In cancer management early diagnosis is crucial for successful treatment. Unfortunately, patients mostly present with advanced disease, limiting therapeutic options. Therefore, screening of the general population for cancer can enhance earlier diagnosis and better treatment, decreasing cancer mortality. Furthermore, close monitoring of patients enables early detection of relapse and more efficient treatment. As proteins reflect the actual state of an organism and are readily measurable in biological matrices such as blood, they can excellently fulfil a role as biomarkers for cancer. Especially the development of mass spectrometry has enhanced fast and easy analysis of the protein content of (clinical) samples. We applied surface-enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI-TOF MS) for the detection of new potential biomarkers for colorectal cancer (CRC) and renal cell cancer (RCC). In a retrospective study, serum protein patterns comprising, among others, apolipoprotein C-I were found that could reliably discriminate patients with advanced CRC from healthy persons. Furthermore, combination of these patterns with the currently used CRC marker CEA showed better performance than CEA alone. The decrease of apolipoprotein C-I serum levels in CRC was validated in a prospective study in patients with mostly early-stage CRC, adenomatous polyps (AP) and controls with an indication for colonoscopy. Comparable to CEA, apolipoprotein C-I levels did not return to normal immediately after surgical resection of the tumour, but gradually within 3 months. In colorectal tissue of these patients, several proteins which were gradually changing in abundance between control, AP and CRC, or between the different histologic subtypes of AP were found. Further structural identification of these proteins can provide insight into the pathophysiological mechanisms underlying or accompanying the development of CRC. For clinical application as a biomarker, quantitative analyses for apolipoprotein C-I need to be developed to establish reliable cut-off levels to identify patients with CRC. Furthermore, strict sample handling protocols are essential for proteomic investigations, as e.g. proteolysis during storage can severely alter protein profiles. To investigate the validity and robustness of reported serum protein profiles for RCC, two distinct patient populations of RCC and controls were assessed in our laboratory. One of the proposed RCC biomarker candidates was indeed validated, but many others were not, exemplifying problems with analytical reproducibility and statistical problems of data over-fitting. Using a new analytical protocol, two new RCC protein profiles could be defined. Since sensitivity and specificity were 60-85%, these profiles are presently not suitable for use in diagnostic screening, although they might have a role in follow-up of RCC patients. However, a five-protein serum profile predicting RCC prognosis could be identified and was demonstrated to be a strong and independent predictor of survival when tested against the extended Memorial Sloan-Kettering Prognostic Factors Model. Concluding, the development of high-throughput mass spectrometric protein profiling approaches such as SELDI-TOF MS has facilitated the comprehensive analysis of a large part of the proteome in clinical samples. Thus, this technique has shown to be very useful in the search for new biomarker candidates for CRC and RCC in human serum and tissue
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