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Li KYC, Dejea H, De Winne K, Bonnin A, D'Onofrio V, Cox JA, Garcia-Canadilla P, Lammens M, Cook AC, Bijnens B, Dendooven A. Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis. Histochem Cell Biol 2023; 160:377-389. [PMID: 37523091 DOI: 10.1007/s00418-023-02220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/01/2023]
Abstract
X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.
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Affiliation(s)
- Kan Yan Chloe Li
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Hector Dejea
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
- ETH Zurich, Zurich, Switzerland
- Department of Biomedical Engineering, Lund University, Lund, Sweden
- MAX IV Laboratory, Lund, Sweden
| | - Koen De Winne
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Anne Bonnin
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Janneke A Cox
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Patricia Garcia-Canadilla
- Interdisciplinary Cardiovascular Research Group, Sant Joan de Déu Research Institute (IRSJD), Barcelona, Spain
- BCNatal Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Andrew C Cook
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Bart Bijnens
- ICREA, Barcelona, Spain
- IDIBAPS, Barcelona, Spain
| | - Amélie Dendooven
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium.
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.
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2
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Merolle L, Pascolo L, Zupin L, Parisse P, Bonanni V, Gariani G, Kenig S, Bedolla DE, Crovella S, Ricci G, Iotti S, Malucelli E, Kourousias G, Gianoncelli A. Impact of Sample Preparation Methods on Single-Cell X-ray Microscopy and Light Elemental Analysis Evaluated by Combined Low Energy X-ray Fluorescence, STXM and AFM. Molecules 2023; 28:molecules28041992. [PMID: 36838979 PMCID: PMC9962160 DOI: 10.3390/molecules28041992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Although X-ray fluorescence microscopy is becoming a widely used technique for single-cell analysis, sample preparation for this microscopy remains one of the main challenges in obtaining optimal conditions for the measurements in the X-ray regime. The information available to researchers on sample treatment is inadequate and unclear, sometimes leading to wasted time and jeopardizing the experiment's success. Many cell fixation methods have been described, but none of them have been systematically tested and declared the most suitable for synchrotron X-ray microscopy. METHODS The HEC-1-A endometrial cells, human spermatozoa, and human embryonic kidney (HEK-293) cells were fixed with organic solvents and cross-linking methods: 70% ethanol, 3.7%, and 2% paraformaldehyde; in addition, HEK-293 cells were subjected to methanol/ C3H6O treatment and cryofixation. Fixation methods were compared by coupling low-energy X-ray fluorescence with scanning transmission X-ray microscopy and atomic force microscopy. RESULTS Organic solvents lead to greater dehydration of cells, which has the most significant effect on the distribution and depletion of diffusion elements. Paraformaldehyde provides robust and reproducible data. Finally, the cryofixed cells provide the best morphology and element content results. CONCLUSION Although cryofixation seems to be the most appropriate method as it allows for keeping cells closer to physiological conditions, it has some technical limitations. Paraformaldehyde, when used at the average concentration of 3.7%, is also an excellent alternative for X-ray microscopy.
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Affiliation(s)
- Lucia Merolle
- AUSL-IRCCS di Reggio Emilia, Transfusion Medicine Unit, 42123 Reggio Emilia, Italy
| | - Lorella Pascolo
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
| | - Luisa Zupin
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
| | - Pietro Parisse
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, 34149 Trieste, Italy
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Valentina Bonanni
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Gianluca Gariani
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Sasa Kenig
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310 Izola, Slovenia
| | - Diana E. Bedolla
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Science, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
| | - Giuseppe Ricci
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
- Department of Medical, Surgical, and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Emil Malucelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - George Kourousias
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
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Surowka AD, Czyzycki M, Ziomber-Lisiak A, Migliori A, Szczerbowska-Boruchowska M. On 2D-FTIR-XRF microscopy - A step forward correlative tissue studies by infrared and hard X-ray radiation. Ultramicroscopy 2021; 232:113408. [PMID: 34706307 DOI: 10.1016/j.ultramic.2021.113408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/28/2022]
Abstract
Correlative Fourier Transform Infra-Red (FTIR) and hard X-Ray Fluorescence (XRF) microscopy studies of thin biological samples have recently evolved as complementary methods for biochemical fingerprinting of animal/human tissues. These are seen particularly useful for tracking the mechanisms of neurological diseases, i.e., in Alzheimer/Parkinson disease, in the brain where mishandling of trace metals (Fe, Cu, Zn) seems to be often associated with ongoing damage to molecular components via, among others, oxidative/reductive stress neurotoxicity. Despite substantial progress in state-of-the-art detection and data analysis methods, combined FTIR-XRF experiments have never benefited from correlation and co-localization analysis of molecular moieties and chemical elements, respectively. We here propose for the first time a completely novel data analysis pipeline, utilizing the idea of 2D correlation spectrometry for brain tissue analysis. In this paper, we utilized combined benchtop FTIR - synchrotron XRF mapping experiments on thin brain samples mounted on polypropylene membranes. By implementing our recently developed Multiple Linear Regression Multi-Reference (MLR-MR) algorithm, along with advanced image processing, artifact-free 2D FTIR-XRF spectra could be obtained by mitigating the impact of spectral artifacts, such as Etalon fringes and mild scattering Mie-like signatures, in the FTIR data. We demonstrated that the method is a powerful tool for co-localizing and correlating molecular arrangements and chemical elements (and vice versa) using visually attractive 2D correlograms. Moreover, the methods' applicability for fostering the identification of distinct (biological) materials, involving chemical elements and molecular arrangements, is also shown. Taken together, the 2D FTIR-XRF method opens up for new measures for in-situ investigating hidden complex biochemical correlations, and yet unraveled mechanisms in a biological sample. This step seems crucial for developing new strategies for facilitating the research on the interaction of metals/nonmetals with organic components. This is particularly important for enhancing our understanding of the diseases associated with metal/nonmetal mishandling.
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Affiliation(s)
- Artur D Surowka
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. A. Mickiewicza 30, Krakow 30-059, Poland.
| | - Mateusz Czyzycki
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. A. Mickiewicza 30, Krakow 30-059, Poland; Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiser Str. 12, Karlsruhe 76131, Germany; Nuclear Science and Instrumentation Laboratory, International Atomic Energy Agency (IAEA) Laboratories, Seibersdorf, Austria
| | - Agata Ziomber-Lisiak
- Department of Pathophysiology, Jagiellonian University, Medical College, Czysta 18, Krakow 31-121, Poland
| | - Alessandro Migliori
- Nuclear Science and Instrumentation Laboratory, International Atomic Energy Agency (IAEA) Laboratories, Seibersdorf, Austria
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Bedolla DE, Birarda G, Giannotta S, Faoro V, Cescato A, Vaccari L, Gianoncelli A. Oxidation of ultralene and paraffin due to radiation damage after exposure to soft X-rays probed by FTIR microspectroscopy and X-ray fluorescence. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:231-239. [PMID: 33399573 DOI: 10.1107/s160057752001471x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Radiation damage upon soft X-ray exposure is an important issue to be considered in soft X-ray microscopy. The work presented here is part of a more extended study on the topic and focuses on the effects of soft X-rays on paraffin, a common embedding medium for soft-tissues, and on ultralene and Si3N4 windows as sample supports. Our studies suggest that the sample environment indeed plays an important role in the radiation damage process and therefore should be carefully taken into account for the analysis and interpretation of new data. The radiation damage effects were followed over time using a combination of Fourier transform infrared (FTIR) microspectroscopy and X-ray fluorescence (XRF), and it was demonstrated that, for higher doses, an oxidation of both embedding medium and ultralene substrate takes place after the irradiated sample is exposed to air. This oxidation is reflected in a clear increase of C=O and O-H infrared bands and on the XRF oxygen maps, correlated with a decrease of the aliphatic infrared signal. The results also show that the oxidation process may affect quantitative evaluation of light element concentrations.
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Affiliation(s)
- Diana E Bedolla
- Elettra-Sincrotrone Trieste, S.S.14 Km 163.5 in Area Science Park, Basovizza, TS 34149, Italy
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste, S.S.14 Km 163.5 in Area Science Park, Basovizza, TS 34149, Italy
| | - Sabina Giannotta
- Laboratori Riuniti - Synlab, Via delle Mura 2, Trieste, TS 34121, Italy
| | - Valentina Faoro
- Laboratori Riuniti - Synlab, Via delle Mura 2, Trieste, TS 34121, Italy
| | - Alberto Cescato
- Laboratori Riuniti - Synlab, Via delle Mura 2, Trieste, TS 34121, Italy
| | - Lisa Vaccari
- Elettra-Sincrotrone Trieste, S.S.14 Km 163.5 in Area Science Park, Basovizza, TS 34149, Italy
| | - Alessandra Gianoncelli
- Elettra-Sincrotrone Trieste, S.S.14 Km 163.5 in Area Science Park, Basovizza, TS 34149, Italy
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5
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Surowka AD, Gianoncelli A, Birarda G, Sala S, Cefarin N, Matruglio A, Szczerbowska-Boruchowska M, Ziomber-Lisiak A, Vaccari L. Soft X-ray induced radiation damage in thin freeze-dried brain samples studied by FTIR microscopy. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1218-1226. [PMID: 32876596 DOI: 10.1107/s1600577520010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
In order to push the spatial resolution limits to the nanoscale, synchrotron-based soft X-ray microscopy (XRM) experiments require higher radiation doses to be delivered to materials. Nevertheless, the associated radiation damage impacts on the integrity of delicate biological samples. Herein, the extent of soft X-ray radiation damage in popular thin freeze-dried brain tissue samples mounted onto Si3N4 membranes, as highlighted by Fourier transform infrared microscopy (FTIR), is reported. The freeze-dried tissue samples were found to be affected by general degradation of the vibrational architecture, though these effects were weaker than those observed in paraffin-embedded and hydrated systems reported in the literature. In addition, weak, reversible and specific features of the tissue-Si3N4 interaction could be identified for the first time upon routine soft X-ray exposures, further highlighting the complex interplay between the biological sample, its preparation protocol and X-ray probe.
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Affiliation(s)
- Artur D Surowka
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - A Gianoncelli
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - G Birarda
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - S Sala
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - N Cefarin
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - A Matruglio
- Department of Chemical Engineering, University College London, London, United Kingdom
| | - M Szczerbowska-Boruchowska
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, Krakow 30-059, Poland
| | - A Ziomber-Lisiak
- Chair of Pathophysiology, Faculty of Medicine, Jagiellonian University, ul. Czysta 18, Kraków 31-121, Poland
| | - L Vaccari
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
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6
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Melo LGA, Hitchcock AP. Electron beam damage of perfluorosulfonic acid studied by soft X-ray spectromicroscopy. Micron 2019; 121:8-20. [PMID: 30875488 DOI: 10.1016/j.micron.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Scanning transmission X-ray microscopy (STXM) was used to study chemical changes to perfluorosulfonic acid (PFSA) spun cast thin films as a function of dose imparted by exposure of a 200 kV electron beam in a Transmission Electron Microscope (TEM). The relationship between electron beam fluence and absorbed dose was calibrated using a modified version of a protocol based on the positive to negative lithography transition in PMMA [Leontowich et al, J. Synchrotron Rad. 19 (2012) 976]. STXM was used to characterize and quantify the chemical changes caused by electron irradiation of PFSA under several different conditions. The critical dose for CF2-CF2 amorphization was used to explore the effects of the sample environment on electron beam damage. Use of a silicon nitride substrate was found to increase the CF2-CF2 amorphization critical dose by ∼x2 from that for free-standing PFSA films. Freestanding PFSA and PMMA films were damaged by 200 kV electrons at ∼100 K and then the damage was measured by STXM at 300 K (RT). The lithography cross-over dose for PMMA was found to be ∼2x higher when the PMMA thin film was electron irradiated at 120 K rather than at 300 K. The critical dose for CF2-CF2 amorphization in PFSA irradiated at 120 K followed by warming and delayed measurement by STXM at 300 K was found to be ∼2x larger than at 300 K. To place these results in the context of the use of electron microscopy to study PFSA ionomer in fuel cell systems, an exposure of 300 e-/nm2 at 300 K (which corresponds to an absorbed dose of ∼20 MGy) amorphizes ∼10% of the CF2-CF2 bonds in PFSA. At this dose level, the spatial resolution for TEM imaging of PFSA is limited to 3.5 nm by radiation damage, if one is using a direct electron detector with DQE = 1. This work recommends caution about 2D and 3D morphological information of PFSA materials based on TEM studies which use fluences higher than 300 e-/nm2.
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Affiliation(s)
- Lis G A Melo
- Dept. Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S4M1, Canada.
| | - Adam P Hitchcock
- Dept. Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S4M1, Canada
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