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Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis
Thesis (MSc)--Stellenbosch University, 2025.
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| Language: | English |
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613784219058176 |
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| access_status_str | Open Access |
| author | Arendse, Shannon Deslene |
| author2 | Snoep, Jacky L. |
| author_browse | Arendse, Shannon Deslene Snoep, Jacky L. |
| author_facet | Snoep, Jacky L. Arendse, Shannon Deslene |
| author_sort | Arendse, Shannon Deslene |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132102 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:41:38.867Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132102 Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis Arendse, Shannon Deslene Snoep, Jacky L. Van Niekerk, D. D. Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. Glycolysis -- Mathematical models HepG2 cells -- Metabolism -- Mathematical models Cancer cells -- Adaptation Cancer cells -- Metabolism -- Regulation Cancer -- Chemotherapy Enzyme inhibitors -- Structure-activity relationships Glycolysis -- Inhibitors -- Mechanism of action UCTD Thesis (MSc)--Stellenbosch University, 2025. Arendse, S. D. 2025.Mathematical Modelling of HepG2 glycolysis; model construction, validation, and analysis. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/21f47ebe-fd33-4e67-a359-bbf7bda27785 ENGLISH ABSTRACT: Cancer is the second leading cause of death worldwide, with diagnosed cases expected to increase in the coming years. Despite the advancements in research and technology, the impact of this disease on humanity remains significant. Areas of cancer research aim to identify potential targets for therapeutic strategies that selectively target cancer cells without harming normal cells or tissues. Cancer cells are able to adapt to oxygen-deprived and nutrient deficient conditions through metabolic reprogramming, a hallmark of cancer. A key characteristic cancer cells exhibit, is an increase in glucose uptake and lactate production, even in the presence of oxygen, known as the Warburg effect. HepG2 cells, the most widely studied human hepatoma cell line, commonly used in drug studies, retain numerous hepatocyte-specific functions, including glucose metabolism. While numerous enzymes have been considered potential therapeutic targets in cancer cells, few reports integrate HepG2 cells into mathematical models to understand the mechanisms of cancer cells, optimise current treatment strategies and develop new therapeutic strategies. In this study, we implement a bottom-up approach to construct two models of metabolism, HepG2-Std (unbranched glycolysis) and HepG2-Ext (with pentose phosphate pathway (PPP) branch), which focus on the characterisation of glycolytic enzymes, and G6PDH. The behaviour of these enzymes is described by kinetic rate equations which are integrated into a detailed mathematical model. The models describe the change in intermediate concentrations and the rate of glycolytic reactions. The glycolytic flux in HepG2 cells was experimentally determined and validated with steady-state model predictions. Results showed that the experimental glycolytic flux was higher than predicted, whereas the experimental lactate flux was lower than predicted, indicating a lack of complete representation of enzyme kinetics, exclusion of branched pathways and transporters in the glycolytic models which may have been amplified in the experimental results. In the analysis of the glycolytic models, metabolic control analysis, supply-demand, and branch-point analyses were applied to determine the regulation of glycolytic enzymes in HepG2 cells. Metabolic control analysis in both models revealed four major flux controlling enzymes to be ATPase, HK, PFK and PGI, and G6PDH in the HepG2-Ext model. The supply and demand rate characteristics of ATP in HepG2 cells were analysed based on the characterisation of PFK, HK, PGK and PK and ATPase activity. Here an increase in ATPase activity in the HepG2-Std and HepG2-Ext models, result in a decrease in ATP concentration. The branch point analysis revealed that enzymes in one branch exert negative control over the flux in the other, with PFK and PGI exhibiting negative control, while G6PDH and HK exerting a high positive control on PPP flux. Notably, ATPase shows positive control by increasing G6P levels, enhancing the PPP over glycolysis, while HK’s stronger positive control on the PPP results in positive control over the coefficient flux ratio between the pathways. These findings highlight the potential targeting for G6PDH, PFK and HK, for therapeutic intervention. This research underscores the pivotal role of glycolysis in cancer metabolism, creating a foundation for future studies aimed at identifying novel drug targets and improve therapeutic outcomes. AFRIKAANSE OPSOMMING: Kanker is die tweede grootste oorsaak van sterftes wêreldwyd, met gediagnoseerde gevalle wat na verwagting in die komende jare sal toeneem. Ten spyte van die vooruitgang in navorsing en tegnologie, bly die impak van hierdie siekte op die mensdom beduidend. Gebiede van kankernavorsing het ten doel om potensiële teikens vir terapeutiese strategieë te identifiseer wat kankerselle selektief teiken sonder om normale selle of weefsels te benadeel. Kankerselle is in staat om aan te pas by toestande wat suurstof ontneem en voedingstowwe tekort is deur metaboliese herprogrammering, ’n kenmerk van kanker. ’n Sleutelkenmerk wat kankerselle vertoon, is ’n toename in glukose-opname en laktaatproduksie, selfs in die teenwoordigheid van suurstof, bekend as die Warburg-effek. HepG2-selle, die mees bestudeerde menslike hepatoomsellyn, wat algemeen in geneesmiddelstudies gebruik word, behou talle hepatosiet-spesifieke funksies, insluitend glukosemetabolisme. Terwyl talle ensieme as potensiële terapeutiese teikens in kankerselle beskou is, integreer min verslae HepG2-selle in wiskundige modelle om die meganismes van kankerselle te verstaan, huidige behandelingstrategieë te optimaliseer en nuwe terapeutiese strategieë te ontwikkel. In hierdie studie implementeer ons ’n bottom-up benadering om twee modelle van metabolisme te konstrueer, HepG2-Std (onvertakte glikolise) en HepG2-Ext (met pentosefosfaatweg (PPP) tak), wat fokus op die karakterisering van glikolitiese ensieme, en G6PDH. Die gedrag van hierdie ensieme word beskryf deur kinetiese tempovergelykings wat in ’n gedetailleerde wiskundige model geïntegreer is. Die modelle beskryf die verandering in intermediêre konsentrasies en die tempo van glikolitiese reaksies. Die glikolitiese vloed in HepG2 selle is eksperimenteel bepaal en bekragtig met bestendige-toestand model voorspellings. Resultate het getoon dat die eksperimentele glikolitiese vloed hoër was as wat voorspel is, terwyl die eksperimentele laktaatvloed laer was as wat voorspel is, wat dui op ’n gebrek aan volledige voorstelling van ensiemkinetika, uitsluiting van vertakte paaie en vervoerders in die glikolitiese modelle wat moontlik in die eksperimentele geamplifiseer is. resultate. In die ontleding van die glikolitiese modelle is metaboliese beheeranalise, vraag-aanbod- en takpunt-analises toegepas om die regulering van glikolitiese ensieme in HepG2-selle te bepaal. Metaboliese beheer analise in beide modelle het vier hoof vloed beheer ensieme geopenbaar as ATPase, HK, PFK en PGI, en G6PDH in die HepG2-Ext model. Die aanbod en vraag tempo eienskappe van ATP in HepG2 selle is ontleed gebaseer op die karakterisering van PFK, HK, PGK en PK en ATPase aktiwiteit. Hier ’n toename in ATPase aktiwiteit in die HepG2-Std en HepG2-Ext modelle, lei tot ’n afname in ATP konsentrasie. Die vertakkingspuntanalise het aan die lig gebring dat ensieme in een tak negatiewe beheer uitoefen oor die vloed in die ander, met PFK en PGI wat negatiewe beheer toon, terwyl G6PDH en HK ’n hoë positiewe beheer op PPP vloed uitoefen. ATPase toon veral positiewe beheer deur G6P-vlakke te verhoog, wat die PPP bo glikolise verbeter, terwyl HK se sterker positiewe beheer op die PPP positiewe beheer oor die koëffisiënt-vloedverhouding tussen die weë tot gevolg het. Hierdie bevindinge beklemtoon die potensiële teiken vir G6PDH, PFK en HK, vir terapeutiese intervensie. Hierdie navorsing beklemtoon die deurslaggewende rol van glikolise in kankermetabolisme, wat ’n grondslag skep vir toekomstige studies wat daarop gemik is om nuwe geneesmiddelteikens te identifiseer en terapeutiese uitkomste te verbeter. Masters 2025-05-23T12:36:09Z 2025-05-23T12:36:09Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132102 en Stellenbosch University xii, 87 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Glycolysis -- Mathematical models HepG2 cells -- Metabolism -- Mathematical models Cancer cells -- Adaptation Cancer cells -- Metabolism -- Regulation Cancer -- Chemotherapy Enzyme inhibitors -- Structure-activity relationships Glycolysis -- Inhibitors -- Mechanism of action UCTD Arendse, Shannon Deslene Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title | Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title_full | Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title_fullStr | Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title_full_unstemmed | Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title_short | Mathematical modelling of HepG2 glycolysis; model construction, validation, and analysis |
| title_sort | mathematical modelling of hepg2 glycolysis model construction validation and analysis |
| topic | Glycolysis -- Mathematical models HepG2 cells -- Metabolism -- Mathematical models Cancer cells -- Adaptation Cancer cells -- Metabolism -- Regulation Cancer -- Chemotherapy Enzyme inhibitors -- Structure-activity relationships Glycolysis -- Inhibitors -- Mechanism of action UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132102 |
| work_keys_str_mv | AT arendseshannondeslene mathematicalmodellingofhepg2glycolysismodelconstructionvalidationandanalysis |