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PubMed2006

Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within.

The predominance of tissues stored worldwide in hospitals and clinical laboratories exist in formalin-fixed paraffin-embedded (FFPE) blocks that are generated by simple and well-established protocols. Although generation of FFPE tissues has facilitated their characterization by such techniques as histopathology, they have proven refractory to biomarker discovery investigations using state-of-the-art MS-based proteomic methodologies. Very recently new methods have been developed that enable proteins extracted from FFPE tissues to be analyzed by MS. This review will highlight and discuss those efforts that have led to this exciting recent progress. Although these developments are quite new, the ability to conduct MS-based proteomic analyses of FFPE tissues opens heretofore intractable clinical samples for discovery-based biomarker research.

Cryopreservation↗
PubMed2005

The application of a monoclonal antibody to CD62L on paraffin-embedded tissue samples in the assessment of the cutaneous T-cell infiltrates.

BACKGROUND: A reduction in the expression of the pan T-cell markers CD7 and CD62L supports an endogenous T-cell dyscrasia. Previously, clone availability for CD62L restricted its application to frozen tissue sections. MATERIALS AND METHODS: A nonavidin/biotin technique to examine CD3, CD62L, and CD7 in paraffin formalin-fixed tissue in non-neoplastic and neoplastic T-cell infiltrates. RESULTS: In the reactive group, CD62L manifested a 15 and 22% reduction in epidermal and dermal staining, respectively; there was a 42 and 31% reduction in epidermal and dermal CD7 staining. In lymphomatoid hypersensitivity, CD62L showed a 24 and 9% reduction in epidermal and dermal staining, respectively; CD7 staining demonstrated reduced staining by 70 and 66% in the epidermis and dermis. In the non-lymphomatous endogenous T-cell dyscrasia and lymphoma categories, an 80% diminution in CD62L and CD7 expression was seen. CONCLUSIONS: CD62L can be successfully applied in formalin-fixed tissue and exhibits enhanced specificity compared to CD7 in the evaluation of cutaneous T-cell infiltrates. Both CD62L and CD7 in paraffin-embedded, formalin-fixed tissue are useful diagnostic adjuncts, especially in regard to the discrimination of lymphomatoid hypersensitivity reactions from true endogenous T-cell dyscrasia.

Antibodies, Monoclonal↗
PubMed1982

Demonstration of AA-protein in formalin-fixed, paraffin-embedded tissues.

AA-protein was identified by SDS-acrylamide electrophoresis in amyloid fibrils fixed in formalin after isolation from fresh-frozen tissues obtained from patients with familial Mediterranean fever (FMF) amyloidosis and idiopathic AA-amyloidosis and, following deparaffination, rehydration and homogenization of embedded formalin-fixed tissues of old autopsy cases of the hereditary amyloidosis of FMF and amyloidosis acquired in association with tuberculosis, bronchiectasis, and rheumatoid arthritis. That AA-protein is unaltered by formalin was firmly established by agar gel diffusion using specific rabbit anti-AA serum. By contrast, AL proteins could not be demonstrated either in formalin-fixed amyloid fibrils derived from fresh-frozen tissues of a patient with presumably AL-amyloidosis dominated by cardiomegaly and one with AL-kappa amyloidosis or in blocks of cases of familial neuropathic amyloidosis, multiple myeloma, and idiopathic amyloidosis with cardiopathy. AA-protein is not denatured by formalin and retains its typical electrophoretic, chromatographic, and immunologic characteristics even 30 years after fixation and paraffin-embedding.

Amyloid↗
PubMed1994

Detection of ptc in archival formalin-fixed, paraffin-embedded tissues. Comparison of radiolabeled DNA hybridization and direct incorporation of digoxigenin-11-dUTP into RT-PCR products.

Archival pathological specimens are a source of RNA and DNA for clinical surveillance or retrospective studies. We employed a modification of the acid guanidium thiocyanate-phenol-chloroform extraction method for the recovery of total RNA from formalin-fixed, paraffin-embedded neoplastic thyroid tissue. The extracted RNA was used for reverse transcription of ptc and subsequent amplification of the complementary DNA (cDNA) by the reverse transcription-polymerase chain reaction (RT-PCR). In lieu of 32P-labeled DNA for hybridization studies, we supplemented the nucleotide pool in the amplification reaction with a modified pyrimidine, digoxigenin-11-dUTP. Digoxigenin-11-dUTP was incorporated directly into the PCR product, eliminating the need for hybridization, posthybridization washes, and prolonged autoradiography. These products were resolved by electrophoresis on agarose gels, Southern blotted to nylon membranes, and rapidly detected by chemiluminescence. This nonradioisotopic method has expedited and reduced the cost for molecular investigations with archival pathological specimens by providing equal sensitivity to or greater sensitivity than that of DNA-labeled radionuclides without the associated biological hazards.

Carcinoma, Papillary↗
PubMed1983

Demonstration of Aujeszky's disease virus antigen in trypsin-digested paraffin-embedded tissue sections by immunofluorescence.

After trypsin digestion of buffered formalin-fixed, paraffin-embedded brain section, immunofluorescent indication of Aujeszky's disease virus antigen was successful in experimentally infected cow and goat. This result was comparable to those obtained with light and electron microscopic examinations. This method will be diagnostically useful where fresh-frozen tissue is not available.

Animals↗
PubMed2006

SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues.

These studies attempt to understand more fully the host response and pathogenesis associated with severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) by monitoring gene expression using formalin-fixed paraffin-embedded (FFPE) pulmonary autopsy tissues. These tissues were from patients in different hospitals in Singapore who were diagnosed with various microbial infections, including SARS-CoV, that caused acute respiratory distress syndrome (ARDS). Global expression patterns showed limited correlation between end-stage ARDS and the initiating pathogen, but when focusing on a subset of genes implicated in pulmonary pathogenesis, molecular signatures of pulmonary disease were obtained and appeared to be influenced by preexisting pulmonary complications and also bacterial components of infection. Many factors detected during pulmonary damage and repair, such as extracellular matrix (ECM) components, transforming growth factor (TGF) enhancers, acute-phase proteins, and antioxidants, were included in the molecular profiles of these ARDS lung tissues. In addition, differential expression of cytokines within these pulmonary tissues were observed, including notable genes involved in the interferon (IFN) pathway, such as Stat1, IFN regulatory factor-1 (IRF-1), interleukin-6 (IL-6), IL-8, and IL-18, that are often characterized as elevated in ARDS patients.

Aged↗
PubMed1988

Southern blot analysis of DNA extracted from formal-saline fixed and paraffin wax embedded tissue.

Model experiments were designed to assess whether DNA could be recovered from formol-saline fixed peripheral blood lymphocytes and tonsil tissue for use in Southern blot gene analysis. Lymphocytes were fixed for 30 min and tonsil for 6 and 24 h, then paraffin embedded. High molecular weight DNA was extracted by prolonged digestion (2-7 days) with proteinase K or protease XXIV in the presence of 1 per cent sodium dodecyl sulphate. Restriction, transfer and hydridization were possible without modification of standard procedures. Multiple copy sequences were demonstrated using Mspl and Bst Nl restriction and hybridization for the Y chromosome (pHY 2.1 probe), single copy genes using EcoRI and BamHl restriction for the T-cell receptor beta chain (T beta probe), and Bgl II and Hind III for the immunoglobulin heavy chain (JH probe). Identical banding to unfixed tissue was achieved except when 24 h fixed extracts were used. With these, demonstration of the 24 KB Bam Hl/T beta and 9.2 KB Hind III/JH bands was not obtained. These findings suggest that as the fixation time is extended, alterations to DNA will limit the available range of restriction enzyme/probe combinations. However, with careful choice of these the extraction of DNA from formalin fixed and paraffin embedded pathological tissue for Southern blotting should be profitable.

DNA↗
PubMed1998

Release and analysis of polypeptides and glycopolypeptides from formalin-fixed, paraffin wax-embedded tissue.

Archival tissue specimens are commonly stored as formalin-fixed, paraffin wax-embedded blocks. Formalin fixation facilitates excellent morphological preservation, and the immunoreactivity of many antigens is preserved, but formalin-induced chemical cross-linking of proteins renders them insoluble and inaccessible to standard biochemical extraction and analytical methods. Thus, biochemical analysis of tissue components identified by histochemistry, with the advantage of long-term clinical follow-up, is precluded. We have applied cyanogen bromide cleavage, a technique used routinely for fragmenting proteins for sequencing experiments, to solubilize transferrin polypeptides and glycopolypeptides from formalin-fixed, paraffin wax-embedded rat liver. Cyanogen bromide cleaves protein specifically at methionine residues, yielding a predictable array of polypeptide fragments. Subsequent oligosaccharide analysis of the transferrin glycopolypeptides by anion exchange chromatography confirmed that, in addition to successful release of polypeptide chains, sialylated oligosaccharide structures remained intact after cyanogen bromide cleavage. This approach may have wide applicability to a range of research interests in which correlation of tissue biochemistry with long-term follow-up is advantageous.

Animals↗
PubMedDate not supplied

A polychromatic staining method for epoxy embedded tissue: a new combination of methylene blue and basic fuchsine for light microscopy.

A simple and rapid method is described for staining semithin sections of material embedded in epoxy resin for observing tissues prior to transmission electron microscopy. The method is suitable for tissue fixed with a glutaraldehyde-formaldehyde mixture and postfixed in osmium tetroxide. No etching or oxidizing procedures are necessary. Sections 0.5-0.8 microm thick are dried onto a slide and stained with either 0.75% methylene blue and 0.25% azure B or 0.5% methylene blue and 0.5% azure II in 0.5% aqueous borax and heated over a flame for 8-10 sec. The slides are rinsed with water, then stained the same way with 0.1% basic fuchsine in 5% aqueous ethanol. Cytoplasm stains blue; nuclei darker blue; collagen, mucus and elastin pink to red; fat and intracellular lipid droplets gray-green.

Animals↗
PubMed1980

Diagnosis of hairy-cell leukaemia by tartrate-resistant acid phosphatase activity in paraffin-embedded tissue sections.

Tartrate-resistant acid phosphatase activity may be demonstrated in paraffin-embedded liver and spleen specimens as well as in decalcified bone marrow biopsies after fixation in a mixed glutaraldehyde-formaldehyde-calcium acetate solution. This technique may routinely be applied to haematologically relevant material and aids in the differential diagnosis of hairy-cell leukaemia.

Acid Phosphatase↗
PubMed1989

Fat intestinal absorption in the catfish--a histochemical study in glycol methacrylate embedded tissue.

The intestinal absorption of lipids was investigated in plastic sections from glycol methacrylate embedded intestine after fat administration. In the catfish, the lipids are absorbed by the enterocytes of the proximal intestinal segment, thus forming fat cytoplasmic inclusions that were demonstrated by Sudan black B staining. The histochemical characterization of lipids by the Nile blue sulphate test revealed the neutral or triglyceride nature of the cytoplasmic droplets, both after the corn oil and oleic acid feeding. There is lipid accumulation in the lamina propria and lymphatic vessels.

Animals↗
PubMedDate not supplied

Immunohistochemical demonstration of various antigens in tissues embedded in plastic.

In the course of a chronic experimental study of polyarthritis in rats, we have established a plastic embedding technique which allows the processing not only of soft tissues but also of tissues such as cartilage, intraarticular ligaments, and even undecalcified whole rat joints and provides broad survival of enzymes and antigens. Preservation of morphological details and the precision of antigen localization are superior to those seen in cryostat and paraffin sections. The method seems to have much diagnostic and investigative value, especially in arthritis research.

Animals↗
PubMed1987

A freeze-dried paraffin-embedded tissue technique for immunohistochemical studies requiring unfixed tissue from the nervous system.

Immunohistochemical studies using monoclonal antibodies against epitopes in neural tissues frequently require tissue which has not been fixed in formalin. In the past, such studies have been performed on frozen (cryostat) sections despite the general loss of morphological preservation compared with paraffin sections. In the present report, a detailed, versatile method for obtaining improved morphological preservation of "unfixed" neural tissue is described which utilizes freeze-dried paraffin-embedded sections (a modified Altmann-Gersh technique). The advantages of using mercury flotation of freeze-dried sections are particularly stressed.

Animals↗
PubMed1977

Organometallic and organometalloid compounds as standards for microprobe analysis of epoxy resin embedded tissue.

X-ray microanalysis of phosphorus, transition elements and heavy metals in biological tissue is frequently carried out on thin sections of specimens embedded in epoxy resin. A logical choice for the quantitive microprobe analysis of these specimens is a standard, consisting of a homogenous solution of the elements of interest in the epoxy resin. Four kinds of compounds were found suitable for this purpose: (1) phenyl compounds containing group Vb elements, (2) cyclopentadienyl-derivatives, (3) a pentanedione derivative (acetylacetonate) and (4) complexes of metals with dialkyldithiocarbamates. In the latter case, the standard also contains sulphur. Standards for P, Sb (1) Mn, Fe (2) Ni (3) Cu, Zn, Cd, Hg, Pb, Bi (4) were prepared in Epon 812 or Spurr epoxy resin. The compounds were mixed with the resin (without accelerator) to which some propylene oxide may be added, and dissolved immediately or after short heating. The maximal concentration of metal was in the order of magnitude of several promilles to 1%. Solubility in the Spurr resin was better than in Epon 812. After addition of the accelerator, polymerization was carried out as usual. The compounds used are commercially availalbe at low cost or can be easily prepared.

Alkanes↗
PubMed1994

Multiple PCR analyses on trace amounts of DNA extracted from fresh and paraffin wax embedded tissues after random hexamer primer PCR amplification.

AIM: To establish a simple and reliable polymerase chain reaction (PCR) methodology for random amplification of whole genomic DNA from limited histopathological samples. METHODS: Trace amounts of genomic DNA extracted from fresh tissue and individual lymphoid follicles microdissected from archival paraffin wax tissue sections were amplified using a two-phase PCR protocol with random hexamers as primers (RP-PCR). The randomly amplified DNA samples were used as templates for specific PCR amplifications. To check the fidelity of the RP-PCR, products of the specific PCR amplifications were further analysed by single stranded conformation polymorphism (SSCP) or sequencing. RESULTS: Using a minute fraction of RP-PCR template pool, multiple PCR analyses, including those for beta globin gene, p53 gene (exon 5-6, exon 7, exon 8-9 and exon 7-9), and rearranged immunoglobulin heavy chain gene fragments (VH framework 3 to JH and VH framework 2 to JH) were successfully performed. No artefactual mutations were identified in the products of these specific PCR reactions by SSCP or sequencing when compared with the products from the original DNA. CONCLUSION: This method is simple and reliable, and permits multiple genetic analyses when only a limited amount of tissue is available.

Base Sequence↗
PubMed2001

[Extraction of RNA from paraffin embedded tissues and analysis of p53 gene expression in colonic cancer].

We examined, immunohistochemically and molecular biologically, p53 gene expression in 10 patients with colonic cancer. RNA was extracted from paraffin embedded normal and colonic cancer tissues by using RNA isolator kit and proteinase K. The most effective time and concentration of proteinase K for RNA extraction was 24 hours and 100 micrograms/ml, respectively. P53 gene expression was analyzed by ABI PRISM 7700 Sequence Detection System(ABI 7700 System, Perkinelmer). Gene expression level in each sample was estimated on the basis of the standard curve of ABI 7700 System. Human G3PDH gene was used as the internal control. Immunohistochemically, the tumor cells in all examined cases showed a strong positivity for anti-p53 gene antibody. In ABI 7700 System, expression of p53 gene in the malignant tissues revealed a high level in only 2 cases that had a clinical stage IV, however, in remaining 8 cases a clinical stage was I to III and expression level of p53 was relatively lower. These results suggest that colonic cancer cells show mutant-p53 gene expression, and a ratio of mutant- to wild-p53 gene may have something to do with a relationship between gene expression and clinical stage.

Adenocarcinoma↗
PubMed1996

Estrogen receptor immunocytochemistry in paraffin embedded tissues with ER1D5 predicts breast cancer endocrine response more accurately than H222Sp gamma in frozen sections or cytosol-based ligand-binding assays.

BACKGROUND: Historically, estrogen receptor (ER) determinations have been made by the ligand-binding assay of tumor homogenates, primarily by the dextran-coated charcoal method (DCC). Immunocytochemical assays (ICA) for ER are more recent and have been executed mostly on frozen sections with the monoclonal antibody H222Sp gamma (H222). Lately, new monoclonal antibodies derived by recombinant ER technology have been developed that work well on paraffin embedded, formalin fixed tissue sections. However, there is little information as to whether such assays prognosticate endocrine response. METHODS: Using antigen retrieval, the immunoglobulin G1 monoclonal antibody ER1D5, and the streptavidin-biotin detection system, 74 patients with breast cancer in whom endocrine response was known were assayed and the results compared with ER by DCC and ER by ICA in frozen section with H222. RESULTS: ER1D5 in paraffin provided the highest correlation with endocrine response (Kendall's tau [r] = 0.57; P<0.001) whereas ER by DCC failed to correlate (r= -0.002; P<0.99). ER1D5 in paraffin correlated weakly though significantly with DCC (Kappa Statistic [K] = 0.204; P<0.02). H222 in frozen sections also correlated moderately with endocrine response (r = 0.34; P<0.001). CONCLUSIONS: ER can be detected in routine tissue sections processed with antigen retrieval and ER1D5, and can be relied upon to provide accurate prognostic information regarding response to endocrine therapies in breast cancer patients.

Adult↗
PubMed2004

Quantitative analysis of mast cells in benign and malignant breast lesions. Immunohistochemical study on formalin-fixed, paraffin-embedded tissues.

BACKGROUND: It has been reported that the number of mast cells was significantly greater in malignant breast carcinomas than in benign breast lesions. This was due to tryptase-containing mast cells while tryptase, chymase-containing mast cells had no effect. However, analysis of mast cells in breast carcinomas and benign breast lesions based on their histological findings remains to be elucidated. METHODS: Using immunohistochemical methods morphological examinations of mast cells were undertaken in benign and malignant breast tissues from 51 patients (30 benign, 21 malignant), which were formalin-fixed and paraffin-embedded. In the study with malignant breast tissues, samples of malignant tissues and adjacent healthy tissues were obtained from a single patient, and the number of mast cells was compared. RESULTS: Among benign breast tissues, the number of mast cells in intracanalicular fibroadenoma was significantly lower than that in pericanalicular fibroadenoma as well as that in mastopathy. The number of mast cells was significantly greater in malignant lesions than that in benign lesions. The number of mast cells in scirrhous carcinoma and that in solid-tubular carcinoma were significantly increased compared with that in adjacent healthy tissues. In addition, the number of mast cells in scirrhous carcinoma was highest among breast carcinomas, and significantly greater than that in papillotubular carcinoma. CONCLUSION: We were the first to find the significant lower number of mast cells in intracanalicular breast fibroadenoma when compared with that in pericanalicular fibroadenoma as well as that in mastopathy. Moreover, the number of mast cells in scirrhous carcinoma was significantly greater than that in papillotubular carcinoma.

Adult↗