Systems Biology of Protein Secretion in Human Cells: Multi-omics Analysis and Modeling of the Protein Secretion Process in Human Cells and its Application.
Doctoral thesis, 2021
This thesis focuses on different aspects of the protein secretion process, including its engineering for cell factory development and analysis in diseases associated with its deregulation. A major part of this thesis involved the use of HEK293 cells as a human model cell-line for investigating the protein secretion process by generating different types of omics data and developing a computational model of the human protein secretion pathway. We compared the transcriptomic profile of cell lines producing erythropoietin (EPO; as a model secretory protein) at different rates to identify key genes that potentially contributed to higher rates of protein secretion. Moreover, by performing a transcriptomic comparison of cells producing green fluorescent protein (GFP; as a model non-secretory protein) with EPO producers, we captured differences that specifically relate to secretory protein production. We sought to further investigate the factors contributing to increased recombinant protein production by analyzing additional omic layers such as proteomics and metabolomics in cells that exhibited different rates of EPO production. Moreover, we developed a toolbox (HumanSec) to extend the reference human genome-scale metabolic model (Human1) to encompass protein-specific reactions for each secretory protein detected in our proteomics dataset. By generating cell-line specific protein secretion models and constraining the models using metabolomics data, we could predict the top host cell proteins (HCPs) that compete with EPO for metabolic and energetic resources. Finally, based on the detected patterns of changes in our multi-omics investigations combined with a protein secretion sensitivity analysis using the metabolic model, we identified a list of genes and pathways that potentially play a key role in recombinant protein production and could serve as promising candidates for targeted cell factory design.
In another part of the thesis, we studied the link between the expression profiles of genes involved in the protein secretory pathway (PSP) and various hallmarks of cancer. By implementing a dual approach involving differential expression analysis and eight different machine learning algorithms, we investigated the expression changes in secretory pathway components across different cancer types to identify PSP genes whose expression was associated with tumor characteristics. We demonstrated that a combined machine learning and differential expression approach have a complementary nature and could highlight key PSP components relevant to features of tumor pathophysiology that may constitute potential therapeutic targets.
cancer protein secretory pathway
protein secretion modeling
Integrative omics analysis
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Machine learning-based investigation of the cancer protein secretory pathway
PLoS Computational Biology,; Vol. 17(2021)
Evolution from adherent to suspension: systems biology of HEK293 cell line development
Scientific Reports,; Vol. 10(2020)
C3SE (Chalmers Centre for Computational Science and Engineering)
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 4984
To be held online through Zoom
Opponent: Prof. Lars Keld Nielsen, The University of Queensland, Australia