Bioinformatic Analysis of the Urine Proteome of Acute Allograft Rejection

Abstract

Abstract. The urinary proteome in health and disease attracts increasing attention because of the potential diagnostic and pathophysiologic biomarker information carried by specific excreted proteins or their constellations. This cross-sectional study aimed to analyze the urinary proteome in patients with biopsy-proven acute rejection (n ϭ 23) compared with transplant recipients with stable graft function (n ϭ 22) and healthy volunteers (n ϭ 20) and to correlate this with clinical, morphologic, and laboratory data. Urine samples were preadsorbed on four different protein chip surfaces, and the protein composition was analyzed using a surface-enhanced laser desorption/ionization time-of-flight mass spectrometer platform. The data were analyzed using two independent approaches to sample classification. Patients who experienced acute rejection could be distinguished from stable patients with a sensitivity of 90.5 to 91.3% and a specificity of 77.2 to 83.3%, depending on the classifier used. Protein masses that were important in constructing the classification algorithms included those of mass 2003.0, 2802.6, 4756.3, 5872.4, 6990.6, 19,018.8, and 25,665.7 Da. Normal urine was distinguished from transplant urine using a protein marker of mass 78,531.2 Da with both a sensitivity and a specificity of 100%. In conclusion, (1) urine proteome in transplant recipients with stable graft function was significantly different from healthy control subjects, and (2) acute rejections were characterized by a constellation of excreted proteins. Analysis of the urinary proteome may expedite the noninvasive prediction of acute graft rejection, thus importantly assisting in establishing the diagnosis.

Proximal tubular dysfunction as an indicator of chronic graft dysfunction

“…Urinary proteomic analyses have already been shown to identify a specific profile in acute rejection with more than 90% sensitivity (58,59). Its role in detecting proximal tubular dysfunction is totally undefined, although it has long been established that this condition alters the profile of urinary proteins compared to normal urinary proteome.…”

A better understanding of molecular mechanisms underlying human disease

“…Three independent approaches demonstrated the ability of SELDI-TOF to identify the presence of acute rejection analysing urine samples [194][195][196]. In a recent approach, urinary protein pattern in type 1 diabetic adolescents with early diabetic nephropathy was identified using high-resolution CE coupled with MS [197].…”

Proteomics and Renal Transplantation: Searching for Novel Biomarkers and Therapeutic Targets

“…Interestingly, each group found a different set of urinary proteins that are associated with the investigated process. To understand these apparent discrepancies, one must consider that in each study disease definition, sample collection, [15,26] found that decreasing levels of urinary ␤-defensin-1 and increasing levels of a fragment of ␣ 1 -antichymotrypsin were associated with renal allograft rejection. Although we identified a different protein as a potential biomarker for renal allograft rejection (i.e.…”

“…allograft rejection, polyoma BK virus nephropathy) [13][14][15][16][17]. Urine might be a valuable source for biomarker development of processes primarily affecting the tubulointerstitial compartment (e.g.…”

“…Although there are several different proteomic platforms, high-throughput technologies such as surface-enhanced laser desorption/ionization time-offlight mass spectrometry (SELDI-TOF MS) [13][14][15]17] and capillary electrophoresis coupled to mass spectrometry (CE-MS) [16] were used in all currently published studies searching for novel urine biomarkers in renal transplantation. Therefore, in the following paragraphs these two platforms will be described and discussed in more detail, while referring to recently published reviews regarding advantages and limitations of other proteomic approaches [20,21].…”