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Abstract
Proteomic studies have generated numerous datasets of potential diagnostic, prognostic, and therapeutic significance in human cancer. Two key technologies underpinning these studies in cancer tissue are two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Although surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-MS is the mainstay for serum or plasma analysis, other methods including isotope-coded affinity tag technology, reverse-phase protein arrays, and antibody microarrays are emerging as alternative proteomic technologies. Because there is little overlap between studies conducted with these approaches, confirmation of these advanced technologies remains an elusive goal. This problem is further exacerbated by lack of uniform patient inclusion and exclusion criteria, low patient numbers, poor supporting clinical data, absence of standardized sample preparation, and limited analytical reproducibility (in particular of 2D-PAGE). Despite these problems, there is little doubt that the proteomic approach has the potential to identify novel diagnostic biomarkers in cancer. In therapeutic proteomics, the challenge is significant due to the complexity systems under investigation (i.e., cells generate over 10(5) different polypeptides). However, the most significant contribution of therapeutic proteomics research is expected to derive not from single experiments, but from the synthesis and comparison of large datasets obtained under different conditions (e.g., normal, inflammation, cancer) and in different tissues and organs. Thus, standardized processes for storing and retrieving data obtained with different technologies by different research groups will have to be developed. Shifting the emphasis of cancer proteomics from technology development and data generation to careful study design, data organization, formatting, and mining is crucial to answer clinical questions in cancer research.
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Affiliation(s)
- M A Reymond
- Department of Surgery, University of Magdeburg, Germany
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Lexander H, Hellman U, Palmberg C, Auer G, Hellström M, Franzén B, Jörnvall H, Egevad L. Evaluation of two sample preparation methods for prostate proteome analysis. Proteomics 2006; 6:3918-25. [PMID: 16767792 DOI: 10.1002/pmic.200600104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
For laboratory techniques that require well-preserved proteins, such as 2-DE, fresh tissue must be harvested and processed as fast as possible to avoid proteolytic degradation. We describe a modified method for harvesting tissue from radical prostatectomy specimens for proteome analysis and compare it with the standard technique. Cells were scraped from cut surfaces of 11 prostate specimens. A fraction of the material was smeared on a glass slide and Giemsa stained for morphological control. The sample was collected in a medium with protease inhibitors, and the protein material was prepared for 2-DE. Filtering and Percoll centrifugation were omitted. Sample locations were noted on a specimen map. From the same area, a tissue block was harvested for comparison. The block was processed with the conventional technique including mechanical disintegration, filtering and Percoll centrifugation. Quality measures of 2-DE were similar with both methods. With the scrape sampling technique, control smears showed abundant epithelial cells and a cleaner background and processing was faster than with tissue block sampling. For proteomic analysis, the scrape sample technique has several advantages over the tissue block method.
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Affiliation(s)
- Helena Lexander
- Department of Oncology and Pathology, Karolinska Hospital, Karolinska Institute, SE-171 76 Stockholm, Sweden
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Besada V, Diaz M, Becker M, Ramos Y, Castellanos-Serra L, Fichtner I. Proteomics of xenografted human breast cancer indicates novel targets related to tamoxifen resistance. Proteomics 2006; 6:1038-48. [PMID: 16385476 DOI: 10.1002/pmic.200500151] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tamoxifen is the most frequently used drug for hormone therapy of breast cancer patients, even though a high percentage of women are (or become) refractory to this treatment. The proteins involved in tamoxifen resistance of breast tumor cells as well as the mechanisms by which they interact, are still unknown. Some years ago, we established the xenograft breast tumor 3366, sensitive to tamoxifen and the 3366/TAM, resistant to tamoxifen, derived after two years of in vivo passages of the parental 3366 under tamoxifen treatment. Here, we compare the protein expression levels of both xenografts. 2-DE of proteins from total cell extracts showed very high reproducibility among tumors from each group (tamoxifen sensitive and tamoxifen resistant). The heuristic clustering analysis of these gels pooled them correctly in both groups. Twelve proteins were found up-regulated in the tamoxifen-resistant line, while nine were down-regulated. The proteins differentially expressed were identified by MS and sequence database analysis. Biological functions of these proteins are related to cell-cell adhesion and interaction, signal transduction, DNA and protein synthesis machinery, mitochondrial respiratory chain, oxidative stress processes and apoptosis. Three of the identified proteins (ALG-2 interacting protein and two GDP-dissociation inhibitors) could be directly involved in the resistance phenomenon.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antineoplastic Agents, Hormonal/therapeutic use
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/drug therapy
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cluster Analysis
- Drug Resistance, Neoplasm
- Electrophoresis, Gel, Two-Dimensional
- Female
- Humans
- Mice
- Mice, Nude
- Molecular Sequence Data
- Proteomics
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tamoxifen/therapeutic use
- Transplantation, Heterologous
- Tumor Cells, Cultured
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Affiliation(s)
- Vladimir Besada
- Department for Proteome Analysis, Centre for Genetic Engineering and Biotechnology, Havana, Cuba
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Hellman K, Alaiya AA, Schedvins K, Steinberg W, Hellström AC, Auer G. Protein expression patterns in primary carcinoma of the vagina. Br J Cancer 2004; 91:319-26. [PMID: 15199389 PMCID: PMC2409807 DOI: 10.1038/sj.bjc.6601944] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Protein patterns in six samples from primary vaginal cancers, in five from normal vaginal tissue and in five primary cervical cancers, were analysed using two-dimensional polyacrylamide gel electrophoresis (2-DE). Protein expression profile was evaluated by computer-assisted image analysis (PDQUEST) and proteins were subsequently identified using matrix-assisted laser desorption/ionisation mass spectrometry. The aim was to analyse the protein expression profiles using the hierarchical clustering method in vaginal carcinoma and to compare them with the protein pattern in cervical carcinoma in order to find a helpful tool for correct classification and for increased biomedical knowledge. Protein expression data of a distinct set of 33 protein spots were differentially expressed. These differences were statistically significant (Mann-Whitney signed-Ranked Test, P<0.05) between normal tissue, vaginal and cervical cancer. Furthermore, protein profiles of pairs of primary vaginal and cervical cancers were found to be very similar. Some of the protein spots that have so far been identified include Tropomyosin 1, cytokeratin 5, 15 and 17, Apolipoprotein A1, Annexin V, Glutathione-S-transferase. Others are the stress-related proteins, calreticulin, HSP 27 and HSP 70. We conclude that cluster analysis of proteomics data allows accurate discrimination between normal vaginal mucosa, primary vaginal and primary cervical cancer. However, vaginal and cervical carcinomas also appear to be relatively homogeneous in their gene expression, indicating similar carcinogenic pathways. There might, further, be a possibility to identify tumour-specific markers among the proteins that are differentially expressed. The results from this study have to be confirmed by more comprehensive studies in the future.
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Affiliation(s)
- K Hellman
- Department of Gynecologic Oncology, Radiumhemmet, Karolinska Hospital, S-171 76 Stockholm, Sweden
- Department of Gynecologic Oncology, Radiumhemmet, Karolinska Hospital, S-171 76 Stockholm, Sweden. E-mail:
| | - A A Alaiya
- Unit of Cancer Proteomics, Department of Oncology and Pathology, Karolinska Institute and Hospital, Stockholm, Sweden
- Unit of Cancer Proteomics, Department of Oncology and Pathology, Karolinska Institute and Hospital, Stockholm, Sweden. E-mail:
| | - K Schedvins
- Division of Obstetrics and Gynecology, Department of Woman and Child Health, Karolinska Institute and Hospital, S-171 76 Stockholm, Sweden
| | - W Steinberg
- Institution of Cytological Diagnosis (Kloster-Paradiese), Im Stiftsfeld 159494 Soest, Germany
| | - A-C Hellström
- Department of Gynecologic Oncology, Radiumhemmet, Karolinska Hospital, S-171 76 Stockholm, Sweden
| | - G Auer
- Unit of Cancer Proteomics, Department of Oncology and Pathology, Karolinska Institute and Hospital, Stockholm, Sweden
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Abstract
Proteome technology has been used widely in cancer research and is a useful tool for the identification of new cancer markers and treatment-related changes in cancer. This article details the use of proteome technology in cancer research, and laboratory-based and clinical cancer research studies are described. New developments in proteome technology that enable higher sample-throughput are evaluated and methods for enhancing conventional proteome analysis (based on two-dimensional electrophoresis) discussed. The need to couple laboratory-based proteomics research with clinically relevant models of the disease is also considered, as this remains the next main challenge of cancer-related proteome research.
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Affiliation(s)
- Miriam V Dwek
- Breast Cancer Research Group, Department of Surgery, Royal Free and University College London Medical School, Institute of Surgical Studies, UK.
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Ott V, Guenther K, Steinert R, Tortola S, Borisch B, Schlegel W, Reymond MA. Accuracy of two-dimensional electrophoresis for target discovery in human colorectal cancer. THE PHARMACOGENOMICS JOURNAL 2002; 1:142-51. [PMID: 11911441 DOI: 10.1038/sj.tpj.6500024] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is increasingly used for target discovery in human disease to complement genomic studies. We have assessed the possibilities and limits of 2-D PAGE applied to human colorectal cancer. Up to 10(8) epithelial cells were purified from paired normal and pathological biopsies using Ber-EP4 coated magnetic beads, allowing the elimination of cellular and fluid contaminations. The mean coefficient of variation (CVAR) of repeated 2-D PAGE analysis with silver staining was lying between 20 and 28%. However, only 47% (interrun) to 76% (intrarun) of spots could be matched within a triplicate experiment. Interindividual phenotypic variability was high. Intratumoral phenotypic variability was not found to be significant. When method and tumor variability were added, 90% of CVAR were inferior to 48%. Thus, two-fold up- or down-regulation of protein expression reveals biological significance. Serial paired comparison of 923 proteins in 10 patients showed highly reproducible differences between normal and cancer tissues. Under well defined experimental conditions and after the high variability of the technique has been considered, 2-D PAGE parallel analysis of paired colorectal samples allows patient-specific tumor profiling.
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Affiliation(s)
- V Ott
- Department of Surgery, University of Geneva, Switzerland
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Krieg RC, Paweletz CP, Liotta LA, Petricoin EF. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol Cancer Res Treat 2002; 1:263-72. [PMID: 12625785 DOI: 10.1177/153303460200100407] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the "software" of protein pathway networks and circuitry. The deranged circuitry of the cell as the drug target itself as well as the effect of the drug on not just the target, but also the entire network, is what we now are striving towards. Clinical proteomics, as a new and most exciting sub-discipline of proteomics, involves the bench-to-bedside clinical application of proteomic tools. Unlike the genome, there are potentially thousands of proteomes: each cell type has its own unique proteome. Moreover, each cell type can alter its proteome depending on the unique tissue microenvironment in which it resides, giving rise to multiple permutations of a single proteome. Since there is no polymerase chain reaction equivalent to proteomics- identifying and discovering the "wiring diagram" of a human diseased cell in a biopsy specimen remains a daunting challenge. New micro-proteomic technologies are being and still need to be developed to drill down into the proteomes of clinically relevant material. Cancer, as a model disease, provides a fertile environment to study the application of proteomics at the bedside. The promise of clinical proteomics and the new technologies that are developed is that we will detect cancer earlier through discovery of biomarkers, we will discover the next generation of targets and imaging biomarkers, and we can then apply this knowledge to patient-tailored therapy.
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Affiliation(s)
- Rene C Krieg
- FDA-NCI Clinical Proteomics Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Ardekani AM, Ardekani AM, Herman EH, Sistare FD, Liotta LA, Petricoin EF. Molecular profiling of cancer and drug-induced toxicity using new proteomic technologies. Curr Ther Res Clin Exp 2001. [DOI: 10.1016/s0011-393x(01)80087-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Reymond MA, Sanchez JC, Schneider C, Rohwer P, Tortola S, Hohenberger W, Kirchner T, Hochstrasser DF, Köckerling F. Specific sample preparation in colorectal cancer. Electrophoresis 1997; 18:622-4. [PMID: 9150950 DOI: 10.1002/elps.1150180346] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Large tissue samples from ten patients operated for colorectal cancer were prepared in the operating room in iced phosphate buffered saline, containing ethylene diaminetetraacetic acid and protease inhibitors. After cutting the specimens into small fragments, the tissues were gently pressed through a steel mesh. Membranes were permeabilized in chilled ethanol 70% to allow cytosolic fluoresceine isothiocyanate labeling, performed with anti-cytokeratin (CAM 5.2) antibodies. Samples were quantitatively sorted with a fluorescence activated cell sorter (FACS) and denatured before processing separation by two-dimensional electrophoresis on polyacrylamide gels. This procedure made it possible to sample about 4 x 10(7) viable normal and tumoral cells before fixation, and up to 4 x 10(6) cells after FACS. The gels run before and after fixation showed no major differences. The rate of cytokeratin-positive cells in the samples was the following (mean, CI 5-95%): mucosa 29.5% (8.9-66.7%), tumor 44.3% (6.6-94.8%). The epithelial cell content in colorectal cancer and normal mucosa shows important intersample variations. This is important for any comparison of fresh samples, whether at DNA, RNA, or at the protein level. We propose a method allowing the preparation of pure epithelial cell samples from normal and tumoral colonic fresh mucosa.
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Affiliation(s)
- M A Reymond
- Department of Surgery, University of Erlangen, Germany
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Franzén B, Hirano T, Okuzawa K, Uryu K, Alaiya AA, Linder S, Auer G. Sample preparation of human tumors prior to two-dimensional electrophoresis of proteins. Electrophoresis 1995; 16:1087-9. [PMID: 7498151 DOI: 10.1002/elps.11501601184] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Sample preparation procedures are critical for obtaining high quality two-dimensional electrophoresis (2-DE) separations from clinical tumor materials. In this communication, we describe procedures which we have found satisfactory for preparing various tumor samples for 2-DE. By these procedures, tumor cells are enriched from serum proteins and contaminating stromal cells. Tumors can be prepared with good reproducibility to obtain high resolution using these techniques.
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Affiliation(s)
- B Franzén
- Department of Cell and Molecular Analysis, Karolinska Institute, Stockholm, Sweden
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Abstract
Two-dimensional electrophoresis is increasingly being used as an important tool for biological research although it continues to have few direct clinical applications. In the absence of simple systems to identify and quantify individual proteins or groups of proteins it is unlikely that clinical applications will increase. Measurement of some individual proteins, for example a single acute phase reactant, often yields as much clinically useful information as could be currently expected from quantitation of several proteins with the same physiological role. Cost-containment pressures within the clinical laboratory will prevent the technique from becoming widely used in the clinical laboratory until it can clearly demonstrate that it can produce clinically important and necessary information that can not be obtained by other means. We continue to believe that the technique's greatest potential lies in identifying a protein or proteins whose concentration can be correlated with a disease and whose concentration varies with the progress of the disease. Antibodies to such proteins can then be produced and used to quantify the disease-associated proteins by a simple procedure, such as nephelometry. In spite of our belief of the likely clinical application of the technique there appears to be no systematic use of two-dimensional electrophoresis for this purpose. With clinical specimens a few investigators still run gels of serum or urine from patients with apparently unusual disorders and compare them visually with gels from healthy individuals. Nevertheless, the technique continues to have considerable unmet promise for clinical applications.
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Affiliation(s)
- D S Young
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia 19104-4283, USA
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Okuzawa K, Franzén B, Lindholm J, Linder S, Hirano T, Bergman T, Ebihara Y, Kato H, Auer G. Characterization of gene expression in clinical lung cancer materials by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 1994; 15:382-90. [PMID: 7914486 DOI: 10.1002/elps.1150150157] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fourteen human lung tumors of various histopathological types were subjected to two-dimensional gel electrophoresis (2-DE). Samples were prepared for 2-DE using a nonenzymatic sample preparation (NESP) technique recently established in our laboratory. Variations in the expression of some polypeptides were observed between tumors of different histopathological types. To this end, high expression of beta-tubulin, heat shock proteins 73 and 90, lamin B, and proliferating cell nuclear antigen (PCNA) were observed in small cell lung carcinomas (SCLC). One polypeptide of unknown identity (35 kDa, pI 5.5) was significantly overexpressed in primary lung adenocarcinomas compared with SCLC, squamous cell lung carcinomas, metastatic lung adenocarcinomas from colon and rectum, and normal tissue. The amino acid composition of this polypeptide is presented. In summary, combining the NESP technique and 2-DE is an effective approach to define tumor-specific markers.
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Affiliation(s)
- K Okuzawa
- Department of Surgery, Tokyo Medical College
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Wimmer K, Harant H, Reiter M, Blüml G, Gaida T, Katinger H. Two-dimensional gel electrophoresis for controlling and comparing culture supernatants of mammalian cell culture productions systems. Cytotechnology 1994; 16:137-46. [PMID: 7766141 DOI: 10.1007/bf00749900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A recombinant Chinese hamster ovary cell line, producing human erythropoietin, was cultivated in a continuous mode in a stirred tank reactor applying different dilution rates. In order to monitor the stability of this expression system, product and non-product proteins of the cell culture supernatant were analyzed by two-dimensional electrophoresis. The consistency of the isoforms of the recombinant product was determined by western blot combined with specific staining. The same cell line was propagated in a high cell density cultivation system based on macro-cell-aggregates. The patterns of secreted proteins of the cell line cultivated in the different systems were compared in order to detect modifications in protein expression of the product and of non product proteins relevant for cell culture supernatant. Hardly any alterations in two-dimensional pattern were detectable. The isoforms of erythropoietin, as well as the overall pattern of secreted proteins, detectable with the two-dimensional electrophoresis method were remarkably stable under different cultivation conditions.
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Affiliation(s)
- K Wimmer
- Institute of Applied Microbiology, University of Agriculture and Forestry, Vienna, Austria
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Franzén B, Linder S, Okuzawa K, Kato H, Auer G. Nonenzymatic extraction of cells from clinical tumor material for analysis of gene expression by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 1993; 14:1045-53. [PMID: 8125054 DOI: 10.1002/elps.11501401167] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have compared different methods of preparation of malignant cells for two-dimensional electrophoresis (2-DE). We found all methods using fresh tissue to be superior compared to methods using frozen tissue. Our results indicate that nonenzymatic methods of preparation of tumor cells, including fine needle aspiration, scraping and squeezing, have advantages over methods using enzymatic extraction of cells. Nonenzymatic methods are rapid, appear to reduce loss of high molecular protein species, and alleviate the necessity of separating viable and nonviable cells by Percoll gradient centrifugation. Using these techniques, high-quality 2-DE maps were derived from tumors of the lung and breast. In the resulting polypeptide patterns, heat shock proteins, non-muscle tropomyosins and intermediate filament were identified. We conclude that nonenzymatic extraction of malignant cells from fresh tumor tissue improves the possibilities that these techniques may be useful in clinical diagnosis.
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Affiliation(s)
- B Franzén
- Department of Pathology, Karolinska Hospital and Institute, Stockholm, Sweden
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