Fundamentals of a systems biology approach to In Vitro tissue growth

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Fundamentals of a systems biology approach to In Vitro tissue growth

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Beck, Richard Joseph

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2013-05

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Abstract

Tissue engineering needs a paradigm shift in order to generate clinically useful products. The field has yet to regularly produce implantable tissue-engineered products. The conventional manner in which input stimuli are applied without consideration of current cellular activity level is certainly suboptimal. The objective of this line of research is to produce a method for rationally choosing input stimuli that drive the cells toward optimal tissue growth. Transient phosphorylation of signaling proteins after a perturbation in stimuli contains biological information concerning downstream tissue growth. The overall project aims to build a statistical model predictive of tissue growth via information of the upstream phosphoproteome minutes after a change in stimuli. The validity of such a statistical model can be tested based on its utility to direct tissue growth: stimuli will be chosen on the basis of which corresponding phosphoproteome profile(s) is predicted to yield the best downstream tissue growth; this can be directly compared to conventional tissue engineering methods. This doctoral project focused on obtaining sample types and tailoring methods appropriate for a systems biology and statistical approach, especially in regard to the label-free quantification of phosphopeptide enrichments. Neonatal human dermal fibroblasts (nhDF) were expanded to near confluence, at which point basal medium for tissue production was applied. After two days, nhDF were perturbed with basal medium supplemented with 1 or 10 ng/mL TGF-β1. Cells were harvested at 10, 20, or 30 minutes for intracellular proteins. Resultant protein lysates were digested to peptides via trypsin and enriched for phosphopeptides via Iron Immobilized Metal Affinity Chromatography (IMAC). Phosphopeptide enrichments were analyzed by tandem mass spectrometry. A total of 1689 peptides were both identified with phosphorylation and quantified using distinct algorithms. Under strict statistical tests, 22 of these peptides were found to differ between treatments/time. Corresponding downstream collagen deposition was also found to differ between treatments. These results indicate that the type of quantitative data needed for the overall project can be acquired. The methods developed can be used in finding a statistical relationship between tissue growth and upstream phosphoproteome profiles.

Keywords

Cell culture

Mass spectrometry

Phosphopeptide

Proteomics

Systems biology

Tissue engineering

Description

University of Minnesota Ph.D. dissertation. May 2013. Major: Biomedical Engineering. Advisor: Robert T. Tranquillo. 1 computer file (PDF); xii, 53 pages.

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Beck, Richard Joseph. (2013). Fundamentals of a systems biology approach to In Vitro tissue growth. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/152426.

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