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

Bibliographic Details
Main Author:	Agana, Bernice A.
Language:	English
Published:	The Ohio State University / OhioLINK 2019
Subjects:	Biochemistry
Online Access:	http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436

id	ndltd-OhioLink-oai-etd.ohiolink.edu-osu1574636665012436
record_format	oai_dc
spelling	ndltd-OhioLink-oai-etd.ohiolink.edu-osu15746366650124362021-12-17T05:24:09Z Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism. Agana, Bernice A. Biochemistry 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. 2019 English text The Ohio State University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436 http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection	NDLTD
language	English
sources	NDLTD
topic	Biochemistry
spellingShingle	Biochemistry Agana, Bernice A. Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
author	Agana, Bernice A.
author_facet	Agana, Bernice A.
author_sort	Agana, Bernice A.
title	Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
title_short	Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
title_full	Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
title_fullStr	Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
title_full_unstemmed	Mass Spectrometry-Based Proteomics and Metabolomics: Understanding Protein Interactions, Proteome Complexity and Perturbations in Cellular Metabolism.
title_sort	mass spectrometry-based proteomics and metabolomics: understanding protein interactions, proteome complexity and perturbations in cellular metabolism.
publisher	The Ohio State University / OhioLINK
publishDate	2019
url	http://rave.ohiolink.edu/etdc/view?acc_num=osu1574636665012436
work_keys_str_mv	AT aganabernicea massspectrometrybasedproteomicsandmetabolomicsunderstandingproteininteractionsproteomecomplexityandperturbationsincellularmetabolism
_version_	1723964517532041216

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

Similar Items