The Tissue Procurement and Sequencing Core (TPSC) is essential in providing support and resources for the Urologic Oncology Branch (UOB) and for our collaborators. It is the TPSC's responsibility to handle every biospecimen that is generated within the UOB, to process each specimen in order to preserve biomolecules, to keep an accurate inventory of each procurement, and to assist in the scientific analysis of select specimens, for the ultimate goal of elucidating biological pathways relating to kidney, prostate, and bladder cancers. The TPSC processes tissue from nearly 100% of UOB surgeries, as well as a subset of biopsies and other medical procedures. Typically, there are between two and five surgeries per week, resulting in surgical samples from over 100 patients procured per year, including kidney, prostate, and bladder carcinomas, adrenal tumors, uterine leiomyomas, lymph node metastases, and other specimens relating to sporadic and familial urologic cancer syndromes. Tissue is always procured in cooperation with Surgical Pathology, to ensure proper handling and accurate diagnosis. Tissue is snap frozen, preserved in formalin or glutaraldehyde, or processed for biomolecule purification and analysis. In addition, blood samples are regularly taken from patients with inherited syndromes, in order to prepare DNA for analysis. Serum or plasma is also collected from select patients for analysis of proteins and other biomarkers. In select cases, whole blood is frozen for future studies, and on rare occasions, RNA is also prepared from blood. Two to three dozen blood samples may be processed per week. Finally, the core also processes additional body fluids, such as urine, ascites or thoracic fluids, and cyst fluids, that may be taken from surgical or other medical procedures. Frozen samples are stored in liquid nitrogen or a -80 degree centigrade freezer. All specimens are assigned a de-identified lab number and entered into a secure database, Labmatrix. In all, over a thousand tissue and blood specimens have been procured within the last year. The entire UOB tissue repository contains in excess of 16,000 tissue samples and DNA from 1,200 blood samples from over 1,000 patients. Most of the samples were collected at the NIH Clinical Center, and full patient histories are incorporated into Labmatrix. Older samples currently in the FreezerWorks biorepository are also being entered promptly into Labmatrix, with the aim of completing the incorporation into Labmatrix in the near future. A future goal is for all clinical and laboratory findings to be incorporated into Labmatrix to provide an accessible resource for all of our studies from bench to bedside. A key function of the TPSC is to support clinical trials in progress within the Branch. We are currently involved in two clinical trials: Bevacizumab and Erlotinib for patients with type 1 papillary kidney cancer or HLRCC, and AstraZeneca ZD6474 for patients with VHL or sporadic clear cell kidney cancer. Blood samples are processed regularly by the TPSC, for the purpose of investigating pharmacodynamic and phamacokinetic effects of the drugs, as well as the study of other cancer biomarkers. In addition, for the Glaxo GSK1363089 study, we obtained and coordinated processing and evaluation of tumor specimens from patients in collaborative effort with other laboratories to ascertain tumor histology, gene mutations and chromosomal aberrations, for subsequent correlation with response to the drug. These studies are integral to the GSK1363089 drug protocol. Many of the tumor samples from kidney cancer surgeries are procured under sterile conditions to establish new cell cultures and mouse xenografts. We have generated over 300 kidney cancer cell lines, 43 of which have been extensively characterized for cancer gene mutations. These include lines generated from familial kidney cancer syndromes (BHD, SDHB, VHL, and 2 HLRCC lines) that provide unique reagents for studying the activity of these respective tumor suppressor genes. In the last year, approximately two dozen kidney tumors have been placed in cell culture and/or in SCID/BEIG or nude mice, with a subset of these growing viably in the short-term and a small number successfully established as immortal lines (four within the past year). These lines are invaluable for studying both the molecular basis of tumor development and prospective therapies. Cell lines are kept in standard carbon dioxide or low oxygen incubators or stored in liquid nitrogen, and mice are housed in an appropriate on-site facility. The BHD, HLRCC, SDHB, and VHL lines are being extensively characterized by DNA sequencing of selected genes, array CGH, realtime PCR, Western blotting, oxygen consumption and extracellular acidification rate, and metabolomics. In addition, 6 selected sporadic clear cell lines are being subjected to whole exome sequencing and metabolomic characterization. The Branch has also generated immortal B cell line samples from several hundred UOB patients from families with VHL, BHD, HPRC, HLRCC, or unknown familial kidney cancer syndromes. These lines provide an unlimited resource for germline DNA in order to characterize genetic aberrations of known genes of interest, as well as the potential to discover new genes that may involved in inherited kidney cancer in patients that have not yet been diagnosed. In addition, these lines provide the opportunity to study genes of interest at the RNA expression level. The collection of DNA samples for the detection and characterization of germline disease mutations has been at the heart of the gene discovery process in the UOB. Several dozen blood samples per year are analyzed by DNA sequencing, comparative genome hybridization (CGH) analysis, fluorescent in-situ hybridization (FISH), and/or other genetic studies. Furthermore, during a three year study using array CGH, we have performed fine mapping of germline deletions in 66 VHL families, 6 BHD families, 3 HLRCC families and one SDHB family, as well as one novel partial gene duplication in a BHD family. The goal has been twofold: to characterize previously undiagnosed clinically affected patients, and to correlate the sizes and locations of these deletions with the severity of disease and/or response to clinical treatments. We continue to use these techniques to discover new mutations, deletions, and amplifications. Both frozen and formalin-fixed tissues from kidney, prostate, and bladder cancers that have been processed by the TPSC have been used extensively by the UOB for characterization using techniques such as immunohistochemistry, quantitative PCR, expression microarrays, Northern and Western blotting, immunoprecipitation, and DNA sequencing. Glutaraldehyde-fixed tissues have been used for electron microscopy, in order to characterize subcellular organelles. Proper handling of our surgical specimens has been an essential factor in assuring the best quality laboratory results. The UOB is involved in providing aliquots of many of its procured tumor tissues and blood samples to collaborating laboratories. The Branch has long-standing collaborations in which we distribute tissue to other laboratories for cell culture and immunotherapy for kidney cancer patients, analysis of kidney cancer stem cell markers, protein and RNA studies of adrenal masses (pheochromocytomas), and molecular epidemiology studies of prostate cancers. We are now participating in both the Cancer Genome Atlas project by contributing clear cell and papillary kidney cancers, and the CCR Multi-Laboratory XMRV Prevalence Study by providing prostate cancer blood and tumor tissue. The sizeable biospecimen collection amassed by the UOB over the last 20 years provides an invaluable resource for both basic and clinical research regarding kidney, prostate and bladder cancers.
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