ABSTRACT
OBJECTIVES: To evaluate the PAXgene tissue fixation system. METHODS: Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]). RESULTS: PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results. CONCLUSIONS: While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
Subject(s)
Gene Expression Profiling/methods , Tissue Fixation/methods , Acetic Acid , Adult , Aged , Carcinoma/diagnosis , Colonic Neoplasms/diagnosis , Ethanol , Female , Humans , Immunohistochemistry , Lung Neoplasms/diagnosis , Male , Methanol , Middle Aged , Paraffin Embedding , Polymerase Chain Reaction , Proteomics/methods , Pulmonary Aspergillosis/diagnosis , Tissue Array AnalysisABSTRACT
This biospecimen research case study illustrates the importance of a neglected pre-analytical factor, the polypropylene type of storage tubes. We measured amyloid ß1-42 peptide and showed that a non-irradiated, homopolymer type of polypropylene has the lowest adsorption properties.
Subject(s)
Alzheimer Disease/cerebrospinal fluid , Amyloid beta-Peptides/cerebrospinal fluid , Polypropylenes/chemistry , Specimen Handling/methods , Adsorption , Alzheimer Disease/diagnosis , Amyloid beta-Peptides/chemistry , Biological Specimen Banks , Biomarkers/chemistry , Diagnostic Errors , Enzyme-Linked Immunosorbent Assay , Humans , Polymers/chemistry , TemperatureABSTRACT
The impact of shipping temperatures and preservation media used during transport of either peripheral blood mononuclear cells (PBMCs) or Jurkat cells was assessed, in view of implementing of a proficiency testing scheme on mononuclear cell viability. Samples were analyzed before and after shipment at different temperatures (ambient temperature, dry ice, and liquid nitrogen) and in different preservation media (serum with cryoprotectant, commercial cryopreservation solution, and room temperature transport medium). Sample quality was assessed by viability assays (Trypan Blue dye exclusion, flow cytometry, Cell Analysis System cell counting (CASY)), and by ELISpot functional assay. The liquid nitrogen storage and shipment were found to be the most stable conditions to preserve cell viability and functionality. However, we show that alternative high quality shipment conditions for viable cells are dry ice shipment and commercial cryopreservation solution. These were also cost-efficient shipment conditions, satisfying the requirements of a proficiency testing scheme for viable mononuclear cells. Room temperature transport medium dramatically and adversely affected the integrity of mononuclear cells.
Subject(s)
Blood Preservation/methods , Blood Specimen Collection/methods , Cryoprotective Agents/pharmacology , Nitrogen/pharmacology , Cell Survival , Humans , Jurkat Cells , Leukocytes, Mononuclear/cytology , Quality Control , TemperatureABSTRACT
This case study illustrates the usefulness of the DNA fingerprinting method in biobank quality control (QC) procedures and emphasizes the need for detailed and accurate record keeping during processing of biological samples. It also underlines the value of independent third-party assessment to identify points at which errors are most likely to have occurred when unexpected results are obtained from biospecimens.
Subject(s)
Biological Specimen Banks/standards , DNA Fingerprinting , Case-Control Studies , DNA/analysis , DNA/isolation & purification , Electrophoresis, Agar Gel , Humans , Quality ControlABSTRACT
Proteomic research requires high-quality, standardized samples. Quality control (QC) biomarkers, which are sensitive to the collection, processing or storage conditions, would be useful tools to identify compromised samples. This study evaluates the usefulness of renal lithostatine as a QC tool for urine sample processing in daily biobank work. Four factors (pre-analytical variations) were examined for their effect on renal lithostatine as measured by ELISA: time from sample collection to centrifugation, number of specimen freeze-thaw cycles, specimen preservation with protease inhibitors, and the inclusion or exclusion of urinary sediment.
Subject(s)
Biomarkers/urine , Lithostathine/urine , Biological Specimen Banks , Centrifugation , Freezing , Humans , Male , Quality Control , Specimen Handling/methodsABSTRACT
Preanalytical conditions applied during sample collection and processing can affect the detection or quantification of unstable phosphoprotein biomarkers. We evaluated the consequences of tissue stabilization and protein extraction methods on phosphoprotein analysis. The effects of stabilization techniques (heat stabilization, snap-freezing) and time on the levels of phosphoproteins, including phospho-Akt, p-ERK 1/2, p-IkBα, p-JNK, and p38 MAPK, were evaluated using a BioPlex phosphoprotein assay. Additionally, two different protein extraction protocols, using different extraction buffers (8 M urea buffer, or Bio-Rad buffer without urea) were tested. For snap-frozen samples, protein extraction yields were comparable with the two buffer systems. For heat-stabilized samples, total protein yields were significantly lower following extraction in non-urea buffer. However, the concentrations of specific phosphoproteins were significantly higher in heat-stabilized samples than in the corresponding snap-frozen samples, indicating that this tissue processing method better preserved phosphoproteins. Significant differences were found between the measured phosphoprotein levels in heat-stabilized and snap-frozen tissue, suggesting that alterations occur very rapidly after tissue excision. Our results suggest that heat stabilization can be used as a tissue processing method for subsequent phosphoprotein analyses, but also suggest that the BioPlex phosphoprotein assay could be used as a possible quality control method to assess tissue sample integrity.
Subject(s)
Phosphoproteins/analysis , Phosphoproteins/isolation & purification , Specimen Handling/methods , Tissue Preservation/methods , Animals , Biomarkers/analysis , Brain , Buffers , Male , Mice , Mice, SCID , Reference Standards , TemperatureABSTRACT
Changes of the intracellular Ca2+ content in human red blood cells (RBCs) in glycerol-containing solutions and after freeze-thawing the cells with glycerol and subsequent deglycerolization were investigated with the Ca2+-sensitive fluorescent dye fluo-4 using fluorescence microscopy. In the glycerol-containing solutions the Ca2+ content increased when compared with a physiological medium (Hepes buffered saline solution (HBSS)). This effect was most likely a result of an inhibition of the Ca2+ pump. After inhibiting the Ca2+ pump using o-vanadate, the Ca2+ uptake was not significantly different in the cells in glycerol-containing and physiological medium. Freeze-thawing and deglycerolization of RBCs resulted in a more pronounced increase in the Ca2+ content. Also in this case, the Ca2+ pump seemed to play a major role.
