University of Illinois Urbana-Champaign

Proteomics and peptidomics for the study of neurological and metabolic disorders

De La Toba, Eduardo Alejandro

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DELATOBA-DISSERTATION-2022.pdf

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https://hdl.handle.net/2142/115560

Description

Title
Proteomics and peptidomics for the study of neurological and metabolic disorders
Author(s)
De La Toba, Eduardo Alejandro
Issue Date
2022-04-19
Director of Research (if dissertation) or Advisor (if thesis)
Sweedler, Jonathan V
Doctoral Committee Chair(s)
Sweedler, Jonathan V
Committee Member(s)
  • van der Donk, Wilfred A
  • Chan, Jefferson
  • Yau, Peter M
Department of Study
Chemistry
Discipline
Chemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
  • Proteomics
  • Peptidomics
  • Mass Spectrometry
  • Liquid Chromatography
  • Peptides
  • Neuropeptides
Abstract
The basic tenets of the central dogma of biology assert that genetic information in a biological organism is transferred through the transcription of DNA into RNA or the reverse, as well as through the translation of RNA into the amino acid sequences that make up a protein. While this concept provides the framework for many insights and advances in molecular biology, there is an added layer of complexity at the protein and peptide level. For instance, while a particular gene encodes a protein, it cannot be known from the gene alone how the protein expression profile in the tissue or cell is altered, how the protein may be post-translationally modified, or how the protein will be transferred to other regions to exert its biological functions. Furthermore, most bioactive signaling peptides are derived from precursor proteins that are differentially processed in different tissues and cell types. Protein expression levels cannot always be relied upon for predicting the processing of the multitude of bioactive peptides that can be generated from a prohormone precursor. Additionally, as our current understanding of various physiological processes expands, it is becoming clear that a specific protein may possess multiple distinct functions. A well-known example of this phenomenon is hemoglobin, whose main role is to serve as an oxygen-transport metalloprotein in red blood cells; however, over recent years it has been shown that several hemoglobin-derived peptides have different pharmacological properties involved in pain relief and immunity. Thus, it is clear that there is not only a tremendous level of structural complexity at the protein and peptide level, but also complexity in terms of protein functions. Here, these issues between gene expression and protein translation and function are addressed. Proteomic and peptidomics are the primary techniques used to characterize proteins and endogenous peptides, respectively, in a biological specimen. These approaches allow an accurate representation of their in vivo molecular profiles in response to certain diseases or stimuli. Furthermore, with these approaches, potentially hundreds to thousands of proteins and peptides can be quantified in both untargeted and targeted studies to understand their dysregulation under various pathological conditions. However, various challenges are often associated with these types of measurements with regards to the appropriate sampling techniques employed for preserving the integrity of the endogenous protein and peptide profiles, instrumentation that enables sensitive identification for often trace-level biomarkers, and the appropriate bioinformatic tools for accurate processing and assessment of the proteomic and peptidomic data. Therefore, in this thesis, these challenges will be addressed through the discussion of several projects that incorporated liquid chromatography-mass spectrometry, and various bioinformatic tools to assess how bioactive proteins and peptides are altered in various metabolic and neurological disorders in various sample types including neuronal tissues, plasma, and pericyte-derived exosomes. Furthermore, different search engines will be compared to assess various metrics for peptidomic applications. From these studies, we further our understanding of how various proteins and endogenous bioactive peptides play a role in disease progression and regulation.
Graduation Semester
2022-05
Type of Resource
Thesis
Handle URL
https://hdl.handle.net/2142/115560
Copyright and License Information
Copyright 2022 Eduardo Alejandro De La Toba

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