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Final Dissertation_Agana.pdf (8.37 MB)

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Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.

Agana, Bernice A
http://orcid.org/0000-0002-8947-6413
http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436

Abstract Details

2019, Doctor of Philosophy, Ohio State University, Biochemistry Program, Ohio State.
In recent years, mass spectrometry (MS) has become the analytical technique of choice with broad applications in biomedical and biochemical research. This dissertation highlights the development of proteomics and metabolomics techniques to study protein interactions, the proteome complexity and perturbations in cellular metabolism. Chapters 2 and 3 outline work done in collaboration with Dr. Daniel Schoenberg’s lab to study the cytoplasmic capping enzyme interactome as well as its role in diversifying the proteome. Mammalian cells possess cytoplasmic machinery capable of restoring a cap structure onto uncapped and/or partially degraded RNA 5’ ends. To gain a better understanding of the cellular context of cytoplasmic recapping, we identified the protein interactome of cytoplasmic capping enzyme (CE) using two complementary approaches: chemical crosslinking and recovery with cytoplasmic CE and BioID coupled to mass spectrometry. Chapter 2 describes the capping enzyme interactome study and identified HSP90 as a client protein. This publication challenged a key paradigm of the mechanism of HSP90 inhibitors in clinical trials for chemotherapy. Chapter 3 describes total proteins and N-terminal truncated proteins expressed from mRNAs that are recapped downstream of canonical 5’ends. Here the results show that cytoplasmic capping has a limited overall impact on the proteome but has the potential to expand the protein coding capacity of a given mRNA by enabling translation to initiate at sites downstream of a recapped 5’ end. Chapters 4 and 5 focus on collaborations with Dr. David Carbone’s lab. Combined proteomics, phosphoproteomics and metabolomics is applied to understand deregulated pathways in LKB1 mutant non-small cell lung cancers (NSCLC). In the past decade, advances in gene sequencing technology, the use of mouse models and the availability of human tumor databases have enhanced our understanding of the molecular mechanisms underlying NSCLC. Although large-scale genomic analyses and gene expression profiles of patient tumors have provided information on the molecular alterations in lung cancer, there is still the need to decode the signaling pathways deregulated in tumor progression and metastases. Chapter 4 describes a multi-omics approach used to study the proteomic, phosphoproteomic and metabolomic signatures of LKB1-loss tumors. This study identified dysregulated production of metabolites such spermidine and arginine that contribute to microenvironment-mediated immune suppression in LKB1-loss tumors. Chapter 5 characterizes the proteins from extracellular vesicles that have been secreted by lung cancer cell lines as potential clinical biomarkers. Cancer-derived extracellular vesicles have been reported to create a pro-metastatic niche by nurturing angiogenesis, invasion, and proliferation in recipient cells to support tumor progression. This study shows that serum deprivation in tissue culture has a significant effect on protein contents of extracellular vesicles. These findings suggest that future studies consider nutrient conditions (serum-starvation or exosome-depleted serum supplementation) as well as mutations in key metabolic regulators such as LKB1.
Vicki Wysocki (Advisor)
186 p.
Biochemistry

Recommended Citations

Citations

  • Agana, B. A. (2019). Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism. [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436

    APA Style (7th edition)

  • Agana, Bernice. Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism. 2019. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436.

    MLA Style (8th edition)

  • Agana, Bernice. "Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism." Doctoral dissertation, Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436

    Chicago Manual of Style (17th edition)

osu1574636665012436
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© 2019, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.