Protein interaction networks are key determinants of protein function in biological systems. Despite the potential that quantitative protein interaction information could have for all areas of cancer research, global or large-scale quantitation of protein interactions within native living systems is a challenge that is unmet by today's technology. Improved capabilities to quantitate protein interactions will have a major impact on the understanding of cancer, metastasis and the development of anti-cancer drug resistance, among many other areas. This project aims to develop and apply novel Protein Interaction Reporter (PIR) technology in conjunction with stable isotope labeling and label-free methods to enable large-scale quantitation of protein interactions and topological features in cancer cells. PIRs are chemical cross-linkers that possess cleavable bonds that allow the compounds to be dissociated with high specificity within the mass spectrometer. This allows complex cross-linking products that result from on-cell cross-linking reactions to be measured as an intact complex and then, identified through the detection of an expected mass reporter ion and intact peptide ions that are released upon PIR activation. In this project, PIR compounds will be synthesized and used to identify protein interactions in cancer cells using mass spectrometry. This will be done by establishing cross-linked peptide connectivity through expected PIR mass relationships and targeted MS/MS on released peptides to identify proteins. The next phase of research will involve the combined application of PIR technology with isotope labeling and label-free methods to cancer cells, cells that have been treated with anticancer drugs, and cancer cells that have developed drug resistance. Successful application of this technology will for the first time, demonstrate the potential for large-scale quantitation of protein interactions in cells and will identify protein interactions relevant to cancer cell drug resistance.

Public Health Relevance

The relevance of the proposed research to public health relates to the identification of protein interactions involved in cancer cell progression and the development of drug resistance. Identification of changes in protein interactions that occur in cancer cells with the onset of drug resistance can lead to alternative strategies to help overcome anti-cancer drug resistance in cancer cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086688-02
Application #
7934512
Study Section
Drug Discovery and Molecular Pharmacology Study Section (DMP)
Program Officer
Edmonds, Charles G
Project Start
2009-09-18
Project End
2011-09-29
Budget Start
2010-09-01
Budget End
2011-09-29
Support Year
2
Fiscal Year
2010
Total Cost
$365,067
Indirect Cost
Name
University of Washington
Department
Genetics
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Chavez, Juan D; Lee, Chi Fung; Caudal, Arianne et al. (2018) Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Cell Syst 6:136-141.e5
Vreven, Thom; Schweppe, Devin K; Chavez, Juan D et al. (2018) Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking. J Mol Biol 430:1814-1828
Xu, Li; Gordon, Ryan; Farmer, Rebecca et al. (2018) Precision therapeutic targeting of human cancer cell motility. Nat Commun 9:2454
Park, Sung-Gun; Anderson, Gordon A; Bruce, James E (2018) Parallel detection in a single ICR cell: Spectral averaging and improved S/N without increased acquisition time. Int J Mass Spectrom 427:29-34
Mohr, Jared P; Perumalla, Poorna; Chavez, Juan D et al. (2018) Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem 90:6028-6034
Chavez, Juan D; Bruce, James E (2018) Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Curr Opin Chem Biol 48:8-18
Zhong, Xuefei; Navare, Arti T; Chavez, Juan D et al. (2017) Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers. J Proteome Res 16:720-727
Kaufman, Daniel M; Wu, Xia; Scott, Barbara A et al. (2017) Ageing and hypoxia cause protein aggregation in mitochondria. Cell Death Differ 24:1730-1738
Schweppe, Devin K; Chavez, Juan D; Lee, Chi Fung et al. (2017) Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci U S A 114:1732-1737
Nygren, Patrick J; Mehta, Sohum; Schweppe, Devin K et al. (2017) Intrinsic disorder within AKAP79 fine-tunes anchored phosphatase activity toward substrates and drug sensitivity. Elife 6:

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