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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: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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52
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Abstract
MALDI MS imaging (MALDI-MSI) offers a capability to not only evaluate the distribution, localization and metabolism of drugs within tissues but also allow correlative tissue measurement of the effect of the drug on biomolecules in the targeted pathway. Particularly for MALDI-MSI, lipid molecules are readily detectable within tissues. Case study examples are provided for two different drugs targeting the sphingosine-1-phosphate/ceramide nexus in tumor xenograft tissues. A workflow combining high-resolution MALDI-MSI with on-tissue confirmation of targeted compounds using a structural library and on-tissue enzymatic digestion strategy is described. Representative images of drug metabolite distribution that correlate to an increase or decrease in sphingosine-1-phosphate or ceramide species are provided.
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53
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Martin-Lorenzo M, Balluff B, Maroto AS, Carreira RJ, van Zeijl RJ, Gonzalez-Calero L, de la Cuesta F, Barderas MG, Lopez-Almodovar LF, Padial LR, McDonnell LA, Vivanco F, Alvarez-Llamas G. Lipid and protein maps defining arterial layers in atherosclerotic aorta. Data Brief 2015; 4:328-31. [PMID: 26217810 PMCID: PMC4510571 DOI: 10.1016/j.dib.2015.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 11/24/2022] Open
Abstract
Subclinical atherosclerosis cannot be predicted and novel therapeutic targets are needed. The molecular anatomy of healthy and atherosclerotic tissue is pursued to identify ongoing molecular changes in atherosclerosis development. Mass Spectrometry Imaging (MSI) accounts with the unique advantage of analyzing proteins and metabolites (lipids) while preserving their original localization; thus two dimensional maps can be obtained. Main molecular alterations were investigated in a rabbit model in response to early development of atherosclerosis. Aortic arterial layers (intima and media) and calcified regions were investigated in detail by MALDI-MSI and proteins and lipids specifically defining those areas of interest were identified. These data further complement main findings previously published in J Proteomics (M. Martin-Lorenzo et al., J. Proteomics. (In press); M. Martin-Lorenzo et al., J. Proteomics 108 (2014) 465-468.) [1,2].
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Affiliation(s)
- Marta Martin-Lorenzo
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aroa S. Maroto
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
| | - Ricardo J. Carreira
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rene J.M. van Zeijl
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Fernando de la Cuesta
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | - Maria G Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | | | - Luis R Padial
- Department of Cardiology, Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - Liam A. McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Fernando Vivanco
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
- Department of Biochemistry and Molecular Biology I, Universidad Complutense, Madrid, Spain
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54
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Martin-Lorenzo M, Balluff B, Maroto AS, Carreira RJ, van Zeijl RJM, Gonzalez-Calero L, de la Cuesta F, Barderas MG, Lopez-Almodovar LF, Padial LR, McDonnell LA, Vivanco F, Alvarez-Llamas G. Molecular anatomy of ascending aorta in atherosclerosis by MS Imaging: Specific lipid and protein patterns reflect pathology. J Proteomics 2015; 126:245-51. [PMID: 26079611 DOI: 10.1016/j.jprot.2015.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 12/22/2022]
Abstract
The molecular anatomy of healthy and atherosclerotic tissue is pursued here to identify ongoing molecular changes in atherosclerosis development. Subclinical atherosclerosis cannot be predicted and novel therapeutic targets are needed. Mass spectrometry imaging (MSI) is a novel unexplored ex vivo imaging approach in CVD able to provide in-tissue molecular maps. A rabbit model of early atherosclerosis was developed and high-spatial-resolution MALDI-MSI was applied to comparatively analyze histologically-based arterial regions of interest from control and early atherosclerotic aortas. Specific protocols were applied to identify lipids and proteins significantly altered in response to atherosclerosis. Observed protein alterations were confirmed by immunohistochemistry in rabbit tissue, and additionally in human aortas. Molecular features specifically defining different arterial regions were identified. Localized in the intima, increased expression of SFA and lysolipids and intimal spatial organization showing accumulation of PI, PG and SM point to endothelial dysfunction and triggered inflammatory response. TG, PA, SM and PE-Cer were identified specifically located in calcified regions. Thymosin β4 (TMSB4X) protein was upregulated in intima versus media layer and also in response to atherosclerosis. This overexpression and localization was confirmed in human aortas. In conclusion, molecular histology by MS Imaging identifies spatial organization of arterial tissue in response to atherosclerosis.
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Affiliation(s)
- Marta Martin-Lorenzo
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aroa S Maroto
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain
| | - Ricardo J Carreira
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rene J M van Zeijl
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Fernando de la Cuesta
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | - Maria G Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | | | - Luis R Padial
- Department of Cardiology, Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Fernando Vivanco
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain; Department of Biochemistry and Molecular Biology I, Universidad Complutense, Madrid, Spain
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55
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Flatley B, Quaye C, Johnson E, Freeman A, Muneer A, Minhas S, Paterson JC, Musa F, Malone P, Cramer R. Distribution analysis of the putative cancer marker S100A4 across invasive squamous cell carcinoma penile tissue. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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56
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MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice. J Transl Med 2015; 95:422-31. [PMID: 25621874 DOI: 10.1038/labinvest.2014.156] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 01/14/2023] Open
Abstract
MALDI Imaging mass spectrometry has entered the field of tissue-based research by providing unique advantages for analyzing tissue specimen in an unprecedented detail. A broad spectrum of analytes ranging from proteins, peptides, protein modification over small molecules, drugs and their metabolites as well as pharmaceutical components, endogenous cell metabolites, lipids, and other analytes are made accessible by this in situ technique in tissue. Some of them were even not accessible in tissues within the histological context before. Thereby, the great advantage of MALDI Imaging is the correlation of molecular information with traditional histology by keeping the spatial localization information of the analytes after mass spectrometric measurement. This method is label-free and allows multiplex analysis of hundreds to thousands of molecules in the very same tissue section simultaneously. Imaging mass spectrometry brings a new quality of molecular data and links the expert discipline of pathology and deep molecular mass spectrometric analysis to tissue-based research. This review will focus on state-of-the-art of MALDI Imaging mass spectrometry, its recent applications by analyzing tissue specimen and the contributions in understanding the biology of disease as well as its perspectives for pathology research and practice.
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57
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Heijs B, Carreira RJ, Tolner EA, de Ru AH, van den Maagdenberg AMJM, van Veelen PA, McDonnell LA. Comprehensive Analysis of the Mouse Brain Proteome Sampled in Mass Spectrometry Imaging. Anal Chem 2015; 87:1867-75. [DOI: 10.1021/ac503952q] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Ricardo J. Carreira
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Else A. Tolner
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arnoud H. de Ru
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arn M. J. M. van den Maagdenberg
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Department
of Human Genetics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Peter A. van Veelen
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Liam A. McDonnell
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Fondazione Pisana
per la Scienza ONLUS, Pisa, 56121 Italy
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58
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Wang X, Han J, Yang J, Pan J, Borchers CH. Matrix coating assisted by an electric field (MCAEF) for enhanced tissue imaging by MALDI-MS. Chem Sci 2015; 6:729-738. [PMID: 28706636 PMCID: PMC5494562 DOI: 10.1039/c4sc01850h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 09/09/2014] [Indexed: 01/13/2023] Open
Abstract
A novel technique, termed matrix coating assisted by an electric field (MCAEF), for enhancing tissue imaging by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was developed in this study. In this technique a static and uniform electric field is applied to sliced tissue sections during matrix spray-coating, resulting in the enrichment of positively or negatively chargeable analytes in the MALDI matrix layer. Experimental results show that MCAEF not only increased the sensitivity of lipid and protein detection across the board in the subsequent MALDI-MS analyses, but also resulted in successful imaging of a larger number of analytes. MALDI imaging enhancement with MCAEF was observed for various tissues (rat liver, rat brain, and porcine adrenal gland) and with different MALDI matrices (e.g., quercetin, 2-mercaptobenzothiazole, dithranol, 9-aminoacridine, and sinapinic acid) and the sensitivity increases were independent of the solvent compositions and pH values of the matrix solutions. Taking rat brain as an example, MCAEF led to the on-tissue detection and imaging of 648 identified lipids by combining positive and negative ion detection by MALDI-Fourier transform ion cyclotron resonance MS and with quercetin as the matrix, as compared to only 344 lipids without MCAEF. For protein imaging, up to 232 protein signals were successfully detected in rat brain tissue sections by MALDI-time-of-flight MS within a mass range of 3500 to 37 000 Da, as compared to 119 without MCAEF. MCAEF also enabled the detection of higher molecular-weight proteins. These results demonstrate the advantages of MCAEF for overall performance improvements in MALDI imaging and we believe that this technique has the potential to become a standard practice for MALDI tissue imaging.
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Affiliation(s)
- Xiaodong Wang
- University of Victoria - Genome British Columbia Proteomics Centre , Vancouver Island Technology Park, #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . ; ; Tel: +1-250-483-3221
| | - Jun Han
- University of Victoria - Genome British Columbia Proteomics Centre , Vancouver Island Technology Park, #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . ; ; Tel: +1-250-483-3221
| | - Juncong Yang
- University of Victoria - Genome British Columbia Proteomics Centre , Vancouver Island Technology Park, #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . ; ; Tel: +1-250-483-3221
| | - Jingxi Pan
- University of Victoria - Genome British Columbia Proteomics Centre , Vancouver Island Technology Park, #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . ; ; Tel: +1-250-483-3221
| | - Christoph H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre , Vancouver Island Technology Park, #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . ; ; Tel: +1-250-483-3221
- Department of Biochemistry and Microbiology , University of Victoria , Petch Building Room 207, 3800 Finnerty Rd. , Victoria , BC V8P 5C2 , Canada
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59
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Rawlins CM, Salisbury JP, Feldman DR, Isim S, Agar NYR, Luther E, Agar JN. Imaging and Mapping of Tissue Constituents at the Single-Cell Level Using MALDI MSI and Quantitative Laser Scanning Cytometry. Methods Mol Biol 2015; 1346:133-49. [PMID: 26542720 DOI: 10.1007/978-1-4939-2987-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For nearly a century, histopathology involved the laborious morphological analyses of tissues stained with broad-spectrum dyes (i.e., eosin to label proteins). With the advent of antibody-labeling, immunostaining (fluorescein and rhodamine for fluorescent labeling) and immunohistochemistry (DAB and hematoxylin), it became possible to identify specific immunological targets in cells and tissue preparations. Technical advances, including the development of monoclonal antibody technology, led to an ever-increasing palate of dyes, both fluorescent and chromatic. This provides an incredibly rich menu of molecular entities that can be visualized and quantified in cells-giving rise to the new discipline of Molecular Pathology. We describe the evolution of two analytical techniques, cytometry and mass spectrometry, which complement histopathological visual analysis by providing automated, cellular-resolution constituent maps. For the first time, laser scanning cytometry (LSC) and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) are combined for the analysis of tissue sections. The utility of the marriage of these techniques is demonstrated by analyzing mouse brains with neuron-specific, genetically encoded, fluorescent proteins. We present a workflow that: (1) can be used with or without expensive matrix deposition methods, (2) uses LSC images to reveal the diverse landscape of neural tissue as well as the matrix, and (3) uses a tissue fixation method compatible with a DNA stain. The proposed workflow can be adapted for a variety of sample preparation and matrix deposition methods.
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Affiliation(s)
- Catherine M Rawlins
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA.
| | - Joseph P Salisbury
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA.
| | - Daniel R Feldman
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Sinan Isim
- Life Sciences Department, Brandeis University, Waltham, MA, USA.
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ed Luther
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Jeffery N Agar
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA. .,Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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60
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Crecelius AC, Schubert US, von Eggeling F. MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage. Analyst 2015; 140:5806-20. [DOI: 10.1039/c5an00990a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a method that allows the investigation of the molecular content of surfaces, in particular, tissues, within its morphological context.
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Affiliation(s)
- A. C. Crecelius
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - U. S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - F. von Eggeling
- Jena Center for Soft Matter (JCSM)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Institute of Physical Chemistry
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61
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Kriegsmann J, Kriegsmann M, Casadonte R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). Int J Oncol 2014; 46:893-906. [PMID: 25482502 DOI: 10.3892/ijo.2014.2788] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 11/06/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.
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Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - Mark Kriegsmann
- Institute for Pathology, University of Heidelberg, Heidelberg, Germany
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62
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Balluff B, Frese CK, Maier SK, Schöne C, Kuster B, Schmitt M, Aubele M, Höfler H, Deelder AM, Heck A, Hogendoorn PCW, Morreau J, Maarten Altelaar AF, Walch A, McDonnell LA. De novo discovery of phenotypic intratumour heterogeneity using imaging mass spectrometry. J Pathol 2014; 235:3-13. [PMID: 25201776 DOI: 10.1002/path.4436] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/31/2022]
Abstract
An essential and so far unresolved factor influencing the evolution of cancer and the clinical management of patients is intratumour clonal and phenotypic heterogeneity. However, the de novo identification of tumour subpopulations is so far both a challenging and an unresolved task. Here we present the first systematic approach for the de novo discovery of clinically detrimental molecular tumour subpopulations. In this proof-of-principle study, spatially resolved, tumour-specific mass spectra were acquired, using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry, from tissues of 63 gastric carcinoma and 32 breast carcinoma patients. The mass spectra, representing the proteomic heterogeneity within tumour areas, were grouped by a corroborated statistical clustering algorithm in order to obtain segmentation maps of molecularly distinct regions. These regions were presumed to represent different phenotypic tumour subpopulations. This was confirmed by linking the presence of these tumour subpopulations to the patients' clinical data. This revealed several of the detected tumour subpopulations to be associated with a different overall survival of the gastric cancer patients (p = 0.025) and the presence of locoregional metastases in patients with breast cancer (p = 0.036). The procedure presented is generic and opens novel options in cancer research, as it reveals microscopically indistinct tumour subpopulations that have an adverse impact on clinical outcome. This enables their further molecular characterization for deeper insights into the biological processes of cancer, which may finally lead to new targeted therapies.
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Affiliation(s)
- Benjamin Balluff
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, The Netherlands
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63
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Park JM, Han NY, Han YM, Chung MK, Lee HK, Ko KH, Kim EH, Hahm KB. Predictive proteomic biomarkers for inflammatory bowel disease-associated cancer: Where are we now in the era of the next generation proteomics? World J Gastroenterol 2014; 20:13466-13476. [PMID: 25309077 PMCID: PMC4188898 DOI: 10.3748/wjg.v20.i37.13466] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/10/2014] [Accepted: 06/17/2014] [Indexed: 02/06/2023] Open
Abstract
Recent advances in genomic medicine have opened up the possibility of tailored medicine that may eventually replace traditional “one-size-fits all” approaches to the treatment of inflammatory bowel disease (IBD). In addition to exploring the interactions between hosts and microbes, referred to as the microbiome, a variety of strategies that can be tailored to an individual in the coming era of personalized medicine in the treatment of IBD are being investigated. These include prompt genomic screening of patients at risk of developing IBD, the utility of molecular discrimination of IBD subtypes among patients diagnosed with IBD, and the discovery of proteome biomarkers to diagnose or predict cancer risks. Host genetic factors influence the etiology of IBD, as do microbial ecosystems in the human bowel, which are not uniform, but instead represent many different microhabitats that can be influenced by diet and might affect processes essential to bowel metabolism. Further advances in basic research regarding intestinal inflammation may reveal new insights into the role of inflammatory mediators, referred to as the inflammasome, and the macromolecular complex of metabolites formed by intestinal bacteria. Collectively, knowledge of the inflammasome and metagenomics will lead to the development of biomarkers for IBD that target specific pathogenic mechanisms involved in the spontaneous progress of IBD. In this review article, our recent results regarding the discovery of potential proteomic biomarkers using a label-free quantification technique are introduced and on-going projects contributing to either the discrimination of IBD subtypes or to the prediction of cancer risks are accompanied by updated information from IBD biomarker research.
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64
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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65
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Moore JL, Caprioli RM, Skaar EP. Advanced mass spectrometry technologies for the study of microbial pathogenesis. Curr Opin Microbiol 2014; 19:45-51. [PMID: 24997399 PMCID: PMC4125470 DOI: 10.1016/j.mib.2014.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/12/2014] [Accepted: 05/28/2014] [Indexed: 02/08/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been successfully applied to the field of microbial pathogenesis with promising results, principally in diagnostic microbiology to rapidly identify bacteria based on the molecular profiles of small cell populations. Direct profiling of molecules from serum and tissue samples by MALDI MS provides a means to study the pathogen-host interaction and to discover potential markers of infection. Systematic molecular profiling across tissue sections represents a new imaging modality, enabling regiospecific molecular measurements to be made in situ, in both two-dimensional and three-dimensional analyses. Herein, we briefly summarize work that employs MALDI MS to study the pathogenesis of microbial infection.
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Affiliation(s)
- Jessica L Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States.
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66
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Longuespée R, Tastet C, Desmons A, Kerdraon O, Day R, Fournier I, Salzet M. HFIP extraction followed by 2D CTAB/SDS-PAGE separation: a new methodology for protein identification from tissue sections after MALDI mass spectrometry profiling for personalized medicine research. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:374-84. [PMID: 24841221 DOI: 10.1089/omi.2013.0176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and profiling technology have become the easiest methods for quickly accessing the protein composition of a tissue area. Unfortunately, the demand for the identification of these proteins remains unmet. To overcome this bottleneck, we combined several strategies to identify the proteins detected via MALDI profiling including on-tissue protein extraction using hexafluoroIsopropanol (1,1,1,3,3,3-hexafluoro-2-propanol, HFIP) coupled with two-dimensional cetyl trimethylammonium bromide/sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D CTAB/SDS-PAGE) for separation followed by trypsin digestion and MALDI-MS analyses for identification. This strategy was compared with an on-tissue bottom-up strategy that we previously developed. The data reflect the complementarity of the approaches. An increase in the number of specific proteins identified has been established. This approach demonstrates the potential of adapted extraction procedures and the combination of parallel identification approaches for personalized medicine applications. The anatomical context provides important insight into identifying biomarkers and may be considered a first step for tissue-based biomarker research, as well as the extemporaneous examination of biopsies during surgery.
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Affiliation(s)
- Rémi Longuespée
- 1 Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), MALDI Imaging Team, Université de Lille 1 , Cité Scientifique, Lille, France
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Jones EE, Powers TW, Neely BA, Cazares LH, Troyer DA, Parker AS, Drake RR. MALDI imaging mass spectrometry profiling of proteins and lipids in clear cell renal cell carcinoma. Proteomics 2014; 14:924-35. [PMID: 24497498 DOI: 10.1002/pmic.201300434] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/05/2013] [Accepted: 12/21/2013] [Indexed: 01/08/2023]
Abstract
Reducing the incidence and mortality rates for clear cell renal cell carcinoma (ccRCC) remains a significant clinical challenge with poor 5-year survival rates. A unique tissue cohort was assembled of matched ccRCC and distal nontumor tissues (n = 20) associated with moderate risk of disease progression, half of these from individuals who progressed to metastatic disease and the other half who remained disease free. These tissues were used for MALDI imaging MS profiling of proteins in the 2-20 kDa range, resulting in a panel of 108 proteins that had potential disease-specific expression patterns. Protein lysates from the same tissues were analyzed by MS/MS, resulting in identification of 56 proteins of less than 20 kDa molecular weight. The same tissues were also used for global lipid profiling analysis by MALDI-FT-ICR MS. From the cumulative protein and lipid expression profile data, a refined panel of 26 proteins and 39 lipid species was identified that could either distinguish tumor from nontumor tissues, or tissues from recurrent disease progressors from nonrecurrent disease individuals. This approach has the potential to not only improve prognostic assessment and enhance postoperative surveillance, but also to inform on the underlying biology of ccRCC progression.
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Affiliation(s)
- Elizabeth Ellen Jones
- Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Medical University of South Carolina, Charleston, SC, USA
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68
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Beyoğlu D, Idle JR. Painting the liver with lasers: the future of liver histology? Hepatology 2014; 59:757-60. [PMID: 24009190 DOI: 10.1002/hep.26734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Diren Beyoğlu
- Hepatology Research Group, Department of Clinical Research, University of Bern, Bern, Switzerland
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Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, Chinot O, Lafitte D. MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics 2014; 14:1290-301. [PMID: 24376047 DOI: 10.1002/pmic.201300329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023]
Abstract
Glioblastoma multiforme is one of the most common intracranial tumors encountered in adults. This tumor of very poor prognosis is associated with a median survival rate of approximately 14 months. One of the major issues to better understand the biology of these tumors and to optimize the therapy is to obtain the molecular structure of glioblastoma. MALDI molecular imaging enables location of molecules in tissues without labeling. However, molecular identification in situ is not an easy task. In this paper, we used MALDI imaging coupled to in-source decay to characterize markers of this pathology. We provided MALDI molecular images up to 30 μm spatial resolution of mouse brain tissue sections. MALDI images showed the heterogeneity of the glioblastoma. In the various zones and at various development stages of the tumor, using our top-down strategy, we identified several proteins. These proteins play key roles in tumorigenesis. Particular attention was given to the necrotic area with characterization of hemorrhage, one of the most important poor prognosis factors in glioblastoma.
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