Aims

The Johns Hopkins University Proteomics Center applies state-of-the-art methods and develops new approaches and techniques to investigate a biological process of broad interest to heart, lung and blood diseases: adaptation to ischemia/hypoxia.  In the course of minute-to-minute physiological function, all mammalian tissues experience variable blood supply and changing oxygen availability.  To satisfy energetic and metabolic needs, cells and tissues must adapt quickly to such changes in perfusion or oxygenation. Adaptive changes to hypoxia and ischemia become even more prominent in pathological states such as coronary artery disease, thrombosis and hypoxic lung injury. The mechanisms that govern such adaptive responses are central to biology but remain poorly-understood. Because hypoxia and ischemia trigger immediate responses in the affected tissues, post-translational modification of the proteome will dominate the initial response (whether or not longer-term changes in gene expression also occur).  Identification and detailed characterization of the normal and diseased proteomes in response to ischemia/hypoxia over time is a necessary step in understanding the adaptive mechanisms. The goal will be to eventually obtain ?disease protein fingerprints? of numerous ischemic/hypoxic disorders, which may then provide a unified picture of the pathogenesis ? the unique features in, and commonalities among, the various stages of injury and tissue types. State-of-the-art and innovative methods, coupled with equally state-of-the-art and innovative biology, form the cornerstone of the Hopkins proposal.

Philosophy and goals: The central philosophy of our Center is as follows: compelling biological questions will drive innovation in technologies of protein chemistry, instrumentation and data analysis. In turn, the application of innovative technologies will revolutionize our understanding of the biology of ischemia/hypoxia. Two types of projects drive our proposal: biological challenges and technological innovations.  The biological challenges motivate six projects that are unified by the theme of adaptation to ischemia/hypoxia:

1. Post-translational modifications of HIF-1a and their functional significance (G. Semenza)
2. Lung endothelial cytoskeletal responses to ischemia (J. Garcia)
3. Proteomic consequences of hypoxia on cell proliferation (C. Dang)
4. Mechanisms of ischemic preconditioning and cardioprotection (E. Marbán)
5. Functional importance of proteomic changes in myocardial stunning (A. Murphy)
6. Identification and detection of novel serum biomarkers of myocardial ischemia in humans (J. Van Eyk)

 The technological innovations feature:

1.      Development of novel proteomic methods to study glycosylation and phosphorylation and dynamic changes to the proteome (G. Hart, A. Pandey, R. Cole)

2.      Development of novel mass spectrometry instrumentation and methods for proteomics (R. Cotter)

3.      Technological innovation in informatics and modeling of proteome dynamics (R. Winslow)

We view the biology and the technology as being highly synergistic, and have structured our proposal to foster such synergy as much as possible. A key feature is the central role for a Technical Implementation and Coordination Core (TICC) facility.  As the name implies, the TICC?s major functions are: (1) coordination of the interaction among biological samples, protein chemistry, analysis, data storage and data dissemination; and (2) reduction to practice and implementation of novel technologies to be developed by the Center.