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Condori RE, Niezgoda M, Lopez G, Matos CA, Mateo ED, Gigante C, Hartloge C, Filpo AP, Haim J, Satheshkumar PS, Petersen B, Wallace R, Olson V, Li Y. Using the LN34 Pan-Lyssavirus Real-Time RT-PCR Assay for Rabies Diagnosis and Rapid Genetic Typing from Formalin-Fixed Human Brain Tissue. Viruses 2020; 12:v12010120. [PMID: 31963651 PMCID: PMC7019996 DOI: 10.3390/v12010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/10/2020] [Accepted: 01/15/2020] [Indexed: 11/16/2022] Open
Abstract
Human rabies post mortem diagnostic samples are often preserved in formalin. While immunohistochemistry (IHC) has been routinely used for rabies antigen detection in formalin-fixed tissue, the formalin fixation process causes nucleic acid fragmentation that may affect PCR amplification. This study reports the diagnosis of rabies in an individual from the Dominican Republic using both IHC and the LN34 pan-lyssavirus real-time RT-PCR assay on formalin-fixed brain tissue. The LN34 assay generates a 165 bp amplicon and demonstrated higher sensitivity than traditional PCR. Multiple efforts to amplify nucleic acid fragments larger than 300 bp using conventional PCR were unsuccessful, probably due to RNA fragmentation. Sequences generated from the LN34 amplicon linked the case to the rabies virus (RABV) strain circulating in the Ouest Department of Haiti to the border region between Haiti and the Dominican Republic. Direct sequencing of the LN34 amplicon allowed rapid and low-cost rabies genetic typing.
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Affiliation(s)
- Rene Edgar Condori
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Michael Niezgoda
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Griselda Lopez
- Laboratorio de Salud Pública “Dr. Defillo”, 10105 Santo Domingo, Dominican Republic
| | | | - Elinna Diaz Mateo
- Centro de Prevención y Control de Enfermedades Transmitidas por Vectores y Zoonosis (CECOVEZ), 10308 Santo Domingo, Dominican Republic
| | - Crystal Gigante
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Claire Hartloge
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | | | - Joseph Haim
- Ministère de l’Agriculture, des Resources Naturelles et du Développement Rural, Department of Animal Health, HT 6110, Republic of Haiti
| | | | - Brett Petersen
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ryan Wallace
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Victoria Olson
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yu Li
- Pox and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Correspondence:
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Behrmann O, Hügle M, Bronsert P, Herde B, Heni J, Schramm M, Hufert FT, Urban GA, Dame G. A lab-on-a-chip for rapid miRNA extraction. PLoS One 2019; 14:e0226571. [PMID: 31856234 PMCID: PMC6922460 DOI: 10.1371/journal.pone.0226571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/28/2019] [Indexed: 12/16/2022] Open
Abstract
We present a simple to operate microfluidic chip system that allows for the extraction of miRNAs from cells with minimal hands-on time. The chip integrates thermoelectric lysis (TEL) of cells with native gel-electrophoretic elution (GEE) of released nucleic acids and uses non-toxic reagents while requiring a sample volume of only 5 μl. These properties as well as the fast process duration of 180 seconds make the system an ideal candidate to be part of fully integrated point-of-care applications for e.g. the diagnosis of cancerous tissue. GEE was characterized in comparison to state-of-the-art silica column (SC) based RNA recovery using the mirVana kit (Ambion) as a reference. A synthetic miRNA (miR16) as well as a synthetic snoRNA (SNORD48) were subjected to both GEE and SC. Subsequent detection by stem-loop RT-qPCR demonstrated a higher yield for miRNA recovery by GEE. SnoRNA recovery performance was found to be equal for GEE and SC, indicating yield dependence on RNA length. Coupled operation of the chip (TEL + GEE) was characterized using serial dilutions of 5 to 500 MCF7 cancer cells in suspension. Samples were split and cells were subjected to either on-chip extraction or SC. Eluted miRNAs were then detected by stem-loop RT-qPCR without any further pre-processing. The extraction yield from cells was found to be up to ~200-fold higher for the chip system under non-denaturing conditions. The ratio of eluted miRNAs is shown to be dependent on the degree of complexation with miRNA associated proteins by comparing miRNAs purified by GEE from heat-shock and proteinase-K based lysis.
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Affiliation(s)
- Ole Behrmann
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Matthias Hügle
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Bettina Herde
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julian Heni
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Marina Schramm
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Frank T. Hufert
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Gerald A. Urban
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Gregory Dame
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
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Panzacchi S, Gnudi F, Mandrioli D, Montella R, Strollo V, Merrick BA, Belpoggi F, Tibaldi E. Effects of short and long-term alcohol-based fixation on Sprague-Dawley rat tissue morphology, protein and nucleic acid preservation. Acta Histochem 2019; 121:750-760. [PMID: 31277893 DOI: 10.1016/j.acthis.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022]
Abstract
Safety concerns on the toxic and carcinogenic effects of formalin exposure have drawn increasing attention to the search for alternative low risk fixatives for processing tissue specimens in laboratories worldwide. Alcohol-based fixatives are considered some of the most promising alternatives. We evaluated the performance of alcohol-fixed paraffin-embedded (AFPE) samples from Sprague-Dawley (SD) rats analyzing tissue morphology, protein and nucleic acid preservation after short and extremely long fixation times (up to 7 years), using formalin-fixed paraffin-embedded (FFPE) samples as a comparator fixative. Following short and long-term alcohol fixation, tissue morphology and cellular details in tissues, evaluated by scoring stained sections (Hematoxylin-Eosin and Mallory's trichrome), were optimally preserved if compared to formalin fixation. Immunoreactivity of proteins (Ki67, CD3, PAX5, CD68), evaluated by immunohistochemistry, showed satisfactory results when the fixation period did not exceed 1 year. Finally, we confirm the superiority of alcohol fixation compared to formalin, in terms of quantity of nucleic acid extracted from paraffin blocks, even after an extremely long time of alcohol fixation. Our results confirm that alcohol fixation is a suitable and safe alternative to formalin for pathological evaluations. There is a need for standardization of formalin-free methods and harmonization of diagnosis in pathology department worldwide.
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Pelisek J, Hegenloh R, Bauer S, Metschl S, Pauli J, Glukha N, Busch A, Reutersberg B, Kallmayer M, Trenner M, Wendorff H, Tsantilas P, Schmid S, Knappich C, Schaeffer C, Stadlbauer T, Biro G, Wertern U, Meisner F, Stoklasa K, Menges AL, Radu O, Dallmann-Sieber S, Karlas A, Knipfer E, Reeps C, Zimmermann A, Maegdefessel L, Eckstein HH. Biobanking: Objectives, Requirements, and Future Challenges-Experiences from the Munich Vascular Biobank. J Clin Med 2019; 8:jcm8020251. [PMID: 30781475 PMCID: PMC6406278 DOI: 10.3390/jcm8020251] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/01/2019] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
Collecting biological tissue samples in a biobank grants a unique opportunity to validate diagnostic and therapeutic strategies for translational and clinical research. In the present work, we provide our long-standing experience in establishing and maintaining a biobank of vascular tissue samples, including the evaluation of tissue quality, especially in formalin-fixed paraffin-embedded specimens (FFPE). Our Munich Vascular Biobank includes, thus far, vascular biomaterial from patients with high-grade carotid artery stenosis (n = 1567), peripheral arterial disease (n = 703), and abdominal aortic aneurysm (n = 481) from our Department of Vascular and Endovascular Surgery (January 2004–December 2018). Vascular tissue samples are continuously processed and characterized to assess tissue morphology, histological quality, cellular composition, inflammation, calcification, neovascularization, and the content of elastin and collagen fibers. Atherosclerotic plaques are further classified in accordance with the American Heart Association (AHA), and plaque stability is determined. In order to assess the quality of RNA from FFPE tissue samples over time (2009–2018), RNA integrity number (RIN) and the extent of RNA fragmentation were evaluated. Expression analysis was performed with two housekeeping genes—glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (ACTB)—using TaqMan-based quantitative reverse-transcription polymerase chain reaction (qRT)-PCR. FFPE biospecimens demonstrated unaltered RNA stability over time for up to 10 years. Furthermore, we provide a protocol for processing tissue samples in our Munich Vascular Biobank. In this work, we demonstrate that biobanking is an important tool not only for scientific research but also for clinical usage and personalized medicine.
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Affiliation(s)
- Jaroslav Pelisek
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
| | - Renate Hegenloh
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sabine Bauer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Susanne Metschl
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Jessica Pauli
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Nadiya Glukha
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Albert Busch
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Benedikt Reutersberg
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Michael Kallmayer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Matthias Trenner
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Heiko Wendorff
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Pavlos Tsantilas
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sofie Schmid
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christoph Knappich
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christoph Schaeffer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Thomas Stadlbauer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Gabor Biro
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Uta Wertern
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Franz Meisner
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Kerstin Stoklasa
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Anna-Leonie Menges
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Oksana Radu
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sabine Dallmann-Sieber
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Angelos Karlas
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Eva Knipfer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christian Reeps
- University Centre for Vascular Medicine and Department of Vascular Surgery, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany.
| | - Alexander Zimmermann
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Lars Maegdefessel
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
| | - Hans-Henning Eckstein
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
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Arber DA, Borowitz MJ, Cessna M, Etzell J, Foucar K, Hasserjian RP, Rizzo JD, Theil K, Wang SA, Smith AT, Rumble RB, Thomas NE, Vardiman JW. Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology. Arch Pathol Lab Med 2017; 141:1342-1393. [PMID: 28225303 DOI: 10.5858/arpa.2016-0504-cp] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - A complete diagnosis of acute leukemia requires knowledge of clinical information combined with morphologic evaluation, immunophenotyping and karyotype analysis, and often, molecular genetic testing. Although many aspects of the workup for acute leukemia are well accepted, few guidelines have addressed the different aspects of the diagnostic evaluation of samples from patients suspected to have acute leukemia. OBJECTIVE - To develop a guideline for treating physicians and pathologists involved in the diagnostic and prognostic evaluation of new acute leukemia samples, including acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemias of ambiguous lineage. DESIGN - The College of American Pathologists and the American Society of Hematology convened a panel of experts in hematology and hematopathology to develop recommendations. A systematic evidence review was conducted to address 6 key questions. Recommendations were derived from strength of evidence, feedback received during the public comment period, and expert panel consensus. RESULTS - Twenty-seven guideline statements were established, which ranged from recommendations on what clinical and laboratory information should be available as part of the diagnostic and prognostic evaluation of acute leukemia samples to what types of testing should be performed routinely, with recommendations on where such testing should be performed and how the results should be reported. CONCLUSIONS - The guideline provides a framework for the multiple steps, including laboratory testing, in the evaluation of acute leukemia samples. Some aspects of the guideline, especially molecular genetic testing in acute leukemia, are rapidly changing with new supportive literature, which will require on-going updates for the guideline to remain relevant.
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Bammert TD, Hijmans JG, Kavlich PJ, Lincenberg GM, Reiakvam WR, Fay RT, Greiner JJ, Stauffer BL, DeSouza CA. Influence of sex on the number of circulating endothelial microparticles and microRNA expression in middle-aged adults. Exp Physiol 2017; 102:894-900. [PMID: 28568648 DOI: 10.1113/ep086359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/24/2017] [Indexed: 12/13/2022]
Abstract
NEW FINDINGS What is the central question of this study? Are there sex-related differences in the number of circulating endothelial microparticles (EMPs) and microparticle microRNA expression in middle-aged adult humans? What is the main finding and its importance? Although the numbers of circulating endothelial microparticles do not differ between middle-aged men and women, there are sex-related differences in the expression of miR-125a in activation-derived EMPs and miR-34a in apoptosis-derived EMPs. Differences in circulating endothelial microparticle microRNA content may provide new insight into the sex-related disparity in the risk and prevalence of vascular disease in middle-aged adults. The aims of this study were to determine: (i) whether circulating concentrations of endothelial microparticles (EMPs) differ in middle-aged men compared with women; and (ii) whether there are sex-related differences in microRNA expression in EMPs. Peripheral blood was collected from 30 sedentary adults: 15 men (56 ± 6 years old) and 15 women (56 ± 5 years old). Endothelial microparticles were defined by markers of activation (CD62e+ ) or apoptosis (CD31+ /CD42b- ) by flow cytometry. Expression of microRNA (miR-34a, 92a, 125a and 126) in activation- and apoptosis-derived EMPs was measured by RT-PCR. Circulating activation- (33 ± 31 versus 39 ± 35 microparticles μl-1 ) and apoptosis-derived EMPs (49 ± 54 versus 42 ± 43 microparticles μl-1 ) were not significantly different between men and women. Expression of miR-125a (2.23 ± 2.01 versus 6.95 ± 3.99 a.u.) was lower (∼215%; P < 0.05) in activation-derived EMPs, whereas expression of miR-34a (1.17 ± 1.43 versus 0.38 ± 0.35 a.u.) was higher (∼210%; P < 0.05) in apoptosis-derived EMPs from men compared with women. Expression of microRNA in circulating EMPs may provide new insight into sex-related differences in cardiovascular disease.
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Affiliation(s)
- Tyler D Bammert
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Jamie G Hijmans
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Philip J Kavlich
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Grace M Lincenberg
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Whitney R Reiakvam
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Ryan T Fay
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Jared J Greiner
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Brian L Stauffer
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA.,Department of Medicine, University of Colorado Anschutz Medical Center, Denver, CO, USA.,Denver Health Medical Center, Denver, CO, USA
| | - Christopher A DeSouza
- Integrative Vascular Biology Laboratory, Department of Integrative Physiology, University of Colorado, Boulder, CO, USA.,Department of Medicine, University of Colorado Anschutz Medical Center, Denver, CO, USA
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Signal Transducer and Activator of Transcription 1 (STAT1) Knock-down Induces Apoptosis in Malignant Pleural Mesothelioma. Pathol Oncol Res 2016; 23:595-605. [DOI: 10.1007/s12253-016-0157-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 12/08/2016] [Indexed: 02/05/2023]
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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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Cho WJ, Oliveira DSM, Najy AJ, Mainetti LE, Aoun HD, Cher ML, Heath E, Kim HRC, Bonfil RD. Gene expression analysis of bone metastasis and circulating tumor cells from metastatic castrate-resistant prostate cancer patients. J Transl Med 2016; 14:72. [PMID: 26975354 PMCID: PMC4791970 DOI: 10.1186/s12967-016-0829-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background Characterization of genes linked to bone metastasis is critical for identification of novel prognostic or predictive biomarkers and potential therapeutic targets in metastatic castrate-resistant prostate cancer (mCRPC). Although bone marrow core biopsies (BMBx) can be obtained for gene profiling, the procedure itself is invasive and uncommon practice in mCRPC patients. Conversely, circulating tumor cells (CTCs), which are likely to stem from bone metastases, can be isolated from blood. The goals of this exploratory study were to establish a sensitive methodology to analyze gene expression in BMBx and CTCs, and to determine whether the presence or absence of detectable gene expression is concordant in matching samples from mCRPC patients. Methods The CellSearch® platform was used to enrich and enumerate CTCs. Low numbers of PC3 prostate cancer (PCa) cells were spiked into normal blood to assess cell recovery rate. RNA extracted from recovered PC3 cells was amplified using an Eberwine-based procedure to obtain antisense mRNA (aRNA), and assess the linearity of the RNA amplification method. In this pilot study, RNAs extracted from CTCs and PCa cells microdissected from formalin-fixed paraffin-embedded BMBx, were amplified to obtain aRNA and assess the expression of eight genes functionally relevant to PCa bone metastasis using RT-PCR. Results RNAs were successfully extracted from as few as 1–5 PCa cells in blood samples. The relative expression levels of reference genes were maintained after RNA amplification. The integrity of the amplified RNA was also demonstrated by RT-PCR analysis using primer sets that target the 5′-end, middle, and 3′-end of reference mRNA. We found that in 21 out of 28 comparisons, the presence or absence of detectable gene expression in CTCs and PCa cells microdissected from single bone lesions of the same patients was concordant. Conclusions This exploratory analysis suggests that aRNA amplification through in vitro transcription may be useful as a method to detect gene expression in small numbers of CTCs and tumor cells microdissected from bone metastatic lesions. In some cases, gene expression in CTCs and BMBxs was not concordant, raising questions about using CTC gene expression to make clinical decisions. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0829-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Won Jin Cho
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Daniel S M Oliveira
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Abdo J Najy
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Leandro E Mainetti
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Hussein D Aoun
- Department of Radiology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Michael L Cher
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA.,Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Elisabeth Heath
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Hyeong-Reh C Kim
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - R Daniel Bonfil
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA. .,Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA. .,Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA.
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Bussolati G, Annaratone L, Maletta F. The pre-analytical phase in surgical pathology. Recent Results Cancer Res 2015; 199:1-13. [PMID: 25636424 DOI: 10.1007/978-3-319-13957-9_1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Several sequential passages are involved in the pre-analytical handling of surgical specimens from resection in the surgical theater to paraffin-embedding and storage. Each passage is highly critical and can significantly affect the preservation of morphology, antigens, and nucleic acids. Some key points in this process are still undefined and are subject to high variability among hospitals. High quality and standardization are demanded and pathologists should therefore work to comply with all novel clinical requests (such as genomic and antigenic testing for targeted molecular therapies). Under-vacuum sealing of surgical pieces can be a safe and reliable alternative to storage in large formalin-filled boxes; it prevents dehydration and favors cooling by removing air. Moreover, it implements tissue banking and preservation of nucleic acids. After transport of specimens to pathological anatomy laboratories, the next passage, fixation, has been the object of several attempt to find alternatives to formalin. However, none of the substitutes proved successful, and formalin fixation is still considered the gold standard for preservation of morphology and antigens. RNA has instead been found to be heavily affected by degradation and fragmentation in formalin-fixed tissues. Based on the hypothesis that RNA degradation would be inhibited by maintaining a low temperature, a protocol based on processing tissues with formalin at low temperature (cold fixation) was evaluated and proved useful in obtaining a reduction in RNA fragmentation. Finally, the problem of storage is discussed, in order to find ways to guarantee feasibility of molecular analyses even years after the original diagnosis.
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Affiliation(s)
- Gianni Bussolati
- Department of Medical Sciences, University of Turin, via Santena 7, 10126, Turin, Italy,
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11
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The tissue is the issue: improved methylome analysis from paraffin-embedded tissues by application of the HOPE technique. J Transl Med 2014; 94:927-33. [PMID: 24933424 DOI: 10.1038/labinvest.2014.79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/25/2014] [Accepted: 05/14/2014] [Indexed: 01/07/2023] Open
Abstract
Alterations in the DNA methylome are characteristic for numerous diseases and a typical hallmark of cancer. Therefore, DNA methylation is currently under investigation in research labs and has also entered diagnostics. Recently, protocols like the BeadChip technology have become commercially available to study DNA methylation in an array format and semiquantitative fashion. However, it is known that fixation of the sample material with formalin prior to BeadChip analysis can affect the results. In this study we compared the influence of fixation on the outcome of BeadChip analysis. From six patients each a lung cancer tissue sample and a corresponding tumor-free lung tissue sample were collected. The samples were separated into three pieces. One piece of each sample was fixed with formalin, another one by the non-cross-linking HOPE technique (Hepes-glutamic acid buffer mediated Organic solvent Protection Effect). Subsequently, both became paraffin embedded. As a reference, the remaining third piece was cryopreserved. In addition we used three adenocarcinoma cell lines (H838, A549, and H1650) to validate the results from patient tissues. We show that using the HOPE technique instead of formalin largely prevents the introduction of formalin-fixation related artifacts. An ANOVA analysis significantly separated HOPE- and cryopreserved from formalin-fixed samples (FDR<0.05), while differences in the methylation data obtained from HOPE-fixed and cryopreserved material were minor. Consequently, HOPE fixation is superior to formalin fixation if a subsequent BeadChip analysis of paraffin-embedded sample material is intended.
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Limited expression of APRIL and its receptors prior to intestinal IgA plasma cell development during human infancy. Mucosal Immunol 2014; 7:467-77. [PMID: 24045575 PMCID: PMC3959635 DOI: 10.1038/mi.2013.64] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/26/2013] [Accepted: 08/07/2013] [Indexed: 02/04/2023]
Abstract
The absence of immunoglobulin A (IgA) in the intestinal tract renders young infants highly susceptible to enteric infections. However, mediators of initial IgA induction in this population are undefined. We determined the temporal acquisition of plasma cells by isotype and expression of T cell-independent (TI) and -dependent (TD) IgA class switch factors in the human intestinal tract during early infancy. We found that IgA plasma cells were largely absent in the infant intestine until after 1 month of age, approaching adult densities later in infancy than both IgM and IgG. The restricted development of IgA plasma cells in the first month was accompanied by reduced expression of the TI factor a proliferation-inducing ligand (APRIL) and its receptors TACI (transmembrane activator and calcium-modulator and cyclophilin ligand interactor) and B cell maturation antigen (BCMA) within isolated lymphoid follicles (ILFs). Moreover, both APRIL and BCMA expression strongly correlated with increasing IgA plasma cell densities over time. Conversely, TD mediators (CD40 ligand (CD40L) and CD40) were expressed within ILFs before 1 month and were not associated with IgA plasma cell generation. In addition, preterm infants had lower densities of IgA plasma cells and reduced APRIL expression compared with full-term infants. Thus, blunted TI responses may contribute to the delayed induction of intestinal IgA during early human infancy.
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Abstract
Powerful technologies critical to personalized medicine and targeted therapeutics require the analysis of carefully validated, procured, stored, and managed biospecimens. Reflecting advancements in biospecimen science, the National Cancer Institute and the International Society for Biological and Environmental Repositories are periodically publishing best practices that can guide the biobanker. The modern biobank will operate more like a clinical laboratory with formal accreditation, standard operating procedures, and quality assurance protocols. This chapter highlights practical issues of consent, procurement, storage, quality assurance, disbursement, funding, and space. Common topics of concern are discussed including the differences between clinical and research biospecimens, stabilization of biospecimens during procurement, optimal storage temperatures, and technical validation of biospecimen content and quality. With quickly expanding biospecimen needs and limited healthcare budgets, biobanks may need to be selective as to what is stored. Furthermore, a shift to room-temperature storage modalities where possible can reduce long-term space and fiscal requirements.
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Affiliation(s)
- William H Yong
- Translational Pathology Core Laboratory, Brain Tumor Translational Resource, Department of Pathology and Laboratory Medicine, Center for Health Sciences, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, 18-161 CHS, Los Angeles, CA, 90095, USA,
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Lou JJ, Mirsadraei L, Sanchez DE, Wilson RW, Shabihkhani M, Lucey GM, Wei B, Singer EJ, Mareninov S, Yong WH. A review of room temperature storage of biospecimen tissue and nucleic acids for anatomic pathology laboratories and biorepositories. Clin Biochem 2013; 47:267-73. [PMID: 24362270 DOI: 10.1016/j.clinbiochem.2013.12.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/03/2013] [Accepted: 12/08/2013] [Indexed: 11/28/2022]
Abstract
UNLABELLED Frozen biospecimens are crucial for translational research and contain well-preserved nucleic acids and protein. However, the risks of freezer failure as well as space, cost, and environmental concerns of frozen biospecimens are substantial. OBJECTIVE The purpose of the study was to review the current status of room temperature biospecimen storage. METHODS We searched Pubmed and vendor websites to identify relevant information. RESULTS Formalin-fixed paraffin embedded (FFPE) tissues have great value but their use is limited by cross-linking and fragmentation of nucleic acids, as well as loss of enzymatic activity. Stabilization solutions can now robustly preserve fresh tissue for up to 7days at room temperature. For longer term storage, commercial vendors of chemical matrices claim real time stability of nucleic acids of over 2 years and their accelerated aging studies to date suggest stability for 12years for RNA and 60years for DNA. However, anatomic pathology biorepositories store mostly frozen tissue rather than nucleic acids. Small quantities of tissue can be directly placed on some chemical matrices to stabilize DNA, however RNA and proteins are not preserved. Current lyophilization approaches can preserve histomorphology, DNA, RNA, and proteins though RNA shows moderate degradation after 1-2years. Formalin-free fixatives show improved but varying abilities to preserve nucleic acids and face validation as well as cost barriers in replacing FFPE specimens. The paraffin embedding process can degrade RNA. CONCLUSION Development of robust long-term room temperature biospecimen tissue storage technology can potentially reduce costs for the biomedical community in the face of growing targeted therapy needs and decreasing budgets.
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Affiliation(s)
- Jerry J Lou
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Leili Mirsadraei
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Desiree E Sanchez
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Ryan W Wilson
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Maryam Shabihkhani
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Gregory M Lucey
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Bowen Wei
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Elyse J Singer
- Department of Neurology, David Geffen School of Medicine at UCLA, 710 Westwood Plaza, Los Angeles, CA 90095-1769, USA; Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - Sergey Mareninov
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
| | - William H Yong
- Department of Pathology and Laboratory Medicine (Neuropathology), David Geffen School of Medicine at UCLA, Los Angeles CA, USA; Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles CA, USA.
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Mu Y, Zhou H, Li W, Hu L, Zhang Y. Evaluation of RNA quality in fixed and unembedded mouse embryos by different methods. Exp Mol Pathol 2013; 95:206-12. [DOI: 10.1016/j.yexmp.2013.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
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Becker N, Lockwood CM. Pre-analytical variables in miRNA analysis. Clin Biochem 2013; 46:861-8. [PMID: 23466658 DOI: 10.1016/j.clinbiochem.2013.02.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 02/21/2013] [Indexed: 01/20/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the regulation of cellular processes and have been shown to be differentially expressed in neoplasia and other disease states. This renders miRNAs promising diagnostic and prognostic biomarkers in tissues and body fluids, especially in blood. However, numerous variables can influence the detection of miRNAs in the pre-analytical phase and lead to erroneous results. This is of particular concern when miRNA profiles are used clinically and alter diagnosis and patient treatment. Since miRNAs have been discovered relatively recently, systematic studies examining pre-analytical variables are rare. Therefore, this review comprehensively summarizes the current knowledge of pre-analytical variables that influence miRNA analysis in general, as well as pre-analytical variables that are specific to the detection of circulating miRNAs and tissue miRNAs.
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Affiliation(s)
- Nils Becker
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Non-formalin fixative versus formalin-fixed tissue: A comparison of histology and RNA quality. Exp Mol Pathol 2013; 94:188-94. [DOI: 10.1016/j.yexmp.2012.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
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Kaneko Y, Wu GS, Saraswathy S, Vasconcelos-Santos DV, Rao NA. Immunopathologic processes in sympathetic ophthalmia as signified by microRNA profiling. Invest Ophthalmol Vis Sci 2012; 53:4197-204. [PMID: 22589448 DOI: 10.1167/iovs.12-9465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Recent discovery of microRNAs and their negative gene regulation have provided new understanding in the pathogenesis of inflammatory diseases. This study demonstrated microRNA expression profiling and their likely role in sympathetic ophthalmia, using formalin-fixed, paraffin embedded samples. METHODS Two groups of four enucleated globes (total eight globes) from patients with clinical and histopathological diagnosis of SO (experimental samples) and one group of four age-matched, noninflamed enucleated globes (control samples) were used. Human genome-wide microRNA PCR array was performed and results were subjected to bioinformatics calculation and P values stringency tests. The targets were searched using the recently published and periodically updated miRWalk software. Quantitative real-time PCR and immunohistochemical staining were performed to confirm the validated targets in the mRNA and in the protein levels, respectively. RESULTS No microRNA was significantly upregulated in SO, but 27 microRNAs were significantly downregulated. Among these, four microRNAs (hsa-miR-1, hsa-let-7e, hsa-miR-9, and hsa-miR-182) were known to be associated with the inflammatory signaling pathway. Only hsa-miR-9 has the validated targets, tumor necrosis factor-α, and nuclear factor kappa B1, which have been previously shown to be associated with mitochondrial oxidative stress-mediated photoreceptor apoptosis in eyes with SO. CONCLUSIONS Identification of altered levels of microRNAs by microRNA expression profiling may yield new insights into the pathogenesis of SO by disclosing specific microRNA signatures. In the future these may be targeted by synthetic microRNA mimic-based therapeutic strategies.
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Affiliation(s)
- Yutaka Kaneko
- Doheny Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections. BMC Res Notes 2012; 5:40. [PMID: 22260539 PMCID: PMC3284398 DOI: 10.1186/1756-0500-5-40] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 01/19/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Quantification of microRNAs in specific cell populations microdissected from tissues can be used to define their biological roles, and to develop and deploy biomarker assays. In this study, a number of variables were examined for their effect on the yield of microRNAs in samples obtained from formalin-fixed paraffin-embedded tissues by laser microdissection. RESULTS MicroRNA yield was improved by using cresyl violet instead of hematoxylin-eosin to stain tissue sections in preparation for microdissection, silicon carbide instead of glass fiber as matrix in RNA-binding columns, and overnight digestion of dissected samples with proteinase K. Storage of slides carrying stained tissue sections at room temperature for up to a week before microdissection, and storage of the microdissectates at room temperature for up to a day before RNA extraction did not adversely affect microRNA yield. CONCLUSIONS These observations should be of value for the efficient isolation of microRNAs from microdissected formalin-fixed tissues with a flexible workflow.
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