High-throughput Proteomics for Biomarker Discovery

Description

The ability to reliably, robustly, and reproducibly detect quantitative protein abundance from biofluids and tissues of patients would have many applications in both research and clinical medicine. SGTC enjoys a long-standing collaboration with the laboratory of Richard Smith (Pacific Northwest National Laboratory), one of the leading groups developing the liquid-chromatography mass spectrometry (LC-MS) approach to proteomics, with the aim of developing methods and analysis techniques for proteomics of human clinical samples. We are specifically involved in developing the computational methods for this approach and applying these methods directly to clinical problems

Selected Projects

Characterization of the Human Plasma Proteome

Blood comes into contact with many different tissues in the human body, and is also relatively easy to collect from patients. A better understanding of the human plasma proteome might allow us to better diagnose and treat a wide range of conditions. Using albumin and immunoglobulin depletion followed by 2-dimensional liquid chromatography – mass spectrometry, we were able to characterize about 5,000 proteins in human plasma. Plasma samples were taken from healthy controls, breast cancer patients, and trauma patients. Characterization of the plasma proteome is essential to further advances in plasma marker discovery.

Quantitative Proteome Analysis of Human Plasma Following Trauma, Burns and in vivo Lipopolysaccharide Administration

While the ability to detect presence or absence of a protein in plasma is useful, the availability of a quantitative proteomics platform has the potential to provide greater biological insight. To assess quantitative changes that occur in the plasma proteome in the inflammatory response, we analyzed plasma samples from individuals prior to and after lipopolysaccharide (LPS) exposure. Following severe trauma and burn injury, patients with similar injury characteristics often experience widely different outcomes, from healthy survival, to multiple organ failure, and even death. Many of these responses are thought to be consequences of the body’s own inflammatory response to injury. We have ongoing studies to identify predictive markers in blood plasma of multiple organ failure and survival.

The Immunocellular Proteome

By combining clinical bedside microfluidics with proteomics, we have been able to undertake the study of individual cell populations of T-cells, monocytes, and neutrophils in trauma patients. We have characterized proteins that are present in each of these cell types, and are currently in the process of analyzing quantitative data from each of these cell-type-specific proteomics assays.

Urine Proteome in Renal Transplant Rejection

Following renal transplant, a subset of patients undergo acute graft rejection. Currently the gold standard for reliable diagnosis of graft rejection is renal biopsy, an unconfortable and invasive procedure that can have an adverse impact on the patient. We are analyzing uring from pools of healthy controls, stable transplants, and acute rejection patients to identify potential markers that might help us identify patients undergoing acute rejection. A urine-protein-based approach would allow for cheaper and more frequent testing for acute rejection, possibly leading to earlier diagnosis and treatment and improved patient outcome.

Personnel

Amit Kaushal, Claire Ryu, Hong Gao and Wenzhong Xiao in collaboration with Weijun Chen, David Camp and Dick Smith at the Pacific Northwest National Laboratory.

 

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