ABSTRACT
During the initial phases of a study focussed on discovering new urinary biomarkers for renal cell carcinoma, a number of challenges and limitations were identified, which we subsequently investigated. The purpose of this report is to provide insight into experimental design for such investigations and potential confounding factors that can impact on such studies. Sixty urine samples from 20 patients with clear cell renal cell carcinoma and ten live renal transplant donor patients, pre- and post-nephrectomy, were profiled using SELDI-TOF-MS incorporating stringent quality control and in-house data processing/analysis. There were 65 significantly differentially expressed peaks (five solitary peaks and four peak clusters that increased post nephrectomy and four peak clusters that decreased). Peak 3934 Da m/z and peaks within 11731-11961 Da m/z, which increased post nephrectomy were identified as the 36 amino acid isoform of ß-defensin-1 and ß(2) -microglobulin, respectively. However, changes in these two protein forms were also seen in healthy donors following nephrectomy implying a relationship with kidney removal per se rather than tumour removal. This study indicates the difficulties in identifying SELDI peaks for subsequent validation and illustrates the need for appropriate controls in biomarker studies to determine whether changes are indirect consequences of treatment.