1. Analytical Needs of Personalized Oncology
With the development of personalized therapeutics for oncology, the systematic and targeted analysis of selected proteins in tumor tissues is currently receiving increasing interest. As a matter of fact, the majority of proteins that can be by targeted by therapeutics are cell surface receptors or proteins involved in cellular signaling. Yet, the number of clinically approved biomarkers is much lower than the number of proteins that could potentially be inhibited with small molecule drugs and therapeutic antibodies. Apart from prime examples such as therapeutic antibodies targeting the HER2 receptor in breast cancer or CD20 in malignant lymphoma, the majority of cancer types are still in need of suitable biomarkers that allow patient-tailored treatment. Hence, a systematic characterization of those membrane receptors and signaling proteins that can be targeted with the repertoire of currently available targeted drugs would be required in the first place to advance the personalized treatment of cancer patients. Therefore, immunoassay-based technologies present a promising experimental approach since they can quickly deliver quantitative information on the expression of already known target proteins.
Screening clinical tissues for target proteins of potential pharmaceutical interest requires large numbers of well-documented clinical samples to yield statistically relevant data. High capacity platforms such as reverse phase protein arrays (RPPA), for example, are therefore well suited for this purpose. However, targeted proteomics requires first of all profound insights into cellular processes underlying cellular transformation and metastasis and a good knowledge of biochemistry. Fundamental changes of the cellular proteome occur immediately post-excision, a process described as cold ischemia. In fact, clinical tissues are still alive and biochemical processes will still proceed as long as enzymes are not inactivated by freezing or other suitable measures [1]. Enzymatic activities can also be re-activated during sample-thawing and lysate preparation. With this in mind, suitable measures are required to preserve the cellular proteome during all working steps of sample preparation and sample handling. Especially, the phosphoproteome is subjected to fast regulation since the turnover rates of kinases and phosphatases are high, and protein kinases will particularly benefit from the ample ATP reservoir of cancer cells. Several studies aimed for quantifying the turnover of protein composition as well as the proteome during cold ischemia. Apparently, 30% of all proteins change within the first half hour after surgical excision [2]. However, after 30 min of cold ischemia, about 75% of protein and phosphoproteins seem to be stable until 24 h after surgery [3]. Therefore, biochemical processes occurring post-excision need to be taken into account as an important pre-analytical factor that will influence the resulting sample quality and require standardized procedures regarding tissue handling as well as sample preparation to ensure comparable sample quality. Hence, to set-up a bio-bank, clinical tissues need to be processed under consistent conditions over many years to exclude artifacts resulting from tissue handling and storage.