Host-centric proteomics : laying the foundation to use human stool proteins as biomarkers of gastrointestinal disease
Abstract/Contents
- Abstract
- It is common practice for a physician to request a blood draw at a doctor's visit in order to determine the levels of key molecules in our blood as proxy's for a healthy or diseased state. Though this is a common practice, establishing these molecules' usefulness as diagnostic agents often takes many years. First, it is necessary to determine what molecules are present in blood. Then, extraction protocols for these molecules need to be established in order to ensure reproducible and measurable results. Next, it is necessary to establish the variability of these molecules across healthy people. Finally, it is necessary to ascertain whether these molecules can distinguish states of health or disease based on their abundance or presence in each phenotype. While these steps have been taken countless times in establishing blood biomarkers, thus far human stool has seen limited use as a source of biomarkers. However, new biological discoveries have brought a renewed interest to human stool. In 2013, microbiome sequencing became cheap and high-throughput. The development of this technology allowed researchers to study the microbiome under a multitude of conditions, including how the microbiome changed in the gut. However, these microbes are not living in isolation and constantly interact with and influence the human gut. One avenue through which microbes and their hosts interact is through the use of proteins secreted by cells in the epithelium. Several protein classes are prevalent in stool including structural, immune, and digestion-related proteins. Given the functional importance of gut-related proteins and their relation to the microbiome, it is important to understand their temporal and insult-related changes. The Elias lab has developed a protocol to enrich and purify these proteins from stool and characterize their abundance using mass-spectrometry-based proteomics. Using a mass spectrometer as a diagnostic approach offers the user many excellent attributes in a diagnostic. This host-centric proteomics approach is quantitative, non-invasive, multi-dimensional, and directly gastrointestinally targeted. The goal of this thesis is to further establish the use of human stool proteins as diagnostic markers of gastrointestinal health using mass spectrometry-based proteomics. First, I optimized a protocol focused on human stool that reliably and reproducibly extracts proteins from stool and enables their quantitation on proteomics platform. Next, I describe how these proteins and their relative abundances vary in healthy people. From this study I found that the largest source of variability of human stool protein abundance was between people. This allows us to control for this variability in the future by studying many people to determine "healthy" protein abundance ranges. Finally, I report stool proteins distinguish states of flare or remission in inflammatory bowel disease patients.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2019; ©2019 |
| Publication date | 2019; 2019 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Casavant, Ellen Pun |
|---|---|
| Degree supervisor | Wandless, Thomas |
| Thesis advisor | Wandless, Thomas |
| Thesis advisor | Elias, Joshua |
| Thesis advisor | Holmes, Susan |
| Thesis advisor | Mallick, Parag, 1976- |
| Thesis advisor | Relman, David A |
| Degree committee member | Elias, Joshua |
| Degree committee member | Holmes, Susan |
| Degree committee member | Mallick, Parag, 1976- |
| Degree committee member | Relman, David A |
| Associated with | Stanford University, Department of Chemical and Systems Biology. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Ellen Pun Casavant. |
|---|---|
| Note | Submitted to the Department of Chemical and Systems Biology. |
| Thesis | Thesis Ph.D. Stanford University 2019. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2019 by Ellen Pun Casavant
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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