Combined Blood/Tissue Analysis for Cancer Biomarker Discovery: Application to Renal Cell Carcinoma

Mass spectrometry (MS) methods allowing for the identification of tumor proteins in blood may enable cancer biomarker. Urgent needs in this domain include assays for: cancer diagnosis, therapy selection, prognosis, and monitoring.1 Both cancer biology and clinical oncology are undergoing rapid transformations, specifically, from an organ-centric to molecular pathways focused disciplines. Therefore, methods allowing for an improved molecular characterization of a patient’s actual malignant process/tumor may facilitate the development of advanced assays for personalized cancer diagnosis and management.2 Molecular profiling of a patient’s tumor may provide better insights into the cancer-induced derangements relevant to the malignancy under study, with the eventual and ultimate hope of benefits to patient outcome.2 MS-based proteomics may play an important role in characterizations of proteins within clinical samples. Therefore, innovative approaches focused on method development for proteomic profiling of clinically relevant specimens are critically needed.3 Despite advances in cancer biomarker research, the translation of proteomic methods and findings to applicable clinical assays has been disappointing.4 Principal factors that hinder mass spectrometry (MS)-based biomarker research using clinical samples include: (i) significant heterogeneity of solid tumors,5 (ii) formidable variability of protein expression in the human population proper, serving as a potential source of analytical/statistical bias,4 (iii) significant mismatches between the dynamic range of MS instrumentation and the protein content of clinical specimens,3 and (iv) the majority of proteomics-derived “potential” cancer biomarkers were not germane to the tumor in question.4 Many of these putative cancer biomarkers fall into the categories of acute-phase reactants and likely lack specificity to the pathologic process under study.4 Identifying relevant differences within the blood proteome from healthy and cancer patients is difficult due to the common lack of specificity of the findings. This may be influenced by a plethora of physiological and analytical factors. Additionally, numerous differences can be detected when comparing such cohorts. The major obstacle is proving which differences are dependent on the presence of the cancer and which result from physiological bias or analytical variability. While blood-based biomarkers would revolutionize cancer management, the commonly followed strategy of only analyzing serum or plasma from patients makes it very difficult to trace the origin of proteomic differences back to a tumor. In this study, we present the results from a combined tumor/plasma proteome analysis of samples acquired from a single patient. This strategy aims to recognize tumor proteins within the blood and may possess a higher probability of surviving the rigors of verification and validation necessary for generating useful clinical biomarker candidates. The objective of this investigation was to develop a proteomic method capable of reliably profiling the proteome of a solid tumor, and determine whether any of the identified proteins in the tumor proper are detectable in the blood of a patient newly diagnosed with a non-metastatic cancer.