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Open AccessArticle

Semantic Analysis of Posttranslational Modification of Proteins Accumulated in Thyroid Cancer Cells Exposed to Simulated Microgravity

1
Max-Planck-Institute for Biochemistry, 82152 Martinsried, Germany
2
Clinic and Policlinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University, 39120 Magdeburg, Germany
3
Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark
4
Melissa Informatics, 2550 Ninth Street, Suite 114, Berkeley, CA, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(8), 2257; https://doi.org/10.3390/ijms19082257
Received: 29 June 2018 / Revised: 27 July 2018 / Accepted: 30 July 2018 / Published: 1 August 2018
(This article belongs to the Special Issue Cell and Molecular Biology of Thyroid Disorders)
When monolayers of tissue cancer cells of various origins are exposed to real or simulated microgravity, many cells leave the monolayer and assemble to three-dimensional (3D) aggregates (spheroids). In order to define the cellular machinery leading to this change in growth behavior of FTC-133 human thyroid cancer cells and MCF-7 breast cancer cells, we recently performed proteome analyses on these cell lines and determined the proteins’ accumulation in monolayer cells grown under 1g-conditions as well as in the cells of spheroids assembled under simulated microgravity during three and 14 days, respectively. At that time, an influence of the increment or decrement of some of the more than 5000 proteins detected in each cell line was investigated. In this study, we focused on posttranslational modifications (PTMs) of proteins. For this purpose, we selected candidates from the list of the proteins detected in the two preceding proteome analyses, which showed significant accumulation in spheroid cells as compared to 1g monolayer cells. Then we searched for those PTMs of the selected proteins, which according to the literature have already been determined experimentally. Using the Semantic Protocol and RDF Query Language (SPARQL), various databases were examined. Most efficient was the search in the latest version of the dbPTM database. In total, we found 72 different classes of PTMs comprising mainly phosphorylation, glycosylation, ubiquitination and acetylation. Most interestingly, in 35 of the 69 proteins, N6 residues of lysine are modifiable. View Full-Text
Keywords: mass spectrometry; Knowledge Explorer; Reactome; pathway analysis; random positioning machine; semantic network; SPARQL reasoning mass spectrometry; Knowledge Explorer; Reactome; pathway analysis; random positioning machine; semantic network; SPARQL reasoning
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Bauer, J.; Wehland, M.; Infanger, M.; Grimm, D.; Gombocz, E. Semantic Analysis of Posttranslational Modification of Proteins Accumulated in Thyroid Cancer Cells Exposed to Simulated Microgravity. Int. J. Mol. Sci. 2018, 19, 2257.

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