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Meritet DM, Spagnoli ST, Fischer KA, Löhr CV. Evaluating the Effects of Various Decalcification Protocols on Immunohistochemical Staining in Zebrafish ( Danio rerio). Zebrafish 2019; 16:280-290. [PMID: 31017539 DOI: 10.1089/zeb.2018.1697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Fixation and decalcification can alter protein structure in tissues, influencing the efficacy of primary antibodies routinely used in immunohistochemical (IHC) staining. Histologic examination of zebrafish requires both processes, making staining and analysis potentially challenging. Here, we investigated the effects of common fixation and decalcification protocols on IHC staining in zebrafish. We also identified zebrafish-reactive and -specific antibodies for use in research and diagnostics. For several of the antibodies, time spent in Dietrich's fixative containing 2% glacial acetic acid or 3.4% formaldehyde followed by decalcification with ethylenediaminetetraacetic acid (EDTA) significantly impacted IHC staining quality, particularly regarding staining intensity. Protocols utilizing shorter fixation times produced higher-quality stains. In addition, individual markers were variably affected by the type of fixative. Dietrich's fixative significantly reduced staining quality for the "neural" markers: glial fibrillar acidic protein, chromogranin A, S100. A negative time-dependent effect of fixation on staining quality was found for several antibodies: muscle actin (Dietrich's only), cytokeratin AE1/AE3, chromogranin, and S100. Neither decalcification protocol had a statistically significant negative time-dependent effect on staining quality. Based on our results, we suggest shorter fixation and decalcification protocols to best preserve IHC staining quality as well as recommend deliberate selection of the fixative used depending on the protein of interest.
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Affiliation(s)
- Danielle M Meritet
- 1 Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
| | - Sean T Spagnoli
- 1 Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
| | - Kay A Fischer
- 2 Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
| | - Christiane V Löhr
- 1 Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon
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102
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Neumann EK, Comi TJ, Rubakhin SS, Sweedler JV. Lipid Heterogeneity between Astrocytes and Neurons Revealed by Single‐Cell MALDI‐MS Combined with Immunocytochemical Classification. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812892] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and Beckman Institute for Advanced Science and technologyUniversity of Illinois at Urbana-Champaign 405 N. Matthews Ave. Urbana IL 61801 USA
| | - Troy J. Comi
- Department of Chemistry and Beckman Institute for Advanced Science and technologyUniversity of Illinois at Urbana-Champaign 405 N. Matthews Ave. Urbana IL 61801 USA
| | - Stanislav S. Rubakhin
- Department of Chemistry and Beckman Institute for Advanced Science and technologyUniversity of Illinois at Urbana-Champaign 405 N. Matthews Ave. Urbana IL 61801 USA
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and technologyUniversity of Illinois at Urbana-Champaign 405 N. Matthews Ave. Urbana IL 61801 USA
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103
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Neumann EK, Comi TJ, Rubakhin SS, Sweedler JV. Lipid Heterogeneity between Astrocytes and Neurons Revealed by Single-Cell MALDI-MS Combined with Immunocytochemical Classification. Angew Chem Int Ed Engl 2019; 58:5910-5914. [PMID: 30811763 DOI: 10.1002/anie.201812892] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Indexed: 12/15/2022]
Abstract
Transcriptomics characterizes cells based on their potential molecular repertoire whereas direct mass spectrometry (MS) provides information on the actual compounds present within cells. Single-cell matrix-assisted laser desorption/ionization (MALDI) MS can measure the chemical contents of individual cells but spectra are difficult to correlate to conventional cell types, limiting the metabolic information obtained. We present a protocol that combines MALDI-MS with immunocytochemistry to assay over a thousand individual rat brain cells. The approach entwines the wealth of knowledge obtained by immunocytochemical profiling with mass spectral information on the predominant lipids within each cell. While many lipid species showed a high degree of similarity between neurons and astrocytes, seventeen significantly differed between the two cell types, including four phosphatidylethanolamines elevated in astrocytes and nine phosphatidylcholines in neurons.
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Affiliation(s)
- Elizabeth K Neumann
- Department of Chemistry and Beckman Institute for Advanced Science and technology, University of Illinois at Urbana-Champaign, 405 N. Matthews Ave., Urbana, IL, 61801, USA
| | - Troy J Comi
- Department of Chemistry and Beckman Institute for Advanced Science and technology, University of Illinois at Urbana-Champaign, 405 N. Matthews Ave., Urbana, IL, 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and Beckman Institute for Advanced Science and technology, University of Illinois at Urbana-Champaign, 405 N. Matthews Ave., Urbana, IL, 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and technology, University of Illinois at Urbana-Champaign, 405 N. Matthews Ave., Urbana, IL, 61801, USA
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104
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Öztaş DY, Altunbek M, Uzunoglu D, Yılmaz H, Çetin D, Suludere Z, Çulha M. Tracing Size and Surface Chemistry-Dependent Endosomal Uptake of Gold Nanoparticles Using Surface-Enhanced Raman Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4020-4028. [PMID: 30773019 DOI: 10.1021/acs.langmuir.8b03988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based single-cell analysis is an emerging approach to obtain molecular level information from molecular dynamics in a living cell. In this study, endosomal biochemical dynamics was investigated based on size and surface chemistry-dependent uptake of gold nanoparticles (AuNPs) on single cells over time using SERS. MDA-MB-231 breast cancer cells were exposed to 13 and 50 nm AuNPs and their polyadenine oligonucleotide-modified forms by controlling the order and combination of AuNPs. The average spectra obtained from 20 single cells were analyzed to study the nature of the biochemical species or processes taking place on the AuNP surfaces. The spectral changes, especially from proteins and lipids of endosomal vesicles, were observed depending on the size, surface chemistry, and combination as well as the duration of the AuNP treatment. The results demonstrate that SERS spectra are sensitive to trace biochemical changes not only the size, surface chemistry, and aggregation status of AuNPs but also the endosomal maturation steps over time, which can be simple and fast way for understanding the AuNP behavior in single cell and useful for the assisting and controlling of AuNP-based gene or drug delivery applications.
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Affiliation(s)
- Deniz Yaşar Öztaş
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Mine Altunbek
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Deniz Uzunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Hülya Yılmaz
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | | | | | - Mustafa Çulha
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
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105
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Ethanol fixation method for heart and lung imaging in micro-CT. Jpn J Radiol 2019; 37:500-510. [DOI: 10.1007/s11604-019-00830-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
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106
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Stenzinger A, Allen JD, Maas J, Stewart MD, Merino DM, Wempe MM, Dietel M. Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. Genes Chromosomes Cancer 2019; 58:578-588. [PMID: 30664300 PMCID: PMC6618007 DOI: 10.1002/gcc.22733] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 01/10/2023] Open
Abstract
Characterization of tumors utilizing next‐generation sequencing methods, including assessment of the number of somatic mutations (tumor mutational burden [TMB]), is currently at the forefront of the field of personalized medicine. Recent clinical studies have associated high TMB with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. However, variability in current methods for TMB estimation and reporting is evident, demonstrating a need for standardization and harmonization of TMB assessment methodology across assays and centers. Two uniquely placed organizations, Friends of Cancer Research (Friends) and the Quality Assurance Initiative Pathology (QuIP), have collaborated to coordinate efforts for international multistakeholder initiatives to address this need. Friends and QuIP, who have partnered with several academic centers, pharmaceutical organizations, and diagnostic companies, have adopted complementary, multidisciplinary approaches toward the goal of proposing evidence‐based recommendations for achieving consistent TMB estimation and reporting in clinical samples across assays and centers. Many factors influence TMB assessment, including preanalytical factors, choice of assay, and methods of reporting. Preliminary analyses highlight the importance of targeted gene panel size and composition, and bioinformatic parameters for reliable TMB estimation. Herein, Friends and QuIP propose recommendations toward consistent TMB estimation and reporting methods in clinical samples across assays and centers. These recommendations should be followed to minimize variability in TMB estimation and reporting, which will ensure reliable and reproducible identification of patients who are likely to benefit from immune checkpoint inhibitors.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg (on behalf of QuIP® GmbH, Berlin, Germany), Heidelberg, Germany
| | - Jeffrey D Allen
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Jörg Maas
- Management Department, QuIP® GmbH, Berlin, Germany
| | - Mark D Stewart
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Diana M Merino
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Madison M Wempe
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Manfred Dietel
- Institute of Pathology, Charité Berlin (on behalf of QuIP® GmbH, Berlin, Germany), Berlin, Germany
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107
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Dörfelt S, Matiasek LA, Felten S, Sangl L, Hartmann K, Matiasek K. Antigens under cover-The preservation and demasking of selected antigens for successful poststaining immunocytochemistry of effusion, brain smears, and lymph node aspirates. Vet Clin Pathol 2019; 48 Suppl 1:98-107. [PMID: 30802342 PMCID: PMC7169317 DOI: 10.1111/vcp.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 07/06/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022]
Abstract
Background In clinical cytology, the applicability of an ancillary test such as immunocytochemistry is too often limited by low sample volume, poor cell representation, and sample preservation. Diagnosticians often read Romanowsky‐stained cytology, although specific techniques such as immunocytochemistry are often essential for a definitive diagnosis. Objectives The goal of the present study aimed to investigate if immunocytochemistry on previously‐stained cytologic specimens was possible. Different pretreatments were examined to determine which treatment preserved antigenicity best. Methods One hundred and twenty‐two impression smears and 64 fine‐needle aspirate preparations of brain and lymph nodes were processed and evaluated microscopically. The impact of staining cytologic preparations with a modified Wright's stain, using a destaining method, performing a coverslipping and decoverslipping process, and subjecting smears to a microwave treatment (MWT) were examined for the immunolabeling of selected nuclear, cytoplasmic, and plasmalemmal antigens, as well as intracellular feline coronavirus (FCoV). Biotinylated secondary antibodies were used, and the bound primary antibody was visualized using an ABC amplification kit. Results Cellular antigens were reliably detected with immunocytochemistry after smears were stained with a Romansky stain and were coverslipped early after staining and stayed coverslipped until immediately before immunolabeling. The staining intensity reached the same levels as that of the controls if the films underwent MWT in citrate buffer. In contrast, FCoV antigen detection was abolished after any physicochemical interference. Conclusions Poststaining immunocytochemistry represents a practical tool for additional investigations on prestained cytologic specimens when searching for cellular antigens. Paired untreated samples should be kept in case the workup requires testing for more vulnerable viral antigens.
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Affiliation(s)
- Stefanie Dörfelt
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany
| | - Lara A Matiasek
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany.,Anicura Small Animal Clinic, Babenhausen, Germany
| | - Sandra Felten
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany
| | - Laura Sangl
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximillians-Universitaet, Munich, Germany
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108
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Charvet S, Riemann L, Alneberg J, Andersson AF, von Borries J, Fischer U, Labrenz M. AFISsys - An autonomous instrument for the preservation of brackish water samples for microbial metatranscriptome analysis. WATER RESEARCH 2019; 149:351-361. [PMID: 30469021 DOI: 10.1016/j.watres.2018.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Microbial communities are the main drivers of biogeochemical cycling of multiple elements sustaining life in the ocean. The rapidity of their response to stressors and abrupt environmental changes implies that even fast and infrequent events can affect local transformations of organic matter and nutrients. Modern molecular techniques now allow for monitoring of microbial activities and functions in the environment through the analysis of genes and expressed genes contained in natural microbial assemblages. However, messenger RNA turnover in cells can be as short as 30 seconds and stability varies greatly between transcripts. Sampling of in situ communities involves an inevitable delay between the collection of seawater and the extraction of its RNA, leaving the bacterial communities plenty of time to alter their gene expression. The characteristics of microbial RNA turnover make time-series very difficult because samples need to be processed immediately to limit alterations to the metatranscriptomes. To address these challenges we designed an autonomous in situ fixation multi-sampler (AFISsys) for the reliable sampling of microbial metatranscriptomes at frequent intervals, for refined temporal resolution. To advance the development of this instrument, we examined the minimal seawater volume necessary for adequate coverage of community gene expression, and the suitability of phenol/ethanol fixation for immediate and long-term preservation of transcripts from a microbial community. We then evaluated the field eligibility of the instrument itself, with two case studies in a brackish system. AFISsys is able to collect, fix, and store water samples independently at a predefined temporal resolution. Phenol/ethanol fixation can conserve metatranscriptomes directly in the environment for up to a week, for later analysis in the laboratory. Thus, the AFISsys constitutes an invaluable tool for the integration of molecular functional analyses in environmental monitoring in brackish waters and in aquatic environments in general.
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Affiliation(s)
- Sophie Charvet
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Denmark
| | - Johannes Alneberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | - Anders F Andersson
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | | | - Uwe Fischer
- HYDRO-BIOS Apparatebau GmbH, Altenholz, Germany
| | - Matthias Labrenz
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany.
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109
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Büttner R, Longshore JW, López-Ríos F, Merkelbach-Bruse S, Normanno N, Rouleau E, Penault-Llorca F. Implementing TMB measurement in clinical practice: considerations on assay requirements. ESMO Open 2019; 4:e000442. [PMID: 30792906 PMCID: PMC6350758 DOI: 10.1136/esmoopen-2018-000442] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023] Open
Abstract
Clinical evidence demonstrates that treatment with immune checkpoint inhibitor immunotherapy agents can have considerable benefit across multiple tumours. However, there is a need for the development of predictive biomarkers that identify patients who are most likely to respond to immunotherapy. Comprehensive characterisation of tumours using genomic, transcriptomic, and proteomic approaches continues to lead the way in advancing precision medicine. Genetic correlates of response to therapy have been known for some time, but recent clinical evidence has strengthened the significance of high tumour mutational burden (TMB) as a biomarker of response and hence a rational target for immunotherapy. Concordantly, immune checkpoint inhibitors have changed clinical practice for lung cancer and melanoma, which are tumour types with some of the highest mutational burdens. TMB is an implementable approach for molecular biology and/or pathology laboratories that provides a quantitative measure of the total number of mutations in tumour tissue of patients and can be assessed by whole genome, whole exome, or large targeted gene panel sequencing of biopsied material. Currently, TMB assessment is not standardised across research and clinical studies. As a biomarker that affects treatment decisions, it is essential to unify TMB assessment approaches to allow for reliable, comparable results across studies. When implementing TMB measurement assays, it is important to consider factors that may impact the method workflow, the results of the assay, and the interpretation of the data. Such factors include biopsy sample type, sample quality and quantity, genome coverage, sequencing platform, bioinformatic pipeline, and the definitions of the final threshold that determines high TMB. This review outlines the factors for adoption of TMB measurement into clinical practice, providing an understanding of TMB assay considerations throughout the sample journey, and suggests principles to effectively implement TMB assays in a clinical setting to aid and optimise treatment decisions.
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Affiliation(s)
- Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - John W Longshore
- Atrium Health, Carolinas Pathology Group, Charlotte, North Carolina, USA
| | - Fernando López-Ríos
- Laboratorio de Dianas Terapéuticas, Hospital Universitario HM Sanchinarro, Madrid, Spain
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Naples, Italy
| | - Etienne Rouleau
- Department of Pathology and Medical Biology, Institut Gustave Roussy, Villejuif, France
| | - Frédérique Penault-Llorca
- Department of Biopathology, Centre Jean Perrin, Clermont-Ferrand, France.,UMR INSERM 1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont-Auvergne, Clermont-Ferrand, France
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110
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Blanco-Rayón E, Soto M, Izagirre U, Marigómez I. Enhanced discrimination of basophilic cells on mussel digestive gland tissue sections by means of toluidine-eosin staining. J Invertebr Pathol 2019; 161:29-39. [PMID: 30615864 DOI: 10.1016/j.jip.2019.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 11/16/2022]
Abstract
Changes in the cell type composition of the digestive gland epithelium constitute a common and recognized biological response to stress in mussels. Usually, these changes are identified as alterations in the relative proportion of basophilic cells, determined in tissue sections stained with hematoxylin-eosin (H&E) and measured in terms of volume density of basophilic cells (VvBAS) after stereological quantification. However, the identification and discrimination of basophilic cells may be a difficult issue, even for a trained operator, especially when, in circumstances of environmental stress, basophilic cells lose their basophilia and the perinuclear area of digestive cells gains basophilia. Thus, the present study was aimed at exploring the best available practices (BAPs) to identify and discriminate basophilic cells on tissue sections of mussel digestive gland. In a first step, a thorough screening of potentially suitable staining methods was carried out; the final selection included several trichrome staining methods and some of their variants, as well as toluidine-based stains. Next, the sample processing (fixation/dehydration steps) was optimized. Toluidine-eosin (T&E) staining after fixation in 4% formaldehyde at 4 °C for 24 h was considered the BAP to identify and discriminate basophilic cells in the digestive gland of mussels. Using the mussel Mytilus galloprovincialis as a target organism, this approach was successfully applied to quantify VvBAS values after automated image analysis and compared with the conventional H&E staining in different field and laboratory tests. It is worth noting that VvBAS values were always higher after T&E staining than after H&E staining, apparently because discrimination of basophilic cells was enhanced. Thus, until more data are available, any comparison with VvBAS values obtained in previous studies using H&E staining must be done cautiously. Finally, the T&E staining was successfully used to discriminate basophilic cells in tissue sections of other marine molluscs of ecotoxicological interest, including Mytilus edulis, Mytilus trossulus, Crassostrea gigas and Littorina littorea.
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Affiliation(s)
- E Blanco-Rayón
- CBET Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology (ZTF/FCT) & Research Centre of Experimental Marine Biology and Biotechnology (Plentzia Marine Station; PiE-UPV/EHU), University of the Basque Country, Bilbo 48080, Basque Country, Spain
| | - M Soto
- CBET Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology (ZTF/FCT) & Research Centre of Experimental Marine Biology and Biotechnology (Plentzia Marine Station; PiE-UPV/EHU), University of the Basque Country, Bilbo 48080, Basque Country, Spain
| | - U Izagirre
- CBET Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology (ZTF/FCT) & Research Centre of Experimental Marine Biology and Biotechnology (Plentzia Marine Station; PiE-UPV/EHU), University of the Basque Country, Bilbo 48080, Basque Country, Spain
| | - I Marigómez
- CBET Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology (ZTF/FCT) & Research Centre of Experimental Marine Biology and Biotechnology (Plentzia Marine Station; PiE-UPV/EHU), University of the Basque Country, Bilbo 48080, Basque Country, Spain.
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111
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Pluhacek T, Skriba A, Novak J, Luptakova D, Havlicek V. Analysis of Microbial Siderophores by Mass Spectrometry. Methods Mol Biol 2019; 1996:131-153. [PMID: 31127553 DOI: 10.1007/978-1-4939-9488-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Siderophores represent important microbial virulence factors and infection biomarkers. Their monitoring in fermentation broths, bodily fluids, and tissues should be reproducible. Similar isolation, characterization, and quantitation studies can often have conflicting results, and without proper documentation of sample collection, data processing, and analysis methods, it is difficult to reexamine the data and reconcile these differences. In this Springer Nature Protocol, we present the procedure optimized for ferricrocin/triacetylfusarinine C extraction from biological material as well as for tissue fixation and cryosectioning for optical microscopy and for both elemental and molecular mass spectrometry imaging. Special attention is paid to siderophore data mining from conventional and product ion mass spectra, liquid chromatography, and mass spectrometry imaging datasets, performed here by our free software called CycloBranch.
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Affiliation(s)
- Tomas Pluhacek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anton Skriba
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Novak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dominika Luptakova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Havlicek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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112
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Hutson HN, Kujawa C, Eliceiri K, Campagnola P, Masters KS. Impact of tissue preservation on collagen fiber architecture. Biotech Histochem 2018; 94:134-144. [PMID: 30354688 DOI: 10.1080/10520295.2018.1530373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Microarchitectural features of collagen-rich extracellular matrices provide the mechanical foundation for tissue function and exhibit topographical cues that influence cellular behavior including proliferation, migration and protein expression. Preservation of tissue microarchitecture is required for accurate evaluation of tissue characteristics and pathology. It is unclear whether common tissue preservation methods possess equal ability to preserve microarchitecture. We investigated collagen microarchitecture in samples that had been flash frozen, fixed in formalin or preserved in RNAlater®, and which contained both collagen-rich and collagen-sparse regions. Fibrillar collagen organization was characterized using picrosirius red staining and second harmonic generation (SHG) microscopy. Maintenance of collagen fiber characteristics compared to the gold standard of flash freezing depended on both the method of preservation and the local collagen content of the tissue. Both formalin fixation and RNAlater® preserved collagen fiber characteristics similar to flash freezing in collagen-rich areas of the tissue, but not in collagen-sparse regions. Analysis using picrosirius red staining indicated preservation-dependent changes in overall tissue architecture and suprafibrillar organization. Together with considerations of cost, ease of use, storage conditions and ability to use the preserved tissue for RNA or protein analysis, our quantitative characterization of the effects of preservation method on collagen microarchitecture may help investigators select the most appropriate preservation approach for their needs.
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Affiliation(s)
- H N Hutson
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - C Kujawa
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K Eliceiri
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA.,b Laboratory for Optical and Computational Instrumentation, Laboratory of Cell and Molecular Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - P Campagnola
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K S Masters
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
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113
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Cisne R, Souza AMT, Pereira-Sampaio MA, Babinski MA, Gorniak SL, Papa PC. Tannic Acid Solution: A Better Fixative Solution Than Formalin for Elastin and Collagen-Toxic and Morphological Assessment. Anat Rec (Hoboken) 2018; 301:1544-1550. [DOI: 10.1002/ar.23894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/02/2018] [Accepted: 02/21/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Rafael Cisne
- Department of Morphology, Biomedical Center; Fluminense Federal University; Niterói RJ Brazil
| | - Alessandra M. T. Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Center of Health Sciences; Federal University of Rio de Janeiro (UFRJ), 21941-590; Rio de Janeiro RJ Brazil
| | | | - Marcio A. Babinski
- Department of Morphology, Biomedical Center; Fluminense Federal University; Niterói RJ Brazil
| | - Silvana L. Gorniak
- Research Center for Veterinary Toxicology (CEPTOX), Department of Pathology; School of Veterinary Medicine, University of São Paulo; São Paulo Brazil
| | - Paula C. Papa
- Department of Surgery, School of the Veterinary Medicine and Animal Science; University of São Paulo; São Paulo Brazil
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114
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Olsen LR, Leipold MD, Pedersen CB, Maecker HT. The anatomy of single cell mass cytometry data. Cytometry A 2018; 95:156-172. [DOI: 10.1002/cyto.a.23621] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lars R. Olsen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Michael D. Leipold
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
| | - Christina B. Pedersen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
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115
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Khetani S, Mohammadi M, Nezhad AS. Filter-based isolation, enrichment, and characterization of circulating tumor cells. Biotechnol Bioeng 2018; 115:2504-2529. [DOI: 10.1002/bit.26787] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sultan Khetani
- Department of Mechanical and Manufacturing Engineering, BioMEMS and Bioinspired Microfluidic Laboratory; University of Calgary; Calgary Canada
- Center for BioEngineering Research and Education, University of Calgary; Calgary Canada
| | - Mehdi Mohammadi
- Department of Mechanical and Manufacturing Engineering, BioMEMS and Bioinspired Microfluidic Laboratory; University of Calgary; Calgary Canada
- Center for BioEngineering Research and Education, University of Calgary; Calgary Canada
- Department of Biological Sciences; University of Calgary; Calgary Canada
| | - Amir Sanati Nezhad
- Department of Mechanical and Manufacturing Engineering, BioMEMS and Bioinspired Microfluidic Laboratory; University of Calgary; Calgary Canada
- Center for BioEngineering Research and Education, University of Calgary; Calgary Canada
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Lee DW, Han SW, Kang JK, Bae JM, Kim HP, Won JK, Jeong SY, Park KJ, Kang GH, Kim TY. Association Between Fusobacterium nucleatum, Pathway Mutation, and Patient Prognosis in Colorectal Cancer. Ann Surg Oncol 2018; 25:3389-3395. [PMID: 30062471 DOI: 10.1245/s10434-018-6681-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND There is a close link between Fusobacterium nucleatum and colorectal cancer (CRC) tumorigenesis and chemoresistance. However, the genetic characteristics and clinical significance of CRC related with F. nucleatum remains unclear. This study evaluated the relationship between F. nucleatum, pathway mutation, and patient prognosis. METHODS Fusobacterium nucleatum amount in the tumor tissue and adjacent normal tissue were measured by quantitative polymerase chain reaction in adjuvant (N = 128) and metastatic (N = 118) cohorts. Patients were divided into binary (F. nucleatum-high and F. nucleatum-low) according to F. nucleatum amount. Targeted next-generation sequencing of 40 genes included in the 5 critical pathways (WNT, P53, RTK-RAS, PI3 K, and TGF-β) was performed in the adjuvant cohort. RESULTS Patients with MSI-H and CIMP-H had higher amount of F. nucleatum in tumor tissue. Fusobacterium nucleatum-high patients had higher rates of transition mutation and C to T (G to A) nucleotide change regardless of MSI status. In addition, mutation rate of AMER1 and ATM genes, and TGF-β pathway was higher in F. nucleatum-high patients. Fusobacterium nucleatum-high was associated with poor overall survival (OS) in the palliative cohort (26.4 vs. 30.7 months, p = 0.042). Multivariate analysis revealed F. nucleatum-high as an independent negative prognostic factor for OS [adjusted hazard ratio of 1.69 (95% confidence interval 1.04-2.75), p = 0.034]. However, F. nucleatum amount was not associated with recurrence in the adjuvant cohort. CONCLUSIONS F. nucleatum-high was associated with poor survival in metastatic CRC. In addition, we identified mutational characteristics of colorectal cancer according to F. nucleatum amount.
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Affiliation(s)
- Dae-Won Lee
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehang-Ro, Jongno-Gu, Seoul, 110-744, Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehang-Ro, Jongno-Gu, Seoul, 110-744, Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
| | - Jun-Kyu Kang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seung-Yong Jeong
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Kyu Joo Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehang-Ro, Jongno-Gu, Seoul, 110-744, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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117
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Martinez M, Pallares F, Soler M, Agut A. Relationship between ultrasonographic and histopathological measurements of small intestinal wall layers in fresh cat cadavers. Vet J 2018; 237:1-8. [DOI: 10.1016/j.tvjl.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 04/26/2018] [Accepted: 05/01/2018] [Indexed: 12/31/2022]
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118
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Janardhan KS, Jensen H, Clayton NP, Herbert RA. Immunohistochemistry in Investigative and Toxicologic Pathology. Toxicol Pathol 2018; 46:488-510. [PMID: 29966501 PMCID: PMC6033701 DOI: 10.1177/0192623318776907] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Immunohistochemistry (IHC) is a valuable tool in pathology. This review provides a brief description of the technical aspects of IHC and a detailed discussion on the variables that affect the results, interpretation, and reproducibility of IHC results. Lists of antibodies that have and have not worked in IHC on various mouse and rat tissues in our laboratory are provided as a guidance for selection of antibodies. An approach to IHC method optimization is presented. Finally, the critical information that should be included as a part of peer-reviewed manuscript is also discussed.
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Affiliation(s)
| | - Heather Jensen
- The Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Natasha P. Clayton
- The Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Ronald A. Herbert
- The Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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119
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Inoue A, Ohta S, Nitta N, Yoshimura M, Sonoda H, Shimizu T, Tani M, Kushima R, Murata K. Ex vivo MR imaging of colorectal carcinoma before and after formalin fixation: correlation with histopathologic findings. Abdom Radiol (NY) 2018; 43:1524-1530. [PMID: 29492606 DOI: 10.1007/s00261-018-1538-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PURPOSE We aimed to assess and compare ex vivo MRI of resected colorectal carcinoma before and after formalin fixation. METHODS We enrolled 45 consecutive patients (47 carcinomas) who underwent colorectal carcinoma surgery. Specimens underwent two MR scans at 1.5 T (after resection and 24 h after formalin fixation). Two radiologists evaluated all MR images independently regarding T-staging and the subserosal linear architecture. T-stage accuracy and frequency of linear architecture were calculated. A third radiologist measured vertical tumor distance and contrast-to-noise ratio (CNR) of the mucosa, submucosa, muscularis propria, subserosa, and tumor. RESULTS T-stage accuracy compared to histopathology by the two readers was 91.5% and 87.2% before fixation and 91.5% and 85.1% after fixation, respectively. Linear architecture was observed in 11.1% of T2 tumors and 100% of T3 tumors by both readers. The vertical tumor distance between histopathological and MRI findings was well correlated before and after fixation. The measurement error of the vertical tumor distance between before and after fixation was within 3 mm. CNR of the tumor was significantly lower than those of the submucosa and subserosa before and after fixation (p < 0.05). CNRs of the tumor and muscularis propria were decreased after formalin fixation (p < 0.05). CONCLUSIONS Subserosal linear architecture represented fibrosis with tumoral invasion, suggesting a T3-4 tumor. The submucosa and subserosa showed high intensity and the mucosa and muscularis propria showed low intensity compared with tumor. CNRs of the tumor and muscularis propria were decreased by formalin fixation.
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Affiliation(s)
- Akitoshi Inoue
- Department of Radiology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.
| | - Shinichi Ohta
- Department of Radiology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Norihisa Nitta
- Department of Radiology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Masahiro Yoshimura
- Department of Radiology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Hiromichi Sonoda
- Department of Surgery, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Tomoharu Shimizu
- Department of Surgery, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Masaji Tani
- Department of Surgery, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Ryoji Kushima
- Department of Pathology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Kiyoshi Murata
- Department of Radiology, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
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Kramer EE, Steadman PE, Epp JR, Frankland PW, Josselyn SA. Assessing Individual Neuronal Activity Across the Intact Brain: Using Hybridization Chain Reaction (HCR) to DetectArcmRNA Localized to the Nucleus in Volumes of Cleared Brain Tissue. ACTA ACUST UNITED AC 2018; 84:e49. [DOI: 10.1002/cpns.49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Emily E. Kramer
- Program in Neurosciences and Mental Health, Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Sciences, University of Toronto; Toronto Ontario Canada
| | - Patrick E. Steadman
- Program in Neurosciences and Mental Health, Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Sciences, University of Toronto; Toronto Ontario Canada
| | - Jonathan R. Epp
- Program in Neurosciences and Mental Health, Hospital for Sick Children; Toronto Ontario Canada
- Department of Cell Biology and Anatomy, University of Calgary; Calgary Alberta Canada
- Current address: Hotchkiss Brain Institute, Cumming School of Medicine; Calgary Alberta Canada
| | - Paul W. Frankland
- Program in Neurosciences and Mental Health, Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Sciences, University of Toronto; Toronto Ontario Canada
- Department of Psychology, University of Toronto; Toronto Ontario Canada
- Department of Physiology, University of Toronto; Toronto Ontario Canada
- Brain, Mind & Consciousness Program, Canadian Institute for Advanced Research; Toronto Ontario Canada. Child & Brain Development Program, Canadian Institute for Advanced Research; Toronto Ontario Canada
| | - Sheena A. Josselyn
- Program in Neurosciences and Mental Health, Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Sciences, University of Toronto; Toronto Ontario Canada
- Department of Psychology, University of Toronto; Toronto Ontario Canada
- Department of Physiology, University of Toronto; Toronto Ontario Canada
- Brain, Mind & Consciousness Program, Canadian Institute for Advanced Research; Toronto Ontario Canada. Child & Brain Development Program, Canadian Institute for Advanced Research; Toronto Ontario Canada
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Lam-Ubol A, Kitrueangphatchara K, Putthanuparp T, Arayakhun R, Kwanthong R, Choonhawarakorn K. Nonformalin Fixative Agents: A Comparative Study of Fixative Efficacy and Histomorphology. Int J Surg Pathol 2018; 26:701-706. [PMID: 29873279 DOI: 10.1177/1066896918779450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Formalin is a gold standard fixative agent. However, formalin possesses health hazards and is not always available in rural areas. The objective of this study was to compare tissue fixative efficacy of nonformalin fixative agents with formalin. METHODS Oral tissues obtained during impacted tooth removal were collected. The tissue fragments were sectioned and fixed in 4 different fixatives; 30% jaggery, 70% ethanol, 2% mepivacaine with 1:100 000 epinephrine, or formalin for 24 and 72 hours. All specimens were then immersed in formalin for another 24 hours and processed according to standard protocol. Hematoxylin and eosin-stained sections were evaluated by a pathologist. The cellular structure, cellular outline, and quality of staining were graded from 1 to 3 and average fixative efficacy scores were compared using 1-way analysis of variance. Fixative artifacts were described. RESULTS Fixative efficacy scores of 70% ethanol and 30% jaggery at 24 and 72 hours were not statistically different from those of formalin. Conversely, 2% mepivacaine demonstrated significantly lower fixative efficacy scores than other agents. Although efficacy of each fixative was not statistically different between 24 and 72 hours, efficacy of 70% ethanol was markedly reduced at 72 hours when compared with others. Acantholysis of epithelial cells was the most notable artifact at 72 hours when fixed with nonformalin fixative agents. CONCLUSION Both 70% ethanol and 30% jaggery provided acceptable fixative efficacy at 24 hours. However, only 30% jaggery maintained fixative efficacy at 72 hours. Nevertheless, negative effects on the epithelial cells were unavoidable and should be interpreted with caution.
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122
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Aljdaimi A, Devlin H, Dickinson M, Alfutimie A. Effect of 2.94 µm Er: YAG laser on the chemical composition of hard tissues. Microsc Res Tech 2018; 81:887-896. [PMID: 29785759 DOI: 10.1002/jemt.23051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/23/2018] [Accepted: 04/18/2018] [Indexed: 11/06/2022]
Abstract
The aim was to investigate the effect of the Er-YAG laser radiation on morphology and chemical composition of enamel, dentin, and bone. The specimens of the three groups were irradiated with a very long pulse mode (VLP) of 2.94 µm Er-YAG laser with 100 mJ pulse energy and energy density of 8.42 J/ c m 2 for 30 s, at a repetition rate of 15 Hz. The organic and inorganic content of the samples were investigated by Fourier Transforms Infrared spectroscopy (FTIR). The morphological characteristics were investigated with scanning electron microscopy (SEM) and elemental analysis (calcium and phosphorus) with energy-dispersive X-ray spectroscopy (EDX). FTIR data were analyzed with a One-Way ANCOVA test and EDX data with the independent sample t-test. Following the laser radiation, FTIR showed a significant decrease in the organic content of all tissues. The weight percentage (wt %) calcium content of dentin and bone increased significantly following irradiation with a p-value of .002 for both tissues, but the wt % of phosphorus content was not influenced significantly. The morphological alterations expressed signs of fusion in all the samples.
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Affiliation(s)
- Abtesam Aljdaimi
- Division of Dentistry, University of Manchester, United Kingdom.,College of Dentistry, Asmarya University, Libya
| | - Hugh Devlin
- Division of Dentistry, University of Manchester, United Kingdom
| | - Mark Dickinson
- Photon Science Institute, School of Physics and Astronomy, University of Manchester, United Kingdom
| | - Abdullatif Alfutimie
- School of Chemical Engineering and Analytical Science, University of Manchester, United Kingdom
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123
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Kresse SH, Namløs HM, Lorenz S, Berner JM, Myklebost O, Bjerkehagen B, Meza-Zepeda LA. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples. PLoS One 2018; 13:e0197456. [PMID: 29771965 PMCID: PMC5957415 DOI: 10.1371/journal.pone.0197456] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.
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Affiliation(s)
- Stine H. Kresse
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Heidi M. Namløs
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Jeanne-Marie Berner
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Leonardo A. Meza-Zepeda
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- * E-mail:
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Lepert G, Gouveia RM, Connon CJ, Paterson C. Assessing corneal biomechanics with Brillouin spectro-microscopy. Faraday Discuss 2018; 187:415-28. [PMID: 27051893 DOI: 10.1039/c5fd00152h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new Brillouin spectro-microscope was designed and built to investigate the mechanical properties of bovine and human corneas. This instrument integrates a single-stage virtually imaged phased array spectrometer with a novel adaptive-optics interferometric filter to achieve unprecedented rejection of the elastic background signal. As a result, highly-resolved, reproducible data from both thin and thick collagen-based materials were obtained. In particular, this technique is capable of rigorously measuring the relative stiffness of different areas of human corneas, thus providing a true non-contact method to characterise the fundamental mechanical features of both live and fixed biological tissue samples.
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Affiliation(s)
- Guillaume Lepert
- Imperial College London, Blackett Laboratory, London, SW7 2BW, UK.
| | - Ricardo M Gouveia
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Che J Connon
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Carl Paterson
- Imperial College London, Blackett Laboratory, London, SW7 2BW, UK.
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Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics. J Pharm Biomed Anal 2018; 155:125-134. [PMID: 29627729 DOI: 10.1016/j.jpba.2018.03.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 02/07/2023]
Abstract
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.
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126
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Jansen I, Lucas M, Savci-Heijink CD, Meijer SL, Marquering HA, de Bruin DM, Zondervan PJ. Histopathology: ditch the slides, because digital and 3D are on show. World J Urol 2018; 36:549-555. [PMID: 29396786 PMCID: PMC5871638 DOI: 10.1007/s00345-018-2202-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/19/2018] [Indexed: 02/08/2023] Open
Abstract
Due to the growing field of digital pathology, more and more digital histology slides are becoming available. This improves the accessibility, allows teleconsultations from specialized pathologists, improves education, and might give urologist the possibility to review the slides in patient management systems. Moreover, by stacking multiple two-dimensional (2D) digital slides, three-dimensional volumes can be created, allowing improved insight in the growth pattern of a tumor. With the addition of computer-aided diagnosis systems, pathologist can be guided to regions of interest, potentially reducing the workload and interobserver variation. Digital (3D) pathology has the potential to improve dialog between the pathologist and urologist, and, therefore, results in a better treatment selection for urologic patients.
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Affiliation(s)
- Ilaria Jansen
- Department of Urology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Marit Lucas
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Sybren L. Meijer
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Henk A. Marquering
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
- Department of Radiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Daniel M. de Bruin
- Department of Urology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Patricia J. Zondervan
- Department of Urology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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127
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Sinha N, Nayak MT, Sunitha JD, Dawar G, Rallan N, Gupta S. Comparitive efficacies of a natural fixative with a conventional fixative. J Oral Maxillofac Pathol 2018; 21:458. [PMID: 29391731 PMCID: PMC5763879 DOI: 10.4103/jomfp.jomfp_236_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Introduction: The quest for formalin substitutes has long been going on due to its health hazards. Honey has been recognized as a safe substitute for formalin. However, we explored jaggery as a natural substitute for formalin. The aim of this study was to compare the tissue fixation abilities of jaggery syrup (30%) with that of 10% neutral-buffered formalin (NBF) and to determine the best fixative among both. Materials and Methods: A study was conducted with 65 pathological tissues. Each specimen was divided into two equal parts. One part was fixed in 30% jaggery solution (Group A), while the other half was fixed in 10% NBF solution (Group B). 24 h tissue fixation was attained at room temperature followed by evaluation of pre- and post-fixation, tissue shrinkage, weight difference and ease of sectioning, followed by evaluation of conventional processing and staining. The histomorphological assessment for each slide was made based on evaluation of cellular outline, cytoplasmic details, nuclear details, staining quality and overall morphology under light microscopy. Each criterion was rated on a scale of 1–4. Nominal categorical data between the groups were compared using Chi-squared test. Results: The preservation of tissue specimen by jaggery syrup was comparable to that of formalin and surprisingly overall nuclear detail of the tissue was better than conventional formalin fixative. Conclusion: Jaggery can be successfully adopted in routine histopathology laboratories in place of formalin.
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Affiliation(s)
- Nidhi Sinha
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
| | - Meghanand T Nayak
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
| | - J D Sunitha
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
| | - Geetanshu Dawar
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
| | - Neelakshi Rallan
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
| | - Shreya Gupta
- Department of Oral Pathology and Microbiology, Teerthanker Mahaveer Dental College and Research Centre, Moradabad, Uttar Pradesh, India
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Giraldo A, Talavera López J, Fernandez-Del-Palacio MJ, García-Nicolás O, Seva J, Brooks G, Moraleda JM. Percutaneous Contrast Echocardiography-guided Intramyocardial Injection and Cell Delivery in a Large Preclinical Model. J Vis Exp 2018:56699. [PMID: 29443073 PMCID: PMC5908667 DOI: 10.3791/56699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cell and gene therapy are exciting and promising strategies for the purpose of cardiac regeneration in the setting of heart failure with reduced ejection fraction (HFrEF). Before they can be considered for use, and implemented in humans, extensive preclinical studies are required in large animal models to evaluate the safety, efficacy, and fate of the injectate (e.g., stem cells) once delivered into the myocardium. Small rodent models offer advantages (e.g., cost effectiveness, amenability for genetic manipulation); however, given inherent limitations of these models, the findings in these rarely translate into the clinic. Conversely, large animal models such as rabbits, have advantages (e.g., similar cardiac electrophysiology compared to humans and other large animals), whilst retaining a good cost-effective balance. Here, we demonstrate how to perform a percutaneous contrast echocardiography-guided intramyocardial injection (IMI) technique, which is minimally invasive, safe, well tolerated, and very effective in the targeted delivery of injectates, including cells, into several locations within the myocardium of a rabbit model. For the implementation of this technique, we also have taken advantage of a widely available clinical echocardiography system. After putting in practice the protocol described here, a researcher with basic ultrasound knowledge will become competent in the performance of this versatile and minimally invasive technique for routine use in experiments, aimed at hypothesis testing of the capabilities of cardiac regenerative therapeutics in the rabbit model. Once competency is achieved, the whole procedure can be performed within 25 min after anaesthetizing the rabbit.
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Affiliation(s)
- Alejandro Giraldo
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading;
| | - Jesús Talavera López
- Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad de Murcia;
| | | | - Obdulio García-Nicolás
- Institute of Virology and Immunology (IVI); Departamento de Anatomía y Anatomía Comparada, Facultad de Veterinaria, Universidad de Murcia
| | - Juan Seva
- Departamento de Anatomía y Anatomía Comparada, Facultad de Veterinaria, Universidad de Murcia
| | - Gavin Brooks
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading
| | - José María Moraleda
- Unidad de Trasplante Hematopoyético y Terapia Celular, Departamento de Hematología, Hospital Universitario Virgen de la Arrixaca, IMIB, Universidad de Murcia
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Lutter JC, Zaleski CM, Pecoraro VL. Metallacrowns: Supramolecular Constructs With Potential in Extended Solids, Solution-State Dynamics, Molecular Magnetism, and Imaging. ADVANCES IN INORGANIC CHEMISTRY 2018. [DOI: 10.1016/bs.adioch.2017.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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130
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Moorcraft SY, Gonzalez de Castro D, Cunningham D, Jones T, Walker BA, Peckitt C, Yuan LC, Frampton M, Begum R, Eltahir Z, Wotherspoon A, Teixeira Mendes LS, Hulkki Wilson S, Gillbanks A, Baratelli C, Fotiadis N, Patel A, Braconi C, Valeri N, Gerlinger M, Rao S, Watkins D, Chau I, Starling N. Investigating the feasibility of tumour molecular profiling in gastrointestinal malignancies in routine clinical practice. Ann Oncol 2018; 29:230-236. [PMID: 29361134 DOI: 10.1093/annonc/mdx631] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Targeted capture sequencing can potentially facilitate precision medicine, but the feasibility of this approach in gastrointestinal (GI) malignancies is unknown. Patients and methods The FOrMAT (Feasibility of a Molecular Characterisation Approach to Treatment) study was a feasibility study enrolling patients with advanced GI malignancies from February 2014 to November 2015. Targeted capture sequencing (mainly using archival formalin-fixed paraffin-embedded diagnostic/resection samples) was carried out to detect mutations, copy number variations and translocations in up to 46 genes which had prognostic/predictive significance or were targets in current/upcoming clinical trials. Results Of the 222 patients recruited, 215 patients (96.8%) had available tissue samples, 125 patients (56.3%) had ≥16 genes successfully sequenced and 136 patients (61.2%) had ≥1 genes successfully sequenced. Sample characteristics influenced the proportion of successfully sequenced samples, e.g. tumour type (colorectal 70.9%, biliary 52.6%, oesophagogastric 50.7%, pancreas 27.3%, P = 0.002), tumour cellularity (high versus low: 78.3% versus 13.3%, P ≤ 0.001), tumour content (high versus low: 78.6% versus 27.3%, P = 0.001) and type of sample (resection versus biopsy: 82.4% versus 47.6%, P ≤ 0.001). Currently, actionable alterations were detected in 90 (40.5%) of the 222 patients recruited (66% of the 136 patients sequenced) and 2 patients subsequently received a targeted therapy. The most frequently detected currently actionable alterations were mutations in KRAS, BRAF, TP53 and PIK3CA. For the 205 patients with archival samples, the median time to obtain sequencing results was 18.9 weeks, including a median of 4.9 weeks for sample retrieval and 5.1 weeks for sequencing. Conclusions Targeted sequencing detected actionable alterations in formalin-fixed paraffin-embedded samples, but tissue characteristics are of critical importance in determining sequencing success. Routine molecular profiling of GI tumours outside of clinical trials is not an effective use of healthcare resources unless more targeted drugs become available. ClinicalTrials.gov identifier NCT02112357.
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Affiliation(s)
- S Y Moorcraft
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - D Gonzalez de Castro
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - D Cunningham
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - T Jones
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - B A Walker
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - C Peckitt
- Department of Statistics, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - L C Yuan
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - M Frampton
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - R Begum
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Z Eltahir
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - A Wotherspoon
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - L S Teixeira Mendes
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - S Hulkki Wilson
- Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - A Gillbanks
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - C Baratelli
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - N Fotiadis
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - A Patel
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - C Braconi
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
- The Institute of Cancer Research, London and Sutton, UK
| | - N Valeri
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
- The Institute of Cancer Research, London and Sutton, UK
| | - M Gerlinger
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
- The Institute of Cancer Research, London and Sutton, UK
| | - S Rao
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - D Watkins
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - I Chau
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - N Starling
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London and Sutton, UK
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Bouatou Y, Kers J, Chevalier-Florquin MSN, Claessen N, Nguyen TQ, Damman J, Proença H, Roelofs JJTH, Florquin S. Diagnostic accuracy of immunofluorescence versus immunoperoxidase staining to distinguish immune complex-mediated glomerulonephritis and C3 dominant glomerulopathy. Histopathology 2017; 72:601-608. [PMID: 28881045 DOI: 10.1111/his.13385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/03/2017] [Indexed: 11/29/2022]
Abstract
AIMS The technique used for classification of membranoproliferative glomerulonephritis (MPGN) has been changed from an electron microscopy-based to an immunofluorescence (IF)-based semiquantitative technique with immunoperoxidase (IP) staining as a backup option when IF is not possible. Since data on that matter is lacking, our aims were to study the interobserver variability, the correlation and the reclassification of MPGN based on these two techniques. METHODS AND RESULTS We retrospectively analysed cases of type 1 MPGN. We repeated IF staining and performed IP staining for IgG, kappa, lambda, C3c and C4d in 35 renal biopsies, among which 19 biopsies had matched IP and IF samples. We observed substantial to near-perfect agreement among the seven observers for both IF and IP (W coefficients from 0.66 for IF lambda to 0.89 for IF C4d). Of the 19 cases with matched IP and IF samples, five (26%) turned out to have different diagnoses on IF and on IP. Also, the ability of C4d to discriminate immune complex-mediated glomerulonephritis (ICGN) from C3 glomerulopathy (C3G) was poor, with areas under the curve of 0.44 [95% confidence interval (CI) 0.24-0.63] and 0.66 (95% CI 0.50-0.81) for the receiver operating characteristic curves of IF and IP respectively. Limitations include the fact that no clinical data regarding complement activation were available. CONCLUSION The diagnosis of ICGN versus C3GN depends on the immunochemical technique used. Also, the use of C4d failed to discriminate ICGN from C3G in our study. Further validation studies are required to avoid misdiagnosis based on kidney biopsy.
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Affiliation(s)
- Yassine Bouatou
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.,Division of Nephrology, Geneva University Hospitals, Geneva, Switzerland
| | - Jesper Kers
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Nike Claessen
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Tri Q Nguyen
- Department of Pathology, University Medical Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jeffrey Damman
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Henrique Proença
- Department of Pathology, Hospital do Rim e Hipertensão, São Paulo, Brazil
| | - Joris J T H Roelofs
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Sandrine Florquin
- Department of Pathology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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Becker RA, Cluff K, Duraisamy N, Casale GP, Pipinos II. Analysis of ischemic muscle in patients with peripheral artery disease using X-ray spectroscopy. J Surg Res 2017; 220:79-87. [PMID: 29180215 PMCID: PMC5708859 DOI: 10.1016/j.jss.2017.06.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/23/2017] [Accepted: 06/28/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND Peripheral artery disease (PAD) is a vascular disease caused by atherosclerosis, resulting in decreased blood flow to the lower extremities. The ankle-brachial index (ABI) is a standard PAD diagnostic test but only identifies reduced blood flow based on blood pressure differences. The early signs of PAD manifest themselves not only at a clinical level but also at an elemental and biochemical level. However, the biochemical and elemental alterations to PAD muscle are not well understood. The objective of this study was to compare fundamental changes in intracellular elemental compositions between control, claudicating, and critical limb ischemia muscle tissue. MATERIALS AND METHODS Gastrocnemius biopsies from three subjects including one control (ABI ≥ 0.9), one claudicating (0.4 ≤ ABI < 0.9), and one critical limb ischemia patient (ABI < 0.4) were evaluated using a scanning electron microscope and energy dispersive X-ray spectroscopy to quantify differences in elemental compositions. Spectra were collected for five myofibers per specimen. An analysis of variance was performed to identify significant differences in muscle elemental compositions. RESULTS This study revealed that intracellular magnesium and calcium were lower in PAD compared with control myofibers, whereas sulfur was higher. Magnesium and calcium are antagonistic, meaning, if magnesium concentrations go down calcium concentrations should go up. However, our findings do not support this antagonism in PAD. Our analysis found decreases in sodium and potassium, in PAD myofibers. CONCLUSIONS These findings may provide insight into the pathologic mechanisms that may operate in ischemic muscle and aid in the development of specialized preventive and rehabilitative treatment plans for PAD patients.
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Affiliation(s)
- Ryan A Becker
- Biomedical Engineering Department, Wichita State University, Wichita, Kansas
| | - Kim Cluff
- Biomedical Engineering Department, Wichita State University, Wichita, Kansas.
| | | | - George P Casale
- Division of General Surgery, Department of Surgery, University of Nebraska Medical Center, Omaha, Nebraska
| | - Iraklis I Pipinos
- Division of General Surgery, Department of Surgery, University of Nebraska Medical Center, Omaha, Nebraska; Department of VA Research Service, VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska
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Undurraga M, Catarino R, Navarria I, Ibrahim Y, Puget E, Royannez Drevard I, Pache JC, Tille JC, Petignat P. User perception of endocervical sampling: A randomized comparison of endocervical evaluation with the curette vs cytobrush. PLoS One 2017; 12:e0186812. [PMID: 29107949 PMCID: PMC5673173 DOI: 10.1371/journal.pone.0186812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022] Open
Abstract
Objectives To evaluate whether the endocervical brush (ECB) is better accepted by patients and health care providers for endocervical evaluation when compared to the endocervical curette (ECC), without a decrease in the quality of sampling. Methods Two hundred patients with cervical dysplasia were randomized at the colposcopy clinic of the University Hospital of Geneva into two groups according to technique. Patients and physicians’ preference regarding the technique as well as the quality of samples were assessed. ECB samples were analyzed using both cytological (cell block) and histologic analysis, while ECC samples were analyzed using standard histologic analysis. Results Of the 200 patients, 89 were randomized to ECC, 101 to ECB and 10 were excluded due to incomplete information or cervical stenosis. Physicians preferred ECB against ECC, classifying it more frequently as an easy technique (94.1% vs.61.4%, p<0.001). Physicians more frequently evaluated the ECB as little or not uncomfortable for patients (28.7% vs.10.2%, p<0.001), though patients themselves didn’t express a preference for either technique. From a quality standpoint, the brush allowed for a better quality of samples, with a lower rate of inadequate samples (2.0% vs 14.3%, p = 0.002) and greater amount of material. Conclusion Endocervical sampling using ECB seems to be easier to perform and provides better quality samples. ECB can therefore be an acceptable alternative to ECC in standard practice. Trial registration ClinicalTrials.gov NCT01435590
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Affiliation(s)
- Manuela Undurraga
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
- * E-mail:
| | - Rosa Catarino
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Isabelle Navarria
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Yasmine Ibrahim
- Division of Clinical Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Evelyne Puget
- Division of Clinical Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Isabelle Royannez Drevard
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Jean-Claude Pache
- Division of Clinical Pathology, Geneva University Hospitals, Geneva, Switzerland
| | | | - Patrick Petignat
- Division of Gynecology, Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
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Mena M, Lloveras B, Tous S, Bogers J, Maffini F, Gangane N, Kumar RV, Somanathan T, Lucas E, Anantharaman D, Gheit T, Castellsagué X, Pawlita M, de Sanjosé S, Alemany L, Tommasino M. Development and validation of a protocol for optimizing the use of paraffin blocks in molecular epidemiological studies: The example from the HPV-AHEAD study. PLoS One 2017; 12:e0184520. [PMID: 29036167 PMCID: PMC5642890 DOI: 10.1371/journal.pone.0184520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/27/2017] [Indexed: 12/11/2022] Open
Abstract
Worldwide use of formalin-fixed paraffin-embedded blocks (FFPE) is extensive in diagnosis and research. Yet, there is a lack of optimized/standardized protocols to process the blocks and verify the quality and presence of the targeted tissue. In the context of an international study on head and neck cancer (HNC)-HPV-AHEAD, a standardized protocol for optimizing the use of FFPEs in molecular epidemiology was developed and validated. First, a protocol for sectioning the FFPE was developed to prevent cross-contamination and distributed between participating centers. Before processing blocks, all sectioning centers underwent a quality control to guarantee a satisfactory training process. The first and last sections of the FFPEs were used for histopathological assessment. A consensus histopathology evaluation form was developed by an international panel of pathologists and evaluated for four indicators in a pilot analysis in order to validate it: 1) presence/type of tumor tissue, 2) identification of other tissue components that could affect the molecular diagnosis and 3) quality of the tissue. No HPV DNA was found in sections from empty FFPE generated in any histology laboratories of HPV-AHEAD consortium and all centers passed quality assurance for processing after quality control. The pilot analysis to validate the histopathology form included 355 HNC cases. The form was filled by six pathologists and each case was randomly assigned to two of them. Most samples (86%) were considered satisfactory. Presence of >50% of invasive carcinoma was observed in all sections of 66% of cases. Substantial necrosis (>50%) was present in <2% of samples. The concordance for the indicators targeted to validate the histopathology form was very high (kappa > 0.85) between first and last sections and fair to high between pathologists (kappa/pabak 0.21-0.72). The protocol allowed to correctly process without signs of contamination all FFPE of the study. The histopathology evaluation of the cases assured the presence of the targeted tissue, identified the presence of other tissues that could disturb the molecular diagnosis and allowed the assessment of tissue quality.
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Affiliation(s)
- Marisa Mena
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO)-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER in primary and secondary prevention of viral induced cancers (CIBERONC), Madrid, Spain
| | - Belen Lloveras
- Department of Pathology. Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Sara Tous
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO)-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER in primary and secondary prevention of viral induced cancers (CIBERONC), Madrid, Spain
| | - Johannes Bogers
- Laboratory of cell biology and histology, University of Antwerp, Antwerp, Belgium
| | - Fausto Maffini
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, India
| | | | | | - Eric Lucas
- International Agency for Research on Cancer, Lyon, France
| | - Devasena Anantharaman
- International Agency for Research on Cancer, Lyon, France
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
| | - Xavier Castellsagué
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO)-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Michael Pawlita
- Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Silvia de Sanjosé
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO)-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Laia Alemany
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO)-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Mehrnezhad A, Park K. Multifrequency Optomechanical Stiffness Measurement of Single Adherent Cells on a Solid Substrate with High Throughput. Anal Chem 2017; 89:10841-10849. [PMID: 28895727 DOI: 10.1021/acs.analchem.7b02356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mechanical properties of a cell reflect its biological and pathological conditions and there have been active research efforts to develop high-throughput platforms to mechanically characterize single cells. Yet, many of these research efforts are focused on suspended cells and use a flow-through configuration. In this paper, the stiffness of single adherent cells are optomechanically characterized using the vibration-induced phase shift (VIPS) without detaching them from the substrate. With the VIPS measurements, the frequency and amplitude dependency of the cell stiffness is investigated and statistically significant difference in the cell stiffness is confirmed after exposure to various drugs affecting cytoskeleton network. Furthermore, a 3-dimensional finite element model of a cell on a vibrating substrate is developed to extract the mechanical property from the measured VIPS. The developed technique can characterize the mechanical properties of single adherent cells at multiple frequencies with high throughput and will provide valuable clues in understanding cell mechanics.
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Affiliation(s)
- Ali Mehrnezhad
- Division of Electrical and Computer Engineering, Electrical Engineering Building, Louisiana State University , Baton Rouge, Louisiana 70809, United States
| | - Kidong Park
- Division of Electrical and Computer Engineering, Electrical Engineering Building, Louisiana State University , Baton Rouge, Louisiana 70809, United States
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Martinić I, Eliseeva SV, Nguyen TN, Foucher F, Gosset D, Westall F, Pecoraro VL, Petoud S. Near-infrared luminescent metallacrowns for combined in vitro cell fixation and counter staining. Chem Sci 2017; 8:6042-6050. [PMID: 28989634 PMCID: PMC5625569 DOI: 10.1039/c7sc01872j] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/21/2017] [Indexed: 01/01/2023] Open
Abstract
Cell fixation is an essential approach for preserving cell morphology, allowing the targeting and labelling of biomolecules with fluorescent probes. One of the key requirements for more efficient fluorescent labelling is the preservation of cell morphology, which usually requires a combination of several fixation techniques. In addition, the use of a counter stain is often essential to improve the contrast of the fluorescent probes. Current agents possess significant limitations, such as low resistance toward photobleaching and sensitivity to changes in the microenvironment. Luminescent Ln3+ 'encapsulated sandwich' metallacrowns (MCs) overcome these drawbacks and offer complementary advantages. In particular, they emit sharp emission bands, possess a large difference between excitation and emission wavelengths and do not photobleach. Herein, MCs formed with pyrazinehydroxamic acid (Ln3+[Zn(ii)MCpyzHA], Ln3+ = Yb, Nd) were used, combined with near-infrared (NIR) counter staining and fixation agents for HeLa cells upon an initial five minute exposure to UV-A light. The validity and quality of the cell fixation were assessed with Raman spectroscopy. Analysis of the NIR luminescence properties of these MCs was performed under different experimental conditions, including in a suspension of stained cells. Moreover, the high emission intensity of Ln3+[Zn(ii)MCpyzHA] in the NIR region allows these MCs to be used for imaging with standard CCD cameras installed on routine fluorescence microscopes. Finally, the NIR-emitting Ln3+[Zn(ii)MCpyzHA] compounds combine, within a single molecule, features such as cell fixation and staining abilities, good photostability and minimal sensitivity of the emission bands to the local microenvironment, and they are highly promising for establishing the next generation of imaging agents with a single biodistribution.
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Affiliation(s)
- Ivana Martinić
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
| | - Svetlana V Eliseeva
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
| | - Tu N Nguyen
- Department of Chemistry , Willard H. Dow Laboratories , University of Michigan , 930 N. University Ave , Michigan 48109 , USA .
| | - Frédéric Foucher
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
| | - David Gosset
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
| | - Frances Westall
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
| | - Vincent L Pecoraro
- Department of Chemistry , Willard H. Dow Laboratories , University of Michigan , 930 N. University Ave , Michigan 48109 , USA .
| | - Stéphane Petoud
- Centre de Biophysique Moléculaire , CNRS , UPR 4301 , 45071 Orléans Cedex 2 , France . ;
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Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H. Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses 2017; 9:E200. [PMID: 28749451 PMCID: PMC5580457 DOI: 10.3390/v9080200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees. Here, we determined two complete variola virus genomes from human tissues kept in a museum in Prague dating back 60 and 160 years, respectively. Moreover, mass spectrometry-based proteomic, chemical, and microscopic examinations were performed. The 60-year-old specimen was most likely an importation from India, a country with endemic smallpox at that time. The genome of the 160-year-old specimen is related to clade 2 West African and variola minor strains. This sequence likely represents a new endemic European variant of variola virus circulating in the midst of the 19th century in Europe.
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Affiliation(s)
- Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Hana Kabíckova
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Libor Písa
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Pavel Aganov
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Karel Fucik
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Tomas Hron
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Vitezslav Kuzelka
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Petr Velemínsky
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Jana Klimentova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Alena Fucikova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Jaroslav Pejchal
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Rita Hrabakova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Tobias Rausch
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Pavel Dundr
- Institute of Pathology of the First Faculty of Medicine and General Teaching Hospital, Studničkova 2, 128 00 Prague, Czech Republic.
| | - Alexander Pilin
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Radomir Cabala
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 166 10 Praha 6, Czech Republic.
| | - Jan Stríbrny
- Military Institute of Forensic Medicine, Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6.
| | - Markus H Antwerpen
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
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138
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Abstract
Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.
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Affiliation(s)
- Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wai-Lung Ng
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Steve M Gentleman
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Research Center of Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Joint Laboratory of Jinan University and The University of Hong Kong, GHM Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
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139
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Blowes LM, Egertová M, Liu Y, Davis GR, Terrill NJ, Gupta HS, Elphick MR. Body wall structure in the starfish Asterias rubens. J Anat 2017; 231:325-341. [PMID: 28714118 PMCID: PMC5554833 DOI: 10.1111/joa.12646] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/25/2022] Open
Abstract
The body wall of starfish is composed of magnesium calcite ossicles connected by collagenous tissue and muscles and it exhibits remarkable variability in stiffness, which is attributed to the mechanical mutability of the collagenous component. Using the common European starfish Asterias rubens as an experimental animal, here we have employed a variety of techniques to gain new insights into the structure of the starfish body wall. The structure and organisation of muscular and collagenous components of the body wall were analysed using trichrome staining. The muscle system comprises interossicular muscles as well as muscle strands that connect ossicles with the circular muscle layer of the coelomic lining. The collagenous tissue surrounding the ossicle network contains collagen fibres that form loop-shaped straps that wrap around calcite struts near to the surface of ossicles. The 3D architecture of the calcareous endoskeleton was visualised for the first time using X-ray microtomography, revealing the shapes and interactions of different ossicle types. Furthermore, analysis of the anatomical organisation of the ossicles indicates how changes in body shape may be achieved by local contraction/relaxation of interossicular muscles. Scanning synchrotron small-angle X-ray diffraction (SAXD) scans of the starfish aboral body wall and ambulacrum were used to study the collagenous tissue component at the fibrillar level. Collagen fibrils in aboral body wall were found to exhibit variable degrees of alignment, with high levels of alignment probably corresponding to regions where collagenous tissue is under tension. Collagen fibrils in the ambulacrum had a uniformly low degree of orientation, attributed to macrocrimp of the fibrils and the presence of slanted as well as horizontal fibrils connecting antimeric ambulacral ossicles. Body wall collagen fibril D-period lengths were similar to previously reported mammalian D-periods, but were significantly different between the aboral and ambulacral samples. The overlap/D-period length ratio within fibrils was higher than reported for mammalian tissues. Collectively, the data reported here provide new insights into the anatomy of the body wall in A. rubens and a foundation for further studies investigating the structural basis of the mechanical properties of echinoderm body wall tissue composites.
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Affiliation(s)
- Liisa M Blowes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK.,School of Engineering & Materials Science, Queen Mary University of London, London, UK
| | - Michaela Egertová
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Yankai Liu
- School of Engineering & Materials Science, Queen Mary University of London, London, UK
| | - Graham R Davis
- Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Himadri S Gupta
- School of Engineering & Materials Science, Queen Mary University of London, London, UK
| | - Maurice R Elphick
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
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140
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Berry AB. Analytic inquiry: Validation and practical considerations. Cancer Cytopathol 2017; 125:465-469. [DOI: 10.1002/cncy.21871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Anna B. Berry
- CellNetix Pathology and Laboratories LLC; Seattle Washington
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141
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Gel-forming mucins form distinct morphologic structures in airways. Proc Natl Acad Sci U S A 2017; 114:6842-6847. [PMID: 28607090 PMCID: PMC5495256 DOI: 10.1073/pnas.1703228114] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gel-forming mucins, the primary macromolecular components of airway mucus, facilitate airway clearance by mucociliary transport. In cystic fibrosis (CF) altered mucus properties impair mucociliary transport. Airways primarily secrete two closely related gel-forming mucins, MUC5B and MUC5AC. However, their morphologic structures and associations in airways that contain abundant submucosal glands and goblet cells are uncertain. Moreover, there is limited knowledge about mucins in airways not affected by inflammation, infection, or remodeling or in CF airways. Therefore, we examined airways freshly excised from newborn non-CF pigs and CF pigs before secondary manifestations develop. We found that porcine submucosal glands produce MUC5B, whereas goblet cells produce predominantly MUC5AC plus some MUC5B. We found that MUC5B emerged from submucosal gland ducts in the form of strands composed of multiple MUC5B filaments. In contrast, MUC5AC emerged from goblet cells as wispy threads and sometimes formed mucin sheets. In addition, MUC5AC often partially coated the MUC5B strands. Compared with non-CF, MUC5B more often filled CF submucosal gland ducts. MUC5AC sheets also accumulated in CF airways overlying MUC5B strands. These results reveal distinct morphology and interactions for MUC5B and MUC5AC and suggest that the two mucins make distinct contributions to mucociliary transport. Thus, they provide a framework for understanding abnormalities in disease.
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142
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Briggs MT, Ho YY, Kaur G, Oehler MK, Everest-Dass AV, Packer NH, Hoffmann P. N-Glycan matrix-assisted laser desorption/ionization mass spectrometry imaging protocol for formalin-fixed paraffin-embedded tissues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:825-841. [PMID: 28271569 DOI: 10.1002/rcm.7845] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) of the proteome of a tissue has been an established technique for the past decade. In the last few years, MALDI-MSI of the N-glycome has emerged as a novel MALDI-MSI technique. To assess the accuracy and clinical significance of the N-linked glycan spatial distribution, we have developed a method that utilises MALDI-MSI followed by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) in order to assign glycan structures to the differentiating MALDI-MSI glycan masses released from the tissue glycoproteins. METHODS AND RESULTS Our workflow presents a comprehensive list of instructions on how to (i) apply MALDI-MSI to spatially map the N-glycome across formalin-fixed paraffin-embedded (FFPE) clinical samples, (ii) structurally characterise N-glycans extracted from consecutive FFPE tissue sections by LC/MS/MS, and (iii) match relevant N-glycan masses from MALDI-MSI with confirmed N-glycan structures determined by LC/MS/MS. CONCLUSIONS Our protocol provides groups that are new to this technique with instructions how to establish N-glycan MALDI-MSI in their laboratory. Furthermore, the method assigns N-glycan structural detail to the masses obtained in the MALDI-MS image. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Matthew T Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia, 5005
| | - Yin Ying Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Martin K Oehler
- Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, 5005, Australia
- Robinson Institute, University of Adelaide, Adelaide, Australia, 5005
| | - Arun V Everest-Dass
- ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, Australia, 5005
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, 2109
| | - Nicolle H Packer
- ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, Australia, 5005
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, 2109
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia, 5005
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143
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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144
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Rouzier R, Roulot A, Jeiranian AH, Ram N, Guinebretiere JM, Salomon AV, Gentien D. Denaturing fixatives are compatible with the NanoString nCounter® platform and the Prosigna® assay. N Biotechnol 2017; 36:37-41. [DOI: 10.1016/j.nbt.2017.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/03/2016] [Accepted: 01/05/2017] [Indexed: 11/29/2022]
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145
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Kim J, Park WY, Kim NKD, Jang SJ, Chun SM, Sung CO, Choi J, Ko YH, Choi YL, Shim HS, Won JK. Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests. J Pathol Transl Med 2017; 51:191-204. [PMID: 28535585 PMCID: PMC5445206 DOI: 10.4132/jptm.2017.03.14] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/14/2017] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.
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Affiliation(s)
- Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nayoung K. D. Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Chang-Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young-Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
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146
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Abstract
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
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Affiliation(s)
- Alexander J. Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- * E-mail:
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147
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Gajda M, Jasztal A, Banasik T, Jasek-Gajda E, Chlopicki S. Combined orcein and martius scarlet blue (OMSB) staining for qualitative and quantitative analyses of atherosclerotic plaques in brachiocephalic arteries in apoE/LDLR -/- mice. Histochem Cell Biol 2017; 147:671-681. [PMID: 28168649 PMCID: PMC5429900 DOI: 10.1007/s00418-017-1538-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2017] [Indexed: 12/23/2022]
Abstract
Numerous cellular and extracellular components should be analyzed in sections of atherosclerotic plaques to assess atherosclerosis progression and vulnerability. Here, we combined orcein (O) staining for elastic fibers and martius scarlet blue (MSB) polychrome to visualize various morphological contents of plaque in brachiocephalic arteries (BCA) of apoE/LDLR−/− mice. Elastic fibers (including broken elastic laminae and ‘buried’ fibrous caps) were stained purple and they could be easily distinguished from collagen fibers (blue). Orcein allowed clear identification of even the finest elastic fibers. Erythrocytes were stained yellow and they could easily be discerned from mature fibrin (red). Old fibrin tends to acquire blue color. The method of OMSB staining is simple, takes less than 1 h to perform and can be adapted to automatic stainers. Most importantly, the color separation is good enough to allow digital automatic segmentation of specific components in tissue section and quantitative analysis of the plaque constituents. OMSB was used to compare atherosclerotic plaques in proximal and distal regions of BCA in apoE/LDLR−/− mice. In conclusion, OMSB staining represents a novel staining that could be routinely used for qualitative and quantitative microscopic assessments of formaldehyde-fixed and paraffin-embedded sections of arteries with atherosclerotic lesions.
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Affiliation(s)
- Mariusz Gajda
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034, Kraków, Poland.
| | - Agnieszka Jasztal
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzyńskiego 14, 30-348, Kraków, Poland
| | - Tomasz Banasik
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzyńskiego 14, 30-348, Kraków, Poland
| | - Ewa Jasek-Gajda
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034, Kraków, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzyńskiego 14, 30-348, Kraków, Poland
- Chair of Pharmacology, Jagiellonian University Medical College, 31-531, Kraków, Poland
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148
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Aboualizadeh E, Carmichael OT, He P, Albarado DC, Morrison CD, Hirschmugl CJ. Quantifying Biochemical Alterations in Brown and Subcutaneous White Adipose Tissues of Mice Using Fourier Transform Infrared Widefield Imaging. Front Endocrinol (Lausanne) 2017; 8:121. [PMID: 28620356 PMCID: PMC5450226 DOI: 10.3389/fendo.2017.00121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023] Open
Abstract
Stimulating increased thermogenic activity in adipose tissue is an important biological target for obesity treatment, and label-free imaging techniques with the potential to quantify stimulation-associated biochemical changes to the adipose tissue are highly sought after. In this study, we used spatially resolved Fourier transform infrared (FTIR) imaging to quantify biochemical changes caused by cold exposure in the brown and subcutaneous white adipose tissues (BAT and s-WAT) of 6 week-old C57BL6 mice exposed to 30°C (N = 5), 24°C (N = 5), and 10°C (N = 5) conditions for 10 days. Fat exposed to colder temperatures demonstrated greater thermogenic activity as indicated by increased messenger RNA expression levels of a panel of thermogenic marker genes including uncoupling protein 1 (UCP-1) and Dio2. Protein to lipid ratio, calculated from the ratio of the integrated area from 1,600 to 1,700 cm-1 (amide I) to the integrated area from 2,830 to 2,980 cm-1 (saturated lipids), was elevated in 10°C BAT and s-WAT compared to 24°C (p = 0.004 and p < 0.0001) and 30°C (p = 0.0033 and p < 0.0001). Greater protein to lipid ratio was associated with greater UCP-1 expression level in the BAT (p = 0.021) and s-WAT (p = 0.032) and greater Dio2 expression in s-WAT (p = 0.033). The degree of unsaturation, calculated from the ratio of the integrated area from 2,992 to 3,020 cm-1 (unsaturated lipids) to the integrated area from 2,830 to 2,980 cm-1 (saturated lipids), showed stepwise decreases going from colder-exposed to warmer-exposed BAT. Complementary 1H NMR measurements confirmed the findings from this ratio in BAT. Principal component analysis applied to FTIR spectra revealed pronounced differences in overall spectral characteristics between 30, 24, and 10°C BAT and s-WAT. Spatially resolved FTIR imaging is a promising technique to quantify cold-induced biochemical changes in BAT and s-WAT in a label-free manner.
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Affiliation(s)
- Ebrahim Aboualizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | | | - Ping He
- Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Diana C. Albarado
- Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | | | - Carol J. Hirschmugl
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
- *Correspondence: Carol J. Hirschmugl,
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149
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Abstract
Mass spectrometry imaging (MSI) has become a valuable tool in cancer research. Even more, due to its capability to directly link molecular changes with histology, it holds the prospect to revolutionize tissue-based diagnostics. In order to learn to walk before running, however, information obtained through classical histology should not be neglected but rather used to its full capacity and integrated with mass spectrometry data to lead to a superior molecular histology synthesis. In order to achieve this, pathomorphological analyses have to be integrated into MSI analyses right from the beginning to avoid errors and pitfalls of MSI application possibly leading to incorrect or imprecise study outcomes. Such errors can be caused by different sample or tissue inherent factors or through factors in sample preparation. Future studies should, therefore, aim for a comprehensive incorporation of histology and pathology characteristics to ensure the generation of high-quality data in MSI to exploit its full capacity in tissue-based basic and translational research.
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150
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Gill EL, Yost RA, Vedam-Mai V, Garrett TJ. Precast Gelatin-Based Molds for Tissue Embedding Compatible with Mass Spectrometry Imaging. Anal Chem 2016; 89:576-580. [PMID: 27935272 DOI: 10.1021/acs.analchem.6b04185] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Preparation of tissue for matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) generally involves embedding the tissue followed by freezing and cryosectioning, usually between 5 and 25 μm thick, depending on the tissue type and the analyte(s) of interest. The brain is approximately 60% fat; it therefore lacks rigidity and poses structural preservation challenges during sample preparation. Histological sample preparation procedures are generally transferable to MALDI-MSI; however, there are various limitations. Optimal cutting temperature compound (OCT) is commonly used to embed and mount fixed tissue onto the chuck inside the cryostat during cryosectioning. However, OCT contains potential interferences that are detrimental to MALDI-MSI, while fixation is undesirable for the analysis of some analytes either due to extraction or chemical modification (i.e., polar metabolites). Therefore, a method for both fixed and fresh tissue compatible with MALDI-MSI and histology is desirable to increase the breadth of analyte(s), maintain the topographies of the brain, and provide rigidity to the fragile tissue while eliminating background interference. The method we introduce uses precast gelatin-based molds in which a whole mouse brain is embedded, flash frozen, and cryosectioned in preparation for mass spectrometry imaging (MSI).
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Affiliation(s)
- Emily L Gill
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida , Gainesville, Florida 32610, United States
| | - Vinata Vedam-Mai
- Department of Neurosurgery, University of Florida , Gainesville, Florida 32610, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida , Gainesville, Florida 32610, United States
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