Our central philosophy is that compelling biological and clinical questions drive innovation through development, optimization and adaption of proteomic technologies, functional analysis, and large-scale data handling. The primary research focuses i) on understanding the molecular mechanism underlying acute and chronic disease and treatment therapies and ii) in the development of clinically robust circulating biomarkers directly or via investigation of secreted proteins. My laboratory has developed technological pipelines to quantify protein isoform and post-translational modifications (PTM) changes of proteins in disease pathways. This includes understanding interplay between competing PTMs like O-GlcNAc and phosphorylation and multiple oxidative modifications. Our group also develops multiple reaction monitoring assays, a MS-based quantitative method, for a number of signaling pathways to determine their absolute concentration. The goal being able to carry out large scale quantification of proteins characterization and quantification of 1000s of samples. Our academic group has its own research but also it acts to facilitate innovative methods to the broader scientific community.
Selected Peer-reviewed Publications (182 peer-reviewed articals/23 chapters/2 books (21 in 2012; 16 in 2013)
1. Murphy AM, Kogler H, Georgakopoulos D, McDonough JL, Kass DA, Van Eyk JE, Marban E. Transgenic mouse model of stunned myocardium. Science2000;287:488. PMID: 10642551
2. Xu W, Liu Y,Wang S, McDonald T, Van Eyk JE, Sidor A, O'Rourke B. Cytoprotective role of the Ca-activated K+ channel in cardiac inner mitochondrial membrane. Science 2002;298: 1029. PMID: 12411707
3. Mathivanan S et al., Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 2008; 26:164-7. PMID: 18259167
4. Gao P, Tchernyshyov I, Chang T-C, Lee Y-S, Kita K, Ochi T, Zeller K, De Marzo AM, Van Eyk JE, Mendell JT, Dang CV. c-Myc suppression of miR-23 enhances mitochondrial glutaminase and glutamine metabolism. Nature 2009: 458:762. PMID: 2729443
5. Matt P, Schoenhoff F, Habashi J, Holm T, Van Erp C, Loch D, Carlson OD, Griswold BF, Fu Q, De Backer J, Loeys B, Huso DL, McDonnell NB, Van Eyk JE, Dietz HC; the GenTAC Consortium. Circulating transforming growth factor-beta in Marfan Syndrome. Circ. 2009:120:526. PMID: 19635970Editorial: Braverman AC. Transforming Growth Factor-beta. A Biomarker in Marfan Syndrome?.
6. Gundry RL, Raginski K, Tarasova Y, Tchernyshyov I, Bausch-Fluck D, Elliott ST, Boheler KR, Van Eyk JE Wollscheid B. The Mouse C2C12 Myoblast Cell Surface N-Linked Glycoprotein Subproteome. Mol. Cell Prot. 2009;8:2555. PMC27773721
7. Agnetti G, Kaludercic N, Kane LA, Elliott ST, Guo Y, Chakir K, Samantapudi D, Paolocci N, Tomaselli GT, Kass DA, Van Eyk JE. Modulation of Mitochondrial Proteome and Improved Mitochondrial Function by Bi- ventricular Pacing of Dyssynchronous Failing Hearts. Circ: Genetics, 2009:3:78. PMC2921909
8. Kane KA, Youngman MJ, Jensen RE, Van Eyk JE. Phosphorylation of the F1Fo ATP synthase ? subunit: Functional and structural consequences assessed in a model system. Circ Res. 2010:106:106504. PMC2835499. Paper was the Editor’s pick
9. Lindsay ME, Schepers D, Bolar NA, Doyle JJ, Gallo E, Fert-Bober J, Kempers MJ, Fishman EK, Chen Y, Myers L, Bjeda D, Oswald G, Elias AF, Levy HP, Anderlid BM, Yang MH, Bongers EM, Timmermans J, Braverman AC, Canham N, Mortier GR, Brunner HG, Byers PH, Van Eyk J, Van Laer L, Dietz, HC, Loeys BL. Loss-of-function mutations in TGFB2 cause a syndromic presentation of thoracic aortic aneurysm. Nat Genet. 2012:8;44:922 PMID: 22772368
10. Wang SB, Foster DB, Rucker J, O'Rourke B, Kass DA, Van Eyk JE. Redox Regulation of Mitochondrial ATP Synthase: Implications for Cardiac Resynchronization Therapy. Circ. Res. 2012.109:750. PMC3500591
11. Gao WD*, Murray CI*, Tian Y, Zhong X, Dumond JF, Shen X, Stanley BA, Foster DB, Wink DA, King SB, Van Eyk JE, Paolocci N. Nitroxyl(HNO)-Mediated Disulfide Bond Formation Between Cardiac Myofilament Cysteines Enhances Contractile Function. Circ Res,2012:111:1002 (*equal) PMC3470471 Editorial; Ge Y and Moss R Circ Res. 2012;111:954-956
12. Murray CI, Uhrigshardt H, O'Meally RN, Cole RN, Van Eyk JE. Identification and quantification of S-nitrosylation by cysteine reactive tandem mass Tag switch assay. Mol Cell Proteomics. 2-12:11:M111.013441. PMC3277766
13. Zhang P, Ji W, dos Remedios CG, Kirk JA, Kass DA, Van Eyk JE*, Murphy AM (*corresponding author). Multiple reaction monitoring to identify site-specific troponin I phosphorylated residues in the failing human heart. Circ. 2012:126:1828. PMC in process Editorial: White M and Cordwell S, Circ Res, in press.
14. Liu X, Jin Z, O'Brien R, Bathon J, Dietz HC, Grote E, Van Eyk JE. Constrained Selected Reaction Monitoring: Quantification of selected post-translational modifications and protein isoforms. Methods. 2013, in press
15. Jin Z, Fu Z, Yang J, Troncosco J, Everett AD, Van Eyk JE. Identification and Characterization of Citrulline-modified Brain Proteins by Combining HCD and CID Fragmentation. Proteomics. 2013, in press.
1. J.E. Van Eyk and M. Dunn. Genomic and Proteomic Analysis of Cardiovascular Disease: moleular mechanism, therapeutic targets and diagnostics. Wiley-VCH Publishers, 2003;
2. J.E. Van Eyk and M. Dunn. Clinical Proteomics: from Diagnosis to Therapy, Wiley-VCH Publishers, 2007\
Guest editor for proteomic or CVD series:
2001–2003.Circ Res (5 articles); 2005.J. Physiology (London) (5 articles);
2008 Proteomics: Clinical Application volume (July);
2010 Circulation Research (5 articles);
2011 Circulation Genetics educational series on Proteomics technology (13 articles).
Patent Applications: 5 patent, 12 applications in proteomic tools and software and protein biomarkers