Banking of fresh-frozen prostate tissue: methods, validation and use

Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility

Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. We sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at -80 °C, vacuumed sealed and stored at -80 °C, with matrix preapplied before storage at -80 °C, under a nitrogen atmosphere and stored at -80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at -80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.

A New Technique in Fresh Prostate Cancer Tissue Biobanking Based on MRI-Transrectal Ultrasound Fusion Biopsy

OBJECTIVE

To present and validate a new technique for biobanking fresh-frozen prostate cancer tissue based on MRI-transrectal ultrasound fusion biopsy.

MATERIALS AND METHODS

From August 2014 to August 2016, patients with elevated levels of PSA and at least 1 suspicious lesion on MRI were invited to this study. Each MRI-suspicious lesion was biopsied repeatedly for at least 2 cores in the same location. These repeated cores were labelled A/A', B/B', etc. The A/B cores were submitted for histologic assessment, and the corresponding A'/B' cores were stored in an -80°C freezer for biobanking. Sixty biobanked samples were processed for histologic assessment to compare their pathologic parameters with their corresponding paraffin samples. Another 20 biobanked samples were processed for RNA quality evaluation.

RESULTS

Fifty-six of the 60 selected banking samples matched their corresponding paraffin samples for benign vs malignant diagnosis, leading an overall concordance rate of 93.3%. There was no significant difference between banking samples and the corresponding paraffin samples in cancer percentage and Gleason score. The RNA Integrity Number value ranged from 6.8 to 9.3 (mean 7.89).

CONCLUSION

The current study demonstrates that the histologic identity of the banked prostate biopsy sample can be accurately predicted by its corresponding paraffin samples. MRI-TRUS fusion biopsy based biobanking method is highly efficient, timesaving, and has high quality tissues both at the histologic and RNA integrity levels.

Fast prostate retrieval in robot-assisted laparoscopic prostatectomy for next-generation biobanking

Robotic-assisted laparoscopic radical prostatectomy (RALP) has become the most widespread treatment for organ-confined prostate cancer. Here, we describe a fast specimen retrieval technique for RALP to obtain high-quality tissue specimen with minimal warm ischemia time for next-generation biobanking. Here, we show that using fast retrieval technique, short warm ischemia times can be achieved while not increasing the surgical time. Patients undergoing RALP with written informed consent participated in Helsinki Urological Bank study. Previously operated RALP patients and those, who were not willing to participate in the study, served as a control group. The study consisted of 1685 patients, 684 in fast retrieval and 1001 in control group. We developed a novel fast retrieval technique in which fascia is opened for camera port according to the prostate size and a running suture is placed and tightened against the camera port in the beginning of the operation. Immediately after prostate is freed from attachments, suture is loosened and the prostate is extirpated inside the endoscopic bag through the camera port fascial opening, then the fascial suture is again tightened against the camera port and the RALP procedure is completed. The mean warm ischemia times in fast retrieval group were 20 min 18 s and 22 min 30 s, respectively, in patients without and with lymphadenectomy. The mean console and surgery times with and without lymphadenectomy were similar in both groups. There were no technique-related complications associated with Fast Retrieval procedure. Tissue integrity test results for the RNA and DNA quality showed good quality for the specimen. Fast retrieval technique can easily and safely be utilized to maximize usefulness of RALP tissue specimen in downstream biobank applications.

A novel technique for biobanking of large sections of radical prostatectomy specimens

AIMS

Harvesting of unfixed tissue from radical prostatectomy specimens for research purposes is challenging. Many prostate cancers cannot be identified at gross inspection, and this tumour is notoriously multifocal and heterogeneous. We aimed to develop a technique to allow detailed topographic analysis and the sampling of a sufficient amount of tumour without jeopardising clinical reporting.

METHODS AND RESULTS

A custom-made double-bladed knife was utilised for cutting a 4-mm-thick horizontal section of the prostate. The slices were split into segments that were frozen in gel, cryosections were cut, and RNA integrity numbers (RINs) were analysed. Sections were cut from all blocks of 20 cases, and the cutting time was monitored. Slides were scanned, and the slices were digitally reconstructed. Cutting frozen sections of an entire slice took 79-253 min (mean 162 min). Tumour was detected in frozen sections of 85% (17/20) of cases and in 46% (72/155) of blocks. The morphological quality was determined to be excellent, and RIN values were high (mean 8.9).

CONCLUSIONS

This novel protocol for biobanking of fresh tissue from prostatectomy specimens provides sufficient tumour material for research purposes, while also enabling reporting of histopathology. The harvesting of a full tissue slice facilitates studies of tumour multifocality and heterogeneity.

Strategies for biochemical and pathologic quality assurance in a large multi-institutional biorepository; The experience of the PROCURE Quebec Prostate Cancer Biobank

Well-characterized, high-quality fresh-frozen prostate tissue is required for prostate cancer research. As part of the PROCURE Prostate Cancer Biobank launched in 2007, four University Hospitals in Quebec joined to bank fresh frozen prostate tissues from radical prostatectomies (RP). As the biobank progressed towards allocation, the nature and quality of the tissues were determined. RP tissues were collected by standardized alternate mirror-image or biopsy-based targeted methods, and frozen for banking. Clinical/pathological parameters were captured. For quality control, two presumed benign and two presumed cancerous frozen, biobanked tissue blocks per case (10/site) were randomly selected during the five years of collection. In a consensus meeting, 4 pathologists blindly evaluated slides (n=160) and graded quality, Gleason score (GS), and size of cancer foci. The quality of tissue RNA (37/40 cases) was assessed using the RNA Integrity Number. The biobank included 1819 patients of mean age: 62.1 years; serum PSA: 8 ng/ml; prostate weight: 47.8 g; GS: 7; and pathological stage: T2 in 64.5%, T3A in 25.5% and T3B in 10% of cases. Of the 157 evaluable slides, 79 and 78 had benign and cancer tissue, respectively. GS for the 37 cancer-positive cases were: 6 in 9, 7 in 18 and >7 in 10 and, in most instances, in concordance with final GS. In 40% of slides containing cancer, foci occupied ≥50% of block surface and 42% had a diameter ≥1 cm. Tissue was well preserved and consistently yielded RNA of very good quality with RNA Integrity Number (RIN) >7 for 97% of cases (mean=8.7 ± 0.7) during the five-year collection period. This study confirms the high quality of randomly selected benign and cancerous fresh-frozen prostate tissues of the PROCURE Quebec Prostate Cancer Biobank. These results strengthen the uniqueness of this large prospective resource for prostate cancer research.

The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings

Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are available, we present a current overview of experimental data regarding procurement, storage, and quality assurance that can inform the handling of frozen biospecimens. Frozen biospecimen degradation can be influenced by factors independent of the collection methodology including tissue type, premortem agonal changes, and warm ischemia time during surgery. Rapid stabilization of tissues by snap freezing immediately can mitigate artifactually altered gene expression and, less appreciated, protein phosphorylation profiles. Collection protocols may be adjusted for specific tissue types as cellular ischemia tolerance varies widely. If data is not available for a particular tissue type, a practical goal is snap freezing within 20min. Tolerance for freeze-thaw events is also tissue type dependent. Tissue storage at -80°C can preserve DNA and protein for years but RNA can show degradation at 5years. For -80°C freezers, aliquots frozen in RNAlater or similar RNA stabilizing solutions are a consideration. It remains unresolved as to whether storage at -150°C provides significant advantages relative to that at -80°C. Histologic quality assurance of tissue biospecimens is typically performed at the time of surgery but should also be conducted on the aliquot to be distributed because of tissue heterogeneity. Biobanking protocols for blood and its components are highly dependent on intended use and multiple collection tube types may be needed. Additional quality assurance testing should be dictated by the anticipated downstream applications.

Tissue banking in ENT: challenges and methods

BACKGROUND

Biobanking is the process of storing high quality human biospecimens alongside linked clinical data, for research purposes. The aim is to identify novel biomarkers with prognostic or diagnostic significance. However, the challenges implicit in the collection and storage of human tissue for research have curtailed the impact of this technique to date.

AIM

This paper aims to summarise the challenges faced by biobanking within the ENT specialty in the UK, and to present protocols used for the routine collection, freezing and storage of tissue specimens at the Royal National Throat, Nose and Ear Hospital. These protocols could be used to guide other ENT departments (in the UK and worldwide) wishing to initiate the routine collection and storage of tissue samples. Their publication could also help to establish basic standards and ensure consistency in ENT tissue storage.

METHODS

Interviews conducted with industry experts, and a literature review of 'best practice' in biobanking.

CONCLUSION

The ENT specialty must stay abreast of progress in human tissue research in order to ensure the best possible management of its patients. Our protocol for the routine banking of ENT tissue at the Royal National Throat, Nose and Ear Hospital could be used as a template for other ENT departments (in the UK and worldwide) to encourage widespread implementation of high quality tissue banking.

Method for sampling tissue for research which preserves pathological data in radical prostatectomy

BACKGROUND

The diagnosis and treatment of prostate cancer is a challenging global healthcare issue requiring significant molecular research. Such research frequently utilizes fresh frozen human tissue which needs to be obtained in a manner acceptable to the pathologist which does not compromise tumor diagnosis or staging.

METHODS

Radical prostatectomy specimens were handled in a standardized method before being sliced fresh. Leaving the margins intact, multiple cylindrical cores were removed using a large skin punch and the sites were marked on a prostate map. The cylindrical cores were placed onto individual, pre-numbered foil squares and snap frozen in liquid nitrogen. Prostate maps were aligned with formalin-fixed paraffin embedded hematoxylin and eosin stained sections of the sampled slice to select tumor regions. Frozen tumor tissue cylinders were processed taking one section for hematoxylin and eosin staining, 6 µm × 50 µm sections for molecular studies and a further section for hematoxylin and eosin staining. This was performed for the length of the cylinder.

RESULTS

A total of 150 prostates have been removed and sliced using this technique. Pathological assessment remained uncompromised. Using the sequential hematoxylin and eosin stained frozen sections, cellularity could be monitored closely in tissues processed for research. The yield of RNA and DNA extracted was high (tumor mean 2.4 µg (RNA) and 12.7 ng per 300 µm tissue) and of high quality (mean tumor RIN 5.9).

CONCLUSIONS

This novel, rapid sampling and processing method provides high quality tissue for research without compromising pathology.

Next-generation prostate cancer biobanking: toward a processing protocol amenable for the International Cancer Genome Consortium

Next-generation DNA and RNA sequencing requires intact nucleic acids from high-quality human tissue samples to better elucidate the molecular basis of cancer. We have developed a prostate biobanking protocol to acquire suitable samples for sequencing without compromising the accuracy of clinical diagnosis. To assess the clinical implications of implementing this protocol, we evaluated 105 consecutive radical prostatectomy specimens from November 2008 to February 2009. Alternating levels of prostate samples were submitted to Surgical Pathology as formalin-fixed, paraffin-embedded blocks and to the institutional biobank as frozen blocks. Differences in reported pathologic characteristics between clinical and procured specimens were compared. Clinical staging and grading were not affected by the biobank protocol. Tumor foci on frozen hematoxylin and eosin slides were identified and high-density tumor foci were scored and processed for DNA and RNA extractions for sequencing. Both DNA and RNA were extracted from 22 cases of 44 with high-density tumor foci. Eighty-two percent (18/22) of the samples passed rigorous quality control steps for DNA and RNA sequencing. To date, DNA extracted from 7 cases has undergone whole-genome sequencing, and RNA from 18 cases has been RNA sequenced. This protocol provides prostate tissue for high-throughput biomedical research and confirms the feasibility of actively integrating prostate cancer into The Cancer Genome Atlas Program, a member of the International Cancer Genome Consortium.

Biobanking after robotic-assisted radical prostatectomy: a quality assessment of providing prostate tissue for RNA studies

BACKGROUND

RNA quality is believed to decrease with ischaemia time, and therefore open radical prostatectomy has been advantageous in allowing the retrieval of the prostate immediately after its devascularization. In contrast, robotic-assisted laparoscopic radical prostatectomies (RALP) require the completion of several operative steps before the devascularized prostate can be extirpated, casting doubt on the validity of this technique as a source for obtaining prostatic tissue. We seek to establish the integrity of our biobanking process by measuring the RNA quality of specimens derived from robotic-assisted laparoscopic radical prostatectomy.

METHODS

We describe our biobanking process and report the RNA quality of prostate specimens using advanced electrophoretic techniques (RNA Integrity Numbers, RIN). Using multivariate regression analysis we consider the impact of various clinicopathological correlates on RNA integrity.

RESULTS

Our biobanking process has been used to acquire 1709 prostates, and allows us to retain approximately 40% of the prostate specimen, without compromising the histopathological evaluation of patients. We collected 186 samples from 142 biobanked prostates, and demonstrated a mean RIN of 7.25 (standard deviation 1.64) in 139 non-stromal samples, 73% of which had a RIN ≥ 7. Multivariate regression analysis revealed cell type--stromal/epithelial and benign/malignant--and prostate volume to be significant predictors of RIN, with unstandardized coefficients of 0.867(p = 0.001), 1.738(p < 0.001) and -0.690(p = 0.009) respectively. A mean warm ischaemia time of 120 min (standard deviation 30 min) was recorded, but multivariate regression analysis did not demonstrate a relationship with RIN within the timeframe of the RALP procedure.

CONCLUSIONS

We demonstrate the robustness of our protocol--representing the concerted efforts of dedicated urology and pathology departments--in generating RNA of sufficient concentration and quality, without compromising the histopathological evaluation and diagnosis of patients. The ischaemia time associated with our prostatectomy technique using a robotic platform does not negatively impact on biobanking for RNA studies.

Pathology in prostate research: optimizing tissue quality

The collection of tissue from the prostate gland for research creates unique challenges in the identification of cancer and in preserving pathological material.

VALUE AND USES OF FORMALIN FIXED TISSUE

Formalin fixed paraffin embedded (FFPE) tissue is often available in abundance after pathological processing and reporting of specimens but is limited in value for detailed molecular tests. Tissue micro-array if carefully performed is a helpful technique for examining many FFPE specimens with immunohistochemical or fluorescence in situ hybridization tests.

VALUE AND USES OF FROZEN TISSUE

The collection of fresh tissue prior to formalin fixation and later validation samples of fresh prostate cancer is difficult as prostate cancer is very difficult to identify macroscopically on cut prostate specimens. Also, the act of manipulation and dissection of the gland while fresh and without compromising surgical margins is challenging. Methods which have been used to dissect the fresh prostate gland and also collect fresh tissue from other prostatic specimens are discussed. The ethical challenges of collecting research tissue without compromising patient care are discussed.

CONCLUSIONS

Prostate cancer tissue banks, particularly of frozen tissue are still relatively few in number. Enhanced collection methods which do not prohibit full pathological examination are available but require expertise to maximize their potential.

A new method to provide a fresh frozen prostate slice suitable for gene expression study and MR spectroscopy

BACKGROUND

Fresh frozen tissue from radical prostatectomy specimens is highly valuable material for research on gene expression and cellular metabolites. The purpose of this study was to develop a standardized method to provide a representative high quality research sample from radical prostatectomy specimens without interfering with the routine histopathological procedure.

METHODS

A complete transversal slice is collected and snap-frozen before formalin fixation and routine processing of the remaining gland. The freezing preserves the original geometric shape, thus allowing subsampling of specific cell populations without thawing. RNA was extracted from 53 cylindrical subsamples (diameter 3 mm, thickness 2 mm) from 16 consecutive frozen slices. The histological pattern was evaluated by microscopy of a cryosection from sample before further analysis.

RESULTS

Using this novel harvesting method close to 400 slices have been collected. Whenever tumor was present in both adjacent surrounding hematoxylin-eosin sections, we found cancer in 88% of the frozen slices. The extracted RNA showed very high quality with a mean RNA integrity number of 9.16 (SD 0.53). The MR spectra showed metabolic profiles containing several resonances, which deserve further evaluation as possible biomarkers for prostate cancer. After MR analysis the RNA was still highly intact with a mean RNA integrity number of 8.40 (SD 1.53), which makes it possible to correlate transcriptomic and metabolomic profiles of the extracted samples.

CONCLUSION

We present a safe and standardized method for procurement of a high quality fresh frozen prostate slice, suitable for gene expression analysis and MR spectroscopy.

Brk protects breast cancer cells from autophagic cell death induced by loss of anchorage

Brk, a tyrosine kinase expressed in a majority of breast tumors, but not normal mammary tissue, promotes breast carcinoma cell proliferation. Normal epithelial cells are dependent on cell-cell or cell-matrix interactions for survival and undergo apoptosis after disruption of these interactions. Tumor cells are less sensitive to the induction of apoptosis and are predicted to have the potential to disseminate. We investigated whether Brk has further roles in breast tumor progression by relating its expression to tumor grade and demonstrating its role in the regulation of carcinoma cell survival under non-adherent conditions. Brk expression was determined by reverse transcription PCR on RNA extracted from surgical samples of human breast cancers. Breast carcinoma cell survival in suspension culture was examined when Brk protein levels were suppressed by RNA interference. Additionally, the effect of experimentally overexpressing Brk in otherwise Brk-negative breast carcinoma cells was assessed. Brk mRNA expression was notably higher in grade 3 breast tumors, as compared with lower tumor grades. In suspension culture, Brk suppression increased the rate of cell death, as compared with controls, and this cell death program exhibited characteristics of autophagy but not of apoptosis. Conversely, experimental expression of Brk in Brk-negative cells increased cell survival whereas kinase-inactive Brk did not. Therefore, Brk enhances breast carcinoma cell survival in suspension, suggesting a role for Brk in supporting breast cancer cell dissemination.

Fresh-frozen, optimal cutting temperature (OCT) compound-embedded bone marrow aspirates: a reliable resource for morphological, immunohistochemical and molecular examinations

The usefulness of fresh-frozen, optimal cutting temperature (OCT) compound-embedded (FFOE) bone marrow (BM) aspirates was evaluated as a reliable resource for morphological, immunohistochemical and molecular examinations. One hundred BM aspirates were collected in polypropylene tubes and immediately frozen for 2 h in a deep freezer. Frozen BM was transferred to a cryomold filled with OCT compound and the prepared samples were stored in a deep freezer. Histological examination and immunohistochemical staining, polymerase chain reaction (PCR), sequencing and reverse transcription (RT)-PCR were performed to evaluate the quality of the FFOE BM sections in 10% of randomly selected samples. FFOE BM sections revealed better morphologies than paraffin-embedded clot sections in haematoxylin and eosin staining because mature erythrocytes were removed during the staining process in frozen BM sections. Immunohistochemical staining for CD34 revealed excellent staining quality and oil red O staining showed that fat vacuoles in cells were well preserved. The quality of genomic DNA in FFOE BM sections was suitable for obtaining about 2000 bp PCR product for the human leucocyte antigen-A locus followed by direct sequencing of the sample, and the quality of total RNA was suitable for detection of BCR-ABL fusion transcript. FFOE BM aspirates are a reliable resource for various laboratory tests of diagnostic and research arenas.

Cryopreservation of prostate cancer tissue during routine processing of fresh unfixed prostatectomy specimen: demonstration and validation of a new technique

BACKGROUND

Most molecular techniques currently require fresh frozen tumor tissue, which in the case of prostatectomy specimen is a challenge to obtain for a variety of intrinsic reasons. Prostate cancers are usually located in the organ periphery and hence meticulous attention has to be paid to the relation between the tumor and the surgical margin. In this article we describe a new technique that allows to obtain fresh frozen tumor material in rather large quantities and without jeopardizing diagnostic accuracy.

METHOD

An inner triangle, representing roughly 50% of the entire prostate tissue, is removed from native prostatectomy specimen and cryopreserved, leaving the periphery of the organ for routine histomorphological analysis. We have validated the technique using a series of 180 archived radical prostatectomy specimen that had been studied by histology in their entirety, as well as 42 prostatectomy specimen worked-up by the new technique.

RESULTS

The described technique is effective, yielding frozen tumor tissue in 84.2% of unilateral (<or=pT2b) and in 91.8% of bilateral (pT2c) carcinomas. The number of tumor containing tissue blocks ranged from 1 to 7 blocks per carcinoma (mean 5.6 +/- 3.2). The remaining peripheral tissue portion subjected to histological analysis allowed to estimate total tumor volume with a high degree to confidentiality (r(2) >or= 0.90 by linear regression analysis). The number of blocks to be routinely examined for each prostatectomy specimen is significantly reduced, thus saving costs without loss of diagnostic accuracy.

CONCLUSION

The described technique for prostate cancer cryoconservtion is feasible, highly standardized, effective, safe, and economic.

Variation in dermcidin expression in a range of primary human tumours and in hypoxic/oxidatively stressed human cell lines

Dermcidin acts as a survival factor in a variety of cancer cell lines under hypoxia or oxidative stress. The aim of this study was to evaluate dermcidin expression in cell lines following simulation of tumour microenvironmental conditions and in a range of primary tumours. Tumour tissues were collected from patients with oesophageal (28 samples), gastric (20), pancreatic (five), bile duct (one) and prostatic (52) carcinomas as well as 30 benign tissue samples, for assessment of dermcidin mRNA levels using real-time PCR. Dermcidin expression was assessed in prostatic and pancreatic cancer cell lines, with and without induction of hypoxia or oxidative stress. Dermcidin mRNA expression was very low or absent in both unstressed and stressed prostate cell lines. None of the primary prostate tissue, benign or malignant, expressed dermcidin mRNA. Only two (4%) of the gastro-oesophageal cancer samples expressed moderate quantities of dermcidin mRNA. However, three (60%) of the pancreatic cancer samples and the single cholangiocarcinoma specimen had moderate/high levels of dermcidin expression. Of the two pancreatic cancer cell lines, one expressed dermcidin moderately but neither showed a response to hypoxia or oxidative stress. Expression of dermcidin in human primary tumours appears highly variable and is not induced substantially by hypoxia/oxidative stress in cell line model systems. The relationship of these findings to dermcidin protein levels and cell survival remains to be determined.

A novel method of obtaining prostate tissue for gene expression profiling

Gene expression profiling by DNA microarray analysis is a technique with great promise in cancer biology. The multifocality and heterogeneity of many prostate cancers makes the collection of adequate biological samples for such profiling particularly challenging. Current methods, such as laser capture microdissection, are not widely available and can have significant limitations. In this article, a novel method of prostatic sampling, which does not affect the histopathological assessment of the surgical specimen and provides adequate RNA yield for microarray analysis is described. This method is simple, inexpensive, easily reproducible, and has been validated as having >95% sensitivity and 99% specificity for histological prediction of tissue obtained. This method can be adopted by other investigators to perform DNA microarray analysis on prostate tumors.

Laser-capture microdissection in prostate cancer research: establishment and validation of a powerful tool for the assessment of tumour-stroma interactions

OBJECTIVES

To describe our experience with the optimization and validation of laser-capture microdissection (LCM) for biomarker analysis in prostate tissues. As LCM allows the separation of benign and malignant epithelial structures and stromal elements, it not only allows identification of the source of the biomarker, but might also accentuate gene or protein expression changes by reducing contamination by other cellular elements.

MATERIALS AND METHODS

In all, 19 fresh-frozen prostate tissue samples were subjected to LCM, with the cDNA being analysed using quantitative polymerase chain reaction for several genes, to identify the optimum number of cells for capture, as well as gene markers assessing for the purity of the captured cells. The localization was further confirmed by in situ hybridization.

RESULTS

Prostate-specific antigen (PSA) and cytokeratin 8, were expressed solely by epithelial cells, whereas hepatocyte growth factor (HGF) and tissue inhibitor of metalloproteinases-3 (TIMP3) were expressed only by stromal cells, and the levels of transcripts of these genes were unaltered between benign and malignant tissues.

CONCLUSIONS

These data suggest that PSA, cytokeratin 8, HGF and TIMP3 are reliable gene markers of purity of epithelial and stromal compartments for LCM of prostate tumours. Although this technique is not new and is increasingly used in laboratories, it needs optimization and stringent validation criteria before data analysis. This applies to all tissue types subjected to LCM.

Human Biobank in Uro-Oncological Research

Purpose

Uro-oncological translational research requires clinical data and human biological tissues collected within a biological tissue bank (BTB). We are hereby outlining ethic-legal, methodological and technical issues of a BTB establishment process, focusing particularly on prostate cancer and Italian setting.

Materials and Methods

Review of literature data, and national and international regulations and guidelines; direct field experience of urological BTB; counseling of the different professionals involved.

Results

Within a BTB establishment process, it is of utmost importance to protect the donors’ privacy and rights through the programmatic adoption of the following procedures: 1) informed consent; 2) confidentiality protection thanks to anonymity of biological specimens and use of an “honest broker” method; 3) identification of a single responsible researcher; 4) dedicated and protected location; 5) approval of the Ethical Committee. There are two main organizational models of BTB: “systematic”, i.e. collecting specimens from all patients and through the same methodology; “project-driven”, i.e. prospectively selecting patients for a specific study and using the specific methods required by researchers. In the preliminary step it is necessary to establish detailed protocols of sampling and crioconservation techniques, and methods of validation and quality control. For prostate tissue sampling, several techniques have been described such as specimens of alternate slices, macro dissection, Tru-Cut.

Conclusions

Today BTBs are necessary in order to support molecular and translational research in uro-oncology and to overcome the limits of the research based only on clinical-pathological data. Ethic-legal and methodological issues related to BTBs are still requiring specific legislation and standardization of techniques.

Isolation of Human Prostatic Epithelial Plasma Membranes for Proteomics Using Mirror Image Tissue Banking of Radical Prostatectomy Specimens

PURPOSE

To isolate human prostatic epithelial plasma membranes for the identification of cell surface proteins in the therapeutic targeting of cancer cells while permitting the retrieval of banked samples for clinical purposes.

EXPERIMENTAL DESIGN

Radical prostatectomies from 84 patients (median, 61 years; prostate-specific antigen, 5.9; 66% nonpalpable) were processed with alternate, mirror image slices submitted for histology and tissue banking. Benign and malignant foci were macrodissected from the banked sections using the pathologically mapped, mirror image histology sections as a guide. Epithelial plasma membranes were isolated using novel immunomagnetic purification and their purity was assessed. Tissue homogenates were probed by Western blot for malignant (AMACR) and benign (p63) markers to test the accuracy of this protocol. Selected banked tissue slices were retrieved, thawed, and compared pathologically to their corresponding routinely processed alternate slices.

RESULTS

Plasma membrane preparations showed the enrichment of epithelial plasma membrane markers (prostate-specific membrane antigen and epithelial-specific antigen) with minimal marker expression from nonepithelial cells or intracellular organelles. Cancer homogenates showed up-regulated AMACR and down-regulated p63, whereas benign homogenates showed up-regulated p63 and down-regulated AMACR. There was 30% benign (p63+) contamination in cancer slices and <6% cancer (AMACR+) contamination in benign slices. Retrieved tissues showed the retention of immunoreactivity while their histology was always adequate for diagnosis.

CONCLUSIONS

We have successfully isolated purified epithelial plasma membranes from benign and malignant human prostates and provided validation data for the accuracy of our protocol in a prostate-specific antigen-screened cohort. Our method also enabled the retrieval of banked tissues for clinical purposes with the retention of good histologic and immunohistochemical quality.

Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens

Molecular tools for tissue profiling, such as expression microarrays and real-time PCR, generally require collection of fresh frozen tissues as sources of high-quality RNA. The fragile nature of RNA prompted us to examine the effects of storage time and transport conditions with regard to RNA integrity and gene expression in nonfixed surgical human specimens. At surgery, fresh normal tonsil and colon tissue was cut into pieces and snap frozen. Additional fresh tissue pieces were (i) left at room temperature, (ii) kept on ice, (iii) in normal saline or (iv) in a commercial RNA-stabilizing buffer (RNAlater) and snap frozen after 0.5, 1, 3, 6 and 16 h. Structural RNA integrity was analysed by microchip electrophoresis. Surprisingly, RNA remained stable in both tissue types under all conditions tested for up to 6-16 h. Gene expression by real-time PCR of cfos, HIF1alpha, Bcl2, PCNA, TGFbeta1 and SMAD7 was analysed at different storage time points in tonsil tissue. Expression levels were essentially stable when samples were kept on ice, while marked regulation of single genes was observed during storage at room temperature, in normal saline and in RNAlater. Furthermore, we analysed selected tissue types from the local biobank representing 47 normal and malignant tissues transported on ice for up to 2-3 h before biobanking. RNA prepared from 45 of the 47 samples exhibited distinct ribosomal peaks indicating intact RNA. This study shows that RNA degradation is a minor problem during handling of fresh human tissue before biobanking. Our data indicate that nonfixed tissue specimens may be transported on ice for hours without any major influence on RNA quality and expression of the selected genes. However, further studies are warranted to clarify the impact of transport logistics on global gene expression.

Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers

Hepsin is a membrane-anchored, trypsin-like serine protease with prominent expression in the human liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1-P4 substrate specificity. Hepsin exhibited strong preference at the P1 position for arginine over lysine, and favoured threonine, leucine or asparagine at the P2, glutamine or lysine at the P3, and proline or lysine at the P4 position. The relative activity of hepsin toward individual AMC (7-amino-4-methylcoumarin)-tetrapeptides was generally consistent with the overall peptide profiling results derived from the PC-SCL screen. The most active tetrapeptide substrate Ac (acetyl)-KQLR-AMC matched with the activation cleavage site of the hepatocyte growth factor precursor sc-HGF (single-chain HGF), KQLR downward arrowVVNG (where downward arrow denotes the cleavage site), as identified by a database analysis of trypsin-like precursors. X-ray crystallographic studies with KQLR chloromethylketone showed that the KQLR peptide fits well into the substrate-binding cleft of hepsin. This hepsin-processed HGF induced c-Met receptor tyrosine phosphorylation in SKOV-3 ovarian cancer cells, indicating that the hepsin-cleaved HGF is biologically active. Activation cleavage site mutants of sc-HGF with predicted non-preferred sequences, DPGR downward arrowVVNG or KQLQ downward arrowVVNG, were not processed, illustrating that the P4-P1 residues can be important determinants for substrate specificity. In addition to finding macromolecular hepsin substrates, the extracellular inhibitors of the HGF activator, HAI-1 and HAI-2, were potent inhibitors of hepsin activity (IC50 4+/-0.2 nM and 12+/-0.5 nM respectively). Together, our findings suggest that the HGF precursor is a potential in vivo substrate for hepsin in tumours, where hepsin expression is dysregulated and may influence tumorigenesis through inappropriate activation and/or regulation of HGF receptor (c-Met) functions.

Identification of degradome components associated with prostate cancer progression by expression analysis of human prostatic tissues

Extracellular proteases of the matrix metalloproteinase (MMP) and serine protease families participate in many aspects of tumour growth and metastasis. Using quantitative real-time RT–PCR analysis, we have undertaken a comprehensive survey of the expression of these enzymes and of their natural inhibitors in 44 cases of human prostate cancer and 23 benign prostate specimens. We found increased expression of MMP10, 15, 24, 25 and 26, urokinase plasminogen activator-receptor (uPAR) and plasminogen activator inhibitor-1 (PAI1), and the newly characterised serine proteases hepsin and matriptase-1 (MTSP1) in malignant tissue compared to benign prostate tissue. In contrast, there was significantly decreased expression of MMP2 and MMP23, maspin, and the protease inhibitors tissue inhibitor of metalloproteinase 3 (TIMP3), TIMP4 and RECK (reversion-inducing cysteine-rich protein with Kazal motifs) in the cancer specimens. The expression of MMP15 and MMP26 correlated positively with Gleason score, whereas TIMP3, TIMP4 and RECK expression correlated negatively with Gleason score. The cellular localisation of the expression of the deregulated genes was evaluated using primary malignant epithelial and stromal cell cultures derived from radical prostatectomy specimens. MMP10 and 25, hepsin, MTSP1 and maspin showed predominantly epithelial expression, whereas TIMP 3 and 4, RECK, MMP2 and 23, uPAR and PAI1 were produced primarily by stromal cells. These data provide the first comprehensive and quantitative analysis of the expression and localisation of MMPs and their inhibitors in human prostate cancer, leading to the identification of several genes involved in proteolysis as potential prognostic indicators, in particular hepsin, MTSP1, MMP26, PAI1, uPAR, MMP15, TIMP3, TIMP4, maspin and RECK.

Processing of radical prostatectomy specimens for correlation of data from histopathological, molecular biological, and radiological studies: a new whole organ technique

AIMS

To develop a method of processing non-formalin fixed prostate specimens removed at radical prostatectomy to obtain fresh tissue for research and for correlating diagnostic and molecular results with preoperative imaging.

METHODS/RESULTS

The method involves a prostate slicing apparatus comprising a tissue slicer with a series of juxtaposed planar stainless steel blades linked to a support, and a cradle adapted to grip the tissue sample and receive the blades. The fresh prostate gland is held in the cradle and the blades are moved through the cradle slits to produce multiple 4 mm slices of the gland in a plane perpendicular to its posterior surface. One of the resulting slices is preserved in RNAlater. The areas comprising tumour and normal glands within this preserved slice can be identified by matching it to the haematoxylin and eosin stained sections of the adjacent slices that are formalin fixed and paraffin wax embedded. Intact RNA can be extracted from the identified tumour and normal glands within the RNAlater preserved slice. Preoperative imaging studies are acquired with the angulation of axial images chosen to be similar to the slicing axis, such that stained sections from the formalin fixed, paraffin wax embedded slices match their counterparts on imaging.

CONCLUSIONS

A novel method of sampling fresh prostate removed at radical prostatectomy that allows tissue samples to be used both for diagnosis and molecular analysis is described. This method also allows the integration of preoperative imaging data with histopathological and molecular data obtained from the prostate tissue slices.

Dysregulated expression of adamalysin-thrombospondin genes in human breast carcinoma

The adamalysin-thrombospondin (ADAMTS) proteinases are a relatively newly described branch of the metzincin family that contain metalloproteinase, disintegrin, and thrombospondin motifs. They have been implicated in various cellular events, including cleavage of proteoglycans, extracellular matrix degradation, inhibition of angiogenesis, gonadal development, and organogenesis. However, in many cases, their normal physiological roles and their potential for dysregulation in malignancy remain to be established. The expression profile of ADAMTS1-20 in human breast carcinoma was undertaken by real-time PCR using RNA isolated from malignant tumors, nonneoplastic mammary tissue, and breast cancer cell lines to identify altered regulation that may have potential pathogenetic and prognostic significance. Our studies show that seven of the ADAMTS genes (ADAMTS1, 3, 5, 8, 9, 10, and 18) are consistently down-regulated in breast carcinomas with respect to nonneoplastic mammary tissue, irrespective of the heterogeneity of the samples and the tumor type or grade (Mann-Whitney U test, P < 0.0001 for each gene). Conversely, ADAMTS4, 6, 14, and 20 are consistently up-regulated in breast carcinomas (P = 0.005, P < 0.0001, P = 0.003, and P = 0.001, respectively). ADAMTS2, 7, 12, 13, 15, 16, 17, and 19 show no significant difference between the sample types. ADAMTS1, 2, 7, 8, 10, and 12 are expressed predominantly in stromal fibroblasts. ADAMTS3, 4, 5, 6, 9, and 13-20 inclusive are expressed predominantly in myoepithelial cells; all appear to be relatively poorly expressed in luminal epithelial cells. ADAMTS15 has emerged as being an independent predictor of survival, with RNA expression levels significantly lower (P = 0.007) in grade 3 breast carcinoma compared with grade 1 and 2 breast carcinoma.

Tissue archives to track blood borne pathogens in people receiving blood products

Tissue banks for surveillance of pathogens, research and transplantation have been established in a variety of settings, and following a variety of guidelines. There are significant and changing ethical, moral, and legal issues in the development and use of such archives. The Association of Hemophilia Clinic Directors of Canada has established an archive of blood samples to test for known and emerging blood borne pathogens, and known and emerging blood clotting genes. Key to the development of the tissue bank was the consent process for sample collection and handling, the establishment of standard operating procedures for the handling of samples and data, and the establishment of an oversight board.