.D.).,German Centre for Cardiovascular Research, Partner Site Heidelberg (C.H., O.J.M., T.J., C.D., H.A.K., S.D.)
| | - Christopher C Glembotski
- From the Department of Biology, San Diego State University Heart Institute, San Diego State University, CA (E.A.B., C.H., M.S.D., A.S.B., A.S., W.S., A.A., D.J.T., F.W.K., C.C.G.)
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12
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Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Friedrich UA, Mauz V, Backs J, Kramer G, Katus HA, Dieterich C, Völkers M. Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress. Circ Res 2019; 125:431-448. [PMID: 31284834 PMCID: PMC6690133 DOI: 10.1161/circresaha.119.314817] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Supplemental Digital Content is available in the text. Rationale: Gene expression profiles have been mainly determined by analysis of transcript abundance. However, these analyses cannot capture posttranscriptional gene expression control at the level of translation, which is a key step in the regulation of gene expression, as evidenced by the fact that transcript levels often poorly correlate with protein levels. Furthermore, genome-wide transcript profiling of distinct cell types is challenging due to the fact that lysates from tissues always represent a mixture of cells. Objectives: This study aimed to develop a new experimental method that overcomes both limitations and to apply this method to perform a genome-wide analysis of gene expression on the translational level in response to pressure overload. Methods and Results: By combining ribosome profiling (Ribo-seq) with a ribosome-tagging approach (Ribo-tag), it was possible to determine the translated transcriptome in specific cell types from the heart. After pressure overload, we monitored the cardiac myocyte translatome by purifying tagged cardiac myocyte ribosomes from cardiac lysates and subjecting the ribosome-protected mRNA fragments to deep sequencing. We identified subsets of mRNAs that are regulated at the translational level and found that translational control determines early changes in gene expression in response to cardiac stress in cardiac myocytes. Translationally controlled transcripts are associated with specific biological processes related to translation, protein quality control, and metabolism. Mechanistically, Ribo-seq allowed for the identification of upstream open reading frames in transcripts, which we predict to be important regulators of translation. Conclusions: This method has the potential to (1) provide a new tool for studying cell-specific gene expression at the level of translation in tissues, (2) reveal new therapeutic targets to prevent cellular remodeling, and (3) trigger follow-up studies that address both, the molecular mechanisms involved in the posttranscriptional control of gene expression in cardiac cells, and the protective functions of proteins expressed in response to cellular stress.
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Affiliation(s)
- Shirin Doroudgar
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Hofmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Etienne Boileau
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Brandon Malone
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Eva Riechert
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Agnieszka A Gorska
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Tobias Jakobi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Clara Sandmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Lonny Jürgensen
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Vivien Kmietczyk
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ellen Malovrh
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Jana Burghaus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Mandy Rettel
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Fereshteh Younesi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ulrike A Friedrich
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Victoria Mauz
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Hugo A Katus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Dieterich
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Mirko Völkers
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
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13
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Jakobi T, Dieterich C. Computational approaches for circular RNA analysis. Wiley Interdiscip Rev RNA 2019; 10:e1528. [PMID: 30788906 DOI: 10.1002/wrna.1528] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) are a recent addition to the expanding universe of RNA species and originate through back-splicing events from linear primary transcripts. CircRNAs show specific expression profiles with regards to cell type and developmental stage. Importantly, only few circRNAs have been functionally characterized to date. The detection of circRNAs from RNA sequencing data is a complex computational workflow that, depending on tissue and condition typically yields candidate sets of hundreds or thousands of circRNA candidates. Here, we provide an overview on different computational analysis tools and pipelines that became available throughout the last years. We outline technical and experimental requirements that are common to all approaches and point out potential pitfalls during the computational analysis. Although computational prediction of circRNAs has become quite mature in recent years, we provide a set of valuable validation strategies, in silico as well as in vitro-based approaches. In addition to circRNA detection via back-splicing junction, we present available analysis pipelines for delineating the primary sequence and for predicting possible functions of circRNAs. Finally, we outline the most important web resources for circRNA research. This article is categorized under: RNA Methods > RNA Analyses in vitro and In Silico RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Tobias Jakobi
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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14
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Bischof LF, Haurat MF, Hoffmann L, Albersmeier A, Wolf J, Neu A, Pham TK, Albaum SP, Jakobi T, Schouten S, Neumann-Schaal M, Wright PC, Kalinowski J, Siebers B, Albers SV. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Front Microbiol 2019; 9:3201. [PMID: 30687244 PMCID: PMC6335949 DOI: 10.3389/fmicb.2018.03201] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.
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Affiliation(s)
- Lisa F Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Astrid Neu
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan Schouten
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Phillip C Wright
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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15
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Abstract
Circular RNAs (circRNAs) have been first described as "scrambled exons" in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure.
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Affiliation(s)
- Tobias Jakobi
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany. .,German Center for Cardiovascular Research (DZHK)-Partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK)-Partner site Heidelberg/Mannheim, Heidelberg, Germany
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16
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Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW. Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Front Genet 2016; 7:5. [PMID: 26904094 PMCID: PMC4748744 DOI: 10.3389/fgene.2016.00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/17/2016] [Indexed: 12/27/2022] Open
Abstract
Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g., modern genomics. This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore, we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand. We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC). Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs) performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead. We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually no additional manual adjustment is required. In contrast, some automatic parallelizers targeting GPUs still lack maturity and are limited to simple statements and structures.
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Affiliation(s)
- Daniel Langenkämper
- Biodata Mining Group, Faculty of Technology, Bielefeld University Bielefeld, Germany
| | - Tobias Jakobi
- Sektion für Bioinformatik und Systemkardiologie, Universitätsklinikum Heidelberg Heidelberg, Germany
| | | | - Lukas Jelonek
- Bioinformatik und Systembiologie, Justus Liebig University Gießen, Germany
| | - Alexander Goesmann
- Bioinformatik und Systembiologie, Justus Liebig University Gießen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Faculty of Technology, Bielefeld University Bielefeld, Germany
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17
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Morgner J, Ghatak S, Jakobi T, Dieterich C, Aumailley M, Wickström SA. Integrin-linked kinase regulates the niche of quiescent epidermal stem cells. Nat Commun 2015; 6:8198. [PMID: 26349061 PMCID: PMC4569844 DOI: 10.1038/ncomms9198] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023] Open
Abstract
Stem cells reside in specialized niches that are critical for their function. Quiescent hair follicle stem cells (HFSCs) are confined within the bulge niche, but how the molecular composition of the niche regulates stem cell behaviour is poorly understood. Here we show that integrin-linked kinase (ILK) is a key regulator of the bulge extracellular matrix microenvironment, thereby governing the activation and maintenance of HFSCs. ILK mediates deposition of inverse laminin (LN)-332 and LN-511 gradients within the basement membrane (BM) wrapping the hair follicles. The precise BM composition tunes activities of Wnt and transforming growth factor-β pathways and subsequently regulates HFSC activation. Notably, reconstituting an optimal LN microenvironment restores the altered signalling in ILK-deficient cells. Aberrant stem cell activation in ILK-deficient epidermis leads to increased replicative stress, predisposing the tissue to carcinogenesis. Overall, our findings uncover a critical role for the BM niche in regulating stem cell activation and thereby skin homeostasis.
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Affiliation(s)
- Jessica Morgner
- Paul Gerson Unna Group ‘Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Sushmita Ghatak
- Paul Gerson Unna Group ‘Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Tobias Jakobi
- Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Christoph Dieterich
- Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Monique Aumailley
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | - Sara A. Wickström
- Paul Gerson Unna Group ‘Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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18
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Baake M, Götze F, Huck C, Jakobi T. Radial spacing distributions from planar point sets. Acta Crystallogr A Found Adv 2014; 70:472-82. [PMID: 25176995 DOI: 10.1107/s2053273314011140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/14/2014] [Indexed: 11/10/2022] Open
Abstract
This paper explores the radial projection method for locally finite planar point sets and provides numerical examples for different types of order. The main question is whether the method is suitable to analyse order in a quantitative way. The findings indicate that the answer is affirmative. In this context, local visibility conditions are also studied for certain types of aperiodic point sets.
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Affiliation(s)
- M Baake
- Department of Mathematics, Bielefeld University, Bielefeld, Germany
| | - F Götze
- Department of Mathematics, Bielefeld University, Bielefeld, Germany
| | - C Huck
- Department of Mathematics, Bielefeld University, Bielefeld, Germany
| | - T Jakobi
- Department of Mathematics, Bielefeld University, Bielefeld, Germany
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Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. J Biotechnol 2014; 190:64-75. [PMID: 25086342 DOI: 10.1016/j.jbiotec.2014.07.437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/18/2014] [Accepted: 07/20/2014] [Indexed: 11/30/2022]
Abstract
Chinese hamster ovary (CHO) cell lines are one of the major production tools for monoclonal antibodies, recombinant proteins, and therapeutics. Although many efforts have significantly improved the availability of sequence information for CHO cells in the last years, forthcoming draft genomes still lack the information depth known from the mouse or human genomes. Many genes annotated for CHO cells and the Chinese hamster reference genome still are in silico predictions, only insufficiently verified by biological experiments. The correct annotation of transcription start sites (TSSs) is of special interest for CHO cells, as these directly define the location of the eukaryotic core promoter. Our study aims to elucidate these largely unexplored regions, trying to shed light on promoter landscapes in the Chinese hamster genome. Based on a 5' enriched dual library RNA sequencing approach 6547 TSSs were identified, of which over 90% were assigned to known genes. These TSSs were used to perform extensive promoter studies using a novel, modular bioinformatics pipeline, incorporating analyses of important regulatory elements of the eukaryotic core promoter on per-gene level and on genomic scale.
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Affiliation(s)
- Tobias Jakobi
- Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Karina Brinkrolf
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Andreas Tauch
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Thomas Noll
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Jens Stoye
- Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany; Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Alexander Goesmann
- Bioinformatik und Systembiologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany.
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20
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Abstract
MOTIVATION The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. RESULTS We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel 'implicit sorting' strategy that enables these benefits to be realized without the overhead of sorting the reads. With these techniques, a 45× coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3 Gb of sequence to fit into only 8.2 GB of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is >4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections. AVAILABILITY Code to construct the BWT and SAP-array on large genomic datasets is part of the BEETL library, available as a github repository at https://github.com/BEETL/BEETL.
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Affiliation(s)
- Anthony J Cox
- Computational Biology Group, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK.
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Hackl M, Jadhav V, Jakobi T, Rupp O, Brinkrolf K, Goesmann A, Pühler A, Noll T, Borth N, Grillari J. Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. J Biotechnol 2012; 158:151-5. [PMID: 22306111 PMCID: PMC3314935 DOI: 10.1016/j.jbiotec.2012.01.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 11/05/2022]
Abstract
MicroRNAs (miRNAs) have recently entered Chinese hamster ovary (CHO) cell culture technology, due to their severe impact on the regulation of cellular phenotypes. Applications of miRNAs that are envisioned range from biomarkers of favorable phenotypes to cell engineering targets. These applications, however, require a profound knowledge of miRNA sequences and their genomic organization, which exceeds the currently available information of ~400 conserved mature CHO miRNA sequences. Based on these recently published sequences and two independent CHO-K1 genome assemblies, this publication describes the computational identification of CHO miRNA genomic loci. Using BLAST alignment, 415 previously reported CHO miRNAs were mapped to the reference genomes, and subsequently assigned to a distinct genomic miRNA locus. Sequences of the respective precursor-miRNAs were extracted from both reference genomes, folded in silico to verify correct structures and cross-compared. In the end, 212 genomic loci and pre-miRNA sequences representing 319 expressed mature miRNAs (approximately 50% of miRNAs represented matching pairs of 5' and 3' miRNAs) were submitted to the miRBase miRNA repository. As a proof-of-principle for the usability of the published genomic loci, four likely polycistronic miRNA cluster were chosen for PCR amplification using CHO-K1 and DHFR (-) genomic DNA. Overall, these data on the genomic context of miRNA expression in CHO will simplify the development of tools employing stable overexpression or deletion of miRNAs, allow the identification of miRNA promoters and improve detection methods such as microarrays.
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Affiliation(s)
- Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tobias Jakobi
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Oliver Rupp
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Karina Brinkrolf
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Alexander Goesmann
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Alfred Pühler
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Thomas Noll
- AG Zellkulturtechnik, Technische Fakultät, Universität Bielefeld, 33549 Bielefeld, Germany
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Becker J, Hackl M, Rupp O, Jakobi T, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Pühler A, Tauch A, Brinkrolf K. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. J Biotechnol 2011; 156:227-35. [PMID: 21945585 DOI: 10.1016/j.jbiotec.2011.09.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 11/17/2022]
Abstract
The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were used to achieve a major step forward to unravel the transcriptome of Chinese hamster ovary (CHO) cells. Normalized cDNA libraries originating from several cell lines and diverse culture conditions were sequenced and the resulting 1.84 million reads were assembled into 32,801 contiguous sequences, 29,184 isotigs, and 24,576 isogroups. A taxonomic classification of the isotigs showed that more than 70% of the assembled data is most similar to the transcriptome of Mus musculus, with most of the remaining isotigs being homologous to DNA sequences from Rattus norvegicus. Mapping of the CHO cell line contigs to the mouse transcriptome demonstrated that 9124 mouse transcripts, representing 6701 genes, are covered by more than 95% of their sequence length. Metabolic pathways of the central carbohydrate metabolism and biosynthesis routes of sugars used for protein N-glycosylation were reconstructed from the transcriptome data. All relevant genes representing major steps in the N-glycosylation pathway of CHO cells were detected. The present manuscript represents a data set of assembled and annotated genes for CHO cells that can now be used for a detailed analysis of the molecular functioning of CHO cell lines.
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Affiliation(s)
- Jennifer Becker
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
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Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner Zu Siederdissen C, Bort JAH, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol 2011; 153:62-75. [PMID: 21392545 PMCID: PMC3119918 DOI: 10.1016/j.jbiotec.2011.02.011] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/24/2011] [Accepted: 02/25/2011] [Indexed: 01/30/2023]
Abstract
Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to identify and annotate both conserved and novel CHO miRNAs in the absence of a Chinese hamster genome, we deep-sequenced small RNA fractions of 6 biotechnologically relevant cell lines and mapped the resulting reads to an artificial reference sequence consisting of all known miRNA hairpins. Read alignment patterns and read count ratios of 5' and 3' mature miRNAs were obtained and used for an independent classification into miR/miR* and 5p/3p miRNA pairs and discrimination of miRNAs from other non-coding RNAs, resulting in the annotation of 387 mature CHO miRNAs. The quantitative content of next-generation sequencing data was analyzed and confirmed using qPCR, to find that miRNAs are markers of cell status. Finally, cDNA sequencing of 26 validated targets of miR-17-92 suggests conserved functions for miRNAs in CHO cells, which together with the now publicly available sequence information sets the stage for developing novel RNAi tools for CHO cell engineering.
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Affiliation(s)
- Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 19, A-1190 Vienna, Austria
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Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 2011; 27:1351-8. [DOI: 10.1093/bioinformatics/btr151] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Jakobi T, Blom J, Jaenicke S, Doppmeier D, Goesmann A. Einsatz von Grafikhardware in der Genomforschung. CHEM-ING-TECH 2010. [DOI: 10.1002/cite.201050431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A. TRUNCATULIX--a data warehouse for the legume community. BMC Plant Biol 2009; 9:19. [PMID: 19210766 PMCID: PMC2654896 DOI: 10.1186/1471-2229-9-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 02/11/2009] [Indexed: 05/08/2023]
Abstract
BACKGROUND Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database - hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data. RESULTS The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage. CONCLUSION The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/.
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Affiliation(s)
- Kolja Henckel
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany
- Technical Faculty, Bielefeld University, Bielefeld, Germany
- Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
| | - Kai J Runte
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
| | - Thomas Bekel
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
| | - Michael Dondrup
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Technical Faculty, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
| | - Helge Küster
- International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
- Genomics of Legume Plants, Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Unit IV – Plant Genomics, Institute for Plant Genetics, Leibniz Universität Hannover, Germany
| | - Alexander Goesmann
- Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Faculty for Biology and Genetics, Bielefeld University, Bielefeld, Germany
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