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Evaluation of colon cancer histomorphology: a comparison between formalin and PAXgene tissue fixation by an international ring trial. Virchows Arch 2014; 465:509-19. [DOI: 10.1007/s00428-014-1624-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/18/2014] [Accepted: 06/30/2014] [Indexed: 01/15/2023]
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52
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Cardiff RD, Miller CH, Munn RJ. Analysis of mouse model pathology: a primer for studying the anatomic pathology of genetically engineered mice. Cold Spring Harb Protoc 2014; 2014:561-80. [PMID: 24890215 DOI: 10.1101/pdb.top069922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This primer of pathology is intended to introduce investigators to the structure (morphology) of cancer with an emphasis on genetically engineered mouse (GEM) models (GEMMs). We emphasize the necessity of using the entire biological context for the interpretation of anatomic pathology. Because the primary investigator is responsible for almost all of the information and procedures leading up to microscopic examination, they should also be responsible for documentation of experiments so that the microscopic interpretation can be rendered in context of the biology. The steps involved in this process are outlined, discussed, and illustrated. Because GEMMs are unique experimental subjects, some of the more common pitfalls are discussed. Many of these errors can be avoided with attention to detail and continuous quality assurance.
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
| | - Claramae H Miller
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
| | - Robert J Munn
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
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53
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Stabilization of biothreat diagnostic samples through vitrification matrices. J Microbiol Methods 2014; 101:81-5. [DOI: 10.1016/j.mimet.2014.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 11/22/2022]
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54
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Abstract
One of the primary goals of fixation is to stop postmortem changes that degrade the tissue and allow optimal preservation of morphologic and cytological detail as well as nucleic acid integrity. Following death, tissues soon undergo autolysis, and if organisms from the gastrointestinal, urinary, or respiratory tracts are present, their colonization can soon cause putrefaction. Time is of the essence because warmer temperatures accelerate both types of degradation. Placing the tissue into a fixative stops the postmortem changes. Fixatives have their effect on tissue by cross-linking, coagulation, or a combination of both. This article outlines the basic tissue fixation procedure and offers guidance on choosing an appropriate fixative, the timing and duration of fixation, sample storage, and quality issues.
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
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55
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Neumeister VM. Tools to assess tissue quality. Clin Biochem 2014; 47:280-7. [PMID: 24565988 DOI: 10.1016/j.clinbiochem.2014.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 01/21/2023]
Abstract
Biospecimen science has recognized the importance of tissue quality for accurate molecular and biomarker analysis and efforts are made to standardize tissue procurement, processing and storage conditions of tissue samples. At the same time the field has emphasized the lack of standardization of processes between different laboratories, the variability inherent in the analytical phase and the lack of control over the pre-analytical phase of tissue processing. The problem extends back into tissue samples in biorepositories, which are often decades old and where documentation about tissue processing might not be available. This review highlights pre-analytical variations in tissue handling, processing, fixation and storage and emphasizes the effects of these variables on nucleic acids and proteins in harvested tissue. Finally current tools for quality control regarding molecular or biomarker analysis are summarized and discussed.
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Affiliation(s)
- Veronique M Neumeister
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, LMP101, New Haven, CT 06520, USA.
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56
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Bonin S, Stanta G. Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics. Expert Rev Mol Diagn 2014; 13:271-82. [DOI: 10.1586/erm.13.14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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57
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Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens. Exp Mol Pathol 2014; 96:168-77. [PMID: 24412268 DOI: 10.1016/j.yexmp.2013.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 11/21/2022]
Abstract
Formalin-fixed tissue has been a mainstay of clinical pathology laboratories, but formalin alters many biomolecules, including nucleic acids and proteins. Meanwhile, frozen tissues contain better-preserved biomolecules, but tissue morphology is affected, limiting their diagnostic utility. Molecular fixatives promise to bridge this gap by simultaneously preserving morphology and biomolecules, enabling clinical diagnosis and molecular analyses on the same specimen. While previous reports have broadly evaluated the use of molecular fixative in various human tissues, we present here the first detailed assessment of the applicability of molecular fixative to both routine histopathological diagnosis and molecular analysis of cervical tissues. Ten specimens excised via the loop electrosurgical excision procedure, which removes conical tissue samples from the cervix, were cut into alternating pieces preserved in either formalin or molecular fixative. Cervical specimens preserved in molecular fixative were easily interpretable, despite featuring more eosinophilic cytoplasm and more recognizable chromatin texture than formalin-fixed specimens. Immunohistochemical staining patterns of p16 and Ki-67 were similar between fixatives, although Ki-67 staining was stronger in the molecular fixative specimens. The RNA of molecular fixative specimens from seven cases representing various dysplasia grades was assessed for utility in expression microarray analysis. Cluster analysis and scatter plots of duplicate samples suggest that data of sufficient quality can be obtained from as little as 50ng of RNA from molecular fixative samples. Taken together, our results show that molecular fixative may be a more versatile substitute for formalin, simultaneously preserving tissue morphology for clinical diagnosis and biomolecules for immunohistochemistry and gene expression analysis.
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58
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Taylor SC, Mrkusich EM. The State of RT-Quantitative PCR: Firsthand Observations of Implementation of Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE). J Mol Microbiol Biotechnol 2014; 24:46-52. [DOI: 10.1159/000356189] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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59
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Kashofer K, Viertler C, Pichler M, Zatloukal K. Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. PLoS One 2013; 8:e70714. [PMID: 23936242 PMCID: PMC3729557 DOI: 10.1371/journal.pone.0070714] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 06/28/2013] [Indexed: 12/20/2022] Open
Abstract
Analysis of RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathological diagnostics. We have performed a comprehensive and systematic investigation of the impact of factors in the pre-analytical workflow, such as different fixatives, fixation time, RNA extraction method and storage of tissues in paraffin blocks, on several downstream reactions including complementary DNA (cDNA) synthesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray hybridization. We compared the effects of routine formalin fixation with the non-crosslinking, alcohol-based Tissue Tek Xpress Molecular Fixative (TTXMF, Sakura Finetek), and cryopreservation as gold standard for molecular analyses. Formalin fixation introduced major changes into microarray gene expression data and led to marked gene-to-gene variations in delta-ct values of qRT-PCR. We found that qRT-PCR efficiency and gene-to-gene variations were mainly attributed to differences in the efficiency of cDNA synthesis as the most sensitive step. These differences could not be reliably detected by quality assessment of total RNA isolated from formalin-fixed tissues by electrophoresis or spectrophotometry. Although RNA from TTXMF fixed samples was as fragmented as RNA from formalin fixed samples, much higher cDNA yield and lower ct-values were obtained in qRT-PCR underlining the negative impact of crosslinking by formalin. In order to better estimate the impact of pre-analytical procedures such as fixation on the reliability of downstream analysis, we applied a qRT-PCR-based assay using amplicons of different length and an assay measuring the efficiency of cDNA generation. Together these two assays allowed better quality assessment of RNA extracted from fixed and paraffin-embedded tissues and should be used to supplement quality scores derived from automated electrophoresis. A better standardization of the pre-analytical workflow, application of additional quality controls and detailed sample information would markedly improve the comparability and reliability of molecular studies based on formalin-fixed and paraffin-embedded tissue samples.
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Affiliation(s)
- Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Martin Pichler
- Division of Oncology, Medical University of Graz, Graz, Austria
| | - Kurt Zatloukal
- Institute of Pathology, Medical University of Graz, Graz, Austria
- * E-mail:
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60
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Staff S, Kujala P, Karhu R, Rökman A, Ilvesaro J, Kares S, Isola J. Preservation of nucleic acids and tissue morphology in paraffin-embedded clinical samples: comparison of five molecular fixatives. J Clin Pathol 2013; 66:807-10. [PMID: 23750036 DOI: 10.1136/jclinpath-2012-201283] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Formalin fixation preserves tissue morphology at the expense of macromolecule integrity. Freshly frozen samples are the golden standard for DNA and RNA analyses but require laborious deep-freezing and frozen sectioning for morphological studies. Alternative tissue stabilisation methods are therefore needed. We analysed the preservation of nucleic acids, immunohistochemical staining properties and tissue morphology in paraffin-embedded clinical tissue samples fixed with Z7, RCL2, PAXgene, Allprotect and RNAlater. Formalin-fixed and deep-frozen samples were used as controls. Immunohistochemical analyses showed good preservation of antigenicity in all except Allprotect and RNAlater-fixed samples. RNA quality, based on RNA integrity number value by Bioanalyzer, was comparable with freshly frozen samples only in PAXgene-fixed samples. According to quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses, RNA from PAXgene samples yielded results similar to freshly frozen samples. No difference between fixatives was seen in DNA analyses (PCR and real-time PCR). In conclusion, PAXgene seems to be superior to other molecular fixatives and formaldehyde.
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Affiliation(s)
- Synnöve Staff
- Laboratory of Cancer Biology, Institute of Biomedical Technology, BioMediTech, University of Tampere, Tampere, Finland
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61
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Dogan S, Becker JC, Rekhtman N, Tang LH, Nafa K, Ladanyi M, Klimstra DS. Use of touch imprint cytology as a simple method to enrich tumor cells for molecular analysis. Cancer Cytopathol 2013; 121:354-60. [DOI: 10.1002/cncy.21292] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/10/2013] [Accepted: 03/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Snjezana Dogan
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Jillian C. Becker
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Natasha Rekhtman
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Laura H. Tang
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Khedoudja Nafa
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Marc Ladanyi
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - David S. Klimstra
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
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62
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Cardiff RD, Hubbard NE, Engelberg JA, Munn RJ, Miller CH, Walls JE, Chen JQ, Velásquez-García HA, Galvez JJ, Bell KJ, Beckett LA, Li YJ, Borowsky AD. Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers. J Transl Med 2013; 93:480-97. [PMID: 23399853 PMCID: PMC3843496 DOI: 10.1038/labinvest.2013.10] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER+/PR+ model (SSM2), a Her2+ model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters.
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Neil E Hubbard
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Jesse A Engelberg
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Robert J Munn
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Claramae H Miller
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Judith E Walls
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Jane Q Chen
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | | | - Jose J Galvez
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institute of Health, Washington, DC, USA
| | - Katie J Bell
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Yue-Ju Li
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Alexander D Borowsky
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
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63
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The PAXgene(®) tissue system preserves phosphoproteins in human tissue specimens and enables comprehensive protein biomarker research. PLoS One 2013; 8:e60638. [PMID: 23555997 PMCID: PMC3612043 DOI: 10.1371/journal.pone.0060638] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 03/01/2013] [Indexed: 11/19/2022] Open
Abstract
Precise quantitation of protein biomarkers in clinical tissue specimens is a prerequisite for accurate and effective diagnosis, prognosis, and personalized medicine. Although progress is being made, protein analysis from formalin-fixed and paraffin-embedded tissues is still challenging. In previous reports, we showed that the novel formalin-free tissue preservation technology, the PAXgene Tissue System, allows the extraction of intact and immunoreactive proteins from PAXgene-fixed and paraffin-embedded (PFPE) tissues. In the current study, we focused on the analysis of phosphoproteins and the applicability of two-dimensional gel electrophoresis (2D-PAGE) and enzyme-linked immunosorbent assay (ELISA) to the analysis of a variety of malignant and non-malignant human tissues. Using western blot analysis, we found that phosphoproteins are quantitatively preserved in PFPE tissues, and signal intensities are comparable to that in paired, frozen tissues. Furthermore, proteins extracted from PFPE samples are suitable for 2D-PAGE and can be quantified by ELISA specific for denatured proteins. In summary, the PAXgene Tissue System reliably preserves phosphoproteins in human tissue samples, even after prolonged fixation or stabilization times, and is compatible with methods for protein analysis such as 2D-PAGE and ELISA. We conclude that the PAXgene Tissue System has the potential to serve as a versatile tissue fixative for modern pathology.
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64
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Non-formalin fixative versus formalin-fixed tissue: A comparison of histology and RNA quality. Exp Mol Pathol 2013; 94:188-94. [DOI: 10.1016/j.yexmp.2012.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
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Verma M, Khoury MJ, Ioannidis JPA. Opportunities and challenges for selected emerging technologies in cancer epidemiology: mitochondrial, epigenomic, metabolomic, and telomerase profiling. Cancer Epidemiol Biomarkers Prev 2013; 22:189-200. [PMID: 23242141 PMCID: PMC3565041 DOI: 10.1158/1055-9965.epi-12-1263] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Remarkable progress has been made in the last decade in new methods for biologic measurements using sophisticated technologies that go beyond the established genome, proteome, and gene expression platforms. These methods and technologies create opportunities to enhance cancer epidemiologic studies. In this article, we describe several emerging technologies and evaluate their potential in epidemiologic studies. We review the background, assays, methods, and challenges and offer examples of the use of mitochondrial DNA and copy number assessments, epigenomic profiling (including methylation, histone modification, miRNAs, and chromatin condensation), metabolite profiling (metabolomics), and telomere measurements. We map the volume of literature referring to each one of these measurement tools and the extent to which efforts have been made at knowledge integration (e.g., systematic reviews and meta-analyses). We also clarify strengths and weaknesses of the existing platforms and the range of type of samples that can be tested with each of them. These measurement tools can be used in identifying at-risk populations and providing novel markers of survival and treatment response. Rigorous analytic and validation standards, transparent availability of massive data, and integration in large-scale evidence are essential in fulfilling the potential of these technologies.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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66
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Gündisch S, Hauck S, Sarioglu H, Schott C, Viertler C, Kap M, Schuster T, Reischauer B, Rosenberg R, Verhoef C, Mischinger HJ, Riegman P, Zatloukal K, Becker KF. Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase. J Proteome Res 2012; 11:5748-62. [PMID: 23134551 DOI: 10.1021/pr300560y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The quality of human tissue specimens can have a significant impact on analytical data sets for biomarker research. The aim of this study was to characterize fluctuations of protein and phosphoprotein levels in human tissue samples during the preanalytical phase. Eleven intestine and 17 liver specimens were surgically resected, aliquoted, and either snap-frozen or fixed in formalin immediately or exposed to different ischemic conditions before preservation. Protein levels in the resultant samples were investigated by reverse phase protein array, Western blot analysis, and liquid chromatography-tandem mass spectrometry. Our data revealed that the degree of sensitivity of proteins and phosphoproteins to delayed preservation varied between different patients and tissue types. For example, up-regulation of phospho-p42/44 MAPK in intestine samples was seen in some patients but not in others. General trends toward up- or down-regulation of most proteins were not evident due to pronounced interpatient variability but signal intensities of only a few proteins, such as cytokeratin 18, were altered from baseline in postresection samples. In contrast, glyceraldehyde 3-phosphate dehydrogenase was found to be stable during periods of cold ischemia. Our study represents a proper approach for studying potential protein fluctuations in tissue specimens for future biomarker development programs.
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Affiliation(s)
- Sibylle Gündisch
- Institute of Pathology, Technische Universität München, Trogerstrasse 18, D-81675 Munich, Germany
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67
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Belloni B, Lambertini C, Nuciforo P, Phillips J, Bruening E, Wong S, Dummer R. Will PAXgene substitute formalin? A morphological and molecular comparative study using a new fixative system. J Clin Pathol 2012; 66:124-35. [DOI: 10.1136/jclinpath-2012-200983] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Formalin fixation and paraffin embedding present the standard procedures for conserving clinical tissues for histological analysis. However, molecular analysis is impaired by the cross linking properties of formalin. The PAXgene tissue system (PreAnalytix, Switzerland) is a new formalin-free tissue collection device.AimsIn this study we aimed to evaluate this new tissue preservation technique in comparison with formalin fixation and fresh frozen tissue samples.Methods12 melanoma biopsy samples were divided and fixed simultaneously with formalin, PAXgene or fresh frozen in liquid nitrogen and analysed with regard to morphology, immunohistochemistry, DNA and RNA content and quality. Markers of melanocytic differentiation and tumour cell proliferation were used.ResultsMorphology was well preserved in PAXPE samples. However, 5 out of 11 immunohistochemical markers showed significantly lower overall staining and staining intensity with PAXPE tissues in comparison with formalin-fixed, paraffin-embedded (FFPE). Increasing membrane permeability through adding a detergent did proportionally increase staining intensity in PAXPE samples. Amplification of different mRNA amplicons showed a direct relationship with the size of the amplicon with greater template integrity observed in PAXPE samples. Sequencing and mutational analysis of DNA samples were comparable for all the different fixation methods, while the level of DNA fragmentation seemed to be lower in PAXPE compared with FFPE tissues.ConclusionsThe switch from formalin to PAXgene fixation would require a re-evaluation of immunohistochemical markers and staining procedures originally developed for FFPE tissues. Our data demonstrate that PAXPE fixation offers some advantages concerning molecular analysis. However, these advantages would not justify substituting formalin fixation in any routine pathology laboratory.
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68
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Wulfkuhle JD, Berg D, Wolff C, Langer R, Tran K, Illi J, Espina V, Pierobon M, Deng J, DeMichele A, Walch A, Bronger H, Becker I, Waldhör C, Höfler H, Esserman L, Liotta LA, Becker KF, Petricoin EF. Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping. Clin Cancer Res 2012; 18:6426-35. [PMID: 23045247 DOI: 10.1158/1078-0432.ccr-12-0452] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Targeting of the HER2 protein in human breast cancer represents a major advance in oncology but relies on measurements of total HER2 protein and not HER2 signaling network activation. We used reverse-phase protein microarrays (RPMA) to measure total and phosphorylated HER2 in the context of HER family signaling to understand correlations between phosphorylated and total levels of HER2 and downstream signaling activity. EXPERIMENTAL DESIGN Three independent study sets, comprising a total of 415 individual patient samples from flash-frozen core biopsy samples and formalin-fixed and paraffin-embedded (FFPE) surgical and core samples, were analyzed via RPMA. The phosphorylation and total levels of the HER receptor family proteins and downstream signaling molecules were measured in laser capture microdissected (LCM) enriched tumor epithelium from 127 frozen pretreatment core biopsy samples and whole-tissue lysates from 288 FFPE samples and these results were compared with FISH and immunohistochemistry (IHC). RESULTS RPMA measurements of total HER2 were highly concordant (>90% all sets) with FISH and/or IHC data, as was phosphorylation of HER2 in the FISH/IHC(+) population. Phosphorylation analysis of HER family signaling identified HER2 activation in some FISH/IHC(-) tumors and, identical to that seen with FISH/IHC(+) tumors, the HER2 activation was concordant with EGF receptor (EGFR) and HER3 phosphorylation and downstream signaling endpoint activation. CONCLUSIONS Molecular profiling of HER2 signaling of a large cohort of human breast cancer specimens using a quantitative and sensitive functional pathway activation mapping technique reveals IHC(-)/FISH(-)/pHER2(+) tumors with HER2 pathway activation independent of total HER2 levels and functional signaling through HER3 and EGFR.
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Affiliation(s)
- Julia D Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, USA
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