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1.
Two methods for proteomic analysis of formalin‐fixed,paraffin embedded tissue result in differential protein identification,data quality,and cost 下载免费PDF全文
Formalin‐fixed paraffin‐embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC‐MS/MS exist, but standardization of procedures and critical analysis of data quality is limited. This study compared and characterized data obtained from FFPE tissue using two methods: a urea in‐solution digestion method (UISD) versus a commercially available Qproteome FFPE Tissue Kit method (Qkit). Each method was performed independently three times on serial sections of homogenous FFPE tissue to minimize pre‐analytical variations and analyzed with three technical replicates by LC‐MS/MS. Data were evaluated for reproducibility and physiochemical distribution, which highlighted differences in the ability of each method to identify proteins of different molecular weights and isoelectric points. Each method replicate resulted in a significant number of new protein identifications, and both methods identified significantly more proteins using three technical replicates as compared to only two. UISD was cheaper, required less time, and introduced significant protein modifications as compared to the Qkit method, which provided more precise and higher protein yields. These data highlight significant variability among method replicates and type of method used, despite minimizing pre‐analytical variability. Utilization of only one method or too few replicates (both method and technical) may limit the subset of proteomic information obtained. 相似文献
2.
Because fresh‐frozen tissue samples associated with long‐term clinical data and of rare diseases are often unobtainable at the present time, formalin‐fixed paraffin‐embedded (FFPE) tissue samples are considered a highly valuable resource for researchers. However, protein extraction from FFPE tissues faces challenges of deparaffinization and cross‐link reversion. Current procedures for protein extraction from FFPE tissue require separate steps and toxic solvents, resulting in inconvenience in protein extraction. To overcome these limitations, an integrated method was developed using nontoxic solvents in four types of FFPE tissues. The average amount of proteins from three replicates of bladder, kidney, liver, and lung FFPE tissues were 442.6, 728.9, 736.4, and 694.7 μg with CVs of 7.5, 5.8, 2.4, and 4.5%, respectively. Proteomic analysis showed that 348, 417, 607, and 304 unique proteins were identified and quantified without specification of isoform by a least two peptides from bladder, kidney, liver, and lung FFPE tissue samples, respectively. The analysis of individual protein CV demonstrated that 97–99% of the proteins were quantified with a CV ≤ 30%, verifying the reproducibility of the integrated protein extraction method. In summary, the developed method is high‐yield, reproducible, convenient, simple, low cost, nonvolatile, nonflammable, and nontoxic. 相似文献
3.
Antigen retrieval (AR) is a technique that re-exposes epitopes in formalin fixed, paraffin embedded sections and makes them detectable by immunohistochemistry. We compared the effects of two AR procedures, enzyme digestion and microwave heating, on immunostaining of vimentin and desmin in formalin fixed, paraffin embedded tissues. Our results showed that AR is necessary for vimentin and desmin immunostaining in tissues fixed in formalin for more than 48 h. With prolonged fixation times, microwave heating showed better results than enzyme digestion for AR. The same results were obtained using 1% zinc sulfate or Citra Plus solution as retrieval solutions for microwave heating. We recommend microwave heating for AR, because it is easier to use and produces better results compared to enzyme treatment. 相似文献
4.
A comparison of microwave heating and proteolytic pretreatment antigen retrieval techniques in formalin fixed, paraffin embedded tissues 总被引:5,自引:0,他引:5
Antigen retrieval (AR) is a technique that re-exposes epitopes in formalin fixed, paraffin embedded sections and makes them detectable by immunohistochemistry. We compared the effects of two AR procedures, enzyme digestion and microwave heating, on immunostaining of vimentin and desmin in formalin fixed, paraffin embedded tissues. Our results showed that AR is necessary for vimentin and desmin immunostaining in tissues fixed in formalin for more than 48 h. With prolonged fixation times, microwave heating showed better results than enzyme digestion for AR. The same results were obtained using 1% zinc sulfate or Citra Plus solution as retrieval solutions for microwave heating. We recommend microwave heating for AR, because it is easier to use and produces better results compared to enzyme treatment. 相似文献
5.
《Biotechnic & histochemistry》2013,88(5):395-399
AbstractParaffin embedded tissue sections and fine needle aspiration biopsy (FNAB) are important methods for diagnosis. We compared thyroid tissue obtained by FNAB to paraffin embedded sections to determine whether there were differences in detection of the amounts of argyrophilic nucleolar organizing region (AgNOR) proteins. Twenty-two patients with papillary thyroid carcinoma were included in the study. Slides were prepared with both FNAB tissue and 3 μm sections of paraffin embedded tissue, and stained for AgNOR. One hundred nuclei per individual were evaluated; total AgNOR number/nucleus (TAn/TNn) and total AgNOR area/nuclear area (TAa/TNa) of individual cells were determined. Mean TAn/TNn and TAa/TNa values were 4.800 ± 1.118 and 13.382 ± 2.612, respectively, for FNAB samples; corresponding values were 2.406 ± 0.649 and 8.49 ± 0.893, respectively, for paraffin embedded sections. The differences between FNAB materials and paraffin embedded tissue sections were significant for the mean TAn/TNn and TAa/TNa values. Significant differences in the amounts of AgNOR protein detected were found between FNAB and paraffin embedded tissue sections. 相似文献
6.
Tissue microarray (TMA) technology has provided a high throughput means of evaluating potential biomarkers and therapeutic
targets in archival pathological specimens. TMAs facilitate the rapid assessment of molecular alterations in hundreds of different
tumours on a single slide. Sections from TMAs can be used for any in situ tissue analysis, including fluorescent in situ hybridization
(FISH). FISH is a molecular technique that detects numerical and structural abnormalities in both metaphase chromosomes and
interphase nuclei. FISH is commonly used as a prognostic and diagnostic tool for the detection of translocations and for the
assessment of gene deletion and amplification in tumours. Performing FISH on TMAs enables researchers to determine the clinical
significance of specific genetic alterations in hundreds of highly characterized tumours. The use of FISH on archival paraffin
embedded tissues is technically demanding and becomes even more challenging when applied to paraffin embedded TMAs. The problems
encountered with FISH on TMAs, including probe preparation, hybridization, and potential applications of FISH, will be addressed
in this review. 相似文献
7.
Fluorescence in situ hybridization has found wide application in the enumeration of gene and chromosome copy number both in isolated cells and
in tissue sections. However, the technique has been less widely used than would be expected in formalin-fixed paraffin processed
(archival) tissue. This article describes a method for assessing archival tissue sections, following pretreatment, before
applying DNA probes, that gives consistent, reliable results. 相似文献
8.
Marie‐Claude Djidja Simona Francese Paul M. Loadman Chris W. Sutton Peter Scriven Emmanuelle Claude Marten F. Snel Julien Franck Michel Salzet Malcolm R. Clench 《Proteomics》2009,9(10):2750-2763
The identification of proteins involved in tumour progression or which permit enhanced or novel therapeutic targeting is essential for cancer research. Direct MALDI analysis of tissue sections is rapidly demonstrating its potential for protein imaging and profiling in the investigation of a range of disease states including cancer. MALDI‐mass spectrometry imaging (MALDI‐MSI) has been used here for direct visualisation and in situ characterisation of proteins in breast tumour tissue section samples. Frozen MCF7 breast tumour xenograft and human formalin‐fixed paraffin‐embedded breast cancer tissue sections were used. An improved protocol for on‐tissue trypsin digestion is described incorporating the use of a detergent, which increases the yield of tryptic peptides for both fresh frozen and formalin‐fixed paraffin‐embedded tumour tissue sections. A novel approach combining MALDI‐MSI and ion mobility separation MALDI‐tandem mass spectrometry imaging for improving the detection of low‐abundance proteins that are difficult to detect by direct MALDI‐MSI analysis is described. In situ protein identification was carried out directly from the tissue section by MALDI‐MSI. Numerous protein signals were detected and some proteins including histone H3, H4 and Grp75 that were abundant in the tumour region were identified. 相似文献
9.
Peter T. Moerkerk Han J. Kessels Joop ten Kate Antony F. P. M. de Goeij Fré T. Bosman 《Virchows Archiv. B, Cell pathology including molecular pathology》1989,58(1):351-355
Two extraction methods for the isolation of DNA from formalin-fixed, paraffin-embedded tissue samples from colonic carcinomas
were compared. The processed DNAs were compared with DNAs from fresh specimens of the same tumors. The two extraction methods
gave similar results. Formalin-fixation and paraffinembedding irreversibly denatured DNA and consequently decreased the extraction
yield and interfered with the quantitative measurement of DNA.
Southern blot and dot blot analysis of processed and native DNA was performed using a c-myc and an actin probe. The results
show that for Southern analysis processed DNA can be used but, due to the generation of random breaks, the restriction fragments
have to be small. Furthermore, the fixation-induced crosslinking of DNA appears to hamper hybridization. For these reasons
processed DNA can be analyzed better by dot blot rather than Southern blot hybridization. 相似文献
10.
S E Goelz S R Hamilton B Vogelstein 《Biochemical and biophysical research communications》1985,130(1):118-126
The ability to isolate DNA from preserved human tissues would provide numerous experimental opportunities. In this report it is shown that DNA can be extracted from tissues prepared for routine histopathological examination (i.e., fixed with formaldehyde and embedded in paraffin). Although the extracted DNA is not intact, it is double stranded, cleavable with restriction endonucleases, and suitable for a variety of standard techniques used in molecular biology. 相似文献
11.
M P Foschini C Ceccarelli P Chieco G Lisignoli V Eusebi 《Basic and applied histochemistry》1987,31(4):493-500
DNA microfluorometry on smears obtained from paraffin embedded tissue has been shown to be a distinctive possibility. In this paper a simple method for the detachment of cells from mammary ducts and ductules is described. Areas of interest were selected in conventional slides stained with Haematoxylin and Eosin. The corresponding paraffin embedded block was then dewaxed. The areas under study were retraced with a stereomicroscope and the cells within ducts and ductules were scraped out with a 0.4 mm diameter fine needle. Cells were isolated with mechanical and enzymatic procedures and stained with the Feulgen reaction. The DNA content of single cells was then measured using a microfluorometer. 相似文献
12.
A simple protocol of tissue preparation was sought, which would enable marker enzymes of bone cells and extracellular matrix antigens to be localized in the same tissue section with high optical resolution. For this purpose, snap-frozen samples of rat fetal skeletal tissues were dried in a FDU 010 freeze-drying unit (Balzers) for 8–12 h at –50 to –40°C and 0.02 bar. Freeze-dried tissues were either vacuum-infiltrated at 45°C and embedded undemineralized in Paraplast, or vacuum-infiltrated overnight at 4°C and embedded undemineralized in glycol methacrylate. These procedures enabled enzyme cytochemistry for alkaline phosphatase and tartrate-resistant acid phosphatase, and immunocytochemical staining for collagen types I, III, and laminin to be performed on the same sections. No pretreatment of the sections was necessary to reveal collagen antigenicity. This study reveals the possibility of complementing immunocytochemical studies of extracellular matrix with enzyme cytochemistry and, above all, with the excellent tissue preservation and high resolution afforded by plastic embedding. 相似文献
13.
14.
A simple protocol of tissue preparation was sought, which would enable marker enzymes of bone cells and extracellular matrix antigens to be localized in the same tissue section with high optical resolution. For this purpose, snap-frozen samples of rat fetal skeletal tissues were dried in a FDU 010 freeze-drying unit (Balzers) for 8-12 h at -50 to -40 degrees C and 0.02 bar. Freeze-dried tissues were either vacuum-infiltrated at 45 degrees C and embedded undemineralized in Paraplast, or vacuum-infiltrated overnight at 4 degrees C and embedded undemineralized in glycol methacrylate. These procedures enabled enzyme cytochemistry for alkaline phosphatase and tartrate-resistant acid phosphatase, and immunocytochemical staining for collagen types I, III, and laminin to be performed on the same sections. No pretreatment of the sections was necessary to reveal collagen antigenicity. This study reveals the possibility of complementing immunocytochemical studies of extracellular matrix with enzyme cytochemistry and, above all, with the excellent tissue preservation and high resolution afforded by plastic embedding. 相似文献
15.
Paul Wallace Medlow Christopher James Steele Andrena Marie McCavigan Wesley Reardon Christopher Michael Brown Shauna May Lambe Felipe Augusto Andre Ishiy Steven Michael Walker Gemma Elizabeth Logan Olaide Yaqeen Raji Viktor Berge Betina Katz Elaine Williamson Kay Katherine Sheehan Ronald William Watson Denis Paul Harkin Richard Darragh Kennedy Laura Anne Knight 《BMC medical genomics》2018,11(1):125
Background
There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. This study describes the analytical validation of one such assay designed to predict metastatic recurrence in prostate cancer using primary formalin fixed paraffin embedded tumour material.Methods
Accuracy was evaluated with a method comparison study between the assay development platform (Prostate Disease Specific Array) and an alternative platform (Xcel? microarray) using 50 formalin-fixed, paraffin-embedded prostate cancer patient samples. An additional 70 samples were used to establish the assay reportable range. Determination of assay precision and sensitivity was performed on multiple technical replicates of three prostate cancer samples across multiple variables (operators, days, runs, reagent lots, and equipment) and RNA/cDNA inputs respectively using the appropriate linear mixed model.Results
The overall agreement between the development and alternative platform was 94.7% (95% confidence interval, 86.9–98.5%). The reportable range was determined to be 0.150 to 1.107 for core needle biopsy samples and???0.214 to 0.844 for radical prostatectomy samples. From the precision study, the standard deviations for assay repeatability and reproducibility were 0.032 and 0.040 respectively. The sensitivity study demonstrated that a total RNA input and cDNA input of 50?ng and 3.5?μg respectively was conservative.Conclusion
The Metastatic Assay was found to be highly reproducible and precise. In conclusion the studies demonstrated an acceptable analytical performance for the assay and support its potential use in the clinic.16.
Lei Zhao Zongsheng Guo Pan Wang Meili Zheng Xiaoyan Yang Ye Liu Zheng Ma Mulei Chen Xinchun Yang 《Journal of cellular and molecular medicine》2020,24(1):511-520
Epicardial adipose tissue (EAT) is a metabolically active visceral fat depot closely linked to the pathogenesis of heart failure (HF). But the molecular signatures related to the mechanism of HF have not been systematically explored. Here, we present comprehensive proteomic analysis of EAT in HF patients and non‐HF patients as controls. A total of 771 proteins were identified in liquid chromatography‐tandem mass spectrometry experiments. Amongst them, 17 increased in abundance in HF and seven decreased. They were involved in HF‐related processes including inflammation and oxidative stress response and lipid metabolism. Of these proteins, serine proteinase inhibitor A3 (Serpina3) levels in EAT were highly up‐regulated in HF, with HF/non‐HF ratio of 4.63 (P = .0047). Gene expression of Serpina3 via quantitative polymerase chain reaction was significantly increased in the HF group. ELISA analysis confirmed a significant increase in circulating plasma Serpina3 levels in the HF group (P = .004). In summary, for the first time, we describe that parts of EAT proteome may be reactive and work as modulators of HF. Our profiling provides a comprehensive basis for linking EAT with pathogenesis of HF. Understanding the role of EAT may offer new insights into the treatment of HF. 相似文献
17.
One of the major questions in the field of obesity is why some humans become obese (obesity prone, OP) and others resist the development of obesity (obesity resistant, OR) when exposed to a high-calorie diet, which has not been completely studied. Therefore, in the present study, in order to gain insight into the molecular mechanisms underlying this propensity, we have performed a comparative analysis of protein expression profiles in white adipose tissue (WAT) and brown adipose tissue (BAT) of rats fed a high-fat diet by 2-DE and MALDI-TOF-MS. Protein mapping of homogenates revealed significant alterations to a number of proteins; 60 and 70 proteins were differentially regulated in BAT and WAT, respectively. For careful interpretation of proteomic results, we categorized the identified proteins into two groups by analysis of both average spot density of pooled six rat adipose tissues and individual spot density of each adipose tissue of six rats as a function of body weight. One of the most striking findings of this study was that significant changes of Ehd1 and laminin receptor in BAT as well as antiquitin, DJ-1 protein, and paraoxonase 2 in WAT were found for the first time in obese rats. In addition, we confirmed the increased expression of some thermogenic enzymes and decreased lipogenic enzymes in adipose tissues of OR rats by immunoblot analysis. To our knowledge, this is the first proteomic study of profiling of protein modulation in OP and OR rats, thereby providing the first global evidence for different propensities to obesity between OP and OR rats. 相似文献
18.
19.
Kroll J Becker KF Kuphal S Hein R Hofstädter F Bosserhoff AK 《Histology and histopathology》2008,23(4):391-395
In general, it is believed that the extraction of proteins from formalin-fixed paraffin embedded samples is not feasible. However, recently a new technique was developed, presenting the extraction of non-degraded, full length proteins from formalin fixed tissues, usable for western blotting and protein arrays. In the study presented here, we applied this technique to punch biopsies of formalin fixed tissues embedded in paraffin to reduce heterogeneity of the tissue represented in sections, and to ensure analysing mainly defined cellular material. Successful extraction was achieved even from very small samples (0.7 mm(3)). Additionally, we were able to detect highly glycosylated proteins and protein modification, such as phosphorylation. Interestingly, with this technique it is feasible to extract high quality proteins from 14 year old samples. In summary, the new technique makes a great pool of material now usable for molecular analysis with high throughput tools. 相似文献
20.
Aging is associated with an accrual of body fat, progressive development of insulin resistance and other obesity comorbidities that contribute to decrease life span. Caloric restriction (CR), which primarily affects energy stores in adipose tissue, is known to extend life span and retard the aging process in animal models. In this study, a proteomic approach combining 2‐DE and MS was used to identify proteins modulated by aging and CR in rat white adipose tissue proteome. Proteomic analysis revealed 133 differentially expressed spots, 57 of which were unambiguously identified by MS. Although CR opposed part of the age‐associated protein expression patterns, many effects of CR were on proteins unaltered by age, suggesting that the effects of CR on adipose tissue are only weakly related to those of aging. Particularly, CR and aging altered glucose, intermediate and lipid metabolism, with CR enhancing the expression of enzymes involved in oxalacetate and NADPH production, lipid biosynthesis and lipolysis. Consistently, insulin‐β and β3‐adrenergic receptors were also increased by CR, which denotes improved sensitivity to lipogenic/lipolytic stimuli. Other beneficial outcomes of CR were an improvement in oxidative stress, preventing the age‐associated decrease in several antioxidant enzymes. Proteins involved in cytoskeleton, iron storage, energy metabolism and several proteins with novel or unknown functions in adipose tissue were also modulated by age and/or CR. Such orchestrated changes in expression of multiple proteins provide insights into the mechanism underlying CR effects, ultimately allowing the discovery of new markers of aging and targets for the development of CR‐mimetics. 相似文献