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Chung JY, Kim K, Ylaya K, Walker-Bawa KE, Perry C, Star RA, Hewitt SM. The Application of Guanidinium to Improve Biomolecule Quality in Fixed, Paraffin-embedded Tissue. J Histochem Cytochem 2023; 71:87-101. [PMID: 36869703 PMCID: PMC10088100 DOI: 10.1369/00221554231159451] [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: 10/04/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
Neutral buffered formalin (NBF) is the most common fixative in clinical applications. However, NBF damages proteins and nucleic acids, limiting the quality of proteomic and nucleic acid-based assays. Prior studies have demonstrated that BE70, a fixative of buffered 70% ethanol, has many benefits over NBF but the degradation of proteins and nucleic acids in archival paraffin blocks remain a challenge. Thus, we evaluated the addition of guanidinium salts to BE70 with the hypothesis that this may protect RNA and protein. Guanidinium salt supplemented BE70 (BE70G)-fixed tissue is comparable with that of BE70 via histology and immunohistochemistry. Western blot analysis also revealed that HSP70, AKT, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) expression signals in BE70G-fixed tissue were higher than those in BE70-fixed tissue. The quality of nucleic acids extracted from BE70G-fixed, paraffin-embedded tissue was also superior, and BE70G provides improved protein and RNA quality at shorter fixation times than its predecessors. The degradation of proteins, AKT and GAPDH, in archival tissue blocks is also decreased with the addition of guanidinium salt to BE70. In conclusion, BE70G fixative improves the quality of molecular analysis with more rapid fixation of tissue and enhanced long-term storage of paraffin blocks at room temperature for evaluation of protein epitopes.
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Affiliation(s)
- Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Kyungeun Kim
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
- Department of Pathology, School of Medicine,
Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, Republic of
Korea
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Katharine E. Walker-Bawa
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Candice Perry
- Antibody Characterization Laboratory, Advanced
Technology Program, Leidos Biomedical Research, Inc., Frederick,
Maryland
| | - Robert A. Star
- Renal Diagnostics and Therapeutics Unit,
National Institutes of Diabetes and Digestive and Kidney Disease, National
Institutes of Health, Bethesda, Maryland
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
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2
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Fusion transcript discovery using RNA sequencing in formalin-fixed paraffin-embedded specimen. Crit Rev Oncol Hematol 2021; 160:103303. [DOI: 10.1016/j.critrevonc.2021.103303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
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3
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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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Wehmas LC, Wood CE, Chorley BN, Yauk CL, Nelson GM, Hester SD. Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples. Toxicol Sci 2020; 170:357-373. [PMID: 31093665 DOI: 10.1093/toxsci/kfz113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues provide an important resource for toxicogenomic research. However, variability in the integrity or quality of RNA obtained from archival FFPE specimens can lead to unreliable data and wasted resources, and standard protocols for measuring RNA integrity do not adequately assess the suitability of FFPE RNA. The main goal of this study was to identify improved methods for evaluating FFPE RNA quality for whole-genome sequencing. We examined RNA quality metrics conducted prior to RNA-sequencing in paired frozen and FFPE samples with varying levels of quality based on age in block and time in formalin. RNA quality was measured by the RNA integrity number (RIN), a modified RIN called the paraffin-embedded RNA metric, the percentage of RNA fragments >100-300 nucleotides in size (DV100-300), and 2 quantitative PCR-based methods. This information was correlated to sequencing read quality, mapping, and gene detection. Among fragmentation-based methods, DV and PCR-based metrics were more informative than RIN or paraffin-embedded RNA metric in determining sequencing success. Across low- and high-quality FFPE samples, a minimum of 80% of RNA fragments >100 nucleotides (DV100 > 80) provided the best indication of gene diversity and read counts upon sequencing. The PCR-based methods further showed quantitative reductions in amplifiable RNA of target genes related to sample age and time in formalin that inform input quantity of FFPE RNA for sequencing. These results should aid in screening and prioritizing archival FFPE samples for retrospective analyses of gene expression.
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Affiliation(s)
- Leah C Wehmas
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Charles E Wood
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709.,Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT 06877
| | - Brian N Chorley
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | - Gail M Nelson
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Susan D Hester
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
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5
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DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9349132. [PMID: 32185225 PMCID: PMC7063185 DOI: 10.1155/2020/9349132] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 12/29/2019] [Accepted: 02/06/2020] [Indexed: 11/28/2022]
Abstract
Poor quality of biological samples will result in an inaccurate analysis of next-generation sequencing (NGS). Therefore, methods to accurately evaluate sample integrity are needed. Among methods for evaluating RNA quality, the RNA integrity number equivalent (RINe) is widely used, whereas the DV200, which evaluates the percentage of fragments of >200 nucleotides, is also used as a quality assessment standard. In this study, we compared the RINe and DV200 RNA quality indexes to determine the most suitable RNA index for the NGS analysis. Seventy-one RNA samples were extracted from formalin-fixed paraffin-embedded tissue samples (n = 30), fresh-frozen samples (n = 25), or cell lines (n = 16). After assessing RNA quality using the RINe and DV200, we prepared two kinds of stranded mRNA sequencing libraries. Finally, we calculated the correlation between each RNA quality index and the amount of library product (1st PCR product per input RNA). The DV200 measure showed stronger correlation with the amount of library product than the RINe (R2 = 0.8208 for the DV200 versus 0.6927 for the RINe). Receiver operating characteristic curve analyses revealed that the DV200 was the better marker for predicting efficient library production than the RINe using a threshold of >10 ng/ng for the amount of the 1st PCR product per input RNA (cutoff value for the RINe and DV200, 2.3 and 66.1%; area under the curve, 0.99 and 0.91; sensitivity, 82% and 92%; and specificity, 93% and 100%, respectively). Our results indicate that NGS libraries prepared using RNA samples with the DV200 value > 66.1% exhibit greater sensitivity and specificity than those prepared with the RINe values > 2.3. These findings suggest that the DV200 is superior to the RINe, especially for low-quality RNA, because it is a more consistent assessment of the amount of the 1st NGS library product per input.
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6
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Trejo CL, Babić M, Imler E, Gonzalez M, Bibikov SI, Shepard PJ, VanSteenhouse HC, Yeakley JM, Seligmann BE. Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue. PLoS One 2019; 14:e0212031. [PMID: 30794557 PMCID: PMC6386473 DOI: 10.1371/journal.pone.0212031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. Fixed and fresh samples prepared in an equivalent manner produced comparable sequencing depth results (+/- 20%), with similar %CV (11.5 and 12.7%, respectively), indicating no significant loss of measurable RNA due to fixation. The sensitivity of the TempO-Seq assay was the same whether the tissue section was fixed or not. The assay performance was equivalent for human, mouse, or rat whole transcriptome. The results from 10 mm2 and 2 mm2 areas of tissue obtained from 5 μm thick sections were equivalent, thus demonstrating high sensitivity and ability to profile focal areas of histology within a section. Replicate reproducibility of separate areas of tissue ranged from R2 = 0.83 (lung) to 0.96 (liver) depending on the tissue type, with an average correlation of R2 = 0.90 across nine tissue types. The average %CVs were 16.8% for genes expressed at greater than 200 counts, and 20.3% for genes greater than 50 counts. Tissue specific differences in gene expression were identified and agreed with the literature. There was negligible impact on assay performance using FFPE tissues that had been archived for up to 30 years. Similarly, there was negligible impact of H&E staining, facilitating accurate visualization for scraping and assay of small focal areas of specific histology within a section.
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Affiliation(s)
- Christy L. Trejo
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Miloš Babić
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Elliot Imler
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Migdalia Gonzalez
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Sergei I. Bibikov
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Peter J. Shepard
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | | | - Joanne M. Yeakley
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Bruce E. Seligmann
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
- * E-mail:
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7
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Dini P, Esteller-Vico A, Scoggin KE, Daels P, Ball BA. Extraction of RNA from formalin-fixed, paraffin-embedded equine placenta. Reprod Domest Anim 2019; 54:627-634. [PMID: 30659674 DOI: 10.1111/rda.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/12/2019] [Indexed: 12/29/2022]
Abstract
Archived formalin-fixed, paraffin-embedded (FFPE) samples represent a valuable resource for the determination of gene expression for physio/pathological conditions. In the present study, we validated a protocol for the extraction of RNA from FFPE samples collected from healthy and diseased equine placenta. The quality and quantity of the extracted RNA from the FFPE and matching RNAlater™-preserved samples and expression levels of common housekeeping genes and reference microRNAs were evaluated. Precision of the expression data was evaluated by comparing relative expression of CYP19A1 and HSD3B1 in FFPE and RNAlater™ samples. The median RNA concentration recovered from FFPE samples was 316.8 ng/mm3 of tissue (ranging between 61.6 and 917.4 ng/mm3 ), average RNA integrity number was 2.3 ± 0.9 (mean ± standard deviation), and 84% of samples had RNA fragments longer than 200 nucleotides (DV200 ). RNA concentrations and CT values for GAPDH, ACTB, miR-8908a and miR-369 in FFPE samples were significantly correlated (r = -0.8, -0.7, -0.4 and -0.4, respectively; p < 0.001). Expression pattern of normalized CYP19A1 and HSD3B1 in paired FFPE and RNAlater™ samples was significantly correlated (r = 0.97 for CYP19A1 and HSD3B1; p < 0.001). This study demonstrates that RNA can be extracted from FFPE equine placental tissue and used for downstream transcriptomic analysis. Similar RNA expression patterns were obtained using RNAlater™ and FFPE tissue samples.
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Affiliation(s)
- Pouya Dini
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.,Department of Veterinary Science, University of Kentucky, Lexington, Kentucky
| | | | - Kirsten E Scoggin
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky
| | - Peter Daels
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Barry A Ball
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky
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8
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Does vacuum centrifugal concentration reduce yield or quality of nucleic acids extracted from FFPE biospecimens? Anal Biochem 2018; 566:16-19. [PMID: 30343041 DOI: 10.1016/j.ab.2018.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 12/30/2022]
Abstract
Vacuum centrifugal (SpeedVac) concentration is commonly applied to nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) sections, but with an unknown impact. We concentrated DNA and RNA from FFPE biospecimens using different time/temperature SpeedVac combinations of up to 30 min concentration at 45 °C, then used spectrophotometry, spectrofluorometry, RIN, PERM, DV200, qRT-PCR, DIN and the Illumina FFPE QC Assay to assess the changes in quantity, purity and integrity induced by the concentration process. We found the effects of SpeedVac concentration to be inconsequential, but an aliquot of elution buffer should be concentrated for use as the blank in spectrophotometry assays.
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9
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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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10
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Bockmeyer CL, Wittig J, Säuberlich K, Selhausen P, Eßer M, Zeuschner P, Modde F, Amann K, Daniel C. Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples. BMC Mol Biol 2018. [PMID: 29534701 PMCID: PMC5850911 DOI: 10.1186/s12867-018-0103-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve research applications. The major challenge for such studies is to obtain good-quality RNA from small amounts of starting material, as applicable for the analysis of glomerular compartments. In this work, we provide data and recommendations for an optimized workflow of glomerular mRNA analysis. Results With a proper resolution of the camera and screen provided by the next generation of micro-dissection systems, we are able to separate parietal epithelial cells from glomerular tufts. Selected compartment-specific transcripts (WT1 and GLEPP1 for glomerular tuft as well as PAX2 for parietal epithelial cells) seem to be reliable discriminators for these micro-dissected glomerular substructures. Using the phenol–chloroform extraction and hemalaun-stained sections (2 µm), high amounts of Bowman’s capsule transections (> 300) reveal sufficient RNA concentrations (> 300 ng mRNA) for further analysis. For comparison, in unstained sections from a number of 60 glomerular transections upwards, a minimum amount of 157 ng mRNA with a reasonable mRNA purity [A260/A280 ratio of 1.5 (1.4/1.7) median (25th/75th percentiles)] was reversely transcribed into cDNA. Comparing the effect of input RNA (20, 60, 150 and 300 micro-dissected glomerular transections), transcript expression of POLR2A significantly correlated when 60 and 150 laser micro-dissected glomerular transections were used for analysis. There was a lower inter-assay coefficient of variability for ADAMTS13, when at least 60 glomerular transections were used. According to the algorithms of geNormPlus and NormFinder, PGK1 and PPIA are more stable glomerular reference transcripts compared to GUSB, GAPDH, POLR2A, RPLPO, TBP, B2M, ACTB, 18SrRNA and HMBS. Conclusions Our approach implements compartment-specific glomerular mRNA expression analysis into research applications, even regarding glomerular substructures like parietal epithelial cells. We recommend using of at least 60 micro-dissected unstained glomerular or 300 hemalaun-stained Bowman’s capsule transections to obtain sufficient input mRNA for reproducible results. Hereby, the range of RNA concentrations in 60 micro-dissected glomeruli is low and appropriate normalization of Cq values using our suggested reference transcripts (PGK1 and PPIA) allows compensation with respect to different amounts of RNA purity and quantity. Electronic supplementary material The online version of this article (10.1186/s12867-018-0103-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clemens L Bockmeyer
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany. .,Institute of Pathology, Hannover Medical School, Hannover, Germany.
| | - Juliane Wittig
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Karen Säuberlich
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Philipp Selhausen
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany
| | - Marc Eßer
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Philip Zeuschner
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Friedrich Modde
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany
| | - Christoph Daniel
- Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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12
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Cui W, Zhang X, Zheng S, Ma Z, Pang X, Li X. Clinicopathological significance of miR-101-3p and c-myc mRNA expression in diffused large B-cell lymphoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:11797-11804. [PMID: 31966543 PMCID: PMC6966081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/10/2017] [Indexed: 06/10/2023]
Abstract
MiR-101-3p has been suggested to be implicated in the pathogenesis of lymphoma, however little is known regarding clinicopathological significance of its expression in diffused large B-cell lymphoma (DLBCL). In contrast, although c-myc has been extensively studied in DLBCL, no direct evidence concerning clinicopathological significance has been well established, either. Given this, in our present study, to understand the significance of both miR-101-3p and c-myc expression on mRNA level in DLBCL, real-time quantitative PCR was used to detect the expression of miR-101-3p and c-myc on mRNA level in 100 cases of DLBCL samples. Association between expression of miR-101-3p and c-myc and clinicopathological variables available was statistically analyzed using Cross-Table test. It was shown that only significant association was observed between miR-101-3p expression and histopathological subtype and therapeutic regimen, no significant relationship was found with other clinicopathological variables. As for c-myc expression, only significant association was found with gender, IPI, and activity of LDH in serum; No significant relations were found with other clinicopathological variables. Together, our study presents the direct evidence regarding clinicopathological significance of miR-101-3p and c-myc expression in DLBCL, which warrants further confirmation in different cohorts with larger sample sizes.
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Affiliation(s)
- Wenli Cui
- Department of Pathology, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
| | - Xingyan Zhang
- Department of Pathology, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
| | - Shutao Zheng
- Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
- State Key Lab Incubation Base of Xinjiang Major Diseases Research, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
| | - Zhiping Ma
- Department of Pathology, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
| | - Xuelian Pang
- Department of Pathology, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
| | - Xinxia Li
- Department of Pathology, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang Uygur Autonomous Region, Urumqi 830011, Xinjiang, P.R. China
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Chung JY, Song JS, Ylaya K, Sears JD, Choi L, Cho H, Rosenberg AZ, Hewitt SM. Histomorphological and Molecular Assessments of the Fixation Times Comparing Formalin and Ethanol-Based Fixatives. J Histochem Cytochem 2017; 66:121-135. [PMID: 29125916 DOI: 10.1369/0022155417741467] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The lack of standardization of tissue handling and processing hinders the development and validation of new biomarkers in research and clinical settings. We compared the histomorphology and the quality and quantity of biomolecules in paraffin-embedded mouse tissues, followed by fixation with neutral buffered formalin (NBF), 70% ethanol, and buffered ethanol (BE70) fixative. The quality of the histomorphology and immunohistochemistry in BE70 was relatively time-independent, whereas those in NBF rapidly decreased after 1 week of fixation. Protein recovered from tissue fixed in 70% ethanol and BE70 was compatible with Western blot and protein array using AKT and GAPDH antibodies, regardless of the fixation time. In addition, the quality and quantity of RNA extracted from tissue in ethanol-based fixative showed minimal changes from 4 hr to 6 months, whereas NBF had a dramatic detrimental change in RNA quality after 1 week of fixation. Furthermore, ethanol-based fixative offers a superior DNA template for PCR amplification-based molecular assays than NBF. In conclusion, coagulative, ethanol-based fixatives show a broader time spectrum than the aldehyde crosslinking fixative NBF in their histomorphological features and the quantity and quality of the biomolecules from paraffin-embedded tissue, and they may facilitate the use of fixative-fixed paraffin-embedded tissues in research and clinical laboratories, avoiding overfixation.
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Affiliation(s)
- Joon-Yong Chung
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joon Seon Song
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kris Ylaya
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - John D Sears
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lauren Choi
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hanbyoul Cho
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
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14
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Baena-Del Valle JA, Zheng Q, Hicks JL, Fedor H, Trock BJ, Morrissey C, Corey E, Cornish TC, Sfanos KS, De Marzo AM. Rapid Loss of RNA Detection by In Situ Hybridization in Stored Tissue Blocks and Preservation by Cold Storage of Unstained Slides. Am J Clin Pathol 2017; 148:398-415. [PMID: 29106457 DOI: 10.1093/ajcp/aqx094] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Recent commercialization of methods for in situ hybridization using Z-pair probe/branched DNA amplification has led to increasing adoption of this technology for interrogating RNA expression in formalin-fixed, paraffin-embedded (FFPE) tissues. Current practice for FFPE block storage is to maintain them at room temperature, often for many years. METHODS To examine the effects of block storage time on FFPE tissues using a number of RNA in situ probes with the Advanced Cellular Diagnostic's RNAscope assay. RESULTS We report marked reductions in signals after 5 years and significant reductions often after 1 year. Furthermore, storing unstained slides cut from recent cases (<1 year old) at -20°C can preserve hybridization signals significantly better than storing the blocks at room temperature and cutting the slides fresh when needed. CONCLUSIONS We submit that the standard practice of storing FFPE tissue blocks at room temperature should be reevaluated to better preserve RNA for in situ hybridization.
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Affiliation(s)
- Javier A Baena-Del Valle
- From the Department of Pathology
- Department of Pathology and Laboratory Medicine, Fundacion Santa Fe de Bogota University Hospital, Bogota DC, Colombia
| | | | | | | | - Bruce J Trock
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle
| | - Eva Corey
- Department of Urology, University of Washington, Seattle
| | - Toby C Cornish
- From the Department of Pathology
- Department of Pathology, University of Colorado School of Medicine, Aurora
| | - Karen S Sfanos
- From the Department of Pathology
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Angelo M De Marzo
- From the Department of Pathology
- Departments of Urology and Oncology
- Sidney Kimmel Comprehensive Cancer Center
- The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, MD
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15
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A melanin-bleaching methodology for molecular and histopathological analysis of formalin-fixed paraffin-embedded tissue. J Transl Med 2016; 96:1116-27. [PMID: 27548802 PMCID: PMC7781076 DOI: 10.1038/labinvest.2016.90] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 01/28/2023] Open
Abstract
Removal of excessive melanin from heavily pigmented formalin-fixed paraffin-embedded (FFPE) melanoma tissues is essential for histomorphological and molecular diagnostic assessments. Although there have been efforts to address this issue, current methodologies remain complex and time-consuming, and are not suitable for multiple molecular applications. Herein, we have developed a robust and rapid melanin-bleaching methodology for FFPE tissue specimens. Our approach is based on quick bleaching (15 min) at high temperature (80 °C) with 0.5% diluted hydrogen peroxide (H2O2) in Tris-HCl, PBS, or Tris/Tricine/SDS buffer. Immunostaining for Ki-67 and HMB45 was enhanced by bleaching with 0.5% H2O2 in Tris/Tricine/SDS and Tris-HCl, respectively. In addition to histopathological applications, our approach also facilitates recovery of protein and nucleic acid from archival melanin-rich FFPE tissue sections. Protein extracted from bleached FFPE tissues was compatible with western blotting using anti-human GAPDH and AKT antibodies. Our bleaching condition significantly improved RNA quality compared with unbleached tissues without compromising the yield. Notably, the RNA/DNA obtained from bleached tissues was suitable for end point PCR and real-time quantitative RT-PCR. In conclusion, this improved melanin-bleaching method enhances and simplifies immunostaining procedures, and facilitates the use of melanin-rich FFPE tissues for histomorphological and PCR amplification-based molecular assays.
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16
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Perry C, Chung JY, Ylaya K, Choi CH, Simpson A, Matsumoto KT, Smith WA, Hewitt SM. A Buffered Alcohol-Based Fixative for Histomorphologic and Molecular Applications. J Histochem Cytochem 2016; 64:425-40. [PMID: 27221702 DOI: 10.1369/0022155416649579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/21/2016] [Indexed: 01/04/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is the predominant preparation for diagnostic histopathological evaluation and increasingly the biospecimen on which molecular diagnostics are performed. However, formalin is carcinogenic and results in cross-linking of proteins and nicking and alterations of nucleic acids. Alternative fixatives, including 70% ethanol, improved biomolecular integrity; however, they have yet to replace neutral-buffered formalin (NBF). Herein, we describe the phosphate-buffered ethanol 70% (BE70) fixative. The histomorphology of BE70-fixed tissue is very similar to that of NBF; however, it is a non-cross-linking fixative and lacks the carcinogenic profile of formaldehyde-based fixatives. RNA isolated from tissue fixed in BE70 was of substantially higher quality and quantity than that was recovered from formalin-fixed tissue. Furthermore, the BE70 fixative showed excellent RNA and DNA integrity compared with that of NBF fixative based on real-time polymerase chain reaction analysis results. Immunohistochemical staining was similar for the antigen tested. In conclusion, BE70 is a non-cross-linking fixative that is superior to NBF and 70% ethanol with reference to biomolecule recovery and quality from paraffin-embedded tissue. Additional studies to compare the histomorphologic and immunohistochemical performance and utility in a clinical setting are required.
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Affiliation(s)
- Candice Perry
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH),Antibody Characterization Laboratory, Advanced Technology Program, Leidos Biomedical Research, Inc., Frederick, Maryland (CP)
| | - Joon-Yong Chung
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Kris Ylaya
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Chel Hun Choi
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH),Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea (CHC)
| | - Amari Simpson
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Kaipo T Matsumoto
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - William A Smith
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (CP, J-YC, KY, CHC, AS, KTM, WAS, SMH)
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