1
|
Wang MM, Tan WJ, Lim TS, Chan ASY. PreservCyt Is an Optimal Fixative that Permits Cytologic and Molecular Analyses of Vitreoretinal Lymphoma Biopsies. Ocul Immunol Inflamm 2019; 29:430-439. [PMID: 31418635 DOI: 10.1080/09273948.2019.1636093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: Vitreoretinal lymphoma (VRL) is a potentially fatal intraocular malignancy. Diagnosis is hampered by poor preservation of morphology and DNA/RNA integrity, which precludes adjunctive molecular analysis. We aimed to determine the optimum fixative protocol for VRL biopsies that permits cytology, IHC/flow cytometry and molecular analyses.Methods: Six fixatives were compared on cultured Pfeiffer cells used as a cellular model. Cells were fixed and evaluated on cellular morphology, antibody staining, DNA/RNA amount and integrity. VRL clinical cases were used as validation and proof-of-concept.Results: PreservCyt was the best fixative for preserving cellular morphology and high-quality RNA/DNA from vitreous fluid biopsies. Cells from clinical VRL cases fixed with PreservCyt showed adequate cellular morphology and IHC positivity. Sufficient DNA was obtained for IgH clonality and MYD88 mutation detection using remnant cytological fluid.Conclusions: PreservCyt maintains good morphology and RNA/DNA integrity suggesting that it is a suitable fixative for VRL diagnosis and molecular analysis.
Collapse
Affiliation(s)
- Mona Meng Wang
- Translational Ophthalmic Pathology Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Wei Jian Tan
- A. Menarini Biomarkers Singapore Pte Ltd, Singapore
| | | | - Anita Sook Yee Chan
- Translational Ophthalmic Pathology Platform, Singapore Eye Research Institute, Singapore, Singapore.,Ocular inflammation and Immunology Department, Singapore National Eye Centre, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore
| |
Collapse
|
2
|
Panzacchi S, Gnudi F, Mandrioli D, Montella R, Strollo V, Merrick BA, Belpoggi F, Tibaldi E. Effects of short and long-term alcohol-based fixation on Sprague-Dawley rat tissue morphology, protein and nucleic acid preservation. Acta Histochem 2019; 121:750-760. [PMID: 31277893 DOI: 10.1016/j.acthis.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022]
Abstract
Safety concerns on the toxic and carcinogenic effects of formalin exposure have drawn increasing attention to the search for alternative low risk fixatives for processing tissue specimens in laboratories worldwide. Alcohol-based fixatives are considered some of the most promising alternatives. We evaluated the performance of alcohol-fixed paraffin-embedded (AFPE) samples from Sprague-Dawley (SD) rats analyzing tissue morphology, protein and nucleic acid preservation after short and extremely long fixation times (up to 7 years), using formalin-fixed paraffin-embedded (FFPE) samples as a comparator fixative. Following short and long-term alcohol fixation, tissue morphology and cellular details in tissues, evaluated by scoring stained sections (Hematoxylin-Eosin and Mallory's trichrome), were optimally preserved if compared to formalin fixation. Immunoreactivity of proteins (Ki67, CD3, PAX5, CD68), evaluated by immunohistochemistry, showed satisfactory results when the fixation period did not exceed 1 year. Finally, we confirm the superiority of alcohol fixation compared to formalin, in terms of quantity of nucleic acid extracted from paraffin blocks, even after an extremely long time of alcohol fixation. Our results confirm that alcohol fixation is a suitable and safe alternative to formalin for pathological evaluations. There is a need for standardization of formalin-free methods and harmonization of diagnosis in pathology department worldwide.
Collapse
|
3
|
Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues. PLoS One 2018; 13:e0203608. [PMID: 30192857 PMCID: PMC6128582 DOI: 10.1371/journal.pone.0203608] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 01/02/2023] Open
Abstract
RNA and DNA analyses from paraffin-embedded tissues (PET) are an important diagnostic tool for characterization of a disease, exploring biomarkers and treatment options. Since nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissue are of limited use for molecular analyses due to chemical modifications of biomolecules alternate, formalin-free fixation reagents such as the PAXgene Tissue system are of evolving interest. Furthermore, biomedical research and biomarker development critically relies on using long-term stored PET from medical archives or biobanks to correlate molecular features with long-term disease outcomes. We therefore performed a comparative study to evaluate the effect of long term storage of FFPE and PAXgene Tissue-fixed and paraffin-embedded (PFPE) tissue at different temperatures on nucleic acid stability and usability in PCR. Matched FFPE and PFPE human tissues from routine clinical setting or rat tissues from a highly controlled animal model were stored at room temperature and 4°C, as well as in case of animal tissues frozen at -20°C and -80°C. RNA and DNA were extracted in intervals for up to nine years, and examined for integrity, and usability in quantitative RT-PCR (RT-qPCR) or PCR (qPCR) assays. PET storage at room temperature led to a degradation of nucleic acids which was slowed down by storage at 4°C and prevented by storage at -20°C or -80°C. Degradation was associated with an amplicon length depending decrease of RT-qPCR and qPCR efficiency. Storage at 4°C improved amplifiability in RT-qPCR and qPCR profoundly. Chemically unmodified nucleic acids from PFPE tissue performed superior compared to FFPE tissue, regardless of storage time and temperature in both human and rat tissues. In conclusion molecular analyses from PET can be greatly improved by using a non-crosslinking fixative and storage at lower temperatures such as 4°C, which should be considered in prospective clinical studies.
Collapse
|
4
|
Neumeister VM, Juhl H. Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis. CURRENT PATHOBIOLOGY REPORTS 2018; 6:265-274. [PMID: 30595971 PMCID: PMC6290693 DOI: 10.1007/s40139-018-0179-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purpose of Review Precision medicine promises patient tailored, individualized diagnosis and treatment of diseases and relies on clinical specimen integrity and accuracy of companion diagnostic testing. Therefore, pre-analytics, which are defined as the collection, processing, and storage of clinical specimens, are critically important to enable optimal diagnostics, molecular profiling, and clinical decision-making around harvested specimens. This review article discusses the impact of tumor pre-analytics on molecular pathology focusing on biospecimen protein expression and analysis. Recent Findings Due to busy clinical schedules and workflows that have been established for many years and to lack of standardization and limited assessment tools to quantify variability in pre-analytical processing, the effects of pre-analytics on biospecimen integrity are often overlooked. Several studies have recently emphasized an emerging crisis in science and reproducibility of results. Summary Biomarker instability due to pre-analytical variables affects comprehensive analysis and molecular phenotyping of patients’ tissue. This problematic emphasizes the critical need for standardized protocols and technologies to be applied in the clinical and research setting.
Collapse
Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
| |
Collapse
|
5
|
Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018; 10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.
Collapse
Affiliation(s)
- Sergiu Susman
- Department of Pathology, Imogen Research Center.,Department of Morphological Sciences
| | | | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ioan-Stefan Florian
- Department of Neurosurgery, Iuliu Hatieganu University of Medicine and Pharmacy
| | | | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ravnit Grewal
- Department of Hematology, Ion Chiricuta Oncology Institute
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine.,Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Haematopathology, Tygerberg Academic Hospital, Tygerberg, South Africa
| |
Collapse
|
6
|
PAXgene fixation enables comprehensive metabolomic and proteomic analyses of tissue specimens by MALDI MSI. Biochim Biophys Acta Gen Subj 2018; 1862:51-60. [DOI: 10.1016/j.bbagen.2017.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/28/2017] [Accepted: 10/08/2017] [Indexed: 12/31/2022]
|
7
|
Chung JY, Song JS, Ylaya K, Sears JD, Choi L, Cho H, Rosenberg AZ, Hewitt SM. Histomorphological and Molecular Assessments of the Fixation Times Comparing Formalin and Ethanol-Based Fixatives. J Histochem Cytochem 2017; 66:121-135. [PMID: 29125916 DOI: 10.1369/0022155417741467] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The lack of standardization of tissue handling and processing hinders the development and validation of new biomarkers in research and clinical settings. We compared the histomorphology and the quality and quantity of biomolecules in paraffin-embedded mouse tissues, followed by fixation with neutral buffered formalin (NBF), 70% ethanol, and buffered ethanol (BE70) fixative. The quality of the histomorphology and immunohistochemistry in BE70 was relatively time-independent, whereas those in NBF rapidly decreased after 1 week of fixation. Protein recovered from tissue fixed in 70% ethanol and BE70 was compatible with Western blot and protein array using AKT and GAPDH antibodies, regardless of the fixation time. In addition, the quality and quantity of RNA extracted from tissue in ethanol-based fixative showed minimal changes from 4 hr to 6 months, whereas NBF had a dramatic detrimental change in RNA quality after 1 week of fixation. Furthermore, ethanol-based fixative offers a superior DNA template for PCR amplification-based molecular assays than NBF. In conclusion, coagulative, ethanol-based fixatives show a broader time spectrum than the aldehyde crosslinking fixative NBF in their histomorphological features and the quantity and quality of the biomolecules from paraffin-embedded tissue, and they may facilitate the use of fixative-fixed paraffin-embedded tissues in research and clinical laboratories, avoiding overfixation.
Collapse
Affiliation(s)
- Joon-Yong Chung
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joon Seon Song
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kris Ylaya
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - John D Sears
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lauren Choi
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hanbyoul Cho
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| |
Collapse
|
8
|
Liu Y, Edward DP. Assessment of PAXgene Fixation on Preservation of Morphology and Nucleic Acids in Microdissected Retina Tissue. Curr Eye Res 2016; 42:104-110. [DOI: 10.3109/02713683.2016.1146777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
9
|
Perry C, Chung JY, Ylaya K, Choi CH, Simpson A, Matsumoto KT, Smith WA, Hewitt SM. A Buffered Alcohol-Based Fixative for Histomorphologic and Molecular Applications. J Histochem Cytochem 2016; 64:425-40. [PMID: 27221702 DOI: 10.1369/0022155416649579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/21/2016] [Indexed: 01/04/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is the predominant preparation for diagnostic histopathological evaluation and increasingly the biospecimen on which molecular diagnostics are performed. However, formalin is carcinogenic and results in cross-linking of proteins and nicking and alterations of nucleic acids. Alternative fixatives, including 70% ethanol, improved biomolecular integrity; however, they have yet to replace neutral-buffered formalin (NBF). Herein, we describe the phosphate-buffered ethanol 70% (BE70) fixative. The histomorphology of BE70-fixed tissue is very similar to that of NBF; however, it is a non-cross-linking fixative and lacks the carcinogenic profile of formaldehyde-based fixatives. RNA isolated from tissue fixed in BE70 was of substantially higher quality and quantity than that was recovered from formalin-fixed tissue. Furthermore, the BE70 fixative showed excellent RNA and DNA integrity compared with that of NBF fixative based on real-time polymerase chain reaction analysis results. Immunohistochemical staining was similar for the antigen tested. In conclusion, BE70 is a non-cross-linking fixative that is superior to NBF and 70% ethanol with reference to biomolecule recovery and quality from paraffin-embedded tissue. Additional studies to compare the histomorphologic and immunohistochemical performance and utility in a clinical setting are required.
Collapse
Affiliation(s)
- Candice Perry
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH),Antibody Characterization Laboratory, Advanced Technology Program, Leidos Biomedical Research, Inc., Frederick, Maryland (CP)
| | - Joon-Yong Chung
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Kris Ylaya
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Chel Hun Choi
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH),Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea (CHC)
| | - Amari Simpson
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Kaipo T Matsumoto
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - William A Smith
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| |
Collapse
|
10
|
Gillio-Meina C, Zielke HR, Fraser DD. Translational Research in Pediatrics IV: Solid Tissue Collection and Processing. Pediatrics 2016; 137:peds.2015-0490. [PMID: 26659457 DOI: 10.1542/peds.2015-0490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 11/24/2022] Open
Abstract
Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.
Collapse
Affiliation(s)
- Carolina Gillio-Meina
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | | | - Douglas D Fraser
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada; Centre for Critical Illness Research, Critical Care Medicine and Pediatrics, Clinical Neurologic Sciences, and Physiology and Pharmacology, Western University, London, Ontario, Canada
| |
Collapse
|
11
|
Roemen GM, zur Hausen A, Speel EJM. Adequate tissue for adequate diagnosis: what do we really need? Lung Cancer 2015. [DOI: 10.1183/2312508x.10010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
12
|
Bussolati G, Annaratone L, Maletta F. The pre-analytical phase in surgical pathology. Recent Results Cancer Res 2015; 199:1-13. [PMID: 25636424 DOI: 10.1007/978-3-319-13957-9_1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Several sequential passages are involved in the pre-analytical handling of surgical specimens from resection in the surgical theater to paraffin-embedding and storage. Each passage is highly critical and can significantly affect the preservation of morphology, antigens, and nucleic acids. Some key points in this process are still undefined and are subject to high variability among hospitals. High quality and standardization are demanded and pathologists should therefore work to comply with all novel clinical requests (such as genomic and antigenic testing for targeted molecular therapies). Under-vacuum sealing of surgical pieces can be a safe and reliable alternative to storage in large formalin-filled boxes; it prevents dehydration and favors cooling by removing air. Moreover, it implements tissue banking and preservation of nucleic acids. After transport of specimens to pathological anatomy laboratories, the next passage, fixation, has been the object of several attempt to find alternatives to formalin. However, none of the substitutes proved successful, and formalin fixation is still considered the gold standard for preservation of morphology and antigens. RNA has instead been found to be heavily affected by degradation and fragmentation in formalin-fixed tissues. Based on the hypothesis that RNA degradation would be inhibited by maintaining a low temperature, a protocol based on processing tissues with formalin at low temperature (cold fixation) was evaluated and proved useful in obtaining a reduction in RNA fragmentation. Finally, the problem of storage is discussed, in order to find ways to guarantee feasibility of molecular analyses even years after the original diagnosis.
Collapse
Affiliation(s)
- Gianni Bussolati
- Department of Medical Sciences, University of Turin, via Santena 7, 10126, Turin, Italy,
| | | | | |
Collapse
|
13
|
Andersen GB, Hager H, Hansen LL, Tost J. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA. Anal Biochem 2015; 468:50-8. [DOI: 10.1016/j.ab.2014.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 01/24/2023]
|
14
|
Immunohistochimie et médecine personnalisée en oncologie pulmonaire: potentialités et limites. Bull Cancer 2014; 101:958-65. [DOI: 10.1684/bdc.2014.2041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
15
|
Boraiy L, Fontao L. Michel's Transport Medium as an Alternative to Liquid Nitrogen for PCR Analysis of Skin Biopsy Specimens. Dermatopathology (Basel) 2014; 1:70-4. [PMID: 27047924 PMCID: PMC4772930 DOI: 10.1159/000368347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Formalin fixation and paraffin embedding are standard procedures for histopathological diagnosis and allow long-term archiving of tissue specimens. The cross-linking properties of formalin cause fragmentation of nucleic acids and reduce the sensitivity of PCR analysis. Michel's medium is a well-established transport medium used by dermatologists for biopsy transport to maintain tissue-fixed immunoreactants prior to direct immunofluorescence and immunoelectron microscopy. Here we report that Michel's medium also allows short-term preservation of DNA for PCR analysis and permits amplification of amplicons larger than 1 kb. Therefore, Michel's medium appears to be a reserve medium for performing PCR when no other samples are available.
Collapse
Affiliation(s)
- Logeina Boraiy
- Departments of Dermatology and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - Lionel Fontao
- Departments of Dermatology and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| |
Collapse
|
16
|
Stanta G, Bonin S, Machado I, Llombart-Bosch A. Models of biobanking and tissue preservation: RNA quality in archival samples in pathology laboratories and "in vivo biobanking" by tumor xenografts in nude mice-two models of quality assurance in pathology. Biopreserv Biobank 2014; 9:149-55. [PMID: 24846260 DOI: 10.1089/bio.2011.0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tissue banks represent essential resources and platforms for biomedical research serving basic, translational, and clinical research projects. In this article, we describe 2 models of biobanking and tissue preservation with different approaches and aims. Archive tissue biobanking is described here as a resource of residual pathology tissues for translational research, which represents the huge clinical heterogeneity. In this context, managing of tissues and RNA quality in archive tissue are discussed. The other model of tissue biobanking is referred to as xenograft tissue banking, which represents an alternative method for obtaining large amounts of tissue, over an indefinite period, in so far as the tumor can be transferred in vivo over generations, maintaining the histological and genetic particularities. A description of the method and examples of the application are given with particular emphasis on sarcomas (Ewing's sarcoma/primitive neuroectodermal sarcoma, synovial sarcomas, and rhabdomyosarcomas) and early stages of tumor angiogenesis in sarcomas.
Collapse
Affiliation(s)
- Giorgio Stanta
- 1 Department of Medical, Surgical and Health Sciences, University of Trieste , Cattinara Hospital, Trieste, Italy
| | | | | | | |
Collapse
|
17
|
Ahmed S, Kashem MA, Sarker R, Ahmed EU, Hargreaves GA, McGregor IS. Neuroadaptations in the Striatal Proteome of the Rat Following Prolonged Excessive Sucrose Intake. Neurochem Res 2014; 39:815-24. [DOI: 10.1007/s11064-014-1274-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 01/30/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
|
18
|
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]
|
19
|
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.
Collapse
|
20
|
Lou JJ, Mirsadraei L, Sanchez DE, Wilson RW, Shabihkhani M, Lucey GM, Wei B, Singer EJ, Mareninov S, Yong WH. A review of room temperature storage of biospecimen tissue and nucleic acids for anatomic pathology laboratories and biorepositories. Clin Biochem 2013; 47:267-73. [PMID: 24362270 DOI: 10.1016/j.clinbiochem.2013.12.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/03/2013] [Accepted: 12/08/2013] [Indexed: 11/28/2022]
Abstract
UNLABELLED Frozen biospecimens are crucial for translational research and contain well-preserved nucleic acids and protein. However, the risks of freezer failure as well as space, cost, and environmental concerns of frozen biospecimens are substantial. OBJECTIVE The purpose of the study was to review the current status of room temperature biospecimen storage. METHODS We searched Pubmed and vendor websites to identify relevant information. RESULTS Formalin-fixed paraffin embedded (FFPE) tissues have great value but their use is limited by cross-linking and fragmentation of nucleic acids, as well as loss of enzymatic activity. Stabilization solutions can now robustly preserve fresh tissue for up to 7days at room temperature. For longer term storage, commercial vendors of chemical matrices claim real time stability of nucleic acids of over 2 years and their accelerated aging studies to date suggest stability for 12years for RNA and 60years for DNA. However, anatomic pathology biorepositories store mostly frozen tissue rather than nucleic acids. Small quantities of tissue can be directly placed on some chemical matrices to stabilize DNA, however RNA and proteins are not preserved. Current lyophilization approaches can preserve histomorphology, DNA, RNA, and proteins though RNA shows moderate degradation after 1-2years. Formalin-free fixatives show improved but varying abilities to preserve nucleic acids and face validation as well as cost barriers in replacing FFPE specimens. The paraffin embedding process can degrade RNA. CONCLUSION Development of robust long-term room temperature biospecimen tissue storage technology can potentially reduce costs for the biomedical community in the face of growing targeted therapy needs and decreasing budgets.
Collapse
Affiliation(s)
- Jerry J Lou
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Leili Mirsadraei
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Desiree E Sanchez
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Ryan W Wilson
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Maryam Shabihkhani
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Gregory M Lucey
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Bowen Wei
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Elyse J Singer
- Department of Neurology, David Geffen School of Medicine at UCLA, 710 Westwood Plaza, Los Angeles, CA 90095-1769, USA; Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Sergey Mareninov
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - William H Yong
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA; Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| |
Collapse
|
21
|
Abstract
Currently, the increasing number of ancillary methods to be performed from tumoral tissues in a pathology laboratory determines the necessity to have an optimal strategy for tissue management. The size of tissue samples dedicated for a pathological examination becomes smaller and smaller, as the diagnosis can be made with non or less invasive methods. However, the samples should also allow to provide the prognosis as well as to realise biological molecular testing in order to found a genomic alteration. Thus, it is critical to think about how to share and to pool the different expertises and abilities in a pathology laboratory in order to optimize the achievement of the different ancillary methods. Thus, following the morphological study made in hematoxylin-eosin staining, it is necessary to preempt the number of immunohistochemical and in situ hybridization studies, which will be potentially done from the tissue samples. Moreover, since the genomic alteration detection in tumours is mainly performed from DNA extracted from tissues, it is necessary to take in account some numerous parameters, in particular the nature and the time of fixation, the percentage of tumour cells, the presence of necrotic area, the percentage of inflammatory cells and the sample size. The strategy for an optimal tissue management in an oncology-pathology laboratory is critical and takes part of the different steps allowing to get an accreditation according the ISO15189 norm.
Collapse
|
22
|
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.
Collapse
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:
| |
Collapse
|
23
|
Abstract
Context.—Cytology relies heavily on morphology to make diagnoses, and morphologic criteria have not changed much in recent years. The field is being shaped predominantly by new techniques for imaging and for acquiring and processing samples, advances in molecular diagnosis and therapeutics, and regulatory issues.
Objective.—To review the importance of classical morphology in the future of cytopathology, to identify areas in which cytology is expanding or contracting in its scope, and to identify factors that are shaping the field.
Data Sources.—Literature review.
Conclusions.—Five stories paint a picture in which classical cytomorphology will continue to have essential importance, both for diagnosis and for improving our understanding of cancer biology. New endoscopy and imaging techniques are replacing surgical biopsies with cytology samples. New molecularly targeted therapies offer a chance for cytology to play a major role, but they pose new challenges. New molecular tests have the potential to synergize with, but not replace, morphologic interpretation of thyroid fine-needle aspirations. Ultrasound-guided fine-needle aspiration performed by cytopathologists is opening a new field of “interventional cytopathology” with unique value. For the productive evolution of the field, it will be important for cytopathologists to play an active role in clinical trials that document the ability of cytology to achieve cost-effective health care outcomes.
Collapse
Affiliation(s)
- Andrew H. Fischer
- From the Department of Pathology, University of Massachusetts Medical Center, Worcester, Massachusetts (Dr Fischer); the Department of Cytopathology, DCL Medical Laboratories, Inc, Indianapolis, Indiana (Dr Benedict); and the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas (Dr Amrikachi)
| | - Cynthia C. Benedict
- From the Department of Pathology, University of Massachusetts Medical Center, Worcester, Massachusetts (Dr Fischer); the Department of Cytopathology, DCL Medical Laboratories, Inc, Indianapolis, Indiana (Dr Benedict); and the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas (Dr Amrikachi)
| | - Mojgan Amrikachi
- From the Department of Pathology, University of Massachusetts Medical Center, Worcester, Massachusetts (Dr Fischer); the Department of Cytopathology, DCL Medical Laboratories, Inc, Indianapolis, Indiana (Dr Benedict); and the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas (Dr Amrikachi)
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
|
26
|
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]
|
27
|
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.
Collapse
|
28
|
Viertler C, Groelz D, Gündisch S, Kashofer K, Reischauer B, Riegman PHJ, Winther R, Wyrich R, Becker KF, Oelmüller U, Zatloukal K. A new technology for stabilization of biomolecules in tissues for combined histological and molecular analyses. J Mol Diagn 2012; 14:458-66. [PMID: 22749745 DOI: 10.1016/j.jmoldx.2012.05.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 11/25/2022] Open
Abstract
For accurate diagnosis, prediction of outcome, and selection of appropriate therapies, the molecular characterization of human diseases requires analysis of a broad spectrum of altered biomolecules, in addition to morphological features, in affected tissues such as tumors. In a high-throughput screening approach, we have developed the PAXgene Tissue System as a novel tissue stabilization technology. Comprehensive characterization of this technology in stabilized and paraffin-embedded human tissues and comparison with snap-frozen tissues revealed excellent preservation of morphology and antigenicity, as well as outstanding integrity of nucleic acids (genomic DNA, miRNA, and mRNA) and phosphoproteins. Importantly, PAXgene-fixed, paraffin-embedded tissues provided RNA quantity and quality not only significantly better than that obtained with neutral buffered formalin, but also similar to that from snap-frozen tissue, which currently represents the gold standard for molecular analyses. The PAXgene tissue stabilization system thus opens new opportunities in a variety of molecular diagnostic and research applications in which the collection of snap-frozen tissue is not feasible for medical, logistic, or ethical reasons. Furthermore, this technology allows performing histopathological analyses together with molecular studies in a single sample, which markedly facilitates direct correlation of morphological disease phenotypes with alterations of nucleic acids and other biomolecules.
Collapse
|
29
|
Erickson HS. Measuring molecular biomarkers in epidemiologic studies: laboratory techniques and biospecimen considerations. Stat Med 2012; 31:2400-13. [PMID: 22593027 DOI: 10.1002/sim.4485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 11/05/2011] [Accepted: 11/14/2011] [Indexed: 12/20/2022]
Abstract
The future of personalized medicine depends on the ability to efficiently and rapidly elucidate a reliable set of disease-specific molecular biomarkers. High-throughput molecular biomarker analysis methods have been developed to identify disease risk, diagnostic, prognostic, and therapeutic targets in human clinical samples. Currently, high throughput screening allows us to analyze thousands of markers from one sample or one marker from thousands of samples and will eventually allow us to analyze thousands of markers from thousands of samples. Unfortunately, the inherent nature of current high throughput methodologies, clinical specimens, and cost of analysis is often prohibitive for extensive high throughput biomarker analysis. This review summarizes the current state of high throughput biomarker screening of clinical specimens applicable to genetic epidemiology and longitudinal population-based studies with a focus on considerations related to biospecimens, laboratory techniques, and sample pooling.
Collapse
Affiliation(s)
- Heidi S Erickson
- Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
30
|
Benerini Gatta L, Cadei M, Balzarini P, Castriciano S, Paroni R, Verzeletti A, Cortellini V, De Ferrari F, Grigolato P. Application of alternative fixatives to formalin in diagnostic pathology. Eur J Histochem 2012; 56:e12. [PMID: 22688293 DOI: 10.4081/ejh.2012.12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 12/30/2011] [Accepted: 01/10/2012] [Indexed: 11/23/2022] Open
Abstract
Fixation is a critical step in the preparation of tissues for histopathology. The objective of this study was to investigate the effects of different fixatives vs formalin on proteins and DNA, and to evaluate alternative fixation for morphological diagnosis and nucleic acid preservation for molecular methods. Forty tissues were fixed for 24 h with six different fixatives: the gold standard fixative formalin, the historical fixatives Bouin and Hollande, and the alternative fixatives Greenfix, UPM and CyMol. Tissues were stained (Haematoxylin-Eosin, Periodic Acid Schiff, Trichromic, Alcian-blue, High Iron Diamine), and their antigenicity was determined by immunohistochemistry (performed with PAN-CK, CD31, Ki-67, S100, CD68, AML antibodies). DNA extraction, KRAS sequencing, FISH for CEP-17, and flow cytometry analysis of nuclear DNA content were applied. For cell morphology the alternative fixatives (Greenfix, UPM, CyMol) were equivalent to formalin. As expected, Hollande proved the best fixative for morphology. The morphology obtained with Bouin was comparable to that with formalin. Hollande was the best fixative for histochemistry. Bouin proved equivalent to formalin. The alternative fixatives were equivalent to formalin, although with greater variability in haematoxylin-eosin staining. It proved possible to obtain immunohistochemical staining largely equivalent to that following formalin-fixation with the following fixatives: Greenfix, Hollande, UPM and CyMol. The tissues fixed in Bouin did not provide results comparable to those obtained with formalin. The DNA extracted from samples fixed with alternative fixatives was found to be suitable for molecular analysis.
Collapse
Affiliation(s)
- L Benerini Gatta
- Second Department of Pathology, School of Medicine, University of Brescia, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Masir N, Ghoddoosi M, Mansor S, Abdul-Rahman F, Florence CS, Mohamed-Ismail NA, Tamby MR, Md-Latar NH. RCL2, a potential formalin substitute for tissue fixation in routine pathological specimens. Histopathology 2012; 60:804-15. [PMID: 22320393 DOI: 10.1111/j.1365-2559.2011.04127.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To investigate RCL2 as a fixative for tissue fixation in routine histopathological examination and to assess tissue suitability for ancillary investigations. METHODS AND RESULTS Forty-nine samples from 36 fresh specimens were cut into three equal pieces and fixed in RCL2 diluted in 100% ethanol, RCL2 in 95% ethanol, or neutral buffered formalin as control. Suitability for microtomy, quality of histomorphology, histochemistry, immunohistochemistry, fluorescent and silver in-situ hybridization analysis and extracted genomic DNA were assessed. Microtomy was straightforward in most tissue blocks, but there was difficulty in cutting in approximately a quarter of samples, which required careful handling by an experienced technician. There were no significant differences in tissue morphology between RCL2- and formalin-fixed tissues (P=0.08). Generally, the quality of histochemical staining, immunohistochemistry and in-situ hybridization were comparable to that of formalin-fixed tissues. Inconsistent immunoreactivity was noted, however, with antibodies against pan-cytokeratin and progesterone receptor. Genomic DNA concentration was higher in RCL2-fixed tissues. Using RCL2 diluted in 95% ethanol did not affect fixation quality. CONCLUSION RCL2 is a potential formalin substitute suitable as a fixative for use in routine histopathological examination; however, difficulty in microtomy and occasional discrepancies in immunohistochemical reactivity require further optimization of the methodology.
Collapse
Affiliation(s)
- Noraidah Masir
- Pathology Department, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Kothmaier H, Popper HH. In Reply. Arch Pathol Lab Med 2012. [DOI: 10.5858/arpa.2011-0423-le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
33
|
Espina V, Mueller C. Reduction of preanalytical variability in specimen procurement for molecular profiling. Methods Mol Biol 2012; 823:49-57. [PMID: 22081338 DOI: 10.1007/978-1-60327-216-2_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Despite the tremendous perceived value, and the predicted high abundance, of disease-associated tissue biomarkers, the number of biomarkers that have been validated for routine clinical use is very low. The major roadblock has been the sample-to-sample variability and perishability of biomolecules in tissue. A chief source of variability is biomolecule perturbation caused by sample handling, the time delays following procurement, and the method of preservation. Living tissue that has been separated from its blood supply during surgical procurement goes through defined stages of reactive changes preceding death, beginning with oxidative, hypoxic, and metabolic stress. These reactive fluctuations in the tissue biomolecules can occur within 20 min postexcision, and can significantly distort the levels of critical diagnostic and prognostic biomolecules. Depending on the delay time ex vivo, and manner of handling, protein biomarkers such as signal pathway phosphoproteins will be elevated or suppressed in a manner that does not represent the biomarker levels at the time of excision. Based on analysis of phosphoproteins, one of the most labile tissue protein biomarkers, we set forth tissue procurement guidelines for clinical research. We further propose the future use of a multipurpose fixative solution designed to stabilize, preserve and maintain proteins, nucleic acids, and tissue architecture.
Collapse
Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
| | | |
Collapse
|
34
|
Moelans CB, ter Hoeve N, van Ginkel JW, ten Kate FJ, van Diest PJ. Formaldehyde substitute fixatives. Analysis of macroscopy, morphologic analysis, and immunohistochemical analysis. Am J Clin Pathol 2011; 136:548-56. [PMID: 21917676 DOI: 10.1309/ajcphh1b0cocbgom] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Because formaldehyde is toxic and creates cross-links that may hinder immunohistochemical studies, we tested 3 new cross-linking (F-Solv [Adamas, Rhenen, the Netherlands]) and non-cross-linking (FineFIX [Milestone, Bergamo, Italy] and RCL2 [Alphelys, Plaisir, France]) alcohol-based fixatives for routine staining in comparison with neutral buffered formalin (NBF) as the "gold standard." Fresh tissue samples were divided into 4 equal pieces and fixed in all fixatives for varying times. After paraffin embedding, H&E staining, 7 common histochemical stains, and 9 common immunohistochemical stains were performed. RCL2 fixation resulted in soft and slippery tissue, causing sectioning difficulties. F-Solv and FineFIX led to partial tissue disintegration during fixation. F-Solv performed morphologically similar to NBF but needed considerable protocol adjustments before being applicable in daily histologic and immunohistochemical practice. FineFIX did not necessitate major protocol changes but caused shrinkage artifacts, degranulation, and lysis of RBCs. RCL2 generated morphologically overall good results without major protocol changes but caused pigment deposition, degranulation, and RBC lysis. The alcohol-based fixatives had positive and negative attributes and environmental drawbacks, and none was overall comparable to NBF with regard to macroscopy, morphologic evaluation, and immunohistochemical studies.
Collapse
Affiliation(s)
- Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Natalie ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan-Willem van Ginkel
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fiebo J. ten Kate
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| |
Collapse
|
35
|
Kothmaier H, Rohrer D, Stacher E, Quehenberger F, Becker KF, Popper HH. Comparison of formalin-free tissue fixatives: a proteomic study testing their application for routine pathology and research. Arch Pathol Lab Med 2011; 135:744-52. [PMID: 21631267 DOI: 10.5858/2009-0676-oa.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Formalin-fixed, paraffin-embedded tissue is the routine processing method for diagnostics practiced in pathology departments worldwide. OBJECTIVE To determine the potential value of non-cross-linking, formalin-free tissue fixation for diagnostics in pathology and proteomic investigations. DESIGN We tested 3 commercially available, formalin-free tissue fixatives-FineFIX, RCL2, and HOPE-in lung cancer specimens from 10 patients. The fixatives were evaluated for their effects on tissue morphology, protein recovery, and immunoreactivity for a selected panel of proteins differently expressed in lung cancer, using immunohistochemistry and Western blotting. RESULTS Tumor-cell analysis with hematoxylin-eosin worked equally well for all tested fixatives when compared with the standard formalin-fixed, paraffin-embedded procedure. Movat pentachrome stains showed comparable results for the different matrices and cellular proteins analyzed. The RCL2 (P = .01) and HOPE fixatives (P = .03) improved protein recovery when compared with formalin-fixed, paraffin-embedded or frozen tissues. Our data clearly show that the fixatives evaluated influenced immunoreactivity to matched, formalin-fixed, paraffin-embedded lung cancer tissue. In particular, membrane-bound proteins, such as epidermal growth factor receptor EGFR, can be detected more efficiently by immunohistochemistry and Western blotting. CONCLUSION We have demonstrated that formalin-free fixatives have the potential in routine pathology and research to replace formalin in histomorphology and protein preservation.
Collapse
Affiliation(s)
- Hannelore Kothmaier
- Institute of Pathology, Research Unit for Molecular Lung and Pleura Pathology, Medical University of Graz, Austria
| | | | | | | | | | | |
Collapse
|
36
|
Evaluation of formalin-fixed paraffin-embedded tissues in the proteomic analysis of parathyroid glands. Proteome Sci 2011; 9:29. [PMID: 21651755 PMCID: PMC3123619 DOI: 10.1186/1477-5956-9-29] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/08/2011] [Indexed: 01/12/2023] Open
Abstract
Background Proteomic research in the field of parathyroid tissues is limited by the very small dimension of the glands and by the low incidence of cancer lesions (1%). Formalin-fixed paraffin-embedded (FFPE) tissue specimens are a potentially valuable resource for discovering protein cancer biomarkers. In this study we have verified the applicability of a heat induced protein extraction from FFPE parathyroid adenoma tissues followed by a gel-based or gel-free proteomic approach in order to achieve protein separation and identification. Results The best results for high quality MS spectra and parameters, were obtained by using a gel-free approach, and up to 163 unique proteins were identified. Similar results were obtained by applying both SDS-out and SDS-out + TCA/Acetone techniques during the gel-free method. Western blot analysis carried out with specific antibodies suggested that the antigenicity was not always preserved, while specific immunoreactions were detected for calmodulin, B box and SPRY domain-containing protein (BSPRY), peroxiredoxin 6 (PRDX 6) and parvalbumin. Conclusions In spite of some limitations mainly due to the extensive formalin-induced covalent cross-linking, our results essentially suggest the applicability of a proteomic approach to FFPE parathyroid specimens. From our point of view, FFPE extracts might be an alternative source, especially in the validation phase of protein biomarkers when a large cohort of samples is required and the low availability of frozen tissues might be constraining.
Collapse
|
37
|
Evaluation of formalin-free tissue fixation for RNA and microRNA studies. Exp Mol Pathol 2011; 91:490-5. [PMID: 21641900 DOI: 10.1016/j.yexmp.2011.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 05/21/2011] [Indexed: 12/30/2022]
Abstract
FineFix, RCL-2 and HOPE, three formalin-free fixatives, were compared to the common used formalin fixed tissue samples of lung cancer and were evaluated for their effects on quality, quantity and integrity of RNA and microRNA. Two commercially available RNA extraction Kits (RNeasy FFPE by Qiagen and RecoverAll™ Nucleic Acid Isolation by Ambion) were tested and optimized in order to determine an extraction protocol for RNA as well as miRNA independent of the fixative. Two selected miRNAs were quantified via TaqMan MicroRNA assays. The optimized RNA extraction protocol for Qiagen's Kit leads to similar results for RNA quality and integrity for all fixatives. Highest RNA yield was obtained for formalin and the highest average miRNA ratio was found for FineFix. RNA fragments smaller than 500 bases were detected in FineFix, formalin and RCL2 fixed tissues; HOPE was the only fixative showing long fragments in one third of the samples. Our findings demonstrate that formalin-free fixatives are in general not superior for RNA studies. With our optimized RNA extraction protocol, there is no difficulty in extracting great amounts of RNA with high quality. According to the quality obtained, quantitative real-time PCR analysis can be performed without any negative impact. Similar results can be achieved for the tested fixatives and therefore no fixative seems to represent a new "gold-standard" for tissue fixation.
Collapse
|
38
|
Dietel M, Denkert C, Hauptmann K, Anagnostopoulos I, Jöhrens K. Konzept der prädiktiven Molekularpathologie. DER ONKOLOGE 2011. [DOI: 10.1007/s00761-011-2057-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
39
|
Groenen PJTA, Blokx WAM, Diepenbroek C, Burgers L, Visinoni F, Wesseling P, van Krieken JHJM. Preparing pathology for personalized medicine: possibilities for improvement of the pre-analytical phase. Histopathology 2011; 59:1-7. [DOI: 10.1111/j.1365-2559.2010.03711.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
40
|
Warren MV, Chan WYI, Ridley JM. Analysis of protein biomarkers in human clinical tumor samples: critical aspects to success from tissue acquisition to analysis. Biomark Med 2011; 5:227-48. [DOI: 10.2217/bmm.11.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There has been increased interest in the analysis of protein biomarkers in clinical tumor tissues in recent years. Tissue-based biomarker assays can add value and aid decision-making at all stages of drug development, as well as being developed for use as predictive biomarkers and for patient stratification and prognostication in the clinic. However, there must be an awareness of the legal and ethical issues related to the sourcing of human tissue samples. This article also discusses the limits of scope and critical aspects on the successful use of the following tissue-based methods: immunohistochemistry, tissue microarrays and automated image analysis. Future advances in standardization of tissue biobanking methods, immunohistochemistry and quantitative image analysis techniques are also discussed.
Collapse
Affiliation(s)
| | - WY Iris Chan
- Pathology Diagnostics Ltd, St John’s Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - John M Ridley
- Pathology Diagnostics Ltd, St John’s Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| |
Collapse
|
41
|
Malinowsky K, Wolff C, Gündisch S, Berg D, Becker K. Targeted therapies in cancer - challenges and chances offered by newly developed techniques for protein analysis in clinical tissues. J Cancer 2010; 2:26-35. [PMID: 21197262 PMCID: PMC3005552 DOI: 10.7150/jca.2.26] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 12/16/2010] [Indexed: 12/20/2022] Open
Abstract
In recent years, new anticancer therapies have accompanied the classical approaches of surgery and radio- and chemotherapy. These new forms of treatment aim to inhibit specific molecular targets namely altered or deregulated proteins, which offer the possibility of individualized therapies.The specificity and efficiency of these new approaches, however, bring about a number of challenges. First of all, it is essential to specifically identify and quantify protein targets in tumor tissues for the reasonable use of such targeted therapies. Additionally, it has become even more obvious in recent years that the presence of a target protein is not always sufficient to predict the outcome of targeted therapies. The deregulation of downstream signaling molecules might also play an important role in the success of such therapeutic approaches. For these reasons, the analysis of tumor-specific protein expression profiles prior to therapy has been suggested as the most effective way to predict possible therapeutic results. To further elucidate signaling networks underlying cancer development and to identify new targets, it is necessary to implement tools that allow the rapid, precise, inexpensive and simultaneous analysis of many network components while requiring only a small amount of clinical material.Reverse phase protein microarray (RPPA) is a promising technology that meets these requirements while enabling the quantitative measurement of proteins. Together with recently developed protocols for the extraction of proteins from formalin-fixed, paraffin-embedded (FFPE) tissues, RPPA may provide the means to quantify therapeutic targets and diagnostic markers in the near future and reliably screen for new protein targets.With the possibility to quantitatively analyze DNA, RNA and protein from a single FFPE tissue sample, the methods are available for integrated patient profiling at all levels of gene expression, thus allowing optimal patient stratification for individualized therapies.
Collapse
Affiliation(s)
- K Malinowsky
- Department of Pathology, Technische Universität München, Munich, Germany
| | | | | | | | | |
Collapse
|
42
|
Ergin B, Meding S, Langer R, Kap M, Viertler C, Schott C, Ferch U, Riegman P, Zatloukal K, Walch A, Becker KF. Proteomic analysis of PAXgene-fixed tissues. J Proteome Res 2010; 9:5188-96. [PMID: 20812734 DOI: 10.1021/pr100664e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Formalin fixation and paraffin embedding is the standard technique for preserving biological material for both storage and histological analysis. Although recent progress has been made in the molecular analysis of formalin-fixed, paraffin-embedded (FFPE) tissues, proteomic applications are a special challenge due to the cross-linking property of formalin. Here we present the results of a new formalin-free tissue fixative, PAXgene, and demonstrate successful extraction of nondegraded and immunoreactive protein for subsequent standard protein assays, such as Western blot analysis and reverse-phase protein arrays. High amounts of protein can be obtained from PAXgene-fixed, paraffin-embedded (PFPE) mouse liver and human spleen, breast, duodenum, and stomach tissues, similar to frozen material. By Western blot analysis, we found that the detection of membrane, cytoplasmic, nuclear, and phosphorylated protein from PAXgene-fixed human tissue samples was comparable to cryopreserved samples. Furthermore, the distribution of protein in PAXgene-fixed human tissue specimens is adequate for matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry for in situ proteomic analysis. Taken together, we demonstrate here that PAXgene has great potential to serve as a novel multimodal fixative for modern pathology, enabling extensive protein biomarker studies on clinical tissue samples.
Collapse
Affiliation(s)
- Bilge Ergin
- Institute of Pathology, Technische Universität München, Munich, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
|
44
|
Hofman V, Ilie M, Gavric-Tanga V, Lespinet V, Mari M, Lassalle S, Butori C, Coelle C, Bordone O, Selva E, Lamy A, Sabourin JC, Hofman P. [Role of the surgical pathology laboratory in the pre-analytical approach of molecular biology techniques]. Ann Pathol 2010; 30:85-93. [PMID: 20451063 DOI: 10.1016/j.annpat.2010.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 03/04/2010] [Accepted: 03/09/2010] [Indexed: 11/15/2022]
Abstract
The advent of the targeted cancer therapies administered to patients, according to the results of molecular biology techniques (in particular, in situ hybridization, "polymerase chain reaction" amplification and sequencing), has modified the practice of the surgical pathology laboratories. The necessity to answer to the needs of physicians for optimizing the medical care for patients who develop cancer has led to a policy of national debate, spurred by the National Institute of Cancer (INCa), in order to implement new procedures in the pathology laboratories. Thus, in addition to the structuring of molecular biology platforms and their labeling by INCa, the upstream control of the steps present between resection of tumor samples and molecular analysis has proved to be crucial. Indeed, the quality of this upstream time, called "pre-analytical" phase, determines the reliability of the molecular biology results and therefore the therapeutic strategy. We describe here the main steps to be checked in the pre-analytical phase. The optimization of this pre-analytical phase within the surgical pathology laboratory aims to reduce or render insignificant the risk of errors of molecular biology tests. These errors can indeed lead to false negative or false positive results whose therapeutic consequences can be particularly harmful to patients with cancer.
Collapse
Affiliation(s)
- Véronique Hofman
- Laboratoire de pathologie clinique et expérimentale, hôpital Pasteur, CHU de Nice, 30, avenue de Voie-Romaine, BP 69, 06002 Nice cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mangé A, Chaurand P, Perrochia H, Roger P, Caprioli RM, Solassol J. Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery. J Proteome Res 2010; 8:5619-28. [PMID: 19856998 DOI: 10.1021/pr9007128] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human tissues are an important source of biological material for the discovery of novel biomarkers. Fresh-frozen tissue could represent an ideal supply of archival material for molecular investigations. However, immediate flash freezing is usually not possible, especially for rare or valuable tissue samples such as biopsies. Here, we investigated the compatibility of RCL2/CS100, a non-cross-linking, nontoxic, and nonvolatile organic fixative, with shotgun proteomic analyses. Several protein extraction protocols compatible with mass spectrometry were investigated from RCL2/CS100-fixed and fresh-frozen colonic mucosa, breast, and prostate tissues. The peptides and proteins identified from RCL2/CS100 tissue were then comprehensively compared with those identified from matched fresh-frozen tissues using a bottom-up strategy based on nano-reversed phase liquid chromatography coupled with tandem mass spectrometry (nanoRPLC-MS/MS). Results showed that similar peptides could be identified in both archival conditions and the proteome coverage was not obviously compromised by the RCL2/CS100 fixation process. NanoRPLC-MS/MS of laser capture microdissected RCL2/CS100-fixed tissues gave the same amount of biological information as that recovered from whole RCL2/CS100-fixed or frozen tissues. We next performed MALDI tissue profiling and imaging mass spectrometry and observed a high level of agreement in protein expression as well as excellent agreement between the images obtained from RCL2/CS100-fixed and fresh-frozen tissue samples. These results suggest that RCL2/CS100-fixed tissues are suitable for shotgun proteomic analyses and tissue imaging. More importantly, this alternate fixative opens the door to the analysis of small, valuable, and rare target lesions that are usually inaccessible to complementary biomarker-driven genomic and proteomic research.
Collapse
Affiliation(s)
- Alain Mangé
- Department of Cellular Biology, CHU Arnaud de Villeneuve, Montpellier, France
| | | | | | | | | | | |
Collapse
|
46
|
Kähler D, Alexander C, Schultz H, Abdullah M, Branscheid D, Lindner B, Zabel P, Vollmer E, Goldmann T. Proteomics out of the archive: Two-dimensional electrophoresis and mass spectrometry using HOPE-fixed, paraffin-embedded tissues. J Histochem Cytochem 2009; 58:221-8. [PMID: 19995946 DOI: 10.1369/jhc.2009.954065] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Proteome analyses provide diagnostic information which can be essential for therapeutic predictions. The application of such techniques for analyzing paraffin-embedded tissue samples is widely hampered by the use of formalin fixation requiring antigen retrieval procedures in molecular pathology. In prior studies, the HEPES-glutamic acid buffer-mediated organic solvent protection effect (HOPE) technique of tissue fixation has been shown to provide a broad array of biochemical investigations with excellent preservation of morphological structures, DNA, RNA, and proteins, thus supporting the multimethod analysis of archived specimens. Here we show that HOPE fixation is also useful in proteomic investigations by allowing two-dimensional electrophoresis (2DE) and mass spectrometry, using lung cancer tissues. Two-dimensional gels of two-protein extraction protocols derived from HOPE-fixed material displayed characteristic spot patterns with high reproducibility. For comparison, 2DE analysis of ethanol-fixed, formalin-fixed, and frozen samples from the same tissues was performed. Western blotting confirmed immunoreactivity of 2DE-separated proteins from HOPE-fixed tissue samples. Additionally, distinct spots were excised from HOPE-derived 2D gels and successfully subjected to peptide mass fingerprinting. In conclusion, paraffin archives containing HOPE-fixed tissues are applicable to a wide spectrum of molecular investigations including common biochemical methods for proteome analyses and therefore represent a unique source for molecular investigations in the rapidly growing field of molecular pathology. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.
Collapse
|
47
|
Lassalle S, Hofman V, Marius I, Gavric-Tanga V, Brest P, Havet K, Butori C, Selva E, Santini J, Mograbi B, Hofman P. Assessment of morphology, antigenicity, and nucleic acid integrity for diagnostic thyroid pathology using formalin substitute fixatives. Thyroid 2009; 19:1239-48. [PMID: 19888862 DOI: 10.1089/thy.2009.0095] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND With the advent of the formaldehyde standard law in France, and because of the impact of new methods for diagnosis and prognosis in pathology, formalin replacement in surgical pathology laboratories is currently being discussed in France. However, a set of criteria must be assessed before introducing a formalin substitute fixative. The objective of this study was to compare formalin substitute fixation with formalin fixation and cryoconservation of tissues from several benign and malignant thyroid pathologies with respect to morphology, antigenicity, and nucleic acid (RNA, DNA, microRNA) integrity. METHODS Calibrated specimens (200 mg, 1 cm(2) each) from four conventional papillary thyroid carcinomas, four follicular variant of papillary thyroid carcinomas, three minimally invasive follicular carcinomas, four thyroid adenomas, five thyroid nodular hyperplasias, and five normal thyroid tissues were fixed for 6, 12, or 24 hours, in different fixatives (formalin, Glyo-Fixx, FineFIX, ExcellPlus, RCL2) at room temperature or at 4 degrees C. Tissues were stained (hematoxylin-eosin, periodic acid Schiff, trichromic Masson, and Sweet-Gordon staining) and their antigenicity determined by immunohistochemistry (performed with HBME-1, galectin-3, CK19, vimentin, CD31, and KL1 antibodies). Evaluation by four pathologists was made blinded. The quantity and quality of DNA, RNA, and two representative microRNA extracted from deparaffinized sections of paraffin embedded specimen were compared with that of cryosections. RESULTS The staining and morphology were not altered by the use of different fixatives. However, formalin, FineFIX, and RCL2 gave the best results for immunohistochemistry. Moreover, FineFIX and RCL2 gave the highest amount of nucleic acids and of the best quality. CONCLUSIONS All the formalin substitute fixatives used in this study provided good histomorphologic quality for the different stained thyroid tissues, but individually, some fixatives performed better for immunohistochemical and molecular biological procedures for different thyroid pathologies.
Collapse
Affiliation(s)
- Sandra Lassalle
- Inserm ERI-21, Faculty of Medicine, University of Nice Sophia Antipolis, 06107 Nice, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Daniele L, Annaratone L, Allia E, Mariani S, Armando E, Bosco M, Macrì L, Cassoni P, D’Armento G, Bussolati G, Cserni G, Sapino A. Technical limits of comparison of step-sectioning,immunohistochemistry and RT-PCR on breast cancer sentinel nodes: a study on methacarn-fixed tissue. J Cell Mol Med 2009; 13:4042-50. [PMID: 18671755 PMCID: PMC4516551 DOI: 10.1111/j.1582-4934.2008.00449.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 07/25/2008] [Indexed: 11/28/2022] Open
Abstract
The optimal pathological assessment of sentinel nodes (SLNs) in breast cancer is a matter of debate. Currently, multilevel histological evaluation and immunohistochemistry (IHC) are recommended, but alternative RT-PCR procedures have been developed. To assess the reliability of these different procedures, we devised a step-sectioning protocol at 100 micron-intervals of 74 SLNs using methacarn fixation. mRNA was extracted from sections collected from levels 4 to 5. Mammaglobin, CEA and CK19 were used for RT-PCR. mRNA extraction was successful in 69 SLNs. Of these, 7 showed macrometastases (>2mm), 2 showed micrometastases (<2 mm) and 7 showed isolated tumour cells (ITC) by IHC. RT-PCR was positive for the three markers in 6 of 7 macrometastases and in 1 of 2 micrometastases. In the 2 RT-PCR negative cases, metastases were detected only on sections distant from those analysed by RT-PCR. CEA and/or CK19 were positive by RT-PCR in 3 of 7 ITC and in 23 morphologically negative SLNs. In conclusion, the main goal of our study was to show that the use of alternate sections of the same sample for different procedures is the key reason for the discrepancies between molecular and morphological analyses of SLN. We believe that only prospective studies with quantitative mRNA analysis of specific metastatic markers on the whole lymph node can elucidate the utility of molecular assessments of SLN.
Collapse
Affiliation(s)
- Lorenzo Daniele
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Laura Annaratone
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Elena Allia
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Sara Mariani
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Enrico Armando
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Martino Bosco
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Luigia Macrì
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Paola Cassoni
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Giuseppe D’Armento
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Gianni Bussolati
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| | - Gabor Cserni
- Department of Surgical Pathology, Bács-Kiskun County Teaching HospitalKecskemét, Hungary
| | - Anna Sapino
- Department of Biomedical Sciences and Human Oncology, University of TurinTurin, Italy
| |
Collapse
|
49
|
Espina V, Mueller C, Edmiston K, Sciro M, Petricoin EF, Liotta LA. Tissue is alive: New technologies are needed to address the problems of protein biomarker pre-analytical variability. Proteomics Clin Appl 2009; 3:874-882. [PMID: 20871745 DOI: 10.1002/prca.200800001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Instability of tissue protein biomarkers is a critical issue for molecular profiling. Pre-analytical variables during tissue procurement, such as time delays during which the tissue remains stored at room temperature, can cause significant variability and bias in downstream molecular analysis. Living tissue, ex vivo, goes through a defined stage of reactive changes that begin with oxidative, hypoxic and metabolic stress, and culminate in apoptosis. Depending on the delay time ex vivo, and reactive stage, protein biomarkers, such as signal pathway phosphoproteins will be elevated or suppressed in a manner which does not represent the biomarker levels at the time of excision. Proteomic data documenting reactive tissue protein changes post collection indicate the need to recognize and address tissue stability, preservation of post-translational modifications, and preservation of morphologic features for molecular analysis. Based on the analysis of phosphoproteins, one of the most labile tissue protein biomarkers, we set forth tissue procurement guidelines for clinical research. We propose technical solutions for (i) assessing the state of protein analyte preservation and specimen quality via identification of a panel of natural proteins (surrogate stability markers), and (ii) using multi-purpose fixative solution designed to stabilize, preserve and maintain proteins, nucleic acids, and tissue architecture.
Collapse
Affiliation(s)
- Virginia Espina
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, VA, USA
| | | | | | | | | | | |
Collapse
|
50
|
Fedorowicz G, Guerrero S, Wu TD, Modrusan Z. Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas. BMC Med Genomics 2009; 2:23. [PMID: 19426511 PMCID: PMC2694827 DOI: 10.1186/1755-8794-2-23] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 05/08/2009] [Indexed: 11/18/2022] Open
Abstract
Background Gene expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples represents a valuable approach for advancing oncology diagnostics and enhancing retrospective clinical studies; however, at present, this methodology still requires optimization and thus has not been extensively used. Here, we utilized thorough quality control methods to assess RNA extracted from FFPE samples and then compared it to RNA extracted from matched fresh-frozen (FF) counterparts. We preformed genome-wide expression profiling of FF and FFPE ovarian serous adenocarcinoma sample pairs and compared their gene signatures to normal ovary samples. Methods RNA from FFPE samples was extracted using two different methods, Ambion and Agencourt, and its quality was determined by profiling starting total RNA on Bioanalyzer and by amplifying increasing size fragments of beta actin (ACTB) and claudin 3 (CLDN3) by reverse-transcriptase polymerase chain reaction. Five matched FF and FFPE ovarian serous adenocarcinoma samples, as well as a set of normal ovary samples, were profiled using whole genome Agilent microarrays. Reproducibility of the FF and FFPE replicates was measured using Pearson correlation, whereas comparison between the FF and FFPE samples was done using a Z-score analysis. Results Data analysis showed high reproducibility of expression within each FF and FFPE method, whereas matched FF and FFPE pairs demonstrated lower similarity, emphasizing an inherent difference between the two sample types. Z-score analysis of matched FF and FFPE samples revealed good concordance of top 100 differentially expressed genes with the highest correlation of 0.84. Genes characteristic of ovarian serous adenocarcinoma, including a well known marker CLDN3, as well as potentially some novel markers, were identified by comparing gene expression profiles of ovarian adenocarcinoma to those of normal ovary. Conclusion Conclusively, we showed that systematic assessment of FFPE samples at the RNA level is essential for obtaining good quality gene expression microarray data. We also demonstrated that profiling of not only FF but also of FFPE samples can be successfully used to identify differentially expressed genes characteristic of ovarian carcinoma.
Collapse
Affiliation(s)
- Grazyna Fedorowicz
- Department of Molecular Biology, Genentech, Inc,, 1 DNA Way, South San Francisco, CA 94080, USA.
| | | | | | | |
Collapse
|