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Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M. Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC). Mol Cell Proteomics 2018; 17:810-825. [PMID: 29363612 PMCID: PMC5880102 DOI: 10.1074/mcp.ra117.000189] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/19/2018] [Indexed: 01/17/2023] Open
Abstract
The interpatient variability of tumor proteomes has been investigated on a large scale but many tumors display also intratumoral heterogeneity regarding morphological and genetic features. It remains largely unknown to what extent the local proteome of tumors intrinsically differs. Here, we used hepatocellular carcinoma as a model system to quantify both inter- and intratumor heterogeneity across human patient specimens with spatial resolution. We defined proteomic features that distinguish neoplastic from the directly adjacent nonneoplastic tissue, such as decreased abundance of NADH dehydrogenase complex I. We then demonstrated the existence of intratumoral variations in protein abundance that re-occur across different patient samples, and affect clinically relevant proteins, even in the absence of obvious morphological differences or genetic alterations. Our work demonstrates the suitability and the benefits of using mass spectrometry-based proteomics to analyze diagnostic tumor specimens with spatial resolution. Data are available via ProteomeXchange with identifier PXD007052.
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Affiliation(s)
- Katarzyna Buczak
- From the ‡European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Alessandro Ori
- From the ‡European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,§Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Joanna M Kirkpatrick
- §Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.,¶European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany
| | - Kerstin Holzer
- ‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Dauch
- **Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany.,‡‡Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Stephanie Roessler
- ‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Volker Endris
- ‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Lasitschka
- ‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Luca Parca
- From the ‡European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | | | - Lars Zender
- **Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany.,‡‡Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.,§§Translational Gastrointestinal Oncology Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Peter Schirmacher
- ‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jeroen Krijgsveld
- ¶European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany.,‖‖European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Singer
- From the ‡European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; .,‖Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Beck
- From the ‡European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; .,European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
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52
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Longuespée R, Alberts D, Baiwir D, Mazzucchelli G, Smargiasso N, De Pauw E. MALDI Imaging Combined with Laser Microdissection-Based Microproteomics for Protein Identification: Application to Intratumor Heterogeneity Studies. Methods Mol Biol 2018; 1788:297-312. [PMID: 29224050 DOI: 10.1007/7651_2017_114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Matrix-assisted laser desorption ionization (MALDI) imaging is widely used for in situ proteomic mapping and finds multiple applications in pathology. However, low fragmentation yields in MALDI avoid an optimal identification of peptides from tissues. On the other hand, LMD-based microproteomic analyses allow for the identification of hundreds to thousands of proteins from small tissue regions. Herein, we present the combination of MALDI imaging and LMD-based microproteomic approaches for parallel identification. We illustrate the workflow with an application to intratumor heterogeneity studies.
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Affiliation(s)
- Rémi Longuespée
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
| | - Deborah Alberts
- Departement of chemistry - Laboratory of mass spectrometry, University of Liége, MolSys, Liége, Belgium
| | - Dominique Baiwir
- Departement of chemistry - Laboratory of mass spectrometry, University of Liége, MolSys, Liége, Belgium
| | - Gabriel Mazzucchelli
- Departement of chemistry - Laboratory of mass spectrometry, University of Liége, MolSys, Liége, Belgium
| | - Nicolas Smargiasso
- Departement of chemistry - Laboratory of mass spectrometry, University of Liége, MolSys, Liége, Belgium
| | - Edwin De Pauw
- Departement of chemistry - Laboratory of mass spectrometry, University of Liége, MolSys, Liége, Belgium
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53
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Longuespée R, Baiwir D, Mazzucchelli G, Smargiasso N, De Pauw E. Laser Microdissection-Based Microproteomics of Formalin-Fixed and Paraffin-Embedded (FFPE) Tissues. Methods Mol Biol 2018; 1723:19-31. [PMID: 29344853 DOI: 10.1007/978-1-4939-7558-7_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Laser microdissection-based proteomics on formalin-fixed and paraffin-embedded tissues is usually performed from relatively large tissue areas or pools of multiple tissue pieces. However, several molecular pathology studies require working on very limited amounts of tissue. This is for example the case when very early cancer lesions have to be handled. Hereby, we present a method for the processing of very small pieces of formalin-fixed and paraffin-embedded tissues for proteomic purposes. This approach is designed in order to avoid sample loss during technical processing and to optimize the digestion of tissue areas containing as little as 2700 cells.
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Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liege, Liège, Belgium.
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liege, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liege, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liege, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liege, Liège, Belgium
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54
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Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
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Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
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55
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Alberts D, Pottier C, Smargiasso N, Baiwir D, Mazzucchelli G, Delvenne P, Kriegsmann M, Kazdal D, Warth A, De Pauw E, Longuespée R. MALDI Imaging-Guided Microproteomic Analyses of Heterogeneous Breast Tumors-A Pilot Study. Proteomics Clin Appl 2017; 12. [DOI: 10.1002/prca.201700062] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Deborah Alberts
- Laboratory of Mass Spectrometry (LSM) - MolSys; Department of Chemistry; University of Liège; Liege Belgium
| | - Charles Pottier
- Department of Pathology; GIGA Cancer; University of Liège Hospital; Liège Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry (LSM) - MolSys; Department of Chemistry; University of Liège; Liege Belgium
| | | | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry (LSM) - MolSys; Department of Chemistry; University of Liège; Liege Belgium
| | - Philippe Delvenne
- Department of Pathology; GIGA Cancer; University of Liège Hospital; Liège Belgium
| | - Mark Kriegsmann
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
| | - Daniel Kazdal
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
| | - Arne Warth
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry (LSM) - MolSys; Department of Chemistry; University of Liège; Liege Belgium
| | - Rémi Longuespée
- Laboratory of Mass Spectrometry (LSM) - MolSys; Department of Chemistry; University of Liège; Liege Belgium
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
- Proteopath GmbH; Trier Germany
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56
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Noberini R, Longuespée R, Richichi C, Pruneri G, Kriegsmann M, Pelicci G, Bonaldi T. PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clin Epigenetics 2017; 9:69. [PMID: 28702092 PMCID: PMC5504751 DOI: 10.1186/s13148-017-0369-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Background Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable epigenetic mechanisms. We have recently developed an approach, termed pathology tissue analysis of histones by mass spectrometry (PAT-H-MS), that allows performing a comprehensive and quantitative analysis of histone PTMs from formalin-fixed paraffin-embedded pathology samples. Despite its great potential, the application of this technique is limited by tissue heterogeneity. Methods In this study, we further implemented the PAT-H-MS approach by coupling it with techniques aimed at reducing sample heterogeneity and selecting specific portions or cell populations within the samples, such as manual macrodissection and laser microdissection (LMD). Results When applied to the analysis of a small set of breast cancer samples, LMD-PAT-H-MS allowed detecting more marked changes between luminal A-like and triple negative patients as compared with the classical approach. These changes included not only the already known H3 K27me3 and K9me3 marks, but also H3 K36me1, which was found increased in triple negative samples and validated on a larger cohort of patients, and could represent a potential novel marker distinguishing breast cancer subtypes. Conclusions These results show the feasibility of applying techniques to reduce sample heterogeneity, including laser microdissection, to the PAT-H-MS protocol, providing new tools in clinical epigenetics and opening new avenues for the comprehensive analysis of histone post-translational modifications in selected cell populations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0369-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@ SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Rémi Longuespée
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.,School of Medicine, University of Milan, 20122 Milan, Italy
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Department of Translational Medicine, Piemonte Orientale University "Amedeo Avogadro", 28100 Novara, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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57
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Herfs M, Longuespée R, Quick CM, Roncarati P, Suarez-Carmona M, Hubert P, Lebeau A, Bruyere D, Mazzucchelli G, Smargiasso N, Baiwir D, Lai K, Dunn A, Obregon F, Yang EJ, Pauw ED, Crum CP, Delvenne P. Proteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma. J Pathol 2017; 241:522-533. [DOI: 10.1002/path.4858] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/21/2016] [Accepted: 11/30/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Rémi Longuespée
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research; University of Liège; Liège Belgium
| | - Charles M Quick
- Department of Pathology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Patrick Roncarati
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Meggy Suarez-Carmona
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Pascale Hubert
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Alizée Lebeau
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Diane Bruyere
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research; University of Liège; Liège Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research; University of Liège; Liège Belgium
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research; University of Liège; Liège Belgium
- GIGA Proteomic Facility; University of Liège; Liège Belgium
| | - Keith Lai
- Department of Pathology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Andrew Dunn
- Department of Pathology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Fabiola Obregon
- Department of Pathology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Eric J Yang
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research; University of Liège; Liège Belgium
| | - Christopher P Crum
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer; University of Liège; Liège Belgium
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58
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Casadonte R, Longuespée R, Kriegsmann J, Kriegsmann M. MALDI IMS and Cancer Tissue Microarrays. Adv Cancer Res 2017; 134:173-200. [PMID: 28110650 DOI: 10.1016/bs.acr.2016.11.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) technology creates a link between the molecular assessment of numerous molecules and the morphological information about their special distribution. The application of MALDI IMS on formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMAs) is suitable for large-scale discovery analyses. Data acquired from FFPE TMA cancer samples in current research are very promising, and applications for routine diagnostics are under development. With the current rapid advances in both technology and applications, MALDI IMS technology is expected to enter into routine diagnostics soon. This chapter is intended to be comprehensive with respect to all aspects and considerations for the application of MALDI IMS on FFPE cancer TMAs with in-depth notes on technical aspects.
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Affiliation(s)
| | | | - J Kriegsmann
- Proteopath GmbH, Trier, Germany; Institute of Molecular Pathology, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - M Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
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59
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Proteomic investigation of human cystic echinococcosis in the liver. Mol Biochem Parasitol 2017; 211:9-14. [DOI: 10.1016/j.molbiopara.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022]
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60
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61
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Longuespée R, Casadonte R, Kriegsmann M, Pottier C, Picard de Muller G, Delvenne P, Kriegsmann J, De Pauw E. MALDI mass spectrometry imaging: A cutting-edge tool for fundamental and clinical histopathology. Proteomics Clin Appl 2016; 10:701-19. [PMID: 27188927 DOI: 10.1002/prca.201500140] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Histopathological diagnoses have been done in the last century based on hematoxylin and eosin staining. These methods were complemented by histochemistry, electron microscopy, immunohistochemistry (IHC), and molecular techniques. Mass spectrometry (MS) methods allow the thorough examination of various biocompounds in extracts and tissue sections. Today, mass spectrometry imaging (MSI), and especially matrix-assisted laser desorption ionization (MALDI) imaging links classical histology and molecular analyses. Direct mapping is a major advantage of the combination of molecular profiling and imaging. MSI can be considered as a cutting edge approach for molecular detection of proteins, peptides, carbohydrates, lipids, and small molecules in tissues. This review covers the detection of various biomolecules in histopathological sections by MSI. Proteomic methods will be introduced into clinical histopathology within the next few years.
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Affiliation(s)
- Rémi Longuespée
- Proteopath GmbH, Trier, Germany.,Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | | | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany.,MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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62
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Marée R, Rollus L, Stévens B, Hoyoux R, Louppe G, Vandaele R, Begon JM, Kainz P, Geurts P, Wehenkel L. Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics 2016; 32:1395-401. [PMID: 26755625 PMCID: PMC4848407 DOI: 10.1093/bioinformatics/btw013] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries. RESULTS We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications. AVAILABILITY AND IMPLEMENTATION Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/ A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available. CONTACT info@cytomine.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Raphaël Marée
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium Bioimage Analysis Unit, Institut Pasteur, Paris, France
| | - Loïc Rollus
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Benjamin Stévens
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Renaud Hoyoux
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Gilles Louppe
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Rémy Vandaele
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Jean-Michel Begon
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Philipp Kainz
- Institute of Biophysics, Medical University of Graz, Graz, Austria
| | - Pierre Geurts
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Louis Wehenkel
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
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