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Quantifying metabolic fluxes using mathematical modeling
Linköping University, Department of Biomedical Engineering. (Integrative Systems Biology)
2018 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Kvantifiering av metabola flöden genom matematisk modellering (Swedish)
Abstract [en]

Background

Cancer is one of the leading causes of death in Sweden. In order to develop better treatments against cancer we need to better understand it. One area of special interest is cancer metabolism and the metabolic fluxes. As these fluxes cannot be directly measured, modeling is required to determine them. Due to the complexity of cell metabolism, some limitations in the metabolism model are required. As the TCA-cycle (TriCarboxylic Acid cycle) is one of the most important parts of cell metabolism, it was chosen as a starting point. The primary goal of this project has been to evaluate the previously constructed TCA-cycle model. The first step of the evaluation was to determine the CI (Confidence Interval) of the model parameters, to determine the parameters’ identifiability. The second step was to validate the model to see if the model could predict data for which the model had not been trained for. The last step of the evaluation was to determine the uncertainty of the model simulation.

Method

The TCA-cycle model was created using Isotopicaly labeled data and EMUs (ElementaryMetabolic Units) in OpenFlux, an open source toolbox. The CIs of the TCA-cycle model parameters were determined using both OpenFlux’s inbuilt functionality for it as well as using amethod called PL (Profile Likelihood). The model validation was done using a leave one out method. In conjunction with using the leave on out method, a method called PPL (Prediction Profile Likelihood) was used to determine the CIs of the TCA-cycle model simulation.

Results and Discussion

Using PL to determine CIs had mixed success. The failures of PL are most likely caused by poor choice of settings. However, in the cases in which PL succeeded it gave comparable results to those of OpenFLux. However, the settings in OpenFlux are important, and the wrong settings can severely underestimate the confidence intervals. The confidence intervals from OpenFlux suggests that approximately 30% of the model parameters are identifiable. Results from the validation says that the model is able to predict certain parts of the data for which it has not been trained. The results from the PPL yields a small confidence interval of the simulation. These two results regarding the model simulation suggests that even though the identifiability of the parameters could be better, that the model structure as a whole is sound.

Conclusion

The majority of the model parameters in the TCA-cycle model are not identifiable, which is something future studies needs to address. However, the model is able to to predict data for which it has not been trained and the model has low simulation uncertainty.

Place, publisher, year, edition, pages
2018. , p. 41
Keywords [en]
Metabolic Flux Analysis, OpenFlux, carbon thirteen, Uncertainty Analysis, Cytoscape, Cancer, TCA-cycle, flux rate, metabolic reactions, systems biology, mathematical modeling, krebs cycle, model validation
National Category
Other Medical Engineering
Identifiers
URN: urn:nbn:se:liu:diva-149588ISRN: LIU-IMT-TFK-A—18/553—SEOAI: oai:DiVA.org:liu-149588DiVA, id: diva2:1231763
Subject / course
Medical Technology
Supervisors
Examiners
Available from: 2018-07-09 Created: 2018-07-09 Last updated: 2018-10-09Bibliographically approved

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