1
|
Quantitative Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded (FFPE) Human Cardiac Tissue. Methods Mol Biol 2021; 2261:525-533. [PMID: 33421012 DOI: 10.1007/978-1-0716-1186-9_33] [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: 01/11/2023]
Abstract
Clinical tissue archives represent an invaluable source of biological information. Formalin-fixed, paraffin-embedded (FFPE) tissue can be used for retrospective investigation of biomarkers of diseases and prognosis.Recently, the number of studies using proteome profiling of samples from clinical archives has markedly increased. However, the application of conventional quantitative proteomics technologies remains a challenge mainly due to the harsh fixation process resulting in protein cross-linking and protein degradation. In the present chapter, we demonstrate a protocol for label-free proteomic analysis of FFPE tissue prepared from human cardiac autopsies. The data presented here highlight the applicability and suitability of FFPE heart tissue for understanding the molecular mechanism of cardiac injury using a proteomics approach.
Collapse
|
2
|
Azimzadeh O, Azizova T, Merl-Pham J, Blutke A, Moseeva M, Zubkova O, Anastasov N, Feuchtinger A, Hauck SM, Atkinson MJ, Tapio S. Chronic Occupational Exposure to Ionizing Radiation Induces Alterations in the Structure and Metabolism of the Heart: A Proteomic Analysis of Human Formalin-Fixed Paraffin-Embedded (FFPE) Cardiac Tissue. Int J Mol Sci 2020; 21:ijms21186832. [PMID: 32957660 PMCID: PMC7555548 DOI: 10.3390/ijms21186832] [Citation(s) in RCA: 12] [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: 06/19/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022] Open
Abstract
Epidemiological studies on workers employed at the Mayak plutonium enrichment plant have demonstrated an association between external gamma ray exposure and an elevated risk of ischemic heart disease (IHD). In a previous study using fresh-frozen post mortem samples of the cardiac left ventricle of Mayak workers and non-irradiated controls, we observed radiation-induced alterations in the heart proteome, mainly downregulation of mitochondrial and structural proteins. As the control group available at that time was younger than the irradiated group, we could not exclude age as a confounding factor. To address this issue, we have now expanded our study to investigate additional samples using archival formalin-fixed paraffin-embedded (FFPE) tissue. Importantly, the control group studied here is older than the occupationally exposed (>500 mGy) group. Label-free quantitative proteomics analysis showed that proteins involved in the lipid metabolism, sirtuin signaling, mitochondrial function, cytoskeletal organization, and antioxidant defense were the most affected. A histopathological analysis elucidated large foci of fibrotic tissue, myocardial lipomatosis and lymphocytic infiltrations in the irradiated samples. These data highlight the suitability of FFPE material for proteomics analysis. The study confirms the previous results emphasizing the role of adverse metabolic changes in the radiation-associated IHD. Most importantly, it excludes age at the time of death as a confounding factor.
Collapse
Affiliation(s)
- Omid Azimzadeh
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
- Correspondence: ; Tel.: +49-89-3187-3887
| | - Tamara Azizova
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Juliane Merl-Pham
- Helmholtz Zentrum München—German Research Centre for Environmental Health, Research Unit Protein Science, 80939 Munich, Germany; (J.M.-P.); (S.M.H.)
| | - Andreas Blutke
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Research Unit Analytical Pathology, 85764 Neuherberg, Germany; (A.B.); (A.F.)
| | - Maria Moseeva
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Olga Zubkova
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Natasa Anastasov
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
| | - Annette Feuchtinger
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Research Unit Analytical Pathology, 85764 Neuherberg, Germany; (A.B.); (A.F.)
| | - Stefanie M. Hauck
- Helmholtz Zentrum München—German Research Centre for Environmental Health, Research Unit Protein Science, 80939 Munich, Germany; (J.M.-P.); (S.M.H.)
| | - Michael J. Atkinson
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
- Chair of Radiation Biology, Technical University of Munich, 81675 Munich, Germany
| | - Soile Tapio
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
| |
Collapse
|
3
|
Morioka T, Blyth BJ, Imaoka T, Nishimura M, Takeshita H, Shimomura T, Ohtake J, Ishida A, Schofield P, Grosche B, Kulka U, Shimada Y, Yamada Y, Kakinuma S. Establishing the Japan-Store house of animal radiobiology experiments (J-SHARE), a large-scale necropsy and histopathology archive providing international access to important radiobiology data. Int J Radiat Biol 2019; 95:1372-1377. [PMID: 31145030 DOI: 10.1080/09553002.2019.1625458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Purpose: Projects evaluating the effects of radiation, within the National Institutes of Quantum and Radiological Science and Technology (QST), National Institute of Radiological Sciences (NIRS), have focused on risk analyses for life shortening and cancer prevalence using laboratory animals. Genetic and epigenetic alterations in radiation-induced tumors have been also analyzed with the aim of better understanding mechanisms of radiation carcinogenesis. As well as the economic and practical limitations of repeating such large-scale experiments, ethical considerations make it vital that we store and share the pathological data and samples of the animal experiments for future use. We are now constructing such an archive called the Japan-Storehouse of Animal Radiobiology Experiments (J-SHARE). Methods: J-SHARE records include information such as detailed experimental protocols, necropsy records and photographs of organs at necropsy. For each animal organs and tumor tissues are dissected, and parts are stored as frozen samples at -80 °C. Samples fixed with formalin are also embedded in paraffin blocks for histopathological analyses. Digital copies of stained tissues are being systematically saved using a virtual slide system linked to original records by barcodes. Embedded and frozen tissues are available for molecular analysis. Conclusion: Similar archive systems for radiation biology have also been under construction in the USA and Europe, the Northwestern University Radiation Archive (NURA), and STORE at the BfS, respectively. The J-SHARE will be linked with the sister-archives and made available for collaborative research to institutions and universities all over the world.
Collapse
Affiliation(s)
- Takamitsu Morioka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Benjamin J Blyth
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Tatsuhiko Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Mayumi Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | | | - Takeo Shimomura
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Jun Ohtake
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Atsuro Ishida
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Paul Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge , UK
| | - Bernd Grosche
- Federal Office for Radiation Protection, Radiation and Health , Oberschleissheim , Germany
| | - Ulrike Kulka
- Federal Office for Radiation Protection, Radiation and Health , Oberschleissheim , Germany
| | | | - Yutaka Yamada
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan.,Fukushima Project Headquarters, NIRS, QST , Chiba , Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| |
Collapse
|
4
|
Nakajima T, Wang B, Ono T, Uehara Y, Nakamura S, Ichinohe K, Braga-Tanaka I, Tanaka S, Tanaka K, Nenoi M. Differences in sustained alterations in protein expression between livers of mice exposed to high-dose-rate and low-dose-rate radiation. JOURNAL OF RADIATION RESEARCH 2017; 58:421-429. [PMID: 28201773 PMCID: PMC5570048 DOI: 10.1093/jrr/rrw133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 05/13/2023]
Abstract
Molecular mechanisms of radiation dose-rate effects are not well understood. Among many possibilities, long-lasting sustained alterations in protein levels would provide critical information. To evaluate sustained effects after acute and chronic radiation exposure, we analyzed alterations in protein expression in the livers of mice. Acute exposure consisted of a lethal dose of 8 Gy and a sublethal dose of 4 Gy, with analysis conducted 6 days and 3 months after irradiation, respectively. Chronic irradiation consisted of a total dose of 8 Gy delivered over 400 days (20 mGy/day). Analyses following chronic irradiation were done immediately and at 3 months after the end of the exposure. Based on antibody arrays of protein expression following both acute lethal and sublethal dose exposures, common alterations in the expression of two proteins were detected. In the sublethal dose exposure, the expression of additional proteins was altered 3 months after irradiation. Immunohistochemical analysis showed that the increase in one of the two commonly altered proteins, MyD88, was observed around blood vessels in the liver. The alterations in protein expression after chronic radiation exposure were different from those caused by acute radiation exposures. Alterations in the expression of proteins related to inflammation and apoptosis, such as caspase 12, were observed even at 3 months after the end of the chronic radiation exposure. The alterations in protein expression depended on the dose, the dose rate, and the passage of time after irradiation. These changes could be involved in long-term effects of radiation in the liver.
Collapse
Affiliation(s)
- Tetsuo Nakajima
- National Institute of Radiological Sciences, National Institutes of Quantum and Radiological Science and Technology, 9-1, Anagawa-4-chome, Inage-ku, Chiba-shi 263-8555, Japan
- Corresponding author. National Institute of Radiological Sciences, National Institutes of Quantum and Radiolgical Science and Technology, 9-1, Anagawa-4-chome, Inage-ku, Chiba-shi 263-8555, Japan. Tel: +81-43-206-3086; Fax: +81-43-255-6497;
| | - Bing Wang
- National Institute of Radiological Sciences, National Institutes of Quantum and Radiological Science and Technology, 9-1, Anagawa-4-chome, Inage-ku, Chiba-shi 263-8555, Japan
| | - Tetsuya Ono
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Yoshihiko Uehara
- Department of Cell Biology, Tohoku University School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Shingo Nakamura
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Kazuaki Ichinohe
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Ignacia Braga-Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Satoshi Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Kimio Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Mitsuru Nenoi
- National Institute of Radiological Sciences, National Institutes of Quantum and Radiological Science and Technology, 9-1, Anagawa-4-chome, Inage-ku, Chiba-shi 263-8555, Japan
| |
Collapse
|
5
|
Tóth E, Vékey K, Ozohanics O, Jekő A, Dominczyk I, Widlak P, Drahos L. Changes of protein glycosylation in the course of radiotherapy. J Pharm Biomed Anal 2015; 118:380-386. [PMID: 26609677 DOI: 10.1016/j.jpba.2015.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 01/11/2023]
Abstract
This is the first study of changes in protein glycosylation due to exposure of human subjects to ionizing radiation. Site specific glycosylation patterns of 7 major plasma proteins were analyzed; 171 glycoforms were identified; and the abundance of 99 of these was followed in the course of cancer radiotherapy in 10 individual patients. It was found that glycosylation of plasma proteins does change in response to partial body irradiation (∼ 60 Gy), and the effects last during follow-up; the abundance of some glycoforms changed more than twofold. Both the degree of changes and their time-evolution showed large inter-individual variability.
Collapse
Affiliation(s)
- Eszter Tóth
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; Semmelweis University, School of Ph.D. Studies, Budapest, Hungary
| | - Károly Vékey
- Core Technologies Centre, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anita Jekő
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Iwona Dominczyk
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
| |
Collapse
|
6
|
Trott K, Grosche B. Obituary Georg Gerber (1926-2014). RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:151-153. [PMID: 25583676 DOI: 10.1007/s00411-015-0583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/04/2015] [Indexed: 06/04/2023]
Affiliation(s)
- K Trott
- University of Pavia, Pavia, Italy
| | | |
Collapse
|
7
|
Qualitative and quantitative proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue. Methods Mol Biol 2015; 1295:109-15. [PMID: 25820718 DOI: 10.1007/978-1-4939-2550-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissue has recently gained interest as an alternative to fresh/frozen tissue for retrospective protein biomarker discovery. However, during the formalin fixation proteins undergo degradation and cross-linking, making conventional protein analysis technologies challenging. Cross-linking is even more challenging when quantitative proteome analysis of FFPE tissue is planned. The use of conventional protein labeling technologies on FFPE tissue has turned out to be problematic as the lysine residue labeling targets are frequently blocked by the formalin treatment. We have established a qualitative and quantitative proteomics analysis technique for FFPE tissues that combines label-free proteomic analysis with optimized protein extraction and separation conditions.
Collapse
|
8
|
Chevalier F, Hamdi DH, Saintigny Y, Lefaix JL. Proteomic overview and perspectives of the radiation-induced bystander effects. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:280-93. [PMID: 25795126 DOI: 10.1016/j.mrrev.2014.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/22/2014] [Accepted: 11/18/2014] [Indexed: 11/28/2022]
Abstract
Radiation proteomics is a recent, promising and powerful tool to identify protein markers of direct and indirect consequences of ionizing radiation. The main challenges of modern radiobiology is to predict radio-sensitivity of patients and radio-resistance of tumor to be treated, but considerable evidences are now available regarding the significance of a bystander effect at low and high doses. This "radiation-induced bystander effect" (RIBE) is defined as the biological responses of non-irradiated cells that received signals from neighboring irradiated cells. Such intercellular signal is no more considered as a minor side-effect of radiotherapy in surrounding healthy tissue and its occurrence should be considered in adapting radiotherapy protocols, to limit the risk for radiation-induced secondary cancer. There is no consensus on a precise designation of RIBE, which involves a number of distinct signal-mediated effects within or outside the irradiated volume. Indeed, several cellular mechanisms were proposed, including the secretion of soluble factors by irradiated cells in the extracellular matrix, or the direct communication between irradiated and neighboring non-irradiated cells via gap junctions. This phenomenon is observed in a context of major local inflammation, linked with a global imbalance of oxidative metabolism which makes its analysis challenging using in vitro model systems. In this review article, the authors first define the radiation-induced bystander effect as a function of radiation type, in vitro analysis protocols, and cell type. In a second time, the authors present the current status of protein biomarkers and proteomic-based findings and discuss the capacities, limits and perspectives of such global approaches to explore these complex intercellular mechanisms.
Collapse
Affiliation(s)
- François Chevalier
- LARIA - iRCM - DSV - CEA, GANIL, Campus Jules Horowitz, Bd Henri Becquerel, BP 55027, Caen 14076, France.
| | - Dounia Houria Hamdi
- LARIA - iRCM - DSV - CEA, GANIL, Campus Jules Horowitz, Bd Henri Becquerel, BP 55027, Caen 14076, France
| | - Yannick Saintigny
- LARIA - iRCM - DSV - CEA, GANIL, Campus Jules Horowitz, Bd Henri Becquerel, BP 55027, Caen 14076, France
| | - Jean-Louis Lefaix
- LARIA - iRCM - DSV - CEA, GANIL, Campus Jules Horowitz, Bd Henri Becquerel, BP 55027, Caen 14076, France
| |
Collapse
|
9
|
Azimzadeh O, Atkinson MJ, Tapio S. Proteomics in radiation research: present status and future perspectives. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2014; 53:31-8. [PMID: 24105449 DOI: 10.1007/s00411-013-0495-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/17/2013] [Indexed: 05/23/2023]
Abstract
Rapidly developing postgenome research has made proteins an attractive target for biological analysis. The well-established term of proteome is defined as the complete set of proteins expressed in a given cell, tissue or organism. Unlike the genome, a proteome is rapidly changing as it tends to adapt to microenvironmental signals. The systematic analysis of the proteome at a given time and state is referred to as proteomics. This technique provides information on the molecular and cellular mechanisms that regulate physiology and pathophysiology of the cell. Applications of proteome profiling in radiation research are increasing. However, the large-scale proteomics data sets generated need to be integrated into other fields of radiation biology to facilitate the interpretation of radiation-induced cellular and tissue effects. The aim of this review is to introduce the most recent developments in the field of radiation proteomics.
Collapse
Affiliation(s)
- Omid Azimzadeh
- Institute of Radiation Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | | |
Collapse
|
10
|
Chaze T, Slomianny MC, Milliat F, Tarlet G, Lefebvre-Darroman T, Gourmelon P, Bey E, Benderitter M, Michalski JC, Guipaud O. Alteration of the serum N-glycome of mice locally exposed to high doses of ionizing radiation. Mol Cell Proteomics 2012; 12:283-301. [PMID: 23146835 DOI: 10.1074/mcp.m111.014639] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Exposure of the skin to ionizing radiation leads to characteristic reactions that will often turn into a pathophysiological process called the cutaneous radiation syndrome. The study of this disorder is crucial to finding diagnostic and prognostic bioindicators of local radiation exposure or radiation effects. It is known that irradiation alters the serum proteome content and potentially post-translationally modifies serum proteins. In this study, we investigated whether localized irradiation of the skin alters the serum glycome. Two-dimensional differential in-gel electrophoresis of serum proteins from a man and from mice exposed to ionizing radiation showed that potential post-translational modification changes occurred following irradiation. Using a large-scale quantitative mass-spectrometry-based glycomic approach, we performed a global analysis of glycan structures of serum proteins from non-irradiated and locally irradiated mice exposed to high doses of γ-rays (20, 40, and 80 Gy). Non-supervised descriptive statistical analyses (principal component analysis) using quantitative glycan structure data allowed us to discriminate between uninjured/slightly injured animals and animals that developed severe lesions. Decisional statistics showed that several glycan families were down-regulated whereas others increased, and that particular structures were statistically significantly changed in the serum of locally irradiated mice. The observed increases in multiantennary N-glycans and in outer branch fucosylation and sialylation were associated with the up-regulation of genes involved in glycosylation in the liver, which is the main producer of serum proteins, and with an increase in the key proinflammatory serum cytokines IL-1β, IL-6, and TNFα, which can regulate the expression of glycosylation genes. Our results suggest for the first time a role of serum protein glycosylation in response to irradiation. These protein-associated glycan structure changes might signal radiation exposure or effects.
Collapse
Affiliation(s)
- Thibault Chaze
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), DRPH, SRBE, LRTE, 92260 Fontenay-aux-Roses, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Gürtler A, Kunz N, Gomolka M, Hornhardt S, Friedl AA, McDonald K, Kohn JE, Posch A. Stain-Free technology as a normalization tool in Western blot analysis. Anal Biochem 2012; 433:105-11. [PMID: 23085117 DOI: 10.1016/j.ab.2012.10.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 10/04/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Western blots are used to specifically measure the relative quantities of proteins of interest in complex biological samples. Quantitative measurements can be subject to error due to process inconsistencies such as uneven protein transfer to the membrane. These non-sample-related variations need to be compensated for by an approach known as normalization. Two approaches to data normalization are commonly employed: housekeeping protein (HKP) normalization and total protein normalization (TPN). In this study, we evaluated the performance of Stain-Free technology as a novel TPN tool for Western blotting experiments in comparison with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a representative of the HKP normalization strategy. The target protein (TP) used for this study was MCM7, a DNA licensing replication factor, which was shown previously to be down-regulated by 20% in irradiated lymphoblastoid cell lines (LCLs). We studied the regulation of MCM7 with a multiplex Western blotting approach based on fluorescently labeled secondary antibodies and found that Stain-Free technology appears to be more reliable, more robust, and more sensitive to small effects of protein regulation when compared with HKP normalization with GAPDH. Stain-Free technology offers the additional advantages of providing checkpoints throughout the Western blotting process by allowing rapid visualization of gel separation and protein transfer.
Collapse
Affiliation(s)
- Anne Gürtler
- Department of Radiation Oncology, LMU, 81377 Munich, Germany
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Pernot E, Hall J, Baatout S, Benotmane MA, Blanchardon E, Bouffler S, El Saghire H, Gomolka M, Guertler A, Harms-Ringdahl M, Jeggo P, Kreuzer M, Laurier D, Lindholm C, Mkacher R, Quintens R, Rothkamm K, Sabatier L, Tapio S, de Vathaire F, Cardis E. Ionizing radiation biomarkers for potential use in epidemiological studies. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2012; 751:258-286. [DOI: 10.1016/j.mrrev.2012.05.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/04/2012] [Accepted: 05/28/2012] [Indexed: 02/07/2023]
|
13
|
Azimzadeh O, Scherthan H, Yentrapalli R, Barjaktarovic Z, Ueffing M, Conrad M, Neff F, Calzada-Wack J, Aubele M, Buske C, Atkinson MJ, Hauck SM, Tapio S. Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation. J Proteomics 2012; 75:2384-95. [DOI: 10.1016/j.jprot.2012.02.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 01/23/2023]
|
14
|
Biologie des radiations : avancées majeures et perspectives pour la radiothérapie. Cancer Radiother 2011; 15:348-54. [DOI: 10.1016/j.canrad.2011.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 05/05/2011] [Accepted: 05/10/2011] [Indexed: 11/22/2022]
|
15
|
Hirst DG, Robson T. Molecular biology: the key to personalised treatment in radiation oncology? Br J Radiol 2011; 83:723-8. [PMID: 20739343 DOI: 10.1259/bjr/91488645] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We know considerably more about what makes cells and tissues resistant or sensitive to radiation than we did 20 years ago. Novel techniques in molecular biology have made a major contribution to our understanding at the level of signalling pathways. Before the "New Biology" era, radioresponsiveness was defined in terms of physiological parameters designated as the five Rs. These are: repair, repopulation, reassortment, reoxygenation and radiosensitivity. Of these, only the role of hypoxia proved to be a robust predictive and prognostic marker, but radiotherapy regimens were nonetheless modified in terms of dose per fraction, fraction size and overall time, in ways that persist in clinical practice today. The first molecular techniques were applied to radiobiology about two decades ago and soon revealed the existence of genes/proteins that respond to and influence the cellular outcome of irradiation. The subsequent development of screening techniques using microarray technology has since revealed that a very large number of genes fall into this category. We can now obtain an adequately robust molecular signature, predicting for a radioresponsive phenotype using gene expression and proteomic approaches. In parallel with these developments, functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) can now detect specific biological molecules such as haemoglobin and glucose, so revealing a 3D map of tumour blood flow and metabolism. The key to personalised radiotherapy will be to extend this capability to the proteins of the molecular signature that determine radiosensitivity.
Collapse
|
16
|
Granzotto A, Joubert A, Viau M, Devic C, Maalouf M, Thomas C, Vogin G, Malek K, Colin C, Balosso J, Foray N. Réponse individuelle aux radiations ionisantes : quel(s) test(s) prédictif(s) choisir ? C R Biol 2011; 334:140-57. [DOI: 10.1016/j.crvi.2010.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/28/2010] [Accepted: 12/29/2010] [Indexed: 12/27/2022]
|
17
|
Bajinskis A, Lindegren H, Johansson L, Harms-Ringdahl M, Forsby A. Low-Dose/Dose-Rate γ Radiation Depresses Neural Differentiation and Alters Protein Expression Profiles in Neuroblastoma SH-SY5Y Cells and C17.2 Neural Stem Cells. Radiat Res 2010; 175:185-92. [DOI: 10.1667/rr2090.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ainars Bajinskis
- Centre for Radiation Protection Research, Department of Genetics, Microbiology and Toxicology, The Arrhenius Laboratories for Natural Science, Stockholm University, Sweden
| | - Heléne Lindegren
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Science, Stockholm University, Stockholm, Sweden
| | - Lotta Johansson
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Science, Stockholm University, Stockholm, Sweden
| | - Mats Harms-Ringdahl
- Centre for Radiation Protection Research, Department of Genetics, Microbiology and Toxicology, The Arrhenius Laboratories for Natural Science, Stockholm University, Sweden
| | - Anna Forsby
- Department of Neurochemistry, The Arrhenius Laboratories for Natural Science, Stockholm University, Stockholm, Sweden
| |
Collapse
|