Shotgun proteomics identifies proteins specific for acute renal transplant rejection

Purpose: Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. Experimental design: We used shotgun proteomics applying LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls. Results: A total of 1446 urinary proteins (UP) were identified along with a number of nonspecific proteinuria-specific, renal transplantation specific and AR-specific proteins. Relative abundance of identified UP was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific UP in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (uromodulin, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these UP in AR. Conclusions and clinical relevance: This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of UP for serial, non-invasive clinical monitoring for graft rejection after kidney transplantation.