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Abuja PM, Pabst D, Bourgeois B, Loibner M, Ulz C, Kufferath I, Fackelmann U, Stumptner C, Kraemer R, Madl T, Zatloukal K. Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability. Int J Mol Sci 2023; 24:8010. [PMID: 37175716 PMCID: PMC10178321 DOI: 10.3390/ijms24098010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Molecular diagnostics in healthcare relies increasingly on genomic and transcriptomic methodologies and requires appropriate tissue specimens from which nucleic acids (NA) of sufficiently high quality can be obtained. Besides the duration of ischemia and fixation type, NA quality depends on a variety of other pre-analytical parameters, such as storage conditions and duration. It has been discussed that the improper dehydration of tissue during processing influences the quality of NAs and the shelf life of fixed tissue. Here, we report on establishing a method for determining the amount of residual water in fixed, paraffin-embedded tissue (fixed by neutral buffered formalin or a non-crosslinking fixative) and its correlation to the performance of NAs in quantitative real-time polymerase chain reaction (qRT-PCR) analyses. The amount of residual water depended primarily on the fixative type and the dehydration protocol and, to a lesser extent, on storage conditions and time. Moreover, we found that these parameters were associated with the qRT-PCR performance of extracted NAs. Besides the cross-linking of NAs and the modification of nucleobases by formalin, the hydrolysis of NAs by residual water was found to contribute to reduced qRT-PCR performance. The negative effects of residual water on NA stability are not only important for the design and interpretation of research but must also be taken into account in clinical diagnostics where the reanalysis of archived tissue from a primary tumor may be required (e.g., after disease recurrence). We conclude that improving the shelf life of fixed tissue requires meticulous dehydration and dry storage to minimize the degradative influence of residual water on NAs.
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Affiliation(s)
- Peter M. Abuja
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Pabst
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Martina Loibner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Christine Ulz
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Iris Kufferath
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Ulrike Fackelmann
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cornelia Stumptner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Rainer Kraemer
- Berghof Products & Instruments GmbH, 72800 Eningen, Germany
| | - Tobias Madl
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
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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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Skoworonska M, Blank A, Centeno I, Hammer C, Perren A, Zlobec I, Rau TT. Real-life data from standardized preanalytical coding (SPREC) in tissue biobanking and its dual use for sample characterization and process optimization. J Pathol Clin Res 2022; 9:137-148. [PMID: 36484086 PMCID: PMC9896154 DOI: 10.1002/cjp2.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
The standardized preanalytical code (SPREC) aggregates warm ischemia (WIT), cold ischemia (CIT), and fixation times (FIT) in a precise format. Despite its growing importance underpinned by the European in vitro diagnostics regulation or broad preanalytical programs by the National Institutes of Health, little is known about its empirical occurrence in biobanked surgical specimen. In several steps, the Tissue Bank Bern achieved a fully informative SPREC code with insights from 10,555 CIT, 4,740 WIT, and 3,121 FIT values. During process optimization according to LEAN six sigma principles, we identified a dual role of the SPREC code as a sample characteristic and a traceable process parameter. With this preanalytical study, we outlined real-life data in a variety of organs with specific differences in WIT, CIT, and FIT values. Furthermore, our FIT data indicate the potential to adapt the SPREC fixation toward concrete paraffin-embedding time points and to extend its categories beyond 72 h due to weekend delays. Additionally, we identified dependencies of preanalytical variables from workload, daytime, and clinics that were actionable with LEAN process management. Thus, streamlined biobanking workflows during the day were significantly resilient to workload peaks, diminishing the turnaround times of native tissue processing (i.e. CIT) from 74.6 to 46.1 min under heavily stressed conditions. In conclusion, there are surgery-specific preanalytics that are surgico-pathologically limited even under process optimization, which might affect biomarker transfer from one entity to another. Beyond sample characteristics, SPREC coding is highly beneficial for tissue banks and Institutes of Pathology to track WIT, CIT, and FIT for process optimization and monitoring measurements.
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Affiliation(s)
| | - Annika Blank
- Institute of PathologyUniversity of BernBern,Institute of PathologyTriemli HospitalZurichSwitzerland
| | | | | | | | - Inti Zlobec
- Institute of PathologyUniversity of BernBern
| | - Tilman T Rau
- Institute of PathologyUniversity of BernBern,Institute of PathologyUniversity Hospital and Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
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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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5
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Alternative tissue fixation for combined histopathological and molecular analysis in a clinically representative setting. Histochem Cell Biol 2021; 156:595-607. [PMID: 34905068 PMCID: PMC8695534 DOI: 10.1007/s00418-021-02029-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/26/2022]
Abstract
Formalin is the principal tissue fixative used worldwide for clinical and research purposes. Despite optimal preservation of morphology, its preservation of DNA and RNA is poor. As clinical diagnostics increasingly incorporates molecular-based analysis, the requirement for maintaining nucleic acid quality is of increasing importance. Here we assess an alternative non-formalin-based tissue fixation method, PAXgene Tissue system, with the aim of better preserving nucleic acids, while maintaining the quality of the tissue to be used for vital existing diagnostic techniques. In this study, these criteria are assessed in a clinically representative setting. In total, 203 paired PAXgene Tissue and formalin-fixed samples were obtained. Blind-scored haematoxylin and eosin (H&E) sections showed comparable and acceptable staining. Immunohistochemistry (IHC) staining was suboptimal using existing protocols but improved with minor method adjustment and optimisation. Quality of DNA and RNA was significantly improved by PAXgene tissue fixation [RIN 2.8 versus 3.8 (p < 0.01), DIN 5.68 versus 6.77 (p < 0.001)], which translated into improved performance on qPCR assay. These results demonstrate the potential of PAXgene Tissue to be used routinely in place of formalin, maintaining adequate histological staining and significantly improving the preservation of biological molecules in the genomic era.
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Lahiri P, Mukherjee S, Ghosh B, Das D, Lahiri B, Varshney SK, Pal M, Paul RR, Chatterjee J. Comprehensive Evaluation of PAXgene Fixation on Oral Cancer Tissues Using Routine Histology, Immunohistochemistry, and FTIR Microspectroscopy. Biomolecules 2021; 11:biom11060889. [PMID: 34203873 PMCID: PMC8232633 DOI: 10.3390/biom11060889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022] Open
Abstract
The choice of tissue fixation is critical for preserving the morphology and biochemical information of tissues. Fragile oral tissues with lower tensile strength are challenging to process for histological applications as they are prone to processing damage, such as tissue tear, wrinkling, and tissue fall-off from slides. This leads to loss of morphological information and unnecessary delay in experimentation. In this study, we have characterized the new PAXgene tissue fixation system on oral buccal mucosal tissue of cancerous and normal pathology for routine histological and immunohistochemical applications. We aimed to minimize the processing damage of tissues and improve the quality of histological experiments. We also examined the preservation of biomolecules by PAXgene fixation using FTIR microspectroscopy. Our results demonstrate that the PAXgene-fixed tissues showed significantly less tissue fall-off from slides. Hematoxylin and Eosin staining showed comparable morphology between formalin-fixed and PAXgene-fixed tissues. Good quality and slightly superior immunostaining for cancer-associated proteins p53 and CK5/6 were observed in PAXgene-fixed tissues without antigen retrieval than formalin-fixed tissues. Further, FTIR measurements revealed superior preservation of glycogen, fatty acids, and amide III protein secondary structures in PAXgene-fixed tissues. Overall, we present the first comprehensive evaluation of the PAXgene tissue fixation system in oral tissues. This study concludes that the PAXgene tissue fixation system can be applied to oral tissues to perform diagnostic molecular pathology experiments without compromising the quality of the morphology or biochemistry of biomolecules.
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Affiliation(s)
- Pooja Lahiri
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
- Correspondence:
| | - Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Biswajoy Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Debnath Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Basudev Lahiri
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Shailendra Kumar Varshney
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research (GNIDSR), Kolkata 700114, India;
| | - Ranjan Rashmi Paul
- Department of Oral & Dental Sciences, JIS University, Kolkata 700109, India;
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
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7
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Frasquilho SG, Sanchez I, Yoo C, Antunes L, Bellora C, Mathieson W. Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor? J Histochem Cytochem 2021; 69:389-405. [PMID: 34010071 DOI: 10.1369/00221554211017859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF-ve, RNA from NBF+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF+ve and NBF-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
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Affiliation(s)
| | | | - Changyoung Yoo
- The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
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8
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Allam A, Elsabahy M, El Badry M, Eleraky NE. Betaxolol-loaded niosomes integrated within pH-sensitive in situ forming gel for management of glaucoma. Int J Pharm 2021; 598:120380. [PMID: 33609725 DOI: 10.1016/j.ijpharm.2021.120380] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 01/20/2023]
Abstract
Blindness and impaired vision are considered as the most troublesome health conditions leading to significant socioeconomic strains. The current study focuses on development of nanoparticulate systems (i.e., niosomes) as drug vehicles to enhance the ocular availability of betaxolol hydrochloride for management of glaucoma. Betaxolol-loaded niosomes were further laden into pH-responsive in situ forming gels to further extend precorneal retention of the drug. The niosomes were evaluated in terms of vesicle size, morphology, size distribution, surface charge and encapsulation efficiency. The optimized niosomes, comprised of Span® 40 and cholesterol at a molar ratio of 4:1, displayed particle size of 332 ± 7 nm, zeta potential of -46 ± 1 mV, and encapsulation efficiency of 69 ± 5%. The optimal nanodispersion was then incorporated into a pH-triggered in situ forming gel comprised of Carbopol® 934P and hydroxyethyl cellulose. The formed gels were translucent, pseudoplastic, mucoadhesive, and displayed a sustained in vitro drug release pattern. Upon instillation of the betaxolol-loaded niosomal gel into rabbits' eyes, a prolonged intraocular pressure reduction and significant enhancement in the relative bioavailability of betaxolol (280 and 254.7%) in normal and glaucomatous rabbits, were attained compared to the marketed eye drops, respectively. Hence, the developed pH-triggered nanoparticulate gelling system might provide a promising carrier for ophthalmic drug delivery and for improved augmentation of glaucoma.
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Affiliation(s)
- Ayat Allam
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; Assiut International Center of Nanomedicine, Al-Rajhy Liver Hospital, Assiut University, Assiut 71515, Egypt
| | - Mahmoud Elsabahy
- Science Academy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Misr University for Science and Technology, 6th of October City 12566, Egypt.
| | - Mahmoud El Badry
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; Assiut International Center of Nanomedicine, Al-Rajhy Liver Hospital, Assiut University, Assiut 71515, Egypt
| | - Nermin E Eleraky
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C. Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures. Neurochem Res 2020; 46:447-454. [PMID: 33249516 DOI: 10.1007/s11064-020-03183-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.
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Affiliation(s)
- Pernille Søs Hovgaard Jensen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Maja Johansen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Christina Kjær
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark. .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
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10
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Fattorini P, Forzato C, Tierno D, De Martino E, Azzalini E, Canzonieri V, Stanta G, Bonin S. A Novel HPLC-Based Method to Investigate on RNA after Fixation. Int J Mol Sci 2020; 21:ijms21207540. [PMID: 33066070 PMCID: PMC7588918 DOI: 10.3390/ijms21207540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different fixatives on RNA. By the application of the presented method, which is based on the Nuclease S1 enzymatic digestion of RNA extracts followed by a HPLC analysis, it is possible to quantify the unmodified nucleotide monophosphates (NMPs) in the mixture and recognize their hydroxymethyl derivatives as well as other un-canonical RNA moieties. The results obtained from a set of mouse livers fixed/embedded with different protocols as well from a set of clinical samples aged 0 to 30 years-old show that alcohol-based fixatives do not induce chemical modification of the nucleic acid under ISO standard recommendations and confirm that pre-analytical conditions play a major role in RNA preservation.
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Affiliation(s)
- Paolo Fattorini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Cristina Forzato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Domenico Tierno
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Doctorate of Nanotechnology, University of Trieste, 34100 Trieste, Italy
| | - Eleonora De Martino
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Eros Azzalini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Vincenzo Canzonieri
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Giorgio Stanta
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Serena Bonin
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Correspondence: ; Tel.: +39-040-399-3266
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11
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Comparative Evaluation of RNAlater Solution and Snap Frozen Methods for Gene Expression Studies in Different Tissues. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Introduction: Freezing of tissues with liquid nitrogen is the most common method in studies performed at the RNA level. However, the use of RNA stabilization solutions has become a popular alternative method. The aim of this study is to investigate the effectiveness of RNAlater on RNA stabilization in different tissues.
Material and Methods: In this study, RNA were isolated from the lung, heart, liver and skeletal muscle tissues of rats that were frozen with liquid nitrogen (snap frozen, SF group) or stored in RNAlater solution (RL group), and the changes in concentration, purity, reference genes expression, and fold-change levels between groups were analyzed.
Results: In the RL group, the concentration of RNA isolated from the liver tissues was higher (P<0.05), whereas the A260/280 ratio was lower in the heart and liver tissues (P<0.05). PPIA and SRP72 genes were found to have lower Ct values in the heart tissues of rats in the RL group (P<0.05 and P<0.001, respectively) than the SF group. Expression levels of PPIA, ACTB, and SRP72 genes across the tissues were found to be different between the groups (P<0.05). The gene expression level examined in terms of fold-change was significantly different in the RL group (upregulated up to 4 folds and downregulated about 0.5 fold) (P< 0.05).
Conclusions: The results showed that RNAlater can maintain the RNA integrity and can also change the results of gene expression because it does not inhibit biological activity. The snap freezing method is more reliable because gene expression is more stable in tissues frozen with liquid nitrogen.
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12
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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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13
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Schubert AD, Channah Broner E, Agrawal N, London N, Pearson A, Gupta A, Wali N, Seiwert TY, Wheelan S, Lingen M, Macleod K, Allen H, Chatterjee A, Vassiliki S, Gaykalova D, Hoque MO, Sidransky D, Suresh K, Izumchenko E. Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer Lett 2020; 471:49-60. [PMID: 31830557 PMCID: PMC6980748 DOI: 10.1016/j.canlet.2019.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) have been linked to risk, progression, and treatment response of head and neck squamous cell carcinoma (HNSCC). Due to their clonal nature and high copy number, mitochondrial mutations could serve as powerful molecular markers for detection of cancer cells in bodily fluids, surgical margins, biopsies and lymph node (LN) metastasis, especially at sites where tumor involvement is not histologically apparent. Despite a pressing need for high-throughput, cost-effective mtDNA mutation profiling system, current methods for library preparation are still imperfect for detection of low prevalence heteroplasmic mutations. To this end, we have designed an ultra-deep amplicon-based sequencing library preparation approach that covers the entire mitochondrial genome. We sequenced mtDNA in 28 HNSCCs, matched LNs, surgical margins and bodily fluids, and applied multiregional sequencing approach on 14 primary tumors. Our results demonstrate that this quick, sensitive and cost-efficient method allows obtaining a snapshot on the mitochondrial heterogeneity, and can be used for detection of low frequency tumor-associated mtDNA mutations in LNs, sputum and serum specimens. These findings provide the foundation for using mitochondrial sequencing for risk assessment, early detection, and tumor surveillance.
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Affiliation(s)
- Adrian D Schubert
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Esther Channah Broner
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Nishant Agrawal
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Nyall London
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Alexander Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Neha Wali
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Tanguy Y Seiwert
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Sarah Wheelan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mark Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Kay Macleod
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Hailey Allen
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Saloura Vassiliki
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Daria Gaykalova
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mohammad O Hoque
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Karthik Suresh
- Division of Pulmonary Critical Care Medicine, Johns Hopkins University School of Medicine. Baltimore, MD, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.
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14
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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15
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Esteva-Socias M, Artiga MJ, Bahamonde O, Belar O, Bermudo R, Castro E, Escámez T, Fraga M, Jauregui-Mosquera L, Novoa I, Peiró-Chova L, Rejón JD, Ruiz-Miró M, Vieiro-Balo P, Villar-Campo V, Zazo S, Rábano A, Villena C. In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network. J Transl Med 2019; 17:370. [PMID: 31718661 PMCID: PMC6852937 DOI: 10.1186/s12967-019-2124-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 01/10/2023] Open
Abstract
The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
| | | | | | - Oihana Belar
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Raquel Bermudo
- Hospital Clínic-IDIBAPS Biobank, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Erika Castro
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Teresa Escámez
- IMIB Biobank, Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Máximo Fraga
- Depto. de Ciencias Forenses, Anatomía Patolóxica, Xinecología e Obstetricia, e Pediatría, Facultade de Medicina, Universidade de Santiago de Compostela (USC), Santiago, Spain.,Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Isabel Novoa
- Vall d'Hebron University Hospital Biobank, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | | | - Juan-David Rejón
- Biobanco del Sistema Sanitario Público de Andalucía, Granada, Spain
| | - María Ruiz-Miró
- IRBLleida Biobank, Instituto de Investigaciones Biomédica de Lleida-Fundación Dr. Pifarre, Lérida, Spain
| | - Paula Vieiro-Balo
- Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Sandra Zazo
- Department of Pathology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Rábano
- Banco de Tejidos, Fundación CIEN, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain. .,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
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16
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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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17
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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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18
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Eid HM, Elkomy MH, El Menshawe SF, Salem HF. Development, Optimization, and In Vitro/In Vivo Characterization of Enhanced Lipid Nanoparticles for Ocular Delivery of Ofloxacin: the Influence of Pegylation and Chitosan Coating. AAPS PharmSciTech 2019; 20:183. [PMID: 31054011 DOI: 10.1208/s12249-019-1371-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/20/2019] [Indexed: 01/08/2023] Open
Abstract
This study aims to investigate whether modification of solid lipid nanoparticles (SLNs) with chitosan (CTS) and polyethylene glycol (PEG) coatings enhances corneal retention time and transcorneal bioavailability. Ofloxacin (OFLOX) was selected as the model drug because of its potential benefits for the treatment of local eye infections. The OFLOX-CTS-PEG-SLN was prepared by a modified emulsion/solvent evaporation technique. A central composite design was implemented to investigate the influence of total lipid/drug ratio, surfactant concentration, PEG stearate concentration in the lipid mixture, and CTS concentration on size, entrapment, transcorneal permeation, and adhesion to the corneal mucosal membrane. The optimized OFLOX-CTS-PEG-SLN was characterized for OFLOX cumulative percentage released in simulated tear fluid and permeated across the excised bovine corneal membrane. Moreover, nanoparticle morphology, eye irritation via histopathological analysis, and OFLOX concentration in the ocular fluids and tissues were determined. A total lipid/drug ratio of 19:1, Tween 80 of 2%, PEG stearate concentration in the lipid mixture (% w/w) of 2.6%, and CTS concentration (% w/v) of 0.23% produced 132.9 nm particles entrapping 74.8% of the total drug added. The particles detached from the corneal membrane at a force of 3700 dyne/cm2. The %OFLOX released from the optimized nanoparticles was 63.3, and 66% of the drug permeated after 24 h. Compared to Oflox® drops, the optimized OFLOX-CTS-PEG-SLN exhibited similar tolerability but two- to threefold higher concentrations in the eyes of rabbits. Coating of SLN with chitosan and PEG augments the ocular bioavailability of OFLOX by increasing transcorneal permeation and enhancing mucoadhesion strength.
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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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20
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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.
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Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
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21
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Lee JH, Song RY, Yi JW, Yu HW, Kwon H, Kim SJ, Chai YJ, Choi JY, Moon JH, Lee KE, Park YJ, Park SK. Case-Control Study of Papillary Thyroid Carcinoma on Urinary and Dietary Iodine Status in South Korea. World J Surg 2018; 42:1424-1431. [PMID: 29067516 DOI: 10.1007/s00268-017-4287-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The association between iodine levels and the risk of papillary thyroid cancer (PTC) has been suggested, but not definitively established. This study is to compare the iodine status of a group of patients with PTC (with and without BRAF V600E) with that of a healthy population cohort. METHODS A cohort of patients scheduled for thyroidectomy was enrolled, along with a community-based health-screening cohort with no known history of thyroid disease. Median urinary iodine (UI) levels, creatinine-adjusted median UI levels, and food frequency questionnaire (FFQ) scores (mean ± SD) were compared. In a subgroup analysis, these values were compared between BRAF V600E-positive and BRAF V600E-negative patients in the PTC group. RESULTS The PTC group consisted of 210 patients, and the control group consisted of 90 healthy individuals. Among the 191 PTC patients whose BRAF V600E mutational status was reported, 169 (88.5%) were revealed positive for the mutation. The median UI levels were significantly higher in the PTC group (786.0 μg/l) than the control group (112.0 μg/l; p < 0.001), as was the case with creatinine-adjusted median UI levels (884.6 μg/g creatinine versus 182.0 μg/g creatinine; p < 0.001) and FFQ scores (66.2 ± 17.5, range 13-114 versus 54.6 ± 21.5, range 16-134; p < 0.001). No significant differences were seen in the subgroup analysis between BRAF V600E-positive and BRAF V600E-negative patients. CONCLUSIONS Our results indicate that iodine status differs significantly between patients with PTC and healthy controls, suggesting that iodine may be involved in the occurrence of PTC, although the association between iodine levels and BRAF mutational status did not reach statistical significance.
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Affiliation(s)
- Joon-Hyop Lee
- Department of Surgery, Seoul National University Bundang Hospital, 300 Gumi-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea.,Thyroid and Endocrine Surgery Section, Department of Surgery, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Ra-Yeong Song
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Jin Wook Yi
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Hyeong Won Yu
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Hyungju Kwon
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Su-Jin Kim
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Jun Chai
- Department of Surgery, Seoul National University Hospital Boramae Medical Center, Seoul, Republic of Korea
| | - June Young Choi
- Department of Surgery, Seoul National University Bundang Hospital, 300 Gumi-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jae Hoon Moon
- Department of Internal Medicine, Seoul National University Bundang Hospital, 300 Gumi-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kyu Eun Lee
- Department of Surgery, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Young Joo Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University Hospital and College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Sue K Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
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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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Molecular Pathology and Pre-Analytic Variables: Impact on Clinical Practice From a Breast Pathology Perspective. CURRENT PATHOBIOLOGY REPORTS 2018. [DOI: 10.1007/s40139-018-0169-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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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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Application of ribonucleoside vanadyl complex (RVC) for developing a multifunctional tissue preservative solution. PLoS One 2018. [PMID: 29538436 PMCID: PMC5851642 DOI: 10.1371/journal.pone.0194393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The quality of biological samples greatly affects the accuracy of scientific results. However, RNA in cryopreserved tissues gradually degrades during storage, leading to errors in the results of subsequent experiments. A suitable sample preservative solution can prolong storage and enhance the research value of samples. Here, we developed a sample preservative solution using the properties of the ribonucleoside vanadyl complex (RVC) and compared its effects on RNA and DNA quality, protein activity, and tissue morphology with the commercially available and widely used RNAlater® Stabilization Solution. The results showed that both the RVC-based preservative solution and RNAlater can effectively delay RNA degradation in tissue samples stored at 4°C or −80°C compared with samples stored without any preservative solution. In contrast to RNAlater, the RVC-based preservative solution did not result in damage to the tissue morphology or a loss of protein activity. Additionally, the RVC-based preservative solution did not affect the RNA and genomic DNA contents of the tissue samples or the results of subsequent experimental analyses. An RVC-based reagent can be used as a multifunctional yet relatively inexpensive tissue preservative solution to provide a comprehensive and cost-effective method for preserving samples for tissue banks.
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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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27
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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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Variability in, variability out: best practice recommendations to standardize pre-analytical variables in the detection of circulating and tissue microRNAs. ACTA ACUST UNITED AC 2017; 55:608-621. [DOI: 10.1515/cclm-2016-0471] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023]
Abstract
Abstract:microRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions. For circulating miRNAs, hemolysis and blood cell contamination significantly affect profiles; samples should be processed within 2 h of collection; ethylene diamine tetraacetic acid (EDTA) is preferred while heparin should be avoided; samples should be “double spun” or filtered; room temperature or 4 °C storage for up to 24 h is preferred; miRNAs are stable for at least 1 year at –20 °C or –80 °C. For tissue-based analysis, warm ischemic time should be <1 h; cold ischemic time (4 °C) <24 h; common fixative used for all specimens; formalin fix up to 72 h prior to processing; enrich for cells of interest; validate candidate biomarkers with in situ visualization. Most importantly, all specimen types should have standard and common workflows with careful documentation of relevant pre-analytical variables.
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KINFix--A formalin-free non-commercial fixative optimized for histological, immunohistochemical and molecular analyses of neurosurgical tissue specimens. Clin Neuropathol 2016; 35:3-12. [PMID: 26521938 PMCID: PMC4766796 DOI: 10.5414/np300907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 12/04/2022] Open
Abstract
An optimal fixative should ideally combine the advantages of formalin fixation and freezing, allowing for good preservation of histology and molecular components, easy handling and storage, lack of toxicity, and low costs. Most of these criteria are fulfilled by ethanol-based solutions, and due to our good experience with the commercial RCL2 fixative, reflected by our published single-center trial, we initiated a multicenter ring trial. However, during its course, RCL2 was discontinued on the market. Therefore, we created our own agent, KINFix, composed of the same main constituents as RCL2, and employed it in our laboratory with similar results. Here we present our evaluation of the three fixatives formalin, RCL2, and KINFix from the perspective of histopathology as well as nucleic acid and protein analyses in comparison to fresh frozen tissues together with the multicenter ring trial data for RCL2. We observe that RCL2 and KINFix offer comparable histomorphology and superior template for molecular analyses than formalin. Moreover, KINFix as freely available fixative might overcome some of the difficulties related to the commercial agents. Therefore, we conclude that KINFix might be an attractive complement to formalin in tissue processing and advocate its use in neuropathological practice.
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30
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Hu Y, Ma Y, Wu S, Chen T, He Y, Sun J, Jiao R, Jiang X, Huang Y, Deng L, Bai W. Protective Effect of Cyanidin-3-O-Glucoside against Ultraviolet B Radiation-Induced Cell Damage in Human HaCaT Keratinocytes. Front Pharmacol 2016; 7:301. [PMID: 27656146 PMCID: PMC5013811 DOI: 10.3389/fphar.2016.00301] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/25/2016] [Indexed: 11/13/2022] Open
Abstract
Ultraviolet radiation is the major environmental harmful factor that has emotional impact on human skin. The aim of the present study was to determine the mechanism of protection of cyanidin-3-O-glucoside against ultraviolet B (UVB)-induced damage to human HaCaT keratinocytes. Our results show that cyanidin-3-O-glucoside decreased the levels of intracellular reactive oxygen species generated by UVB treatment. Cyanidin-3-O-glucoside also decreased the UVB-augmented levels of the DNA damage indicators phospho-p53 and phospho-ATM/ATR. In addition, cyanidin-3-O-glucoside protected keratinocytes from UVB-induced injury by overturning the disruption of mitochondrial membrane potential and reversing apoptosis. The expression of anti-apoptotic protein B-cell lymphoma 2 (Bcl-2) was attenuated in UVB-exposed cells but restored in UVB/cyanidin-3-O-glucoside-treated cells. Furthermore, expression of the proapoptotic proteins Bcl-2-associated X (Bax) and the key apoptosis executer cleaved caspase-3 were increased in UVB-irradiated cells and decreased in UVB/cyanidin-3-O-glucoside-treated cells. For these reasons, the results demonstrate that cyanidin-3-O-glucoside protects human keratinocytes against UVB-induced oxidative stress and apoptosis. Our study provides a theoretical basis for the use of cyanidin-3-O-glucoside in the fight against light damage.
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Affiliation(s)
- Yunfeng Hu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University Guangzhou, China
| | - Yuetang Ma
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University Guangzhou, China
| | - Shi Wu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University Guangzhou, China
| | - Tianfeng Chen
- Department of Food Science and Engineering, Jinan University Guangzhou, China
| | - Yong He
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University Guangzhou, China
| | - Jianxia Sun
- Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology Guangzhou, China
| | - Rui Jiao
- Department of Food Science and Engineering, Jinan University Guangzhou, China
| | - Xinwei Jiang
- Department of Food Science and Engineering, Jinan University Guangzhou, China
| | - Yadong Huang
- Department of Food Science and Engineering, Jinan University Guangzhou, China
| | - Liehua Deng
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University Guangzhou, China
| | - Weibin Bai
- Department of Food Science and Engineering, Jinan University Guangzhou, China
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Abdelbary A, Salem HF, Khallaf RA, Ali AMA. Mucoadhesive niosomal in situ gel for ocular tissue targeting: in vitro and in vivo evaluation of lomefloxacin hydrochloride. Pharm Dev Technol 2016; 22:409-417. [DOI: 10.1080/10837450.2016.1219916] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ahmed Abdelbary
- Department of Pharmaceutics, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Heba F. Salem
- Department of Pharmaceutics, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Rasha A. Khallaf
- Department of Pharmaceutics, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Ahmed M. A. Ali
- Department of Pharmaceutics, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
- Department of Pharmaceutics, Faculty of Pharmacy, Taif University, Taif, KSA
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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]
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Korenkova V, Slyskova J, Novosadova V, Pizzamiglio S, Langerova L, Bjorkman J, Vycital O, Liska V, Levy M, Veskrna K, Vodicka P, Vodickova L, Kubista M, Verderio P. The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data. Sci Rep 2016; 6:29023. [PMID: 27383461 PMCID: PMC4935944 DOI: 10.1038/srep29023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/14/2016] [Indexed: 01/12/2023] Open
Abstract
Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.
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Affiliation(s)
- Vlasta Korenkova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Jana Slyskova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucie Langerova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | | | - Ondrej Vycital
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Vaclav Liska
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Levy
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Karel Veskrna
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Mikael Kubista
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic.,TATAA Biocenter AB, Göteborg, Sweden
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
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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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Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system. Mod Pathol 2016; 29:708-16. [PMID: 27102344 DOI: 10.1038/modpathol.2016.81] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 11/08/2022]
Abstract
Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgene-fixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.
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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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Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis. Biopreserv Biobank 2016; 14:264-70. [PMID: 27158753 PMCID: PMC4991598 DOI: 10.1089/bio.2015.0064] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples.
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Affiliation(s)
- Gema Lucena-Aguilar
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - Ana María Sánchez-López
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | | | - José Antonio Carrillo-Ávila
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - José Antonio López-Guerrero
- 3 Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología , Valencia, Spain .,4 Biobank, Fundación Instituto Valenciano de Oncología , Valencia, Spain
| | - Rocío Aguilar-Quesada
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
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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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Karlsson O, Segerström L, Sjöback R, Nylander I, Borén M. qPCR based mRNA quality score show intact mRNA after heat stabilization. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:21-6. [PMID: 27077049 PMCID: PMC4827693 DOI: 10.1016/j.bdq.2016.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/21/2016] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
Abstract
Analysis of multiple analytes from biological samples can be challenging as different analytes require different preservation measures. Heat induced enzymatic inactivation is an efficient way to preserve proteins and their modifications in biological samples but RNA quality, as measured by RIN value, has been a concern in such samples. Here, we investigate the effect of heat stabilization compared with standard snap freezing on RNA quality using two RNA extraction protocols, QiaZol with and without urea pre-solubilization, and two RNA quality measurements: RIN value, as defined by the Agilent Bioanalyzer, and an alternative qPCR based method. DNA extraction from heat stabilized brain samples was also examined. The snap frozen samples had RIN values about 1 unit higher than heat stabilized samples for the direct QiaZol extraction but equal with stabilized samples using urea pre-solubilization. qPCR based RNA quality measurement showed no difference in quality between snap frozen and heat inactivated samples. The probable explanation for this discrepancy is that the RIN value is an indirect measure based on rRNA, while the qPCR score is based on actual measurement of mRNA quality. The DNA yield from heat stabilized brain tissue samples was significantly increased, compared to the snap frozen tissue, without any effects on purity or quality. Hence, heat stabilization of tissues opens up the possibility for a two step preservation protocol, where proteins and their modifications can be preserved in the first heat based step, while in a second step, using standard RNA preservation strategies, mRNA be preserved. This collection strategy will enable biobanking of samples where the ultimate analysis is not determined without loss of sample quality.
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Affiliation(s)
- Oskar Karlsson
- Department of Clinical Neuroscience, Karolinska Institutet, The Center for Molecular Medicine, Stockholm, Sweden
| | - Lova Segerström
- Department of Pharmaceutical Biosciences/Pharmacology/Neuropharmacology, Addiction & Behavior, Uppsala University, Uppsala, Sweden
| | | | - Ingrid Nylander
- Department of Pharmaceutical Biosciences/Pharmacology/Neuropharmacology, Addiction & Behavior, Uppsala University, Uppsala, Sweden
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Lung J, Lin YC, Hung MS, Jiang YY, Lee KD, Lin PY, Tsai YH. A sensitive and high throughput TaqMan-based reverse transcription quantitative polymerase chain reaction assay efficiently discriminates ALK rearrangement from overexpression for lung cancer FFPE specimens. Lung Cancer 2016; 94:114-20. [PMID: 26973216 DOI: 10.1016/j.lungcan.2016.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/03/2016] [Accepted: 02/06/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVES ALK fusion gene is an oncogenic driver in lung cancer with low prevalence, which can be ameliorated by crizotinib. Currently, ALK fusion gene can be diagnosed by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), but inconstistnt results between the two methods are encountered regularly. To make the ALK fusion gene screening more efficient and to provide a simple solution to clarify the discrepancy between FISH and IHC results, a sensitive TaqMan-based reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay was established. MATERIALS AND METHODS The 3-plex TaqMan-based RT-qPCR assay was established and performed on 102 archived formalin-fixed, paraffin-embedded (FFPE) NSCLC samples to detect ALK rearrangement and overexpression. Break-apart FISH and automatic immunohistochemistry based ALK assays were performed side by side using tissue microarray. RESULTS The RT-qPCR was performed successfully for 80 samples and 10 of them showed positive signals. Three out of the 10 qPCR positive cases were further confirmed by FISH and IHC test. Two others were IHC positive and FISH negative, and expressed full-length ALK transcript. The rest were neither FISH nor IHC positive and their ALK expression level was significantly lower than those FISH or IHC positive cases. CONCLUSION Our RT-qPCR assay demonstrates that the capability and reliability of ALK detection is comparable to FISH and IHC, but it is more effective at discriminating ALK rearrangement from overexpression. The RT-qPCR assay easily clarifies the discrepancy between FISH and IHC, and can be incorporated into routine ALK screening for lung cancer.
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Affiliation(s)
- Jrhau Lung
- Department of Medical Research and Development, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Yu-Ching Lin
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi, Taiwan
| | - Ming-Szu Hung
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi, Taiwan
| | - Yuan Yuan Jiang
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Kuan-Der Lee
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Paul Yann Lin
- Department of Pathology, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Ying Huang Tsai
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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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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Hara K, Watanabe A, Matsumoto S, Matsuda Y, Kuwata T, Kan H, Yamada T, Koizumi M, Shinji S, Yamagishi A, Ishiwata T, Naito Z, Shimada T, Uchida E. Surgical Specimens of Colorectal Cancer Fixed with PAXgene Tissue System Preserve High-Quality RNA. Biopreserv Biobank 2015; 13:325-34. [DOI: 10.1089/bio.2014.0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Keisuke Hara
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Atsushi Watanabe
- Department of Biochemistry and Molecular Biology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Satoshi Matsumoto
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Yoko Matsuda
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | | | - Hayato Kan
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Michihiro Koizumi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Seiichi Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Aya Yamagishi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Toshiyuki Ishiwata
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Zenya Naito
- Department of Pathology and Integrative Oncological Pathology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Takashi Shimada
- Department of Biochemistry and Molecular Biology, Nippon Medical School Graduate School, Tokyo, Japan
| | - Eiji Uchida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
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Björkman J, Švec D, Lott E, Kubista M, Sjöback R. Differential amplicons (ΔAmp)-a new molecular method to assess RNA integrity. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 6:4-12. [PMID: 27077042 PMCID: PMC4822209 DOI: 10.1016/j.bdq.2015.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/26/2015] [Accepted: 09/08/2015] [Indexed: 11/25/2022]
Abstract
Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS), Quantitative real-time PCR (qPCR) or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples before conducting large and costly studies. Most methods today to assess the quality of RNA are ignorant to the nature of the RNA and, therefore, reflect the integrity of ribosomal RNA, which is the dominant species, rather than of mRNAs, microRNAs and long non-coding RNAs, which usually are the species of interest. Here, we present a novel molecular approach to assess the quality of the targeted RNA species by measuring the differential amplification (ΔAmp) of an Endogenous RNase Resistant (ERR) marker relative to a reference gene, optionally combined with the measurement of two amplicons of different lengths. The combination reveals any mRNA degradation caused by ribonucleases as well as physical, chemical or UV damage. ΔAmp has superior sensitivity to common microfluidic electrophoretic methods, senses the integrity of the actual targeted RNA species, and allows for a smoother and more cost efficient workflow.
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Affiliation(s)
| | - D Švec
- TATAA Biocenter AB, Gothenburg, Sweden; Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - E Lott
- TATAA Biocenter AB, Gothenburg, Sweden
| | - M Kubista
- TATAA Biocenter AB, Gothenburg, Sweden; Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - R Sjöback
- TATAA Biocenter AB, Gothenburg, Sweden
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44
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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]
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Abuja PM, Ehrhart F, Schoen U, Schmidt T, Stracke F, Dallmann G, Friedrich T, Zimmermann H, Zatloukal K. Alterations in Human Liver Metabolome during Prolonged Cryostorage. J Proteome Res 2015; 14:2758-68. [DOI: 10.1021/acs.jproteome.5b00025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter M. Abuja
- Institute
of Pathology, Medical University of Graz, Austria Auenbruggerplatz 25, A-8036 Graz, Austria
| | - Friederike Ehrhart
- Fraunhofer Institute of Biomedical Technology, Ensheimer Str. 48, 66386 St. Ingbert, Germany
| | - Uwe Schoen
- Fraunhofer Institute of Biomedical Technology, Ensheimer Str. 48, 66386 St. Ingbert, Germany
| | - Tomm Schmidt
- Fraunhofer Institute of Biomedical Technology, Ensheimer Str. 48, 66386 St. Ingbert, Germany
| | - Frank Stracke
- Fraunhofer Institute of Biomedical Technology, Ensheimer Str. 48, 66386 St. Ingbert, Germany
| | - Guido Dallmann
- BIOCRATES LifeSciences AG, Eduard-Bodem-Gasse
8, 6020 Innsbruck, Austria
| | - Torben Friedrich
- BIOCRATES LifeSciences AG, Eduard-Bodem-Gasse
8, 6020 Innsbruck, Austria
| | - Heiko Zimmermann
- Fraunhofer Institute of Biomedical Technology, Ensheimer Str. 48, 66386 St. Ingbert, Germany
| | - Kurt Zatloukal
- Institute
of Pathology, Medical University of Graz, Austria Auenbruggerplatz 25, A-8036 Graz, Austria
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Modeling, Optimization, and In Vitro Corneal Permeation of Chitosan-Lomefloxacin HCl Nanosuspension Intended for Ophthalmic Delivery. J Pharm Innov 2015. [DOI: 10.1007/s12247-015-9224-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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Kap M, Arron GI, Loibner M, Hausleitner A, Siaulyte G, Zatloukal K, Murk JL, Riegman P. Inactivation of Influenza A virus, Adenovirus, and Cytomegalovirus with PAXgene tissue fixative and formalin. Biopreserv Biobank 2015; 11:229-34. [PMID: 24845590 DOI: 10.1089/bio.2013.0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Formalin fixation is known to inactivate most viruses in a vaccine production context, but nothing is published about virus activity in tissues treated with alternative, non-crosslinking fixatives. We used a model assay based on cell culture to test formalin and PAXgene Tissue fixative for their virus-inactivating abilities. MDCK, A549, and MRC-5 cells were infected with Influenza A virus, Adenovirus, and Cytomegalovirus, respectively. When 75% of the cells showed a cytopathic effect (CPE), the cells were harvested and incubated for 15 min, or 1, 3, 6, or 24 hours, with PBS (positive control), 4% formalin, or PAXgene Tissue Fix. The cells were disrupted and the released virus was used to infect fresh MDCK, A549, and MRC-5 cells cultured on cover slips in 24-well plates. The viral cultures were monitored for CPE and by immunocytochemistry (ICC) to record viral replication and infectivity. Inactivation of Adenovirus by formalin occurred after 3 h, while Influenza A virus as well as Cytomegalovirus were inactivated by formalin after 15 min. All three virus strains were inactivated by PAXgene Tissue fixative after 15 min. We conclude that PAXgene Tissue fixative is at least as effective as formalin in inactivating infectivity of Influenza A virus, Adenovirus, and Cytomegalovirus.
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Affiliation(s)
- Marcel Kap
- 1 Department of Pathology, Josephine Nefkens Institute , Erasmus MC, Rotterdam, Netherlands
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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]
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van der Linden A, Blokker BM, Kap M, Weustink AC, Riegman PHJ, Oosterhuis JW. Post-mortem tissue biopsies obtained at minimally invasive autopsy: an RNA-quality analysis. PLoS One 2014; 9:e115675. [PMID: 25531551 PMCID: PMC4274113 DOI: 10.1371/journal.pone.0115675] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/26/2014] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Bereaved relatives often refuse to give consent for post-mortem investigation of deceased cancer patients, mainly because of the mutilation due to conventional autopsy (CA). Minimally invasive autopsy (MIA) may be a more acceptable alternative and, if implemented in clinical practice, creates an opportunity to more often obtain post-mortem tissue samples of (recurred) primary tumors and metastases for molecular research. As a measure for tissue quality for molecular studies, we hereby present a feasibility study, comparing the RNA quality of MIA and CA samples, and fresh frozen samples as reference. MATERIALS AND METHODS Tissue samples of heart, liver and kidney were prospectively collected from 24 MIAs followed by CA, and compared to corresponding archival fresh frozen tissue. After RNA isolation and RT-qPCR, RNA integrity numbers (RIN) and GAPDH expression (six amplicon sizes ranging from 71 to 530 base pairs) were measured. RIN values and GAPDH Cq values were analyzed and compared between all sample groups and post-mortem intervals (PMI). RESULTS RIN values in MIA samples were significantly higher than those in CA samples. GAPDH was expressed significantly higher in MIA samples than in CA samples and 530 bp PCR products could be measured in all cases. GAPDH expression was significantly lower in samples with PMI >15 hours. As expected, the samples of the fresh frozen reference standard performed best in all analyses. CONCLUSION MIA samples showed better RNA quality than CA samples, probably due to shorter PMI. Both had lower RNA quality and expression levels than fresh frozen tissue, however, remaining GAPDH RNA was still sufficiently intact. Therefore, other highly expressed genes are most likely also detectable. Gene array analysis should be performed to gain insight into the quality of entire post-mortem genomes. Reducing PMI will further improve the feasibility of demanding molecular research on post-mortem tissues, this is most likely more feasible with MIA than CA.
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Affiliation(s)
| | | | - Marcel Kap
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
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