The surgical specimen is the personalized part of personalized cancer medicine

Simulating the contribution of a biospecimen and clinical data repository in a phase II clinical trial: A value of information analysis

The potential contributions of a centralized data warehouse or repository in clinical research include the expedited accrual of subjects for phase II trials. Understanding the contribution of data warehouses that integrate clinical, biospecimen, and molecular data for the conduct of clinical trials is essential to inform private and public decisions on resource allocation and investment. We conducted a value of information analysis using data from recent trials at the Moffitt Cancer Center and simulated the potential reductions in trial size due to possible alternative scenarios of expedited accrual. In this study, we compared alternative data sets using a single model to assess value of information. Our findings suggest that the reductions in trial size range from 0% to 43%, depending on the amount of censoring in overall survival. The ability to expedite the accrual of patients for clinical trial studies using large data repositories that store data on inclusion/exclusion criteria and response to standard of care therapies demonstrated significant improvement in reducing the number of subjects needed to achieve similar end-results, as evaluated using value of information analysis with a limited number of parameters and a parsimonious model of overall survival.

Effect of surgical procedures on prostate tumor gene expression profiles

Current surgical treatment of prostate cancer is typically accomplished by either open radical prostatectomy (ORP) or robotic-assisted laparoscopic radical prostatectomy (RALRP). Intra-operative procedural differences between the two surgical approaches may alter the molecular composition of resected surgical specimens, which are indispensable for molecular analysis and biomarker evaluation. The objective of this study is to investigate the effect of different surgical procedures on RNA quality and genome-wide expression signature. RNA integrity number (RIN) values were compared between total RNA samples extracted from consecutive LRP (n=11) and ORP (n=24) prostate specimens. Expression profiling was performed using the Agilent human whole-genome expression microarrays. Expression differences by surgical type were analyzed by Volcano plot analysis and gene ontology analysis. Quantitative reverse transcription (RT)-PCR was used for expression validation in an independent set of LRP (n=8) and ORP (n=8) samples. The LRP procedure did not compromise RNA integrity. Differential gene expression by surgery types was limited to a small subset of genes, the number of which was smaller than that expected by chance. Unexpectedly, this small subset of differentially expressed genes was enriched for those encoding transcription factors, oxygen transporters and other previously reported surgery-induced stress-response genes, and demonstrated unidirectional reduction in LRP specimens in comparison to ORP specimens. The effect of the LRP procedure on RNA quality and genome-wide transcript levels is negligible, supporting the suitability of LRP surgical specimens for routine molecular analysis. Blunted in vivo stress response in LRP specimens, likely mediated by CO(2) insufflation but not by longer ischemia time, is manifested in the reduced expression of stress-response genes in these specimens.

The Use of Immunohistochemistry for Biomarker Assessment—Can It Compete with Other Technologies?

A morphology-based assay such as immunohistochemistry (IHC) should be a highly effective means to define the expression of a target molecule of interest, especially if the target is a protein. However, over the past decade, IHC as a platform for biomarkers has been challenged by more quantitative molecular assays with reference standards but that lack morphologic context. For IHC to be considered a “top-tier” biomarker assay, it must provide truly quantitative data on par with non-morphologic assays, which means it needs to be run with reference standards. However, creating such standards for IHC will require optimizing all aspects of tissue collection, fixation, section thickness, morphologic criteria for assessment, staining processes, digitization of images, and image analysis. This will also require anatomic pathology to evolve from a discipline that is descriptive to one that is quantitative. A major step in this transformation will be replacing traditional ocular microscopes with computer monitors and whole slide images, for without digitization, there can be no accurate quantitation; without quantitation, there can be no standardization; and without standardization, the value of morphology-based IHC assays will not be realized.

Distribution of CPP-Protein Complexes in Freshly Resected Human Tissue Material

Interest in cell-penetrating peptides (CPPs) as delivery agents has fuelled a large number of studies conducted on cultured cells and in mice. However, only a few studies have been devoted to the behaviour of CPPs in human tissues. Therefore, we performed ex vivo tissue-dipping experiments where we studied the distribution of CPP-protein complexes in samples of freshly harvested human tissue material. We used the carcinoma or hyperplasia-containing specimens of the uterus and the cervix, obtained as surgical waste from nine hysterectomies. Our aim was to evaluate the tissue of preference (epithelial versus muscular/connective tissue, carcinoma versus adjacent histologically normal tissue) for two well-studied CPPs, the transportan and the TAT-peptide. We complexed biotinylated CPPs with avidin--galactosidase (ABG), which enabled us to apply whole-mount X-gal staining as a robust detection method. Our results demonstrate that both peptides enhanced the tissue distribution of ABG. The enhancing effect of the tested CPPs was more obvious in the normal tissue and in some specimens we detected a striking selectivity of CPP-ABG complexes for the normal tissue. This unexpected finding encourages the evaluation of CPPs as local delivery agents in non-malignant situations, for example in the intrauterine gene therapy of benign gynaecological diseases.