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Hernandez-Ronquillo L, Miranzadeh Mahabadi H, Moien-Afshari F, Wu A, Auer R, Zherebitskiy V, Borowsky R, Mickleborough M, Huntsman R, Vrbancic M, Cayabyab FS, Taghibiglou C, Carter A, Tellez-Zenteno JF. The Concept of an Epilepsy Brain Bank. Front Neurol 2020; 11:833. [PMID: 32973652 PMCID: PMC7468480 DOI: 10.3389/fneur.2020.00833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/03/2020] [Indexed: 12/31/2022] Open
Abstract
Epilepsy comprises more than 40 clinical syndromes affecting millions of patients and families worldwide. To decode the molecular and pathological framework of epilepsy researchers, need reliable human epilepsy and control brain samples. Brain bank organizations collecting and supplying well-documented clinically and pathophysiologically tissue specimens are important for high-quality neurophysiology and neuropharmacology studies for epilepsy and other neurological diseases. New development in molecular mechanism and new treatment methods for neurological disorders have evoked increased demands for human brain tissue. An epilepsy brain bank is a storage source for both the frozen samples as well as the formaldehyde fixed paraffin embedded (FFPE) tissue from epilepsy surgery resections. In 2014, the University of Saskatchewan have started collecting human epilepsy brain tissues for the first time in Canada. This review highlights the necessity and importance of Epilepsy Brain bank that provides unique access for research to valuable source of brain tissue and blood samples from epilepsy patients.
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Affiliation(s)
- Lizbeth Hernandez-Ronquillo
- Saskatchewan Epilepsy Program, Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hajar Miranzadeh Mahabadi
- Department of Anatomy, Physiology and Pharmacology, College of Medicine University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Adam Wu
- Division of Neurosurgery, Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
| | - Roland Auer
- Department of Pathology and Laboratory Medicine, Royal University Hospital, Saskatchewan Health Region, University of Saskatchewan, Saskatoon, SK, Canada
| | - Viktor Zherebitskiy
- Department of Pathology and Laboratory Medicine, Royal University Hospital, Saskatchewan Health Region, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ron Borowsky
- Cognitive Neuroscience Laboratory, Department of Psychology, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Marla Mickleborough
- Cognitive Neuroscience Laboratory, Department of Psychology, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard Huntsman
- Division of Pediatric Neurology, Department of Pediatrics, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mirna Vrbancic
- Department of Clinical Health Psychology, Ellis Hall, Royal University Hospital, Saskatoon, SK, Canada
| | - Francisco S Cayabyab
- Division of Neurosurgery, Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
| | - Changiz Taghibiglou
- Department of Anatomy, Physiology and Pharmacology, College of Medicine University of Saskatchewan, Saskatoon, SK, Canada
| | - Alexandra Carter
- Saskatchewan Epilepsy Program, Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jose F Tellez-Zenteno
- Saskatchewan Epilepsy Program, Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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2
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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3
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Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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4
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Ntshangase S, Shobo A, Kruger HG, Asperger A, Niemeyer D, Arvidsson PI, Govender T, Baijnath S. The downfall of TBA-354 - a possible explanation for its neurotoxicity via mass spectrometric imaging. Xenobiotica 2017; 48:938-944. [PMID: 28859520 DOI: 10.1080/00498254.2017.1375168] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
1. TBA-354 was a promising antitubercular compound with activity against both replicating and static Mycobacterium tuberculosis (M.tb), making it the focal point of many clinical trials conducted by the TB Alliance. However, findings from these trials have shown that TBA-354 results in mild signs of reversible neurotoxicity; this left the TB Alliance with no other choice but to stop the research. 2. In this study, mass spectrometric methods were used to evaluate the pharmacokinetics and spatial distribution of TBA-354 in the brain using a validated liquid chromatography tandem-mass spectrometry (LCMS/MS) and mass spectrometric imaging (MSI), respectively. Healthy female Sprague-Dawley rats received intraperitoneal (i.p.) doses of TBA-354 (20 mg/kg bw). 3. The concentrationtime profiles showed a gradual absorption and tissue penetration of TBA-354 reaching the Cmax at 6 h post dose, followed by a rapid elimination. MSI analysis showed a time-dependent drug distribution, with highest drug concentration mainly in the neocortical regions of the brain. 4. The distribution of TBA-354 provides a possible explanation for the motor dysfunction observed in clinical trials. These results prove the importance of MSI as a potential tool in preclinical evaluations of suspected neurotoxic compounds.
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Affiliation(s)
- Sphamandla Ntshangase
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa
| | - Adeola Shobo
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa
| | | | | | - Per I Arvidsson
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa.,c Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Development of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm , Sweden
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa
| | - Sooraj Baijnath
- a Catalysis and Peptide Research Unit, University of KwaZulu-Natal , Durban , South Africa
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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6
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Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Combined MALDI Mass Spectrometry Imaging and Parafilm-Assisted Microdissection-Based LC-MS/MS Workflows in the Study of the Brain. Methods Mol Biol 2017; 1598:269-283. [PMID: 28508367 DOI: 10.1007/978-1-4939-6952-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins and other biomolecules such as lipids are significant players in the central nervous system and are implicated in various neurological disorders. Their identification, quantification, and distribution are thus important not only in understanding the disease but also in developing treatments. A combined workflow allowing the localized microextraction of discrete regions identified by a matrix-assisted laser desorption/ionization mass spectrometry (MSI) imaging experiment for proteomics analysis by liquid chromatography/tandem mass spectrometry (LC MS/MS) is described in this chapter. MSI was initially used to map lipid distributions allowing for the identification of regions of interest (ROIs) that are then subjected to microextraction in a consecutive tissue section. Mounting of consecutive tissue on parafilm allows microdissection of the ROIs, where proteins can then be recovered for processing and LC MS/MS analysis. The PAM method provides a fast and cheap means to perform further downstream analysis after an MSI experiment.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Julien Franck
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
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7
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Tikka S, Monogioudi E, Gotsopoulos A, Soliymani R, Pezzini F, Scifo E, Uusi-Rauva K, Tyynelä J, Baumann M, Jalanko A, Simonati A, Lalowski M. Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules. Neuromolecular Med 2015; 18:109-33. [PMID: 26707855 DOI: 10.1007/s12017-015-8382-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/15/2015] [Indexed: 02/06/2023]
Abstract
Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood encephalopathy.
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Affiliation(s)
- Saara Tikka
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.,Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Evanthia Monogioudi
- Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.,Joint Research Centre, Directorate D-Institute for Reference Materials and Measurements, Standards for Innovation and Sustainable Development, Geel, Belgium
| | - Athanasios Gotsopoulos
- Brain and Mind Laboratory, Department of Biomedical Engineering and Computational Science (BECS), Aalto University School of Science, 02150, Espoo, Finland
| | - Rabah Soliymani
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland
| | - Francesco Pezzini
- Department of Neurological and Movement Sciences, University of Verona, 37134, Verona, Italy
| | - Enzo Scifo
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland.,Doctoral Program Brain & Mind, University of Helsinki, Helsinki, Finland.,Campbell Family Mental Health Research Institute, CAMH, University of Toronto, Toronto, Canada
| | - Kristiina Uusi-Rauva
- Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.,Genomics and Biomarkers, National Institute for Health and Welfare (THL), P.O. Box 30, 00271, Helsinki, Finland
| | - Jaana Tyynelä
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland
| | - Marc Baumann
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine (FIMM), University of Helsinki, 00014, Helsinki, Finland.,Genomics and Biomarkers, National Institute for Health and Welfare (THL), P.O. Box 30, 00271, Helsinki, Finland
| | - Alessandro Simonati
- Department of Neurological and Movement Sciences, University of Verona, 37134, Verona, Italy
| | - Maciej Lalowski
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Room C214a, 00014, Helsinki, Finland. .,Folkhälsan Institute of Genetics, 00014, Helsinki, Finland.
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8
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Martin-Lorenzo M, Alvarez-Llamas G, McDonnell LA, Vivanco F. Molecular histology of arteries: mass spectrometry imaging as a novelex vivotool to investigate atherosclerosis. Expert Rev Proteomics 2015; 13:69-81. [DOI: 10.1586/14789450.2016.1116944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Reductions of docosahexaenoic acid-containing phosphatidylcholine levels in the anterior horn of an ALS mouse model. Neuroscience 2015; 297:127-36. [PMID: 25841322 DOI: 10.1016/j.neuroscience.2015.03.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 12/31/2022]
Abstract
In this study, we analyzed the spatiotemporal alterations of phospholipid composition in the spinal cord of an amyotrophic lateral sclerosis (ALS) mouse model (G93A-mutated human superoxide dismutase 1 transgenic mice [SOD1(G93A) mice]) using imaging mass spectrometry (IMS), a powerful method to visualize spatial distributions of various types of molecules in situ. Using this technique, we deciphered the phospholipid distribution in the pre-symptomatic stage, early stage after disease onset, and terminal stages of disease in female SOD1(G93A) mouse spinal cords. These experiments revealed a significant decrease in levels of docosahexaenoic acid (DHA)-containing phosphatidylcholines (PCs), such as PC (diacyl-16:0/22:6), PC (diacyl-18:0/22:6), and PC (diacyl-18:1/22:6) in the L5 anterior horns of terminal stage (22-week-old) SOD1(G93A) mice. The reduction in PC (diacyl-16:0/22:6) level could be reflecting the loss of motor neurons themselves in the anterior horn of the spinal cord in ALS model mice. In contrast, other PCs, such as PC (diacyl-16:0/16:0), were observed specifically in the L5 dorsal horn gray matter, and their levels did not vary between ALS model mice and controls. Thus, our study showed a significant decrease in DHA-containing PCs, but not other PCs, in the terminal stage of ALS in model mice, which is likely to be a reflection of neuronal loss in the anterior horns of the spinal cords. Given its enrichment in dorsal sensory regions, the preservation of PC (diacyl-16:0/16:0) may be the result of spinal sensory neurons being unaffected in ALS. Taken together, these findings suggest that ALS spinal cords show significant alterations in PC metabolism only at the terminal stage of the disease, and that these changes are confined to specific anatomical regions and cell types.
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10
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Romero-Perez GA, Takei S, Yao I. Imaging Mass Spectrometric Analysis of Neurotransmitters: A Review. Mass Spectrom (Tokyo) 2015; 3:S0049. [PMID: 26819893 PMCID: PMC4353836 DOI: 10.5702/massspectrometry.s0049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/22/2015] [Indexed: 01/19/2023] Open
Abstract
Imaging mass spectrometry (IMS) is a toolbox of versatile techniques that enable us to investigate analytes in samples at molecular level. In recent years, IMS, and especially matrix-assisted laser desorption/ionisation (MALDI), has been used to visualise a wide range of metabolites in biological samples. Simultaneous visualisation of the spatial distribution of metabolites in a single sample with little tissue disruption can be considered as one important advantage of MALDI over other techniques. However, several technical hurdles including low concentrations and rapid degradation rates of small molecule metabolites, matrix interference of signals and poor ionisation, need to be addressed before MALDI can be considered as a reliable tool for the analysis of metabolites such as neurotransmitters in brain tissues from different sources including humans. In the present review we will briefly describe current MALDI IMS techniques used to study neurotransmitters and discuss their current status, challenges, as well as future prospects.
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Affiliation(s)
| | | | - Ikuko Yao
- Hamamatsu University School of Medicine
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11
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Aichler M, Luber B, Lordick F, Walch A. Proteomic and metabolic prediction of response to therapy in gastric cancer. World J Gastroenterol 2014; 20:13648-13657. [PMID: 25320503 PMCID: PMC4194549 DOI: 10.3748/wjg.v20.i38.13648] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
Several new treatment options for gastric cancer have been introduced but the prognosis of patients diagnosed with gastric cancer is still poor. Disease prognosis could be improved for high-risk individuals by implementing earlier screenings. Because many patients are asymptomatic during the early stages of gastric cancer, the diagnosis is often delayed and patients present with unresectable locally advanced or metastatic disease. Cytotoxic treatment has been shown to prolong survival in general, but not all patients are responders. The application of targeted therapies and multimodal treatment has improved prognosis for those with advanced disease. However, these new therapeutic strategies do not uniformly benefit all patients. Predicting whether patients will respond to specific therapies would be of particular value and would allow for stratifying patients for personalized treatment strategies. Metabolic imaging by positron emission tomography was the first technique with the potential to predict the response of esophago-gastric cancer to neoadjuvant therapy. Exploring and validating tissue-based biomarkers are ongoing processes. In this review, we discuss the status of several targeted therapies for gastric cancer, as well as proteomic and metabolic methods for investigating biomarkers for therapy response prediction in gastric cancer.
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12
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Kopp C, Wisztorski M, Revel J, Mehiri M, Dani V, Capron L, Carette D, Fournier I, Massi L, Mouajjah D, Pagnotta S, Priouzeau F, Salzet M, Meibom A, Sabourault C. MALDI-MS and NanoSIMS imaging techniques to study cnidarian-dinoflagellate symbioses. ZOOLOGY 2014; 118:125-31. [PMID: 25447219 DOI: 10.1016/j.zool.2014.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/29/2014] [Accepted: 06/30/2014] [Indexed: 12/22/2022]
Abstract
Cnidarian-dinoflagellate photosynthetic symbioses are fundamental to biologically diverse and productive coral reef ecosystems. The hallmark of this symbiotic relationship is the ability of dinoflagellate symbionts to supply their cnidarian host with a wide range of nutrients. Many aspects of this association nevertheless remain poorly characterized, including the exact identity of the transferred metabolic compounds, the mechanisms that control their exchange across the host-symbiont interface, and the precise subcellular fate of the translocated materials in cnidarian tissues. This lack of knowledge is mainly attributed to difficulties in investigating such metabolic interactions both in situ, i.e. on intact symbiotic associations, and at high spatial resolution. To address these issues, we illustrate the application of two in situ and high spatial resolution molecular and ion imaging techniques-matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and the nano-scale secondary-ion mass spectrometry (NanoSIMS) ion microprobe. These imaging techniques provide important new opportunities for the detailed investigation of many aspects of cnidarian-dinoflagellate associations, including the dynamics of cellular interactions.
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Affiliation(s)
- C Kopp
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - M Wisztorski
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - J Revel
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - M Mehiri
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - V Dani
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - L Capron
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - D Carette
- CCMA, University of Nice-Sophia Antipolis, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - I Fournier
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - L Massi
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - D Mouajjah
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - S Pagnotta
- CCMA, University of Nice-Sophia Antipolis, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - F Priouzeau
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - M Salzet
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - A Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - C Sabourault
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France.
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Acquadro E, Caron I, Tortarolo M, Bucci EM, Bendotti C, Corpillo D. Human SOD1-G93A specific distribution evidenced in murine brain of a transgenic model for amyotrophic lateral sclerosis by MALDI imaging mass spectrometry. J Proteome Res 2014; 13:1800-9. [PMID: 24579824 DOI: 10.1021/pr400942n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disease caused by the degeneration of motor neurons. The transgenic mouse model carrying the human SOD1G93A mutant gene (hSOD1G93A mouse) represents one of the most reliable and widely used model of this pathology. In the present work, the innovative technique of matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) was applied in the study of pathological alterations at the level of small brain regions such as facial and trigeminal nuclei, which in rodents are extremely small and would be difficult to analyze with classical proteomics approaches. Comparing slices from three mice groups (transgenic hSOD1G93A, transgenic hSOD1WT, and nontransgenic, Ntg), this technique allowed us to evidence the accumulation of hSOD1G93A in the facial and trigeminal nuclei, where it generates aggregates. This phenomenon is likely to be correlated to the degeneration observed in these regions. Moreover, a statistical analysis allowed us to highlight other proteins as differentially expressed among the three mice groups analyzed. Some of them were identified by reverse-phase HPLC fractionation of extracted proteins and mass spectrometric analysis before and after trypsin digestion. In particular, the 40S ribosomal protein S19 (RPS19) was upregulated in the parenkyma and reactive glial cells in facial nuclei of hSOD1G93A mice when compared to transgenic hSOD1WT and nontransgenic ones.
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Affiliation(s)
- Elena Acquadro
- ABLE Bioscences, BioIndustry Park Silvano Fumero S.p.A., Via Ribes 5, 10010 Colleretto Giacosa, TO, Italy
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Guo L, Panderi I, Yan DD, Szulak K, Li Y, Chen YT, Ma H, Niesen DB, Seeram N, Ahmed A, Yan B, Pantazatos D, Lu W. A comparative study of hollow copper sulfide nanoparticles and hollow gold nanospheres on degradability and toxicity. ACS NANO 2013; 7:8780-93. [PMID: 24053214 PMCID: PMC3870179 DOI: 10.1021/nn403202w] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Gold and copper nanoparticles have been widely investigated for photothermal therapy of cancer. However, degradability and toxicity of these nanoparticles remain concerns. Here, we compare hollow CuS nanoparticles (HCuSNPs) with hollow gold nanospheres (HAuNS) in similar particle sizes and morphology following intravenous administration to mice. The injected pegylated HCuSNPs (PEG-HCuSNPs) are eliminated through both hepatobiliary (67 percentage of injected dose, %ID) and renal (23 %ID) excretion within one month postinjection. By contrast, 3.98 %ID of Au is excreted from liver and kidney within one month after iv injection of pegylated HAuNS (PEG-HAuNS). Comparatively, PEG-HAuNS are almost nonmetabolizable, while PEG-HCuSNPs are considered biodegradable nanoparticles. PEG-HCuSNPs do not show significant toxicity by histological or blood chemistry analysis. Principal component analysis and 2-D peak distribution plots of data from matrix-assisted laser desorption ionization-time-of-flight imaging mass spectrometry (MALDI-TOF IMS) of liver tissues demonstrated a reversible change in the proteomic profile in mice receiving PEG-HCuSNPs. This is attributed to slow dissociation of Cu ion from CuS nanoparticles along with effective Cu elimination for maintaining homeostasis. Nonetheless, an irreversible change in the proteomic profile is observed in the liver from mice receiving PEG-HAuNS by analysis of MALDI-TOF IMS data, probably due to the nonmetabolizability of Au. This finding correlates with the elevated serum lactate dehydrogenase at 3 months after PEG-HAuNS injection, indicating potential long-term toxicity. The comparative results between the two types of nanoparticles will advance the development of HCuSNPs as a new class of biodegradable inorganic nanomaterials for photothermal therapy.
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Affiliation(s)
- Liangran Guo
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Irene Panderi
- COBRE Center for Cancer Research and Development, Rhode Island Hospital, Rhode Island 02903, United States
- Department of Pharmacy, Division of Pharmaceutical Chemistry, University of Athens, Panepistimiopolis, Zografou, Athens 15771, Greece
| | - Daisy D. Yan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Kevin Szulak
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yajuan Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Hang Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel B. Niesen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Navindra Seeram
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Aftab Ahmed
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Bingfang Yan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Dionysios Pantazatos
- COBRE Center for Cancer Research and Development, Rhode Island Hospital, Rhode Island 02903, United States
- Warren Alpert Medical School, Brown University, Providence, Rhode Island 02903, United States
| | - Wei Lu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Corresponding author: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, USA. Phone: +1-401-874-5517. Fax: +1-401-874-5787.
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Lalowski M, Magni F, Mainini V, Monogioudi E, Gotsopoulos A, Soliymani R, Chinello C, Baumann M. Imaging mass spectrometry: a new tool for kidney disease investigations. Nephrol Dial Transplant 2013; 28:1648-56. [PMID: 23553250 DOI: 10.1093/ndt/gft008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Matrix-assisted laser desorption ionization (MALDI)-profiling and imaging mass spectrometry are promising technologies for measuring hundreds of different molecules directly on tissues. For instance, small molecules, drugs and their metabolites, endogenous lipids, carbohydrates and complex peptides/proteins can be measured at the same time without significant disruption of sample integrity. In this review, the potential of MALDI-profiling/imaging technologies in disease proteomics, drug action and studies of cellular processes in the context of kidney tissue is described. Spatial and sequence information obtained in tissue MALDI-profiling/imaging studies can be correlated with other mass spectrometry-based techniques, auxiliary imaging technologies and routine (immuno) histochemical staining.
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Affiliation(s)
- Maciej Lalowski
- Meilahti Clinical Proteomics Core Facility, Biochemistry and Developmental Biology, Institute of Biomedicine, University of Helsinki, Helsinki, Finland
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16
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Imaging mass spectrometry of thin tissue sections: a decade of collective efforts. J Proteomics 2012; 75:4883-4892. [PMID: 22525544 DOI: 10.1016/j.jprot.2012.04.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 12/21/2022]
Abstract
Imaging mass spectrometry (MS) allows to monitor the spatial distribution and abundance of endogenous and administered compounds present within tissue specimens. Several different but complementary imaging MS technologies have been developed allowing the analysis of a wide variety of compounds including inorganic elementals, metabolites, lipids, peptides, proteins and xenobiotics with spatial resolutions from micrometer to nanometer scales. In the past decade, an enormous collective body of work has been done to develop and improve the imaging MS technology. This article gives a historical perspective, an overview of the principle and status of the technology and lists the main fields of applications. It also enumerates some of the critical challenges we need to collectively address for imaging MS to be considered a mainstream analytical method.
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Zimmerman TA, Debois D, Mazzucchelli G, Bertrand V, De Pauw-Gillet MC, De Pauw E. An Analytical Pipeline for MALDI In-Source Decay Mass Spectrometry Imaging. Anal Chem 2011; 83:6090-7. [DOI: 10.1021/ac201221h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Tyler A. Zimmerman
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
| | - Delphine Debois
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
| | - Virginie Bertrand
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
| | - Marie-Claire De Pauw-Gillet
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, ‡Histology-Cytology Laboratory, GIGA-R Systems Biology and Chemical Biology, University of Liège, B-4000 Liège (Sart-Tilman), Belgium
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18
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Hankin JA, Farias S, Barkley RM, Heidenreich K, Frey LC, Hamazaki K, Kim HY, Murphy RC. MALDI mass spectrometric imaging of lipids in rat brain injury models. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1014-21. [PMID: 21953042 PMCID: PMC4537074 DOI: 10.1007/s13361-011-0122-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 05/03/2023]
Abstract
Matrix-assisted laser desorption ionization/ionization imaging mass spectrometry (MALDI IMS) with a time-of-flight analyzer was used to characterize the distribution of lipid molecular species in the brain of rats in two injury models. Ischemia/reperfusion injury of the rat brain after bilateral occlusion of the carotid artery altered appearance of the phospholipids present in the hippocampal region, specifically the CA1 region. These brain regions also had a large increase in the ion abundance at m/z 548.5 and collisional activation supported identification of this ion as arising from ceramide (d18:1/18:0), a lipid known to be associated with cellular apoptosis. Traumatic brain injury model in the rat was examined by MALDI IMS and the area of damage also showed an increase in ceramide (d18:1/18:0) and a remarkable loss of signal for the potassium adduct of the most abundant phosphocholine molecular species 16:0/18:1 (PC) with a corresponding increase in the sodium adduct ion. This change in PC alkali attachment ion was suggested to be a result of edema and influx of extracellular fluid likely through a loss of Na/K-ATPase caused by the injury. These studies reveal the value of MALDI IMS to examine tissues for changes in lipid biochemistry and will provide data needed to eventually understand the biochemical mechanisms relevant to tissue injury.
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Affiliation(s)
- Joseph A. Hankin
- Department of Pharmacology, University of Colorado Denver, 12801 E. 17
| | - Santiago Farias
- Department of Pharmacology, University of Colorado Denver, 12801 E. 17
| | - Robert M. Barkley
- Department of Pharmacology, University of Colorado Denver, 12801 E. 17
| | - Kim Heidenreich
- Department of Pharmacology, University of Colorado Denver, 12801 E. 17
| | | | - Kei Hamazaki
- Laboratory of Molecular signaling, NIAAA, National Institutes of Health, 5625 Fishers Lane, Bethesda, MD 20892-9410
| | - Hee-Yong Kim
- Laboratory of Molecular signaling, NIAAA, National Institutes of Health, 5625 Fishers Lane, Bethesda, MD 20892-9410
| | - Robert C. Murphy
- Department of Pharmacology, University of Colorado Denver, 12801 E. 17
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Bonnel D, Longuespee R, Franck J, Roudbaraki M, Gosset P, Day R, Salzet M, Fournier I. Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer. Anal Bioanal Chem 2011; 401:149-65. [DOI: 10.1007/s00216-011-5020-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 12/20/2022]
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Rauser S, Deininger SO, Suckau D, Höfler H, Walch A. Approaching MALDI molecular imaging for clinical proteomic research: current state and fields of application. Expert Rev Proteomics 2011; 7:927-41. [PMID: 21142893 DOI: 10.1586/epr.10.83] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MALDI imaging mass spectrometry ('MALDI imaging') is an increasingly recognized technique for biomarker research. After years of method development in the scientific community, the technique is now increasingly applied in clinical research. In this article, we discuss the use of MALDI imaging in clinical proteomics and put it in context with classical proteomics techniques. We also highlight a number of upcoming challenges for personalized medicine, development of targeted therapies and diagnostic molecular pathology where MALDI imaging could help.
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Affiliation(s)
- Sandra Rauser
- Institute of Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg, Germany
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21
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Lorenzen K, van Duijn E. Native mass spectrometry as a tool in structural biology. ACTA ACUST UNITED AC 2011; Chapter 17:Unit17.12. [PMID: 21104986 DOI: 10.1002/0471140864.ps1712s62] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Native mass spectrometry (native MS) gives information about the composition, topological arrangements, dynamics, and structural properties of protein complexes. The mass range is principally unlimited and highly dynamic, allowing the detection of small subunits and large complexes within the same measurement. The amount of protein needed for an analysis is, compared to most other structural biology methods, very low. This unit provides an introduction to native MS. It starts with an explanation of the basic method and details on how to measure intact proteins and protein complexes, and continues with the study of dynamics and complex stability in the gas phase. The final section discusses the most recent extension to the native MS field, ion mobility, which allows the direct assessment of the structural properties of the complexes of interest.
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22
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Van Dyck S, Flammang P, Meriaux C, Bonnel D, Salzet M, Fournier I, Wisztorski M. Localization of secondary metabolites in marine invertebrates: contribution of MALDI MSI for the study of saponins in Cuvierian tubules of H. forskali. PLoS One 2010; 5:e13923. [PMID: 21085713 PMCID: PMC2978086 DOI: 10.1371/journal.pone.0013923] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/16/2010] [Indexed: 11/24/2022] Open
Abstract
Background Several species of sea cucumbers of the family Holothuriidae possess a particular mechanical defense system called the Cuvierian tubules (Ct). It is also a chemical defense system as triterpene glycosides (saponins) appear to be particularly concentrated in Ct. In the present study, the precise localization of saponins in the Ct of Holothuria forskali is investigated. Classical histochemical labeling using lectin was firstly performed but did not generate any conclusive results. Thus, MALDI mass spectrometry Imaging (MALDI-MSI) was directly applied and completed by statistical multivariate tests. A comparison between the tubules of relaxed and stressed animals was realized. Results These analyses allowed the detection of three groups of ions, corresponding to the isomeric saponins of the tubules. Saponins detected at m/z 1287 and 1303 were the most abundant and were apparently localized in the connective tissue of the tubules of both relaxed and stressed individuals. Saponins at m/z 1125 and 1141 were detected in lower amount and were present in tissues of relaxed animals. Finally, saponin ions at 1433, 1449, 1463 and 1479 were observed in some Ct of stressed holothuroids in the outer part of the connective tissue. The saponin group m/z 14xx seems therefore to be stress-specific and could originate from modifications of the saponins with m/z of 11xx. Conclusions All the results taken together indicate a complex chemical defense mechanism with, for a single organ, different sets of saponins originating from different cell populations and presenting different responses to stress. The present study also reflects that MALDI-MSI is a valuable tool for chemical ecology studies in which specific chemical signalling molecules like allelochemicals or pheromones have to be tracked. This report represents one of the very first studies using these tools to provide a functional and ecological understanding of the role of natural products from marine invertebrates.
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Affiliation(s)
- Séverine Van Dyck
- Laboratoire de Biologie marine, Université de Mons - UMONS, Mons, Belgium
| | - Patrick Flammang
- Laboratoire de Biologie marine, Université de Mons - UMONS, Mons, Belgium
| | - Céline Meriaux
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, Université Lille Nord de France (USTL), Villeneuve d'Ascq, France
| | - David Bonnel
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, Université Lille Nord de France (USTL), Villeneuve d'Ascq, France
| | - Michel Salzet
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, Université Lille Nord de France (USTL), Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, Université Lille Nord de France (USTL), Villeneuve d'Ascq, France
| | - Maxence Wisztorski
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, Université Lille Nord de France (USTL), Villeneuve d'Ascq, France
- * E-mail:
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23
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Molecular mass spectrometry imaging in biomedical and life science research. Histochem Cell Biol 2010; 134:423-43. [DOI: 10.1007/s00418-010-0753-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
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Chaurand P, Cornett DS, Angel PM, Caprioli RM. From whole-body sections down to cellular level, multiscale imaging of phospholipids by MALDI mass spectrometry. Mol Cell Proteomics 2010; 10:O110.004259. [PMID: 20736411 DOI: 10.1074/mcp.o110.004259] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Significant progress in instrumentation and sample preparation approaches have recently expanded the potential of MALDI imaging mass spectrometry to the analysis of phospholipids and other endogenous metabolites naturally occurring in tissue specimens. Here we explore some of the requirements necessary for the successful analysis and imaging of phospholipids from thin tissue sections of various dimensions by MALDI time-of-flight mass spectrometry. We address methodology issues relative to the imaging of whole-body sections such as those cut from model laboratory animals, sections of intermediate dimensions typically prepared from individual organs, as well as the requirements for imaging areas of interests from these sections at a cellular scale spatial resolution. We also review existing limitations of MALDI imaging MS technology relative to compound identification. Finally, we conclude with a perspective on important issues relative to data exploitation and management that need to be solved to maximize biological understanding of the tissue specimen investigated.
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Affiliation(s)
- Pierre Chaurand
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8575, USA
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25
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Macagno ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 2010; 11:407. [PMID: 20579359 PMCID: PMC2996935 DOI: 10.1186/1471-2164-11-407] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 06/25/2010] [Indexed: 11/17/2022] Open
Abstract
Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions. Conclusions The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.
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Affiliation(s)
- Eduardo R Macagno
- Division of Biological Sciences, University of California, San Diego, CA, USA.
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Affiliation(s)
- Kamila Chughtai
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ron M.A. Heeren
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
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Reyzer ML, Chaurand P, Angel PM, Caprioli RM. Direct molecular analysis of whole-body animal tissue sections by MALDI imaging mass spectrometry. Methods Mol Biol 2010; 656:285-301. [PMID: 20680598 DOI: 10.1007/978-1-60761-746-4_17] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The determination of the localization of various compounds in a whole animal is valuable for many applications, including pharmaceutical absorption, distribution, metabolism, and excretion (ADME) studies and biomarker discovery. Imaging mass spectrometry is a powerful tool for localizing compounds of biological interest with molecular specificity and relatively high resolution. Utilizing imaging mass spectrometry for whole-body animal sections offers considerable analytical advantages compared to traditional methods, such as whole-body autoradiography, but the experiment is not straightforward. This chapter addresses the advantages and unique challenges that the application of imaging mass spectrometry to whole-body animal sections entails, including discussions of sample preparation, matrix application, signal normalization, and image generation. Lipid and protein images obtained from whole-body tissue sections of mouse pups are presented along with detailed protocols for the experiments.
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Affiliation(s)
- Michelle L Reyzer
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
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Abstract
MALDI imaging as a molecular mass spectrometry imaging technique (MSI) can provide accurate information about molecular composition on a surface. The last decade of MSI development has brought the technology to clinical and biomedical applications as a complementary technique of MRI and other molecular imaging. Then, this IMS technique is used for endogenous and exogenous molecule detection in pharmaceutical and biomedical fields. However, some limitations still exist due to physical and chemical aspects, and sensitivity of certain compounds is very low. Thus, we developed a multiplex technique for fast detection of different compound natures. The multiplex MALDI imaging technique uses a photocleavable group that can be detect easily by MALDI instrument. These techniques of targeted imaging using Tag-Mass molecules allow the multiplex detection of compounds like antibodies or oligonucleotides. Here, we describe how we used this technique to detect huge proteins and mRNA by MALDI imaging in rat brain and in a model for regeneration; the leech.
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Affiliation(s)
- Jonathan Stauber
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, FRE CNRS 3249, MALDI Imaging Team, Université Lille Nord de France, Université Lille 1, Villeneuve d'Ascq, France
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29
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Zimmerman TA, Rubakhin SS, Romanova EV, Tucker KR, Sweedler JV. MALDI mass spectrometric imaging using the stretched sample method to reveal neuropeptide distributions in aplysia nervous tissue. Anal Chem 2009; 81:9402-9. [PMID: 19835365 PMCID: PMC2837479 DOI: 10.1021/ac901820v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuropeptides are a diverse set of complex cell-cell signaling molecules that modulate behavior, learning, and memory. Their spatially heterogeneous distributions, large number of post-translational modifications, and wide range of physiologically active concentrations make their characterization challenging. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging is well-suited to characterizing and mapping neuropeptides in the central nervous system. Because matrix application can cause peptide migration within tissue samples, application parameters for MALDI typically represent a compromise between attaining the highest signal quality and preserving native spatial distributions. The stretched sample approach minimizes this trade-off by fragmenting the tissue section into thousands of spatially isolated islands, each approximately 40 mum in size. This inhibits analyte migration between the pieces and, at the same time, reduces analyte-salt adduct formation. Here, we present methodological improvements that enable the imaging of stretched tissues and reveal neuropeptide distributions in nervous tissue from Aplysia californica. The distributions of known neuropeptides are shown to correspond with previous immunohistochemical results, demonstrating that the stretched imaging method is well-suited for working with easily redistributed molecules and heterogeneous tissues and reduces adducts from physiological salts.
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Affiliation(s)
- Tyler A. Zimmerman
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Stanislav S. Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Elena V. Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Kevin R. Tucker
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
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30
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Liao L, McClatchy DB, Yates JR. Shotgun proteomics in neuroscience. Neuron 2009; 63:12-26. [PMID: 19607789 DOI: 10.1016/j.neuron.2009.06.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/27/2022]
Abstract
Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.
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Affiliation(s)
- Lujian Liao
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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31
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Eijkel GB, Kükrer Kaletaş B, van der Wiel IM, Kros JM, Luider TM, Heeren RMA. Correlating MALDI and SIMS imaging mass spectrometric datasets of biological tissue surfaces. SURF INTERFACE ANAL 2009. [DOI: 10.1002/sia.3088] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Kaletaş BK, van der Wiel IM, Stauber J, Lennard J. Dekker, Güzel C, Kros JM, Luider TM, Heeren RMA. Sample preparation issues for tissue imaging by imaging MS. Proteomics 2009; 9:2622-33. [DOI: 10.1002/pmic.200800364] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Herrmann K, Walch A, Balluff B, Tänzer M, Höfler H, Krause BJ, Schwaiger M, Friess H, Schmid RM, Ebert MPA. Proteomic and metabolic prediction of response to therapy in gastrointestinal cancers. Nat Rev Gastroenterol Hepatol 2009; 6:170-83. [PMID: 19259108 DOI: 10.1038/ncpgasthep1366] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 12/09/2008] [Indexed: 12/17/2022]
Abstract
Despite substantial improvements in the diagnosis and treatment of many gastrointestinal cancers, particularly colorectal cancer, numerous patients are only diagnosed in advanced stages of disease, which can preclude curative treatment. Screening and early diagnosis of high-risk individuals might be the most promising approach to improve prognosis; however, molecular biomarkers for early diagnosis of most gastrointestinal cancers are not yet available. The prognosis of patients with advanced gastrointestinal cancers has improved through the development of multimodal treatments and the introduction of targeted therapies. Nonetheless, not all patients benefit equally from these treatment approaches, and toxicity can be substantial. The ability to predict whether a patient will respond to therapy early in their treatment for gastrointestinal cancer may be of particular value to stratify and individualize patient treatment strategies. Despite improvement in the understanding of cancer pathogenesis and progression at the molecular level, the molecular changes that underlie treatment response and/or drug resistance are still largely unknown. PET is the first technique to show promise in prediction of response to therapy, and has resulted in promising advancements, particularly in esophageal and gastric cancers. Tissue-based and blood-based molecular biomarkers are still subject to validation. Prediction of response to treatment could ultimately lead to an overall improvement in prognosis.
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Affiliation(s)
- Ken Herrmann
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, München, Germany
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34
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Esquenazi E, Yang YL, Watrous J, Gerwick WH, Dorrestein PC. Imaging mass spectrometry of natural products. Nat Prod Rep 2009; 26:1521-34. [DOI: 10.1039/b915674g] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Bakota L, Brandt R. Chapter 2 Live‐Cell Imaging in the Study of Neurodegeneration. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 276:49-103. [DOI: 10.1016/s1937-6448(09)76002-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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36
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Hayasaka T, Goto-Inoue N, Sugiura Y, Zaima N, Nakanishi H, Ohishi K, Nakanishi S, Naito T, Taguchi R, Setou M. Matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight (MALDI-QIT-TOF)-based imaging mass spectrometry reveals a layered distribution of phospholipid molecular species in the mouse retina. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3415-3426. [PMID: 18837478 DOI: 10.1002/rcm.3751] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We recently developed a matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight (MALDI-QIT-TOF)-based imaging mass spectrometry (IMS) system. This system enables us to perform structural analyses using tandem mass spectrometry (MS/MS), as well as to visualize phospholipids and peptides in frozen sections. In the retina, phototransduction is regulated by the light-sensitive interaction between visual pigment-coupled receptor proteins, such as rhodopsin, and G proteins, such as transducin. There are some reports that the conformation of rhodopsin is influenced by the composition of phospholipids in the lipid bilayer membrane. However, these results were based on in vitro experiments and have not been analyzed in vivo. In this study, we visualized and identified phospholipids in mouse retinal sections with the MALDI-QIT-TOF-based IMS system. From a spectrum obtained by raster-scanned analysis of the sections, ions with high signal intensities were selected and analyzed by MS/MS. As a result, sixteen ions were identified as being from four diacyl-phosphatidylcholine (PC) species, i.e., PC (16:0/16:0), PC (16:0/18:1), PC (16:0/22:6), and PC (18:0/22:6), with different ion forms. The ion images revealed different distributions on the retinal sections: PC (16:0/18:1) was distributed in the inner nuclear layer and outer plexiform layer, PC (16:0/16:0) in the outer nuclear layer and inner segment, and both PC (16:0/22:6) and PC (18:0/22:6) in the outer segment and pigment epithelium. In conclusion, our in vivo IMS analyses demonstrated a three-zone distribution of PC species on the retinal sections. This approach may be useful for analyzing lipid changes and their contribution to phototransduction in the retina.
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Affiliation(s)
- Takahiro Hayasaka
- Department of Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
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