1
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Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023; 51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Affiliation(s)
- Tim A Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Genís Parra
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Marta Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Jean-Rémi Trotta
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Raúl Tonda
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Alice Moussy
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
| | - Zuzana Gerber
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Peter M Abuja
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
| | - Marit M Grimsrud
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover 30625, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, Ludwigsburg 71640, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Sebastian Hinz
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Clemens Schafmayer
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Jean-François Deleuze
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Ivo G Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
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2
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Barroux M, Horstmann J, Fricke L, Schömig L, Werner M, Kraynova E, Kamarádová K, Fléjou JF, Maerkel B, Kumarasinghe MP, Vieth M, Westerhoff M, Patil DT, Steiger K, Becker KF, Weichert W, Schmid RM, Quante M, Slotta-Huspenina J. Histological evaluation of PAXgene tissue fixation in Barrett’s esophagus and esophageal adenocarcinoma diagnostics. Virchows Arch 2022; 482:887-898. [PMID: 36527466 PMCID: PMC10156762 DOI: 10.1007/s00428-022-03471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Abstract
The dysplasia grading of Barrett’s esophagus (BE), based on the histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue, suffers from high interobserver variability leading to an unsatisfactory prediction of cancer risk. Thus, pre-analytic preservation of biological molecules, which could improve risk prediction in BE enabling molecular and genetic analysis, is needed. We aimed to evaluate such a molecular pre-analytic fixation tool, PAXgene-fixed paraffin-embedded (PFPE) biopsies, and their suitability for histomorphological BE diagnostics in comparison to FFPE. In a ring trial, 9 GI pathologists evaluated 116 digital BE slides of non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinomas (EAC) using virtual microscopy. Overall quality, cytological and histomorphological parameters, dysplasia criteria, and diagnosis were analyzed. PFPE showed better preservation of nuclear details as chromatin and nucleoli, whereas overall quality and histomorphologic parameters as visibility of basal lamina, goblet cells, and presence of artifacts were scored as equal to FFPE. The interobserver reproducibility with regard to the diagnosis was best for NDBE and EAC (κF = 0.72–0.75) and poor for LGD and HGD (κF = 0.13–0.3) in both. In conclusion, our data suggest that PFPE allows equally confident histomorphological diagnosis of BE and EAC, introducing a novel tool for molecular analysis and parallel histomorphological evaluation.
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Affiliation(s)
- Melissa Barroux
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany.
| | - Julia Horstmann
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Lisa Fricke
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Linus Schömig
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg and Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Ekaterina Kraynova
- Department of Pathology, Yaroslavl Regional Cancer Hospital, Yaroslavl, Russian Federation
| | - Katerina Kamarádová
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Charles University, Hradec Králové, Czech Republic
| | - Jean-François Fléjou
- Service d'Anatomie Pathologique, AP-HP, Faculté de Médecine Sorbonne, Hôpital Saint-Antoine, Université, 75012, Paris, France
| | - Bruno Maerkel
- Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
| | - M Priyanthi Kumarasinghe
- Department of Pathology, PathWest Laboratory-University of Western Australia, WA, Perth, Australia
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | | | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Michael Quante
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
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3
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DeCoste R, Amemiya Y, Nersesian S, Westhaver L, Lee SN, Carter MD, Sapp HL, Stueck AE, Arnason T, Boudreau J, Seth A, Huang WY. PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology. J Clin Med 2022; 11:jcm11144241. [PMID: 35888003 PMCID: PMC9319620 DOI: 10.3390/jcm11144241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling of pancreatic cancer using small core biopsies has taken an increasingly prominent role in precision medicine. However, if not appropriately preserved, nucleic acids (NA) from pancreatic tissues are known to be susceptible to degradation due to high intrinsic levels of nucleases. PAXgene fixation (PreAnalytix, Switzerland) represents a novel formalin-free tissue preservation method. We sought to compare the NA and histomorphological preservation of pancreatic cancer tissues preserved with PAXgene-fixed paraffin-embedding (PFPE) and formalin-fixed paraffin-embedding (FFPE). Tissues from 19 patients were obtained prospectively from pancreaticoduodenectomy specimens and evaluated by four gastrointestinal pathologists. The extracted NA were quantified by Nanodrop and Qubit and assessed for quality by qPCR, targeted next-generation sequencing (NGS) assay, and RNA-sequencing. Our results demonstrated that, when assessed blindly for morphological quality, the four pathologists deemed the PFPE slides adequate for diagnostic purposes. PFPE tissues enable greater yields of less fragmented and more amplifiable DNA. PFPE tissues demonstrated significantly improved quality control (QC) metrics in a targeted NGS assay including Median Absolute Pair-wise Difference (MAPD) scores. Our results support the use of PAXgene fixative for the processing of specimens from pancreatic cancers with the potential benefits of improved yields for more amplifiable DNA in low-yield biopsy specimens and its ideal use for amplicon-based NGS assays.
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Affiliation(s)
- Ryan DeCoste
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Yutaka Amemiya
- Sunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; (Y.A.); (A.S.)
| | - Sarah Nersesian
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Lauren Westhaver
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Stacey N. Lee
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Michael D. Carter
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Heidi L. Sapp
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Ashley E. Stueck
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Thomas Arnason
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Jeanette Boudreau
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Arun Seth
- Sunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; (Y.A.); (A.S.)
- Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Weei-Yuarn Huang
- Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence:
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4
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Radani N, Metwaly A, Reitmeier S, Baumeister T, Ingermann J, Horstmann J, Anand A, Gatz I, Kohlmayer F, Janssen KP, Slotta-Huspenina J, Schmid RM, Haller D, Abrams JA, Quante M. Analysis of Fecal, Salivary, and Tissue Microbiome in Barrett's Esophagus, Dysplasia, and Esophageal Adenocarcinoma. GASTRO HEP ADVANCES 2022; 1:755-766. [PMID: 39131856 PMCID: PMC11307671 DOI: 10.1016/j.gastha.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/05/2022] [Indexed: 08/13/2024]
Abstract
Background and Aims Esophageal adenocarcinoma (EAC) incidence has risen dramatically in the Western countries over the past decades. The underlying reasons are incompletely understood, and shifts in the esophageal microbiome have been postulated to increase predisposition to disease development. Multiple factors including medications, lifestyle, and diet could influence microbiome composition and disease progression. The aim of this study was (1) to identify a feasible method to characterize the tissue-associated microbiome, and (2) to investigate differences in the microbiome of saliva, esophageal tissue, and fecal samples by disease state and validate with 2 external cohorts. Methods Forty-eight patients (15 Barrett's esophagus [BE], 4 dysplasia, 15 EAC, and 14 healthy) were enrolled in this cross-sectional study (Munich cohort). Demographics, epidemiologic and clinical data, medications, smoking, and alcohol consumption were assessed. 16S rRNA Gene sequencing was performed on saliva, tissue biopsy and fecal samples. PAXgene fixation was used as a novel methodology. Microbial community alpha- and beta-diversity, as well as microbial composition at phylum and genus level, were characterized for this cohort and compared with 2 external cohorts: New York cohort and Cooperative Health Research in the Augsburg Region cohort. Results We first established PAXgene fixation is a feasible method for microbiome analysis and utilized it to identify a distinct microbial shift in tissue biopsies from patients with EAC, whereas overall microbial diversity in salivary and fecal samples did not differ significantly between disease states. Our findings were similar in a reanalysis to those from a US cohort that used a standardized fresh frozen biopsy collection protocol (New York cohort, N = 75 biopsies). Nevertheless, we could not distinguish German Munich cohort patients from a German population-based cohort (Cooperative Health Research in the Augsburg Region cohort, N = 2140 individuals) when fecal bacterial profiles were compared between both cohorts. In addition, we used data integration of diagnosis and risk factors of patients and found associations with microbiome alterations. Conclusion Sample collection and microbiome analysis are indeed feasible and can be implemented into clinical routine by an easy-to-use biopsy protocol. The presence of BE and EAC together with epidemiologic factors can be associated with alterations of the salivary, tissue, and fecal microbial community in an easy-to-use data integration concept. Given a possible role of the microbiome in BE and EAC, it will be important in future studies to take tissue-specific microbial communities and individual taxa into account in larger prospective studies.
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Affiliation(s)
- Nikole Radani
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Munich, Germany
| | - Sandra Reitmeier
- ZIEL-Institute for Food and Health, Technical University of Munich, Munich, Germany
| | - Theresa Baumeister
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Jonas Ingermann
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Julia Horstmann
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Akanksha Anand
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Ingrid Gatz
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, TUM, Munich, Germany
| | - Florian Kohlmayer
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, TUM, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, TU München, Munich, Germany
- The Biobank of Klinikum rechts der Isar/Technical University Munich (MTBIO), Munich, Germany
| | - Julia Slotta-Huspenina
- The Biobank of Klinikum rechts der Isar/Technical University Munich (MTBIO), Munich, Germany
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland M. Schmid
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Munich, Germany
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Michael Quante
- Department of Internal Medicine, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II, University of Freiburg, Freiburg, Germany
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5
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Smith J, Faria CSAA, Qvist CC, Melchior LC, Lauridsen T. Prolonging fixation time of an alternative fixative to formalin for dermatological samples using standard laboratory protocols. J Clin Pathol 2020; 74:149-156. [PMID: 32669366 DOI: 10.1136/jclinpath-2020-206612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 11/03/2022]
Abstract
AIMS Though formalin remains to be the gold standard fixative in pathology departments, analytical challenges persist for nucleic acid evaluations. In our laboratory, formalin fixation of skin samples in particular impairs diagnostic accuracy and demands repetition of biopsies and analytical procedures. PAXgene Tissue Systems may be an alternative; however, according to manufacturer specifications it only allows fixation for 48 hours before having to add a stabiliser. This may be a challenge in laboratories, which are closed in weekends and bank holidays. Our aim was to validate this alternative fixative for dermatological samples with prolonged fixation times using standard laboratory protocols developed for formalin-fixed specimens. We compared the results with gold standard formalin fixation. METHODS Skin specimens were formalin or PAXgene fixed for either 2 hours, 24 hours, 3 days or 7 days, paraffin-embedded, analysed and scored by observers. RESULTS Generally, formalin outperformed PAXgene fixation in H&E stains and fluorescence in situ hybridisation (FISH), but both seem usable for diagnostics. Time of PAXgene fixation did not have an impact on alcian blue-Van Gieson (ABVG), H&E (p=0.48), nor immunohistochemistry (p=0.74). There was a tendency towards best PAXgene performance at 24 hours of fixation for FISH, and for DNA integrity analysis 24 hours or 3 days. CONCLUSIONS Prolonging PAXgene fixation time to 3 days before adding stabiliser does not seem to have major impact on performance of general diagnostic analysis, but our preliminary results show optimisation of internal protocols are needed. PAXgene is an expensive alternative and may be confined to some dermatological samples.
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Affiliation(s)
- Julie Smith
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | | | - Camilla Christine Qvist
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Linea C Melchior
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Thomas Lauridsen
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
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Southwood M, Krenz T, Cant N, Maurya M, Gazdova J, Maxwell P, McGready C, Moseley E, Hughes S, Stewart P, Salto-Tellez M, Groelz D, Rassl D. Systematic evaluation of PAXgene® tissue fixation for the histopathological and molecular study of lung cancer. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2019; 6:40-54. [PMID: 31571426 PMCID: PMC6966705 DOI: 10.1002/cjp2.145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022]
Abstract
Whilst adequate for most existing pathological tests, formalin is generally considered a poor DNA preservative and use of alternative fixatives may prove advantageous for molecular testing of tumour material; an increasingly common approach to identify targetable driver mutations in lung cancer patients. We collected paired PAXgene® tissue-fixed and formalin-fixed samples of block-sized tumour and lung parenchyma, Temno-needle core tumour biopsies and fine needle tumour aspirates (FNAs) from non-small cell lung cancer resection specimens. Traditionally processed formalin fixed paraffin wax embedded (FFPE) samples were compared to paired PAXgene® tissue fixed paraffin-embedded (PFPE) samples. We evaluated suitability for common laboratory tests (H&E staining and immunohistochemistry) and performance for downstream molecular investigations relevant to lung cancer, including RT-PCR and next generation DNA sequencing (NGS). Adequate and comparable H&E staining was seen in all sample types and nuclear staining was preferable in PAXgene® fixed Temno tumour biopsies and tumour FNA samples. Immunohistochemical staining was broadly comparable. PFPE samples enabled greater yields of less-fragmented DNA than FFPE comparators. PFPE samples were also superior for PCR and NGS performance, both in terms of quality control metrics and for variant calling. Critically we identified a greater number of genetic variants in the epidermal growth factor receptor gene when using PFPE samples and the Ingenuity® Variant Analysis pipeline. In summary, PFPE samples are adequate for histopathological diagnosis and suitable for the majority of existing laboratory tests. PAXgene® fixation is superior for DNA and RNA integrity, particularly in low-yield samples and facilitates improved NGS performance, including the detection of actionable lung cancer mutations for precision medicine in lung cancer samples.
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Affiliation(s)
- Mark Southwood
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
| | - Tomasz Krenz
- Sample Technologies Department, QIAGEN GmbH, Hilden, Germany
| | - Natasha Cant
- Sample Technologies Department, QIAGEN Ltd., Manchester, UK
| | - Manisha Maurya
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jana Gazdova
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Perry Maxwell
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Claire McGready
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Ellen Moseley
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
| | - Susan Hughes
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Peter Stewart
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel Groelz
- Sample Technologies Department, QIAGEN GmbH, Hilden, Germany
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
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7
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Wiethaler M, Slotta-Huspenina J, Brandtner A, Horstmann J, Wein F, Baumeister T, Radani N, Gerland S, Anand A, Lange S, Schmidt M, Janssen KP, Conrad A, Johannes W, Strauch K, Quante AS, Linkohr B, Kuhn KA, Blaser R, Lehmann A, Kohlmayer F, Weichert W, Schmid RM, Becker KF, Quante M. BarrettNET-a prospective registry for risk estimation of patients with Barrett's esophagus to progress to adenocarcinoma. Dis Esophagus 2019; 32:5479247. [PMID: 31329831 DOI: 10.1093/dote/doz024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Risk stratification in patients with Barrett's esophagus (BE) to prevent the development of esophageal adenocarcinoma (EAC) is an unsolved task. The incidence of EAC and BE is increasing and patients are still at unknown risk. BarrettNET is an ongoing multicenter prospective cohort study initiated to identify and validate molecular and clinical biomarkers that allow a more personalized surveillance strategy for patients with BE. For BarrettNET participants are recruited in 20 study centers throughout Germany, to be followed for progression to dysplasia (low-grade dysplasia or high-grade dysplasia) or EAC for >10 years. The study instruments comprise self-administered epidemiological information (containing data on demographics, lifestyle factors, and health), as well as biological specimens, i.e., blood-based samples, esophageal tissue biopsies, and feces and saliva samples. In follow-up visits according to the individual surveillance plan of the participants, sample collection is repeated. The standardized collection and processing of the specimen guarantee the highest sample quality. Via a mobile accessible database, the documentation of inclusion, epidemiological data, and pathological disease status are recorded subsequently. Currently the BarrettNET registry includes 560 participants (23.1% women and 76.9% men, aged 22-92 years) with a median follow-up of 951 days. Both the design and the size of BarrettNET offer the advantage of answering research questions regarding potential causes of disease progression from BE to EAC. Here all the integrated methods and materials of BarrettNET are presented and reviewed to introduce this valuable German registry.
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Affiliation(s)
- Maria Wiethaler
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Julia Slotta-Huspenina
- Institute of Pathology, University Hospital rechts der Isar, Technical University of Munich.,Tissue Bank of the Klinikum rechts der Isar Munich and Technical University of Munich
| | - Anna Brandtner
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Julia Horstmann
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Frederik Wein
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Theresa Baumeister
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Nikole Radani
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Sophie Gerland
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Akanksha Anand
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Sebastian Lange
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Melissa Schmidt
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Klaus-Peter Janssen
- Klinik und Poliklinik für Chirurgie, University Hospital rechts der Isar, Technical University of Munich
| | - Anja Conrad
- Institute of Pathology, University Hospital rechts der Isar, Technical University of Munich.,Tissue Bank of the Klinikum rechts der Isar Munich and Technical University of Munich
| | - Widya Johannes
- Institute of Pathology, University Hospital rechts der Isar, Technical University of Munich.,Tissue Bank of the Klinikum rechts der Isar Munich and Technical University of Munich
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, München
| | - Anne S Quante
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, München.,Department of Gynecology and Obstetrics, Klinikum rechts der Isar, Technical University of Munich
| | - Birgit Linkohr
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Klaus A Kuhn
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich
| | - Rainer Blaser
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich
| | - Andreas Lehmann
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich
| | - Florian Kohlmayer
- Institute of Medical Informatics, Statistics and Epidemiology, University Hospital rechts der Isar, Technical University of Munich
| | - Wilko Weichert
- Institute of Pathology, University Hospital rechts der Isar, Technical University of Munich.,Tissue Bank of the Klinikum rechts der Isar Munich and Technical University of Munich
| | - Roland M Schmid
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
| | - Karl-Friedrich Becker
- Institute of Pathology, University Hospital rechts der Isar, Technical University of Munich.,Tissue Bank of the Klinikum rechts der Isar Munich and Technical University of Munich
| | - Michael Quante
- Klinik und Poliklinik für Innere Medizin II, University Hospital rechts der Isar, Technical University of Munich
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8
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The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol 2019; 52:69-83. [PMID: 31082574 DOI: 10.1016/j.nbt.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Pre-analytical factors can greatly influence the outcome of molecular analyses in medical diagnostics and research. This also applies to in situ staining techniques such as immunohistochemistry (IHC), where different types of tissue fixation methods lead to different modifications of proteins and thus can affect differently the detection by antibodies. For formalin-fixed paraffin-embedded (FFPE) tissue, antigen retrieval is applied in order to reverse the negative effects of formalin and re-establish immunoreactivity. Most antibodies and protocols used in IHC are optimized for FFPE tissue, but not for paraffin-embedded tissue treated with other fixatives such as non-crosslinking fixatives. We report results from systematic studies on distinct pre-analytical conditions in IHC, immunofluorescence and electron microscopy. Parameters investigated are the impact of crosslinking and non-crosslinking fixatives (comparing formalin and PAXgene Tissue fixation) on whole tissue, subcellular structures and organelles, as well as on ultrastructure. The results generated show that minor changes in antigen retrieval conditions may have a major impact on IHC results and that protocols optimized for crosslinking fixatives may not be used for other fixatives without re-validation. Key antigen retrieval parameters such as buffers with different pH and duration of microwave treatment must be tested systematically for each antibody and fixation protocol.
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9
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Verderio P, Pizzamiglio S, Ciniselli CM. Methodological and statistical issues in developing an External Quality Assessment scheme in laboratory medicine: Focus on biomarker research. N Biotechnol 2019; 52:54-59. [PMID: 31059865 DOI: 10.1016/j.nbt.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 11/16/2022]
Abstract
External Quality Assessment (EQA) schemes are well-established tools with which to evaluate, monitor and improve the output quality of clinical laboratories, recognising that high quality laboratory medicine is essential for patient care. EQA programs involve the testing of multiple laboratories and the statistical comparison of their results, according to a multistep workflow. New clinical laboratory activities, such as biomarker research, require new EQA schemes. Critical elements in designing EQA programs are choosing the statistical methods and defining reference values and control limits. This article summarizes the key features of an EQA scheme, including designing the study, identifying reference values and control limits for qualitative and quantitative data, and graphically reporting laboratory performance statistics. These steps are illustrated with examples taken from the authors' experience in national and international quality assessment schemes for biomarker research.
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Affiliation(s)
- Paolo Verderio
- Bioinformatics and Biostatistics Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Sara Pizzamiglio
- Bioinformatics and Biostatistics Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Maura Ciniselli
- Bioinformatics and Biostatistics Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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10
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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.
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11
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Yamazaki M, Yabuki N, Suzuki Y, Ito M, Ikeda A, Natori O, Suzuki M, Kato A. PAXgene-fixed paraffin-embedded sample is applicable to laser capture microdissection with well-balanced RNA quality and tissue morphology. J Toxicol Pathol 2018; 31:213-220. [PMID: 30093792 PMCID: PMC6077159 DOI: 10.1293/tox.2017-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Assessing how gene expression analysis by RNA sequencing (RNA-Seq) correlates to a unique morphology is increasingly necessary, and laser capture microdissection (LCM) is a critical research tool for discovering the genes responsible in a region of interest (ROI). Because RNA-Seq requires high-quality RNA, a sample preparation procedure that can preserve morphology and give the required quality of RNA is essential. A PAXgene®-fixed paraffin-embedded (XFPE) block can satisfy the need for high-quality RNA, but there are few reports on adapting the method for LCM, such as how small an ROI is analyzable by RNA-Seq. In this study, we confirmed the morphology and preservation of RNA in XFPE and then assessed the relationship between the size of pieces cut by LCM and their RNA quality. In XFPE, the morphology was similar to that in alcohol-based fixed samples, the quality of the RNA extracted from a whole sample was excellent, that is equivalent to that of a fresh frozen sample, and the quality was maintained over one year later. Three sizes of pieces—large (25,000 µm2), medium (5,000 µm2), and small (1,000 µm2)—were cut by LCM so that the total areas of the sections cut per size were the same. RNA quality was found to be best preserved when tissue was cut into pieces of over 5,000 µm2. In summary, XFPE exhibits good morphology and excellent preservation of RNA quality. Furthermore, it can be a good tool when used with LCM and RNA-Seq, giving well-balanced RNA quality and tissue morphology in the ROI.
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Affiliation(s)
- Masaki Yamazaki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Nami Yabuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Yasunori Suzuki
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Mayumi Ito
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Asuka Ikeda
- Chugai Research Institute for Medical Science, Inc., 1-135, Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Osamu Natori
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Masami Suzuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Atsuhiko Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
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12
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Sanchez I, Betsou F, Culot B, Frasquilho S, McKay SC, Pericleous S, Smith C, Thomas G, Mathieson W. RNA and microRNA Stability in PAXgene-Fixed Paraffin-Embedded Tissue Blocks After Seven Years' Storage. Am J Clin Pathol 2018; 149:536-547. [PMID: 29659661 DOI: 10.1093/ajcp/aqy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To evaluate the stability of RNA and microRNA (miRNA) in PAXgene-fixed paraffin-embedded tissue blocks after 7 years' storage. METHODS RNA and miRNA were extracted from PAXgene-fixed paraffin-embedded (PFPE) blocks in 2009 then stored at -80°C. Seven years later, RNA and miRNA were again extracted from the same blocks. RNA and miRNA integrity in the 2009 and 2016 extractions were compared using RNA integrity number (RIN), paraffin-embedded RNA metric (PERM), reverse transcription polymerase chain reaction (RT-PCR) for different amplicon lengths, and quantitative RT-PCR (qRT-PCR) for three mRNA and three miRNA targets. RESULTS In PFPE blocks, mRNA was poorer in 2016 extractions compared to the 2009 extractions in all blocks and all assays applied, with transcripts degrading at different rates in the same blocks. For miRNA, qRT-PCR showed no statistically significant differences between 2009 and 2016 extractions. CONCLUSIONS mRNA in PFPE tissue blocks degrades at room temperature storage over 7 years.
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Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Siobhan C McKay
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Gerry Thomas
- Department of Surgery and Cancer, Imperial College London, London, UK
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13
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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]
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14
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Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol 2017; 42:103-115. [PMID: 28984675 DOI: 10.1097/pas.0000000000000961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied. Our results suggest that it is feasible to use PFPE tissue for routine robot-assisted laparoscopic prostatectomy surgical pathology diagnostics and immunohistochemistry, with the benefit of significantly improvedDNA and RNA quality and RNA picogram yield per nucleus as compared with FFPE tissue. For fresh frozen, FFPE, and PFPE tissues, respectively, the average Genomic Quality Numbers were 7.9, 3.2, and 6.2, average RNA Quality Numbers were 8.7, 2.6, and 6.3, average DNA picogram yields per nucleus were 0.41, 0.69, and 0.78, and average RNA picogram yields per nucleus were 1.40, 0.94, and 2.24. These findings suggest that where DNA and/or RNA analysis of tissue is required, and when tissue size is small, PFPE may provide important advantages over FFPE. The results also suggest several interesting nuances including potential avenues to improve RNA quality in FFPE tissues and confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided.
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Affiliation(s)
- Gunilla Högnäs
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Signal Processing Laboratory, Tampere University of Technology, Pori
| | - Antti Koskenalho
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Department of Urology, University of Tampere
| | | | - Joanna Ilvesaro
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Saara Kares
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | | | - Marita Laurila
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tuomas Mirtti
- Institute for Molecular Medicine Finland, University of Helsinki.,Department of Pathology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Paula M Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
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15
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Loibner M, Oberauner-Wappis L, Viertler C, Groelz D, Zatloukal K. Protocol for HER2 FISH Using a Non-cross-linking, Formalin-free Tissue Fixative to Combine Advantages of Cryo-preservation and Formalin Fixation. J Vis Exp 2017. [PMID: 29364207 PMCID: PMC5908343 DOI: 10.3791/55885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Morphologic assessment of formalin-fixed, paraffin-embedded (FFPE) tissue samples has been the gold standard for cancer diagnostics for decades due to its excellent preservation of morphology. Personalized medicine increasingly provides individually adapted and targeted therapies for characterized individual diseases enabled by combined morphological and molecular analytical technologies and diagnostics. Performance of morphologic and molecular assays from the same FFPE specimen is challenging because of the negative impact of formalin due to chemical modification and cross-linking of nucleic acids and proteins. A non-cross-linking, formalin-free tissue fixative has been recently developed to fulfil both requirements, i.e., to preserve morphology like FFPE and biomolecules like cryo-preservation. Since FISH is often required in combination with histopathology and molecular diagnostics, we tested the applicability of FISH protocols on tissues treated with this new fixative. We found that formalin post-fixation of histological sections of non-cross-linking, formalin-free and paraffin-embedded (NCFPE) breast cancer tissue generated equivalent results to those with FFPE tissue in human epidermal growth factor receptor 2 (HER2) FISH analysis. This protocol describes how a FISH assay originally developed and validated for FFPE tissue can be used for NCFPE tissues by a simple post-fixation step of histological sections.
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Affiliation(s)
- Martina Loibner
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz; Institute of Pathology, Medical University Graz
| | - Lisa Oberauner-Wappis
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz; Institute of Pathology, Medical University Graz
| | | | | | - Kurt Zatloukal
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz; Institute of Pathology, Medical University Graz;
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16
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Abstract
Bone metastasis from primary cancer sites creates diagnostic and therapeutic challenges. Calcified bone is difficult to biopsy due to tissue hardness and patient discomfort, thus limiting the frequency and availability of bone/bone marrow biopsy material for molecular profiling. In addition, bony tissue must be demineralized (decalcified) prior to histomorphologic analysis. Decalcification processes rely on three main principles: (a) solubility of calcium salts in an acid, such as formic or nitric acid; (b) calcium chelation with ethylenediaminetetraacetic acid (EDTA); or (c) ion-exchange resins in a weak acid. A major roadblock in molecular profiling of bony tissue has been the lack of a suitable demineralization process that preserves histomorphology of calcified and soft tissue elements while also preserving phosphoproteins and nucleic acids. In this chapter, we describe general issues relevant to specimen collection and preservation of osseous tissue for molecular profiling. We provide two protocols: (a) one-step preservation of tissue histomorphology and proteins and posttranslational modifications, with simultaneous decalcification of bony tissue, and (b) ethanol-based tissue processing for TheraLin-fixed bony tissue.
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17
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Mathieson W, Marcon N, Antunes L, Ashford DA, Betsou F, Frasquilho SG, Kofanova OA, McKay SC, Pericleous S, Smith C, Unger KM, Zeller C, Thomas GA. A Critical Evaluation of the PAXgene Tissue Fixation System: Morphology, Immunohistochemistry, Molecular Biology, and Proteomics. Am J Clin Pathol 2016; 146:25-40. [PMID: 27402607 DOI: 10.1093/ajcp/aqw023] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To evaluate the PAXgene tissue fixation system. METHODS Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]). RESULTS PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results. CONCLUSIONS While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
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Affiliation(s)
- William Mathieson
- From the Integrated Biobank of Luxembourg, Luxembourg
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | | | - David A. Ashford
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Fay Betsou
- From the Integrated Biobank of Luxembourg, Luxembourg
| | | | | | - Siobhan C. McKay
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Stephan Pericleous
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Colleen Smith
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
| | - Kristian M. Unger
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Constanze Zeller
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Geraldine A. Thomas
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
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18
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Oberauner-Wappis L, Loibner M, Viertler C, Groelz D, Wyrich R, Zatloukal K. Protocol for HER2 FISH determination on PAXgene-fixed and paraffin-embedded tissue in breast cancer. Int J Exp Pathol 2016; 97:202-6. [PMID: 27273709 PMCID: PMC4926048 DOI: 10.1111/iep.12185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/14/2016] [Indexed: 12/24/2022] Open
Abstract
Molecular diagnostics in personalized medicine increasingly relies on the combination of a variety of analytical technologies to characterize individual diseases and to select patients for targeted therapies. The gold standard for tissue‐based diagnostics is fixation in formalin and embedding in paraffin, which results in excellent preservation of morphology but negatively impacts on a variety of molecular assays. The formalin‐free, non‐cross‐linking PAXgene tissue system preserves morphology in a similar way to formalin, but also preserves biomolecules essentially in a similar way to cryopreservation, which markedly widens the spectrum, sensitivity and accuracy of molecular analytics. In this study, we have developed and tested a protocol for PAXgene‐fixed and paraffin‐embedded tissues for fluorescent in situ hybridization (FISH). The implementation of a 24‐h formalin postfixation step of slides from PAXgene‐fixed and paraffin‐embedded tissues allowed us to use the assays approved for formalin‐fixed and paraffin‐embedded tissues. The equivalence of the methodologies was demonstrated by FISH analysis of HER2 amplification in breast cancer cases. The 24‐h postfixation step of the slides used for FISH can be well integrated in the routine diagnostic workflow and allows the remaining PAXgene‐fixed and paraffin‐embedded tissue to be used for further molecular testing.
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Affiliation(s)
- Lisa Oberauner-Wappis
- CD Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria.,Institute of Pathology, Medical University Graz, Graz, Austria
| | - Martina Loibner
- CD Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria.,Institute of Pathology, Medical University Graz, Graz, Austria
| | | | - Daniel Groelz
- Research and Development, Qiagen GmbH, Hilden, Germany
| | - Ralf Wyrich
- Research and Development, Qiagen GmbH, Hilden, Germany
| | - Kurt Zatloukal
- CD Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria.,Institute of Pathology, Medical University Graz, Graz, Austria
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19
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Loibner M, Buzina W, Viertler C, Groelz D, Hausleitner A, Siaulyte G, Kufferath I, Kölli B, Zatloukal K. Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative. PLoS One 2016; 11:e0151383. [PMID: 26974150 PMCID: PMC4790970 DOI: 10.1371/journal.pone.0151383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/26/2016] [Indexed: 11/20/2022] Open
Abstract
Background Requirements on tissue fixatives are getting more demanding as molecular analysis becomes increasingly relevant for routine diagnostics. Buffered formaldehyde in pathology laboratories for tissue fixation is known to cause chemical modifications of biomolecules which affect molecular testing. A novel non-crosslinking tissue preservation technology, PAXgene Tissue (PAXgene), was developed to preserve the integrity of nucleic acids in a comparable way to cryopreservation and also to preserve morphological features comparable to those of formalin fixed samples. Methods Because of the excellent preservation of biomolecules by PAXgene we investigated its pathogen inactivation ability and biosafety in comparison to formalin by in-vitro testing of bacteria, human relevant fungi and human cytomegalovirus (CMV). Guidelines for testing disinfectants served as reference for inactivation assays. Furthermore, we tested the properties of PAXgene for detection of pathogens by PCR based assays. Results All microorganisms tested were similarly inactivated by PAXgene and formalin except Clostridium sporogenes, which remained viable in seven out of ten assays after PAXgene treatment and in three out of ten assays after formalin fixation. The findings suggest that similar biosafety measures can be applied for PAXgene and formalin fixed samples. Detection of pathogens in PCR-based diagnostics using two CMV assays resulted in a reduction of four to ten quantification cycles of PAXgene treated samples which is a remarkable increase of sensitivity. Conclusion PAXgene fixation might be superior to formalin fixation when molecular diagnostics and highly sensitive detection of pathogens is required in parallel to morphology assessment.
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Affiliation(s)
- Martina Loibner
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Walter Buzina
- Medical University Graz, Institute of Hygiene, Microbiology and Environmental Medicine, Graz, Austria
| | | | - Daniel Groelz
- Qiagen GmbH, Research and Development, Hilden, Germany
| | - Anja Hausleitner
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- LKH Hospital Weiz, Laboratory of Medical Department, Weiz, Austria
| | - Gintare Siaulyte
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Iris Kufferath
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Bettina Kölli
- Medical University Graz, Institute of Hygiene, Microbiology and Environmental Medicine, Graz, Austria
| | - Kurt Zatloukal
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
- * E-mail:
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Stumptner C, Gogg-Kamerer M, Viertler C, Denk H, Zatloukal K. Immunofluorescence and Immunohistochemical Detection of Keratins. Methods Enzymol 2016; 568:139-62. [DOI: 10.1016/bs.mie.2015.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Boellner S, Becker KF. Recent progress in protein profiling of clinical tissues for next-generation molecular diagnostics. Expert Rev Mol Diagn 2015. [DOI: 10.1586/14737159.2015.1070098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ciniselli CM, Pizzamiglio S, Malentacchi F, Gelmini S, Pazzagli M, Hartmann CC, Ibrahim-Gawel H, Verderio P. Combining qualitative and quantitative imaging evaluation for the assessment of genomic DNA integrity: The SPIDIA experience. Anal Biochem 2015; 479:60-2. [DOI: 10.1016/j.ab.2015.03.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 11/25/2022]
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Becker KF. Using tissue samples for proteomic studies-Critical considerations. Proteomics Clin Appl 2015; 9:257-67. [DOI: 10.1002/prca.201400106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 01/09/2023]
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