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Jaeschke A, Harvey NR, Tsurkan M, Werner C, Griffiths LR, Haupt LM, Bray LJ. Techniques for RNA extraction from cells cultured in starPEG-heparin hydrogels. Open Biol 2021; 11:200388. [PMID: 34062095 PMCID: PMC8169204 DOI: 10.1098/rsob.200388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Three-dimensional (3D) cell culture models that provide a biologically relevant microenvironment are imperative to investigate cell–cell and cell–matrix interactions in vitro. Semi-synthetic star-shaped poly(ethylene glycol) (starPEG)–heparin hydrogels are widely used for 3D cell culture due to their highly tuneable biochemical and biomechanical properties. Changes in gene expression levels are commonly used as a measure of cellular responses. However, the isolation of high-quality RNA presents a challenge as contamination of the RNA with hydrogel residue, such as polymer or glycosaminoglycan fragments, can impact template quality and quantity, limiting effective gene expression analyses. Here, we compare two protocols for the extraction of high-quality RNA from starPEG–heparin hydrogels and assess three subsequent purification techniques. Removal of hydrogel residue by centrifugation was found to be essential for obtaining high-quality RNA in both isolation methods. However, purification of the RNA did not result in further improvements in RNA quality. Furthermore, we show the suitability of the extracted RNA for cDNA synthesis of three endogenous control genes confirmed via quantitative polymerase chain reaction (qPCR). The methods and techniques shown can be tailored for other hydrogel models based on natural or semi-synthetic materials to provide robust templates for all gene expression analyses.
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Affiliation(s)
- Anna Jaeschke
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia.,School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nicholas R Harvey
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia.,Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - Mikhail Tsurkan
- Leibniz Institute of Polymer Research Dresden, Saxony, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden, Saxony, Germany
| | - Lyn R Griffiths
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia.,Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - Larisa M Haupt
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia.,Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, Australia.,ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - Laura J Bray
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia.,ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, Australia.,School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia
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Martin AD, Chua SW, Au CG, Stefen H, Przybyla M, Lin Y, Bertz J, Thordarson P, Fath T, Ke YD, Ittner LM. Peptide Nanofiber Substrates for Long-Term Culturing of Primary Neurons. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25127-25134. [PMID: 29979564 DOI: 10.1021/acsami.8b07560] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The culturing of primary neurons represents a central pillar of neuroscience research. Primary neurons are derived directly from brain tissue and recapitulate key aspects of neuronal development in an in vitro setting. Unlike neural stem cells, primary neurons do not divide; thus, initial attachment of cells to a suitable substrate is critical. Commonly used polylysine substrates can suffer from batch variability owing to their polymeric nature. Herein, we report the use of chemically well-defined, self-assembling tetrapeptides as substrates for primary neuronal culture. These water-soluble peptides assemble into fibers which facilitate adhesion and development of primary neurons, their long-term survival (>40 days), synaptic maturation, and electrical activity. Furthermore, these substrates are permissive toward neuronal transfection and transduction which, coupled with their uniformity and reproducible nature, make them suitable for a wide variety of applications in neuroscience.
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Affiliation(s)
- Adam D Martin
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
- School of Chemistry, The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science & Technology , University of New South Wales , Sydney , NSW , 2052 , Australia
| | - Sook Wern Chua
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Carol G Au
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Holly Stefen
- Neurodegeneration and Repair Unit, School of Medical Sciences and Neuronal Culture Core Facility , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Magdalena Przybyla
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Yijun Lin
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Josefine Bertz
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Pall Thordarson
- School of Chemistry, The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science & Technology , University of New South Wales , Sydney , NSW , 2052 , Australia
| | - Thomas Fath
- Neurodegeneration and Repair Unit, School of Medical Sciences and Neuronal Culture Core Facility , University of New South Wales , Sydney , NSW 2052 , Australia
- Dementia Research Centre, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Yazi D Ke
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Lars M Ittner
- Dementia Research Unit, School of Medical Sciences, Faculty of Medicine , University of New South Wales , Sydney , NSW 2052 , Australia
- Dementia Research Centre, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , NSW 2109 , Australia
- Neuroscience Research Australia , Sydney , NSW 2031 , Australia
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3
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RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells. PLoS One 2018; 13:e0197517. [PMID: 29864116 PMCID: PMC5986125 DOI: 10.1371/journal.pone.0197517] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/03/2018] [Indexed: 12/21/2022] Open
Abstract
Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution-pronase-was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed.
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Burgess KA, Miller AF, Oceandy D, Saiani A. Western blot analysis of cells encapsulated in self-assembling peptide hydrogels. Biotechniques 2017; 63:253-260. [DOI: 10.2144/000114617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/19/2017] [Indexed: 11/23/2022] Open
Abstract
Continuous optimization of in vitro analytical techniques is ever more important, especially given the development of new materials for tissue engineering studies. In particular, isolation of cellular components for downstream applications is often hindered by the presence of biomaterials, presenting a major obstacle in understanding how cell–matrix interactions influence cell behavior. Here, we describe an approach for western blot analysis of cells that have been encapsulated in self-assembling peptide hydrogels (SAPHs), which highlights the need for complete solubilization of the hydrogel construct. We demonstrate that both the choice of buffer and multiple cycles of sonication are vital in obtaining complete solubilization, thereby enabling the detection of proteins otherwise lost to SAP aggregation. Moreover, we show that the presence of self-assembling peptides (SAPs) does not interfere with the standard immunoblotting technique, offering the potential for use in more full-scale proteomic studies.
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Affiliation(s)
- Kyle A. Burgess
- School of Materials, The University of Manchester, Manchester, UK
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Aline F. Miller
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- School of Chemical Engineering and Analytical Sciences, The University of Manchester, Manchester, UK
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, UK
| | - Alberto Saiani
- School of Materials, The University of Manchester, Manchester, UK
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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Wojciechowski JP, Martin AD, Mason AF, Fife CM, Sagnella SM, Kavallaris M, Thordarson P. Choice of Capping Group in Tripeptide Hydrogels Influences Viability in the Three‐Dimensional Cell Culture of Tumor Spheroids. Chempluschem 2016; 82:383-389. [DOI: 10.1002/cplu.201600464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/28/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Jonathan P. Wojciechowski
- School of Chemistry The University of New South Wales Sydney NSW 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
| | - Adam D. Martin
- School of Chemistry The University of New South Wales Sydney NSW 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
| | - Alexander F. Mason
- School of Chemistry The University of New South Wales Sydney NSW 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
| | - Christopher M. Fife
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
- Tumour Biology and Targeting Program Children's Cancer Institute Lowy Cancer Research Centre UNSW Australia Sydney NSW 2052 Australia
| | - Sharon M. Sagnella
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
- Tumour Biology and Targeting Program Children's Cancer Institute Lowy Cancer Research Centre UNSW Australia Sydney NSW 2052 Australia
| | - Maria Kavallaris
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
- Tumour Biology and Targeting Program Children's Cancer Institute Lowy Cancer Research Centre UNSW Australia Sydney NSW 2052 Australia
| | - Pall Thordarson
- School of Chemistry The University of New South Wales Sydney NSW 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
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