Electronic tracking of human brain samples for research

Insight into the pathogenesis of neurodegenerative disorders requires accurately categorized postmortem human brain tissue. This article introduces electronic tissue tracking and management as implemented at New York Brain Bank (NYBB) through processing of the brain at fresh state and storing standardized frozen samples. NYBB tissue tracking uses a relational database to co-register a bar coded, unique sample identifier to unique coordinates in the three-dimensional freezer space, allowing immediate retrieval of stored samples without further dissection. In the 5 years since the inception of NYBB (2002-2007) 560 brains (63,252 fresh frozen samples) were processed and as of 11/2007, 54,242 samples are stored seven freezers occupying 81% of maximum capacity of NYBB. Within the same time period, 1,094 requests were processed and 9,096 samples were disbursed with an average turnaround time of five working days. The NYBB system of brain banking has the following key advantages: (1) The dissection of the brain and the harvest of samples at the fresh state improve their anatomic specificity and quality; (2) samples are ready for immediate disbursement once categorized diagnostically, reducing the time between the receipt of request and disbursement of samples; (3) the methods prevent thaw-refreeze cycles and carving out of regions of interest from frozen tissue, which is cumbersome and deleterious to the both samples and source brains; (4) accurate quantitative data on stored samples according to anatomical regions and distributive diagnosis guides future sample collection and fosters effective use of limited resources.     

New tissue microarray technology for analyses of gene expression in frozen pathological samples

Tissue microarrays (TMAs) are widely used to analyze gene expression in multiple pathological samples on a single slide. Currently, most TMA slides are made by coring paraffin-embedded tissues and arraying them into a paraffin block, from which TMA sections are cut. However paraffin-based TMA technology may not be compatible with frozen clinical tissue samples, which have a higher quality of RNAs and proteins for preparing TMAs than paraffin-embedded tissue samples. In this study, we developed an alternative TMA technology that is applicable to a broader range of frozen tissue samples. Our method takes advantage of a newly developed array recipient block that can be used to array small tissue cores. After arraying tissue cores, the tissue block can be immediately sectioned on a cryostat microtome to make TMA slides. TMAs made using this method have well-defined array configurations and good tissue/cell morphology. Immunohistochemistry and in situ hybridization study also revealed well-preserved proteins and mRNAs on TMA slides. Our method significantly simplifies TMA preparation and assembly when frozen pathological tissues are used. Our technology provides an alternative tool for creating high-quality TMAs for the general research community to study gene expressions in pathological samples.     

Gross Damage Accumulation in Frozen Rabbit Liver Due to Mechanical Stress at Cryogenic Temperatures

The second phase of a pilot study dealing with the mechanical response of frozen biological tissues to external compressive load is presented. This stage deals with histological observations of the damage accompanying mechanically induced permanent deformation in frozen rabbit liver. No significant gross histological damage was observed in the liver samples due to either processing the tissue in the frozen state, due to slow cooling of the liver tissues down to −20°C, or due to rapid cooling of the samples down to −196°C. No histological changes were observed in tissue samples that were loaded within the elastic regime, that is, below the yield strength of the material. Therefore, it is concluded that histological changes due to mechanical stresses are associated with plastic (permanent) deformations. Histological observations indicate that linear cracks which appear to have no preferred orientation develop due to mechanical stress beyond the yield strength of the frozen tissue. These cracks accumulate until final failure of the frozen tissue, when the tissue sample collapses to rubble. Based on histological observations and concepts from solid mechanics, an interaction between crack formation and irregularities in the frozen medium is suggested. Significant sources for such irregularities, in an homogeneous tissue such as the liver, are blood vessels and bile ducts. These irregularities may either initiate crack formation or, on the other hand, may also arrest propagating cracks.     

The effect of fixation on the chemical extraction of glycogen from rat liver

Synopsis Small samples of rat liver, weighing 15 mg or less, were either (a) frozen in liquid nitrogen or (b) fixed at 4°C for 5 min to 2 hr in absolute alcohol, alcoholic picric acid (Rossman's fluid), or aqueous picric acid (Bouin's fluid). The tissue samples were analysed for total glycogen content by a modification of the procedure described by Goodet al. (1933).Comparable yields of glycogen were extracted from freshly frozen and fixed tissue samples. The time of fixation had no apparent effect on the amount of glycogen that could be extracted chemically. Dissolved glycogen was not detectable in the fixatives.It is concluded that (a) the fixatives used in this study do not significantly affect the yield of chemically extractable glycogen from liver; (b) fixation is extremely rapid; and (c) alcoholic fixatives are not significantly superior to aqueous picric acid fixatives for preservation of chemically extractable glycogen in very small samples of tissue.     

Comparison of vitrification and slow cooling for umbilical tissues

The tissue cryopreservation maintains the cellular metabolism in a quiescence state and makes the conservation possible for an indefinite period of time. The choice of an appropriate cryopreservation protocol is essential for maintenance of cryopreserved tissue banks. This study evaluated 10 samples of umbilical cord, from which small fragments of tissue (Wharton’s jelly and cord lining membrane) were subjected to two protocols of cryopreservation: slow cooling and vitrification. The samples were frozen for a period of time ranging from 5 to 78 days. The efficiency of cryopreservation was evaluated by testing cell viability, histological analysis, cell culture, cytogenetic analysis and comparison with the results of the fresh samples. The results showed that the slow cooling protocol was more efficient than the vitrification for cryopreservation of umbilical cord tissue, because it has caused fewer changes in the structure of tissue (edema and degeneration of the epithelium) and, despite the significant decrease cell viability compared to fresh samples, the ability of cell proliferation in vitro was preserved in most samples. In conclusion, this study showed that it is possible to cryopreserve small fragments of tissue from the umbilical cord and, to obtain viable cells capable of proliferation in vitro after thawing, contributing to the creation of a frozen tissue bank.     

Preservation of gastrointestinal bacteria and their microenvironmental associations in rats by freezing.

The use of frozen rat gastrointestinal tissue samples for both the recovery of viable bacteria and for observation of microbial communities associated with the tissue was investigated. A decrease of 1 log in lactobacilli, bifidobacteria, and anaerobes was observed when the numbers of bacteria recoverable from frozen tissue (stored 7 to 9 days) were compared to those recoverable from fresh nonfrozen tissue (zero time control). However, freezing did not appear to decrease the numbers of recoverable coliforms. Tissues, cleaved with razor blades after being frozen and stored for 7 to 9 days, showed bacterial communities situated on the mucosa and in the lumen of gastrointestinal specimens. This freezing technique preserved structures not previously observed in the gastrointestinal tract. This indicates that freezing is a good method to use to study such fragile microenvironments.     

Standardization of Genomic DNA Isolation from Minute Quantities of Fish Scales and Fins Amenable to RAPD-PCR

The main focus of this study was to standardize a non-destructive procedure for extraction of genomic DNA (gDNA) from minute quantities of scales and fins of two commonly available fishes Labeo bata and Heteropneustes fossilis and also to compare the gDNA yields from live and as well from frozen samples. The spectrophotometric and electrophoretic analyses revealed a significant difference in the DNA yields from live and frozen samples. The isolated gDNAs were used as templates for RAPD-PCR. The quality and consistency of banding pattern showed that gDNA templates from live tissues performed better than that from frozen tissue samples. It was also found that the minute quantities of fresh scales or fin tissues from live fish provided satisfactory quantity and quality of gDNAs that could support several rounds of RAPD-PCR. This non-destructive sampling has a great implication in gDNA based population genetic studies in endangered and vulnerable species of fishes, where killing or sacrificing is an ethical issue.     

Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA isolated from resection specimens from 17 patients with colorectal cancer liver metastases. From ten of these patients, paired fresh frozen and routinely processed FFPE tissue was available for comparative study. Sample quality of FFPE tissues was determined by the amount of amplifiable DNA using qPCR, sequencing libraries were evaluated using Bioanalyzer. Three bioinformatic pipelines were compared for analysis of amplicon sequencing data. Selected hot spot mutations were reviewed using Sanger sequencing. In the sequenced samples from 16 patients, 29 non-synonymous coding mutations were identified in eleven genes. Most frequent were mutations in TP53 (10), APC (7), PIK3CA (3) and KRAS (2). A high concordance of FFPE and paired frozen tissue samples was observed in ten matched samples, revealing 21 identical mutation calls and only two mutations differing. Comparison of these results with two other commonly used variant calling tools, however, showed high discrepancies. Hence, amplicon sequencing can potentially be used to identify hot spot mutations in colorectal cancer metastases in frozen and FFPE tissue. However, remarkable differences exist among results of different variant calling tools, which are not only related to DNA sample quality. Our study highlights the need for standardization and benchmarking of variant calling pipelines, which will be required for translational and clinical applications.     

Comparison of Arcobacter isolation methods, and diversity of Arcobacter spp. in Cheshire, United Kingdom

The aims of this study were, firstly, to compare five published methods for the isolation of Arcobacter spp. from animal feces in order to determine the most sensitive and specific method. Second, we analyzed the resulting isolates by multilocus sequence typing (MLST) in order to investigate the diversity of the isolates recovered. Third, we investigated the ability to recover Arcobacter spp. from frozen fecal samples. Seventy-seven fecal samples from cattle, sheep, and badgers were subjected to five isolation methods, based on published methods for the isolation of Arcobacter and Campylobacter spp. Thirty-nine Arcobacter butzleri isolates were analyzed using a multilocus sequence typing scheme. The survival of Arcobacter spp. in frozen samples was investigated by freezing the fecal samples at -80°C for 7 days and then applying the same five isolation methods. The most sensitive and specific method used an Arcobacter-specific broth in conjunction with modified charcoal cefoperazone deoxycholate agar (mCCDA) with added antibiotics. Freezing of fecal samples led to a reduction in the recovery of Arcobacter spp. by approximately 50%. The 39 allelic profiles obtained by MLST could be divided into 11 sequence types (STs). We have identified the most sensitive and specific method for the isolation of Arcobacter spp. from animal feces and demonstrated that the freezing of fecal samples prior to isolation reduces arcobacter recovery. MLST analysis of the isolates revealed a high level of diversity.     

Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry

Global mass spectrometry (MS) profiling and spectral count quantitation are used to identify unique or differentially expressed proteins and can help identify potential biomarkers. MS has rarely been conducted in retrospective studies, because historically, available samples for protein analyses were limited to formalin-fixed, paraffin-embedded (FFPE) archived tissue specimens. Reliable methods for obtaining proteomic profiles from FFPE samples are needed. Proteomic analysis of these samples has been confounded by formalin-induced protein cross-linking. The performance of extracted proteins in a liquid chromatography tandem MS format from FFPE samples and extracts from whole and laser capture microdissected (LCM) FFPE and frozen/optimal cutting temperature (OCT)–embedded matched control rat liver samples were compared. Extracts from FFPE and frozen/OCT–embedded livers from atorvastatin-treated rats were further compared to assess the performance of FFPE samples in identifying atorvastatin-regulated proteins. Comparable molecular mass representation was found in extracts from FFPE and OCT-frozen tissue sections, whereas protein yields were slightly less for the FFPE sample. The numbers of shared proteins identified indicated that robust proteomic representation from FFPE tissue and LCM did not negatively affect the number of identified proteins from either OCT-frozen or FFPE samples. Subcellular representation in FFPE samples was similar to OCT-frozen, with predominantly cytoplasmic proteins identified. Biologically relevant protein changes were detected in atorvastatin-treated FFPE liver samples, and selected atorvastatin-related proteins identified by MS were confirmed by Western blot analysis. These findings demonstrate that formalin fixation, paraffin processing, and LCM do not negatively impact protein quality and quantity as determined by MS and that FFPE samples are amenable to global proteomic analysis. (J Histochem Cytochem 57:849–860, 2009)     

Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling

Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (R² between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.     

A method for preparing 2- to 50-µm-thick fresh-frozen sections of large samples and undecalcified hard tissues

This article describes a method for preparing 2- to 50-micron-thick fresh-frozen sections from large samples and completely calcified tissue samples. In order to perform the more routine work involved, a tungsten carbide disposable blade was installed to a heavy-duty sledge cryomicrotome. An entire 10-day-old rat and bone and tooth samples from a 7-month-old rat were rapidly frozen. The frozen samples were attached to the cryomicrotome stage. The cutting surface of the samples was covered with a polyvinylidene chloride film coated with synthetic rubber cement and cut at -25 degrees C. The soft tissues and the hard tissues were satisfactorily preserved and all tissue cells were easily identifiable. Enzymatic activity in the fresh sections was much stronger than that in chemically fixed and/or decalcified sections. The sections permitted histological and histochemical studies without trouble. In addition, the sections can be used for multiple experiments such as immunohistochemistry, in situ hybridization, and electron microprobe X-ray micro-analysis. This method can be used with conventional cryomicrotome equipment.     

Quantification of the concentration and 13C tracer enrichment of long-chain fatty acyl-coenzyme A in muscle by liquid chromatography/mass spectrometry

Recent diabetes and obesity research has been focused on the role of intracellular lipids in insulin resistance. Fatty acyl-coenzyme A (CoA) esters play a central role in the trafficking of intracellular lipids, but there has not previously been a method with which to quantify their kinetics using tracer methodology. We have therefore developed a high-performance liquid chromatography (HPLC)-mass spectrometry method to simultaneously measure the (13)C stable isotopic enrichment of palmitoyl-acyl-CoA ester and the concentrations of five individual long-chain fatty acyl-CoA esters extracted from muscle tissue samples. The long-chain fatty acyl-CoA can be effectively extracted from frozen muscle tissue samples and baseline separated by a reverse-phase HPLC with the presence of a volatile reagent-triethylamine. Negative ion electrospray mass spectrometry with selected ion monitoring was used to analyze the fatty acyl-CoAs to achieve reliable quantification of their concentrations and (13)C isotopic enrichment. Applying this protocol to rabbit muscle samples demonstrates that it is a sensitive, accurate, and precise method for the quantification of long-chain fatty acyl-CoA concentrations and enrichment.     

Postmortem Changes in Binding to the Muscarinic Receptor from Human Cerebral Cortex

Abstract: The effects of storage at 4°C on the antagonist and agonist binding properties of the muscarinic acetyl-choline receptor from fresh surgical and frozen autopsy samples from human cerebral cortex were studied. The number of 1-[³H]3-quinuclidinyl benzilate binding sites and their affinities were stable up to 51 h, both when stored as pieces of intact nonfrozen tissue and as a homogenate. The agonist binding properties as measured by the ability of the muscarinic agonist carbachol to compete with l-[³H]3-quinuclidinyl benzilate were also stable up to 51 h when the tissue was stored in the form of pieces. The affinity for carbachol decreased when the tissue was stored as a homogenate. The frozen autopsy samples showed no significant differences in binding properties in comparison with fresh neurosurgical tissue.     

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3′-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01) on both the frozen tissue (∼9.6K genes) and FFPET (∼8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (∼4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.     

Preparation of smears of isolated hepatocytes and the glycogen preservation in them after cryopreservation of the liver tissue

A method is proposed for preparation of smears of isolated hepatocytes from liver samples frozen in liquid nitrogen or dry ice. The thawing of liver samples and the preparation of smears of isolated hepatocytes were produced by a successive maintenance of the samples in a mixture of 0.067 M phosphate buffer and 5% sucrose (pH 8.0) at 20 degrees C, followed by placing in 0.067 M phosphate buffer (pH 7.4) at the same temperature. Then hepatocytes were fixed by methanol. The cytofluorometric analysis has shown that isolation of cells from the frozen and thawing liver tissue using the proposed method does not influence the level of glycogen preservation in the hepatocytes. The proposed method may be used in the clinical practice.     

Immunohistochemical localization of P-glycoprotein in adult human ovary and female genital tract of patients with benign gynecological conditions

The multidrug-resistance gene, MDR1, encodes a plasma membrane glycoprotein termed P-glycoprotein, which mediates active cellular efflux of certain cytotoxic agents. Two mouse monoclonal antibodies (MAb), C219 and JSB-1, were used to identify P-glycoprotein in frozen tissue from the female genital tract of 14 women with benign gynecological conditions; multiple samples from several sites in the genital tract were available from seven patients. P-glycoprotein was detected in the ovarian surface epithelium in four of 14 cases, in the Fallopian tube in three of five cases, in occasional epithelial cells of the endometrial glands in two of five cases, in some endocervical glandular epithelium in three of five cases, in ectocervical squamous epithelium in one of the two cases, and in luteinized cells of the eight cases in which a corpus luteum was present in the specimen. Positive staining with these two MAb was also observed in some endothelial cells in the cortex of the ovary and in the stromal tissue of the myometrium, endometrium, and endocervix. These studies suggest that, if epithelial ovarian cancers are derived from the surface epithelial cells of the ovary, a small proportion of the cancers might be expected to retain the phenotype found in non-cancerous cells and to express P-glycoprotein.     

Membrane transport properties of equine and macaque ovarian tissues frozen in mixtures of dimethylsulfoxide and ethylene glycol

The rate at which equine and macaque ovarian tissue sections are first cooled from +25 degrees C to +4 degrees C has a significant effect on the measured water transport when the tissues are subsequently frozen in 0.85 M solutions of glycerol, dimethylsulfoxide (DMSO), or ethylene glycol (EG). To determine whether the response of ovarian tissues is altered if they are suspended in mixtures of cryoprotective agents (CPAs), rather than in solutions of a single CPA, we have now measured the subzero water transport from ovarian tissues that were suspended in mixtures of DMSO and EG. Sections of freshly collected equine and macaque ovaries were suspended either in a mixture of 0.9 M EG plus 0.7 M DMSO (equivalent to a mixture of approximately 5% vv of EG and DMSO) or in a 1.6M solution of only DMSO or only EG. The tissue sections were cooled from +25 degrees C to +4 degrees C and then frozen to subzero temperatures at 5 degrees C/min. As the tissues were being frozen, a shape-independent differential scanning calorimeter technique was used to measure water loss from the tissues and, consequently, the best fit membrane permeability parameters (L(pg) and E(Lp)) of ovarian tissues during freezing. In the mixture of DMSO+EG, the respective values of L(pg) and E(Lp) for equine tissue first cooled at 40 degrees C/min between +25 degrees C and +4 degrees C before being frozen were 0.15 microm/min atm and 7.6 kcal/mole. The corresponding L(pg) and E(Lp) values for equine tissue suspended in 1.6M DMSO were 0.12 microm/min atm and 27.2 kcal/mole; in 1.6M EG, the values were 0.06 microm/min atm and 21.9 kcal/mole, respectively. For macaque ovarian tissues suspended in the mixture of DMSO+EG, the respective values of L(pg) and E(Lp) were 0.26 microm/min atm and 26.2 kcal/mole. Similarly, the corresponding L(Lg) and E(Lp) values for macaque tissue suspended in 1.6M DMSO were 0.22 microm/min atm and 31.4 kcal/mole; in 1.6 M EG, the values were 0.20 microm/min atm and 27.9 kcal/mole. The parameters for both equine and macaque tissue samples suspended in the DMSO+EG mixture and first cooled at 0.5 degrees C/min between +25 degrees C and +4 degrees C were very similar to the corresponding values for samples cooled at 40 degrees C/min. In contrast, the membrane parameters of equine and macaque samples first cooled at 0.5 degrees C/min in single-component solutions were significantly different from the corresponding values for samples cooled at 40 degrees C/min. These results show that the membrane properties of ovarian cells from two species are different, and that the membrane properties are significantly affected both by the solution in which the tissue is suspended and by the rate at which the tissue is cooled from +25 degrees C to +4 degrees C before being frozen. These observations suggest that these variables ought to be considered in the derivation of methods to cryopreserve ovarian tissues.