Nuclear Proteome Dynamics in Differentiating Embryonic Carcinoma (NTERA-2) Cells

Pewsey, Emma; Bruce, Christine; Tonge, Peter D.; Evans, Caroline; Ow, Sy; As, Georgiou; Wright, Phillip C.; Pw, Andrews; Fazeli, Alireza

doi:10.1021/pr901069d

Cited by 9 publications

(11 citation statements)

References 47 publications

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“…Current neurite outgrowth models routinely used within neuroscience research generally utilise the differentiation of cell monolayer cultures, whether it be of stem cells (Tegengem et al., 2011, Satoh et al., 1997, Pewsey et al., 2010, Roloff et al., 2015), cancer cells (Ferrari-Toninelli et al., 2004, Tucholski et al., 2001, Ross et al., 1983) or primary animal derived cells (Clagett-Dame et al., 2006, Balgude et al., 2001, Fitzgerald et al., 1993). However, quantification of neurite outgrowth in populations of cells grown as monolayers can be challenging using image analysis software, as it can be difficult to individually trace each neurite back to its parent cell body within an intricate neurite network (Radio and Mundy, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…The embryonal carcinoma (EC) stem cell line, TERA2, readily differentiates into neuronal subtypes when exposed to ATRA. EC cells are the malignant counterpart of embryonic stem cells, and cells from the TERA2 lineage have provided the basis for many in vitro models of neural differentiation, function and neurite outgrowth (Tegengem et al., 2011, Satoh et al., 1997, Pewsey et al., 2010, Roloff et al., 2015, Przyborski, 2001, Przyborski et al., 2000, Przyborski et al., 2003, Przyborski et al., 2004, Stewart et al., 2004, Coyne et al., 2011). While such models are valuable, there is significant scope to enhance their reliability in terms of robustness and reproducibility.…”

Section: Introductionmentioning

confidence: 99%

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A robust and reproducible human pluripotent stem cell derived model of neurite outgrowth in a three-dimensional culture system and its application to study neurite inhibition

Clarke

Tams

Henderson

et al. 2017

Neurochemistry International

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The inability of neurites to grow and restore neural connections is common to many neurological disorders, including trauma to the central nervous system and neurodegenerative diseases. Therefore, there is need for a robust and reproducible model of neurite outgrowth, to provide a tool to study the molecular mechanisms that underpin the process of neurite inhibition and to screen molecules that may be able to overcome such inhibition. In this study a novel in vitro pluripotent stem cell based model of human neuritogenesis was developed. This was achieved by incorporating additional technologies, notably a stable synthetic inducer of neural differentiation, and the application of three-dimensional (3D) cell culture techniques. We have evaluated the use of photostable, synthetic retinoid molecules to promote neural differentiation and found that 0.01 μM EC23 was the optimal concentration to promote differentiation and neurite outgrowth from human pluripotent stem cells within our model. We have also developed a methodology to enable quick and accurate quantification of neurite outgrowth derived from such a model. Furthermore, we have obtained significant neurite outgrowth within a 3D culture system enhancing the level of neuritogenesis observed and providing a more physiological microenvironment to investigate the molecular mechanisms that underpin neurite outgrowth and inhibition within the nervous system. We have demonstrated a potential application of our model in co-culture with glioma cells, to recapitulate aspects of the process of neurite inhibition that may also occur in the injured spinal cord. We propose that such a system that can be utilised to investigate the molecular mechanisms that underpin neurite inhibition mediated via glial and neuron interactions.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A robust and reproducible human pluripotent stem cell derived model of neurite outgrowth in a three-dimensional culture system and its application to study neurite inhibition

Clarke

Tams

Henderson

et al. 2017

Neurochemistry International

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“…Thereafter, bioinformatics tools are used to predict the interaction partners of the regulated proteins. This approach has been used for temporal examination of planktonic and biofilm proteomes, the signaling upon brain injury, the differentiation in embryonic carcinoma cells, and the protein interactions related to tyrosine phosphorylation . Interaction maps have been created using bioinformatics tools such as Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Highly Multiplexed Amplicon‐based Phylogenomics (HiMAP) .…”

Section: Protein–protein Interactionsmentioning

confidence: 99%

“…Interaction maps have been created using bioinformatics tools such as Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Highly Multiplexed Amplicon‐based Phylogenomics (HiMAP) . The results are then presented as network clusters, and the most advanced one (which also involves the time aspect) was presented by Pewsey et al . Taking Figure as one example, the importance of time in interactomics studies are clearly visualized.…”

Section: Protein–protein Interactionsmentioning

confidence: 99%

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Mass Spectrometry‐Based Analysis of Time‐Resolved Proteome Quantification

Valdés

Lind

2019

Proteomics

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The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.

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Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms

Mukherjee

Noirel

et al. 2011

Proteomics

Self Cite

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Cell surface physicochemical characterization techniques were combined with quantitative changes in protein expression, to investigate the biological and biophysical changes of Escherichia coli MG1655 cells when grown as a biofilm (BIO). The overall surface charge of BIO cells was found to be less negative, highlighting the need for a lower electrophoretic mobility for attachment to occur. Comparison of the chemical functional groups on the cell surface showed similar profiles, with the absorbance intensity higher for proteins and carbohydrates in the BIO cells. Quantitative proteomic analysis demonstrated that 3 proteins were significantly increased, and 9 proteins significantly decreased in abundance, in cells grown as a BIO compared to their planktonic counterparts, with 7 of these total 12 proteins unique to this study. Proteins showing significant increased or decreased abundance include proteins involved in acid resistance, DNA protection and binding and ABC transporters. Further predictive analysis of the metabolic pathways showed an increased abundance of the amino acid metabolism and tricarboxylic acid (TCA) cycle, with a decrease in expression within the pentose phosphate and glycolysis pathways. It is therefore hypothesized that cells grown as a BIO are still energetically viable potentially using amino acids as an indirect carbon backbone source into the TCA cycle.

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Nuclear Proteome Dynamics in Differentiating Embryonic Carcinoma (NTERA-2) Cells

Cited by 9 publications

References 47 publications

A robust and reproducible human pluripotent stem cell derived model of neurite outgrowth in a three-dimensional culture system and its application to study neurite inhibition

A robust and reproducible human pluripotent stem cell derived model of neurite outgrowth in a three-dimensional culture system and its application to study neurite inhibition

Mass Spectrometry‐Based Analysis of Time‐Resolved Proteome Quantification

Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms

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