Protein interactions 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, unbiased or large-scale quantitation of protein interactions within native living systems is a challenge that is unmet by today's technology. The capacity to identify and quantitate protein interactions on a large-scale within native cells, patient samples, or tissues does not currently exist. 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. This project aims to develop and apply quantitative cross-linking with cancer cells with advanced Protein Interaction Reporter (PIR) technology. Stable Isotope Label of Amino acids in Cell culture (SILAC) will be combined with PIR technology to allow quantitation of protein levels and protein interactions in cells. These capabilities will be applied to cisplatin-, taxol-, and SN-38 resistant cancer cells to allow quantitation of interactions relative to drug sensitive cancer cells. This project will provide the first relative quantitation data on protein interactions in cancer cells and the first unbiased measurements of functional regulation at the protein interaction level relevant to drug resistance.

Public Health Relevance

Drug resistance in cancer treatment is the primary reason for therapy failure and will likely remain a primary factor leading to cancer patient death until functional regulation that supports drug resistance can be better understood. Functional regulation in all cells is achieved by changes in protein abundance, localization, interactions and topological features. This project will develop and apply advanced technology to help visualize changes in functional regulation in cancer cells that have acquired drug resistance.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Drug Discovery and Molecular Pharmacology Study Section (DMP)
Program Officer
Edmonds, Charles G
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University of Washington
Schools of Medicine
United States
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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
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
Chavez, Juan D; Lee, Chi Fung; Caudal, Arianne et al. (2017) Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Cell Syst :
Schweppe, Devin K; Chavez, Juan D; Navare, Arti T et al. (2016) Spectral Library Searching To Identify Cross-Linked Peptides. J Proteome Res 15:1725-31
Wu, Xia; Chavez, Juan D; Schweppe, Devin K et al. (2016) In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nat Commun 7:13414
Schweppe, Devin K; Chavez, Juan D; Bruce, James E (2016) XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Bioinformatics 32:306-8
Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K et al. (2016) A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. PLoS One 11:e0167547
Schweppe, Devin K; Zheng, Chunxiang; Chavez, Juan D et al. (2016) XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data. Bioinformatics 32:2716-8
DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M et al. (2016) Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology. J Virol 90:1973-87
Lee, Chi Fung; Chavez, Juan D; Garcia-Menendez, Lorena et al. (2016) Normalization of NAD+ Redox Balance as a Therapy for Heart Failure. Circulation 134:883-94

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