Fixing archiving

Rahimi F, Shepherd CE, Halliday GM, et al. Antigen-epitope retrieval to facilitate proteomic analysis of formalin-fixed archival brain tissue. Anal. Chem. 2006 78 7216-7221. 

Experimental samples are mainly derived from tissue culture cells, laboratory animals, or human tissues collected from hospitals after surgical biopsies and autopsies. With human and animal tissue specimens, it is important to arrest metabolic processes within 5-10 min of collection in order to preserve mRNAs from degradation by internal enzymatic reactions (26,27). Most hospitals use 10% buffered formalin as a tissue fixative. Subsequently, each tissue slice is trapped in a paraffin block. Series of 4-5-pm-thick sections are cut and mounted on silanated slides. Formalin-fixed archival tissues have been successfully used in in situ PCR and in situ hybridization protocols (28-32). However, the procedure for RNA protection is not always followed. It is often difficult to alter or control the routine procedures of hospitals for the required protection of mRNAs in surgically removed human tissues. 

Immunohistochemistry, on the other hand, enables identification of activated caspases or their cleaved products in fixed archival tissue sections. This technique allows identification of cell(s) undergoing caspase activation, as well as analysis of the distribution of cell(s) in the tissue. Specific antibodies to various caspases are now commercially available, the most frequently studied being caspase-3. Studies in various human tissues and cells have shown that immunohistochemical detection of activated caspase-3 is a useful tool for identifying apoptotic cells in archival material, even before all of the morphological features of apoptosis occur [84-86]. Several target proteins cleaved by caspases can also be detected by immunohistochemistry for example PARP [87], actin [88, 89], and lamin B [90]. 

The Self-defining Text Archive and Retrieval (STAR) file format addresses primarily the problem of the inflexibility of the PDB file format, its fixed sets of allowable fields, and their strong dependence on order, To overcome the problems described, both the data. structure and the actual data items within a STAR file arc self-defined, which means that they are preceeded by corresponding names (labels) which identify and describe the data. The data may be of any type and there is no predefined order of the data. STAR files, in contrast to PDB files, are easy to read and write manually. The whole syntax of STAR files is very simple and is defined by only a few rules ... 

Mass storage device. Typically, fixed-head hard disk drives are used to store ac tive data, including on-line and historical databases and non-memory-resident programs. Memory-resident programs are stored to allow loading at system startups. The tape drives are used for archives and backups. 

Gill et al.21 Archival FFPE spinal cord tissue both paraformaldehyde-fixed frozen rat spinal cord tissue and paraffin-embedded same tissue To establish an optimal protocol for detection of low-abundance protein (NeuN) in human spinal cord FFPE tissue sections, testing three AR solutions of pH 6, alkaline, and acidic buffer, with three heating conditions 95,100, and 105°C Heating FFPE tissue sections in an alkaline buffer yields most effective AR-IHC staining results. 

Baschong W, Suetterlin R, Laeng RH. Control of autofluorescence of archival formaldehyde-fixed, paraffin-embedded tissue in confocal laser scanning microscopy (CLSM)./. Histochem. Cytochem. 2001 49 1565-1571. 

Coombs NJ, Gough AC, Primrose JN. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res. 1999 27 el2-el7. 

Shi S-R, Cote RJ, Wu L, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle heating under the influence of pH. /. Histochem. Cytochem. 2002 50 1005-1011. 

Johnson NA, Hamoudi RA, Ichimura K, et al. Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab. Invest. 2006 86 968-978. 

Liu H, Huang X, Zhang Y, et al. Archival fixed histologic and cytologic specimens including stained and unstained materials are amenable to RT-PCR. Diagn. Mol. Pathol. 2002 11 222-227. 

Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embeddded tumor tissue. Am. J. Pathol. 2001 158 419-429. 

Linton KM, Hey Y, Saunders E, et al. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br. J. Cancer 2008 98 1398-1402. 

The new fixative approach presents very large logistical issues, including a long transition period when both the new fixative and formalin would be in use in different laboratories across the world. In addition, archival banks for FFPE tissues would diminish in value and become worthless as techniques adapted to the new fixative tissues. On the other hand, data are... 

When fresh or frozen tissue is used for proteomic analyses, the results cannot be related directly to the clinical course of diseases in a timely manner. Instead, researchers frequently reduce the number of interesting proteins to a manageable number and then attempt to use immunohistochemistry to understand the implications of proteomic changes in archival formalin-fixed, paraffin-embedded (FFPE) tissue for which the clinical course has been established.3 Unfortunately, immunohistochemistry is a semiquantitative pro-teomic method, and the choice of interesting proteins must occur without advance knowledge of the clinical course of the disease or the response to therapy. If routinely fixed and embedded archival tissues could be used for standard proteomic methods such as 2-D gel electrophoresis and mass spectrometry (MS), these powerful techniques could be used to both qualitatively and quantitatively analyze large numbers of tissues for which the clinical course has been established. However, analysis of archival FFPE tissues by... 

Nirmalan NJ, Harnden P, Selby PJ, et al. Mining the archival formalin-fixed paraffin-embedded tissue proteome opportunities and challenges. Mol. Biosyst. 2008 4 712-720. 

Hwang SI, Thumar J, Lundgren DH, et al. Direct cancer tissue proteomics a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2006 26 65-76. 

Fowler CB, Cunningham RE, O Leary TJ, et al. Tissue surrogates as a model for archival formalin-fixed paraffin-embedded tissues. Lab. Invest. 2007 87 836-846. 

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