Lessons Learned During Three Decades of Operations of Two Prospective Bioresources

Prospective collection is a model through which biospecimens are provided for research. Using this model, biospecimens are collected based on real-time requests from the research community instead of being collected based on the prediction of future requests. We describe the lessons learned by two bioresources that have operated successfully using a prospective model for over three decades. Our goal is to improve other bioresources by increasing utilization of biospecimens that honor consented donors who provide biospecimens to the research community; this provides strong evidence of stewardship of the public trust. The operation of these sites requires flexibility, close communication, and cooperation with the investigator in developing a standard operating procedure (protocol) based on the investigator's needs described in their initial request. If practicable, almost any preparation can be provided, including fresh (nonfrozen) biospecimens and tissue blots. A quality management system includes rigorous quality control of the specific biospecimens provided to an investigator. The informatics approach focuses on the investigator, the investigator's request, and the biospecimens collected for the investigator; the informatics focus of classic biobanks is on the biospecimens collected to match expected future requests. These lessons have been incorporated into our current operations. Standard investigator agreements (e.g., indemnification and no unapproved biospecimen transfers to third parties) replace material transfer agreements. We have operated under the prospective model of the Cooperative Human Tissue Network (CHTN), which has been successful and has provided over 1.2 million biospecimens since it began in 1987. These tissues have supported over 4300 peer-reviewed scientific articles. Since 2012, about 1000 publications have indicated support by CHTN tissues; their average citation rate is 31 with an H factor of 61. Also, during this period, 114 patents cited the CHTN. We also describe disadvantages of prospective bioresources (e.g., inadequate distribution of rare tissues, biospecimens not immediately available, and delayed clinical outcomes).

Archived formalin-fixed paraffin-embedded (FFPE) blocks: A valuable underexploited resource for extraction of DNA, RNA, and protein

Formalin-fixed paraffin-embedded (FFPE) material presents a readily available resource in the study of various biomarkers. There has been interest in whether the storage period has significant effect on the extracted macromolecules. Thus, in this study, we investigated if the storage period had an effect on the quantity/quality of the extracted nucleic acids and proteins. We systematically examined the quality/quantity of genomic DNA, total RNA, and total protein in the FFPE blocks of malignant tumors of lung, thyroid, and salivary gland that had been stored over several years. We show that there is no significant difference between macromolecules extracted from blocks stored over 11-12 years, 5-7 years, or 1-2 years in comparison to the current year blocks.

The effects of frozen tissue storage conditions on the integrity of RNA and protein

Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.

Protein extraction from methanol fixed paraffin embedded tissue blocks: A new possibility using cell blocks

Background:

Methanol fixed and paraffin embedded (MFPE) cellblocks are an essential cytology preparation. However, MFPE cellblocks often contain limited material and their relatively small size has caused them to be overlooked in biomarker discovery. Advances in the field of molecular biotechnology have made it possible to extract proteins from formalin fixed and paraffin embedded (FFPE) tissue blocks. In contrast, there are no established methods for extracting proteins from MFPE cellblocks. We investigated commonly available CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate) buffer, as well as two commercially available Qiagen^® kits and compared their effectiveness on MFPE tissue for protein yields.

Materials and Methods:

MFPE blocks were made by Cellient™ automated system using human tissue specimens from normal and malignant specimens collected in ThinPrep™ Vials. Protein was extracted from Cellient-methanol fixed and paraffin embedded blocks with CHAPS buffer method as well as FFPE and Mammalian Qiagen^® kits.

Results:

Comparison of protein yields demonstrated the effectiveness of various protein extraction methods on MFPE cellblocks.

Conclusion:

In the current era of minimally invasive techniques to obtain minimal amount of tissue for diagnostic and prognostic purposes, the use of commercial and lab made buffer on low weight MFPE scrapings obtained by Cellient^® processor opens new possibilities for protein biomarker research.

Abstract 4213: Gene expression of hsp27 in renal cell carcinoma and the correlation with tumor progression

Background Overexpression of Hsp27 protein has been correlated with tumor progression in a variety of cancers including Renal Cell Carcinoma (RCC). Various phosphorylation patterns of Hsp27 correlate with the aggressiveness of tumor phenotype. Increased Hsp27 phosphorylation was reported to correlate with increased tumor progression in RCC. Since the phosphorylation status of Hsp27 is dependent on phosphorylation by kinases and dephosphorylation by phosphatases, a better understanding of these factors in the tumor microenvironment needed to be analyzed at the gene expression level. Gene expression studies of tumor tissues using microarray routinely fail to identify hsp27 because large amount of transcripts that microarrays analyze may mask the changes observed with hsp27 and its associated genes. Hence, we used quantitative RT-PCR to investigate the relative gene expressions of hsp27 in RCC tumor and normal adjacent tissues (NAT). We examined the gene expression levels of MAP kinases such as Mitogen Activated Protein Kinase 1 (mapk1) and MAPK-activated protein Kinase 5 (mk5) along with a major phosphatase, Protein Phosphatase 2 A (pp2a). Methods RCC tumor and normal control samples were frozen in liquid nitrogen within one hour post surgical excision. Frozen samples were pulverized in Covaris TissueTubes using the Covaris CryoPrep™ system. The pulverized tissue was homogenized for RNA extraction using the Covaris Adaptive Focused Acoustics (AFA) S220 system. Total RNA was extracted using a Qiagen RNeasy Plus kit. The gene expressions for Hsp27, MAPK1, MK5, and PP2A were analyzed by RT-PCR using validated TaqMan assays on an Applied Biosystems 7500 Fast Real-Time PCR System. A house keeping gene, beta actin, was measured in parallel to normalize the differences between samples. Results In RCC, in comparison to NAT, the relative gene expressions of hsp27 increased to 224.44% suggesting an upregulation of hsp27 in cancer tissue. Adding to this microenvironment, the phosphorylating enzymes were also upregulated in the RCC tissue. Expression levels of kinases, mapk1 and mk5 were increased to 22.11% and 37.18% respectively. Interestingly, the level of phosphatase (pp2a) was decreased 67.25 %. These data suggests that the combination of the upregulation of kinases along with down regulation of phosphatase may be a major factor creating the environment of enhanced phosphorylation in overexpressed hsp27. Conclusion Our data shows that the gene expression level increase of hsp27 in RCC is consistent with the predicted increase in protein level expression of Hsp27. However, the dramatic combined effect of the increase in the gene expression of the kinases, along with decrease in the gene expression of the phosphatase may result in a striking increase in phosphorylation. The enhanced phosphorylation will activate Hsp27 in the tumor microenvironment resulting increased tumor progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4213. doi:1538-7445.AM2012-4213

Effect of thaw temperatures in reducing enzyme activity in human thyroid tissues

An identified impediment to the advancement of science in the field of proteomics is the deterioration of proteins in tissue upon removal of the tissue from its natural state. To reduce this degradation, human tissues are frozen and stored in either liquid nitrogen or -80°C environments. It is believed that frozen tissue in ultralow temperatures preserves proteins against enzyme degradation. Various molecular, biophysical, and biochemical analytical studies require that frozen tissues be thawed before being used for analyses. Depending on downstream analyses, tissues are thawed at different temperatures (37°C, room temperature or 4°C). However, there is very little literature that describes the effects of different thaw temperatures on enzymatic inactivation in tissue lysates. We investigated the effects of preprocessing variable thaw temperature on postprocessed lysates using tyrosine phosphatase and phosphatase and tensin homolog activity assays. In our study we examined the thawing of frozen human thyroid tissues at the traditional temperatures of 4°C (on ice), 37°C (in an oven), and the novel temperature of 95°C (using Stabilizor T1™). The tissue lysates were processed without the addition of enzymatic inhibitors. Our results showed that in benign, malignant, and diseased tissues, high temperature thawing is effective in reducing enzymatic activity. In normal tissue, the reduction is dependent on individual enzymes. This suggests that if tissue lysates are to be obtained from frozen tissues without the addition of inhibitors, high temperature thawing might have marked improvement in downstream non-enzymatic analyses of diseased and neoplastic tissues.

Singlet oxygen and superoxide characteristics of a series of novel asymmetric photosensitizers

The singlet oxygen quantum yields and superoxide quantum yields for a series of novel compounds based on an asymmetrical protoporphyrin molecule have been examined. Electron spin resonance was used to measure superoxide yield and time resolved luminescence for singlet oxygen. A comparison between these results and previously published cell survival data was carried out. A broad association was found between singlet oxygen quantum yield and clonogenic cell kill.

The excited states of covalently linked dimeric porphyrins. I: The excited singlet states

The ground state absorbance and emission properties of a series of covalently linked biporphyrins were studied, in both their neutral and dicationic forms. The fluorescence quantum yields determined are comparable in value with that obtained from haematoporphyrin IX. Soret band splitting is observed for porphyrin rings separated by a hydrocarbon chain containing 0-3 carbons joined at the beta,beta' ring positions. The biporphyrin linked directly at the meso position shows considerable steric hindrance and behaves like two independent chromophores.