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Lee YXF, Johansson H, Wood MJA, El Andaloussi S. Considerations and Implications in the Purification of Extracellular Vesicles - A Cautionary Tale. Front Neurosci 2019; 13:1067. [PMID: 31680809 PMCID: PMC6813730 DOI: 10.3389/fnins.2019.01067] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/24/2019] [Indexed: 12/29/2022] Open
Abstract
Extracellular vesicles (EVs) are nano-sized particles constitutively released from cells into all biological fluids. Interestingly, these vesicles contain genetic cargoes including proteins, RNA and bioactive lipids that can be functionally delivered and affect recipient cells. As a result, there is growing interest in studying EVs in pathological conditions, including central nervous system (CNS)-related diseases, as EVs may be used for diagnostic purposes or as therapeutic agents. However, one major bottleneck is the need for better EV purification strategies when considering complex biological sources such as serum/protein-rich media or plasma. In this study, we have performed a systematic comparison study between the current gold-standard method: ultracentrifugation, to an alternative: size-exclusion chromatography (LC), using induced pluripotent stem cell (iPSC) derived complex media as a model system. We demonstrate that LC allows for derivation of purer EVs from iPSCs, which was previously impossible with the original UC method. Importantly, our study further highlights the various drawbacks when using the conventional UC approach that lead to misinterpretation of EV data. Lastly, we describe novel data on our iPSC-EVs; how they could relate to stem cell biology and discuss their potential use as EV therapeutics for CNS diseases.
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Affiliation(s)
- Yi Xin Fiona Lee
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Henrik Johansson
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Samir El Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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Zeidler S, Meckbach C, Tacke R, Raad FS, Roa A, Uchida S, Zimmermann WH, Wingender E, Gültas M. Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development. Front Genet 2016; 7:33. [PMID: 27047536 PMCID: PMC4804722 DOI: 10.3389/fgene.2016.00033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/23/2016] [Indexed: 12/28/2022] Open
Abstract
Transcription factors (TFs) regulate gene expression in living organisms. In higher organisms, TFs often interact in non-random combinations with each other to control gene transcription. Understanding the interactions is key to decipher mechanisms underlying tissue development. The aim of this study was to analyze co-occurring transcription factor binding sites (TFBSs) in a time series dataset from a new cell-culture model of human heart muscle development in order to identify common as well as specific co-occurring TFBS pairs in the promoter regions of regulated genes which can be essential to enhance cardiac tissue developmental processes. To this end, we separated available RNAseq dataset into five temporally defined groups: (i) mesoderm induction stage; (ii) early cardiac specification stage; (iii) late cardiac specification stage; (iv) early cardiac maturation stage; (v) late cardiac maturation stage, where each of these stages is characterized by unique differentially expressed genes (DEGs). To identify TFBS pairs for each stage, we applied the MatrixCatch algorithm, which is a successful method to deduce experimentally described TFBS pairs in the promoters of the DEGs. Although DEGs in each stage are distinct, our results show that the TFBS pair networks predicted by MatrixCatch for all stages are quite similar. Thus, we extend the results of MatrixCatch utilizing a Markov clustering algorithm (MCL) to perform network analysis. Using our extended approach, we are able to separate the TFBS pair networks in several clusters to highlight stage-specific co-occurences between TFBSs. Our approach has revealed clusters that are either common (NFAT or HMGIY clusters) or specific (SMAD or AP-1 clusters) for the individual stages. Several of these clusters are likely to play an important role during the cardiomyogenesis. Further, we have shown that the related TFs of TFBSs in the clusters indicate potential synergistic or antagonistic interactions to switch between different stages. Additionally, our results suggest that cardiomyogenesis follows the hourglass model which was already proven for Arabidopsis and some vertebrates. This investigation helps us to get a better understanding of how each stage of cardiomyogenesis is affected by different combination of TFs. Such knowledge may help to understand basic principles of stem cell differentiation into cardiomyocytes.
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Affiliation(s)
- Sebastian Zeidler
- University Medical Center Göttingen, Institute of Bioinformatics, Georg-August-University GöttingenGöttingen, Germany; Heart Research Center Göttingen, University Medical Center Göttingen, Institute of Pharmacology and Toxicology, Georg-August-University GöttingenGöttingen, Germany; DZHK (German Centre for Cardiovascular Research)Göttingen, Germany
| | - Cornelia Meckbach
- University Medical Center Göttingen, Institute of Bioinformatics, Georg-August-University Göttingen Göttingen, Germany
| | - Rebecca Tacke
- University Medical Center Göttingen, Institute of Bioinformatics, Georg-August-University Göttingen Göttingen, Germany
| | - Farah S Raad
- Heart Research Center Göttingen, University Medical Center Göttingen, Institute of Pharmacology and Toxicology, Georg-August-University GöttingenGöttingen, Germany; DZHK (German Centre for Cardiovascular Research)Göttingen, Germany
| | - Angelica Roa
- Heart Research Center Göttingen, University Medical Center Göttingen, Institute of Pharmacology and Toxicology, Georg-August-University GöttingenGöttingen, Germany; DZHK (German Centre for Cardiovascular Research)Göttingen, Germany
| | - Shizuka Uchida
- Institute of Cardiovascular Regeneration, Goethe University FrankfurtFrankfurt, Germany; DZHK (German Centre for Cardiovascular Research)Frankfurt, Germany
| | - Wolfram-Hubertus Zimmermann
- Heart Research Center Göttingen, University Medical Center Göttingen, Institute of Pharmacology and Toxicology, Georg-August-University GöttingenGöttingen, Germany; DZHK (German Centre for Cardiovascular Research)Göttingen, Germany
| | - Edgar Wingender
- University Medical Center Göttingen, Institute of Bioinformatics, Georg-August-University GöttingenGöttingen, Germany; DZHK (German Centre for Cardiovascular Research)Göttingen, Germany
| | - Mehmet Gültas
- University Medical Center Göttingen, Institute of Bioinformatics, Georg-August-University Göttingen Göttingen, Germany
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Deng XY, Wang H, Wang T, Fang XT, Zou LL, Li ZY, Liu CB. Non-viral methods for generating integration-free, induced pluripotent stem cells. Curr Stem Cell Res Ther 2015; 10:153-8. [PMID: 25248676 PMCID: PMC4460285 DOI: 10.2174/1574888x09666140923101914] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/16/2014] [Indexed: 12/11/2022]
Abstract
Induced pluripotent stem (iPS) cells were created from mouse fibroblasts by induced expression
of Yamanaka factors, Oct3/4, Sox2, Klf4, and c-Myc. This technique has quickly resulted in an exponential
increase in the amount of pluripotency studies, and has provided a valuable tool in regenerative medicine. At
the same time, many methodologies to generate iPS cells have been reported, and are comprised mainly of
viral methods and non-viral methods. Although viral methods may not be applicable for clinical applications, various nonviral
methods have been reported in recent years, including DNA vector-based approaches, transfection of mRNA, transduction
of reprogramming proteins, and use of small molecule compounds. This review summarizes and evaluates these
non-viral methods.
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