1
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Mass spectrometry imaging in gynecological cancers: the best is yet to come. Cancer Cell Int 2022; 22:414. [PMID: 36536419 PMCID: PMC9764543 DOI: 10.1186/s12935-022-02832-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry imaging (MSI) enables obtaining multidimensional results simultaneously in a single run, including regiospecificity and m/z values corresponding with specific proteins, peptides, lipids, etc. The knowledge obtained in this way allows for a multifaceted analysis of the studied issue, e.g., the specificity of the neoplastic process and the search for new therapeutic targets. Despite the enormous possibilities, this relatively new technique in many aspects still requires the development or standardization of analytical protocols (from collecting biological material, through sample preparation, analysis, and data collection, to data processing). The introduction of standardized protocols for MSI studies, with its current potential to extend diagnostic and prognostic capabilities, can revolutionize clinical pathology. As far as identifying ovarian cancer subtypes can be challenging, especially in poorly differentiated tumors, developing MSI-based algorithms may enhance determining prognosis and tumor staging without the need for extensive surgery and optimize the choice of subsequent therapy. MSI might bring new solutions in predicting response to treatment in patients with endometrial cancer. Therefore, MSI may help to revolutionize the future of gynecological oncology in terms of diagnostics, treatment, and predicting the response to therapy. This review will encompass several aspects, e.g., contemporary discoveries in gynecological cancer research utilizing MSI, indicates current challenges, and future perspectives on MSI.
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2
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Alexovič M, Sabo J, Longuespée R. Microproteomic sample preparation. Proteomics 2021; 21:e2000318. [PMID: 33547857 DOI: 10.1002/pmic.202000318] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/11/2022]
Abstract
Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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3
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Pietkiewicz D, Horała A, Plewa S, Jasiński P, Nowak-Markwitz E, Kokot ZJ, Matysiak J. MALDI-MSI-A Step Forward in Overcoming the Diagnostic Challenges in Ovarian Tumors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E7564. [PMID: 33080944 PMCID: PMC7589662 DOI: 10.3390/ijerph17207564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
This study presents the use of matrix-assisted laser desorption and ionization mass spectrometry imaging (MALDI-MSI) directly on the tissue of two ovarian tumors that often present a diagnostic challenge, a low-grade serous borderline ovarian tumor and ovarian fibrothecoma. Different spatial distribution of m/z values within the tissue samples was observed, and regiospecific peaks were identified. Among the 106 peaks in the borderline ovarian tumor five, regiospecific peaks (m/z: 2861.35; 2775.79; 3368.34; 3438.43; 4936.37) were selected using FlexImaging software. Subsequently, the distribution of those selected peaks was visualized on the fibrothecoma tissue section, which demonstrated the differences in the tissue homo-/heterogeneous structure of both tumors. The comparison with the histopathological staining of the ovarian borderline tumor tissue section, obtained during serial sectioning, showed a close correlation of the molecular map with the morphological and histopathological features of the tissue and allowed the identification of different tissue types within the sample. This study highlights the potential significance of MSI in enabling morphological characterization of ovarian tumors as well as correct diagnosis and further prognosis than thus far seen in the literature. Osteopontin, tropomyosin and orosomucoid are only a couple of the molecules investigated using MALDI-MSI in ovarian cancer research. This study, in line with the available literature, proves the potential of MALDI-MSI to overcome the current limitations of classic histopathological examination giving a more in-depth insight into the tissue structure and thus lead to the more accurate differential diagnosis of ovarian tumors, especially in the most challenging cases.
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Affiliation(s)
- Dagmara Pietkiewicz
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland; (D.P.); (S.P.)
| | - Agnieszka Horała
- Gynecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (A.H.); (E.N.-M.)
| | - Szymon Plewa
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland; (D.P.); (S.P.)
| | - Piotr Jasiński
- Department of Pathology Gynecological and Obstetric Clinical Hospital, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland;
| | - Ewa Nowak-Markwitz
- Gynecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (A.H.); (E.N.-M.)
| | - Zenon J. Kokot
- Faculty of Health Sciences, Calisia University, 13 Kaszubska Street, 62-800 Kalisz, Poland;
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland; (D.P.); (S.P.)
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4
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Fung AWS, Sugumar V, Ren AH, Kulasingam V. Emerging role of clinical mass spectrometry in pathology. J Clin Pathol 2019; 73:61-69. [PMID: 31690564 DOI: 10.1136/jclinpath-2019-206269] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry-based assays have been increasingly implemented in various disciplines in clinical diagnostic laboratories for their combined advantages in multiplexing capacity and high analytical specificity and sensitivity. It is now routinely used in areas including reference methods development, therapeutic drug monitoring, toxicology, endocrinology, paediatrics, immunology and microbiology to identify and quantify biomolecules in a variety of biological specimens. As new ionisation methods, instrumentation and techniques are continuously being improved and developed, novel mass spectrometry-based clinical applications will emerge for areas such as proteomics, metabolomics, haematology and anatomical pathology. This review will summarise the general principles of mass spectrometry and specifically highlight current and future clinical applications in anatomical pathology.
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Affiliation(s)
- Angela W S Fung
- Department of Pathology and Laboratory Medicine, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vijithan Sugumar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Annie He Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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5
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Bashizadeh Fakhar H, Rezaie-Tavirani M, Zali H, Darkhaneh RF, Nejad EK, Aghazadeh MH. Proteomic Analysis of Low-Grade Serous Ovarian Cancer and Comparing It with Non-cancerous Ovarian. INDIAN JOURNAL OF GYNECOLOGIC ONCOLOGY 2018. [DOI: 10.1007/s40944-018-0187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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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: 33] [Impact Index Per Article: 4.7] [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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7
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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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8
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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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9
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Elzek MA, Rodland KD. Proteomics of ovarian cancer: functional insights and clinical applications. Cancer Metastasis Rev 2016; 34:83-96. [PMID: 25736266 DOI: 10.1007/s10555-014-9547-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the past decade, there has been an increasing interest in applying proteomics to assist in understanding the pathogenesis of ovarian cancer, elucidating the mechanism of drug resistance, and in the development of biomarkers for early detection of ovarian cancer. Although ovarian cancer is a spectrum of different diseases, the strategies for diagnosis and treatment with surgery and adjuvant therapy are similar across ovarian cancer types, increasing the general applicability of discoveries made through proteomics research. While proteomic experiments face many difficulties which slow the pace of clinical applications, recent advances in proteomic technology contribute significantly to the identification of aberrant proteins and networks which can serve as targets for biomarker development and individualized therapies. This review provides a summary of the literature on proteomics' contributions to ovarian cancer research and highlights the current issues, future directions, and challenges. We propose that protein-level characterization of primary lesion in ovarian cancer can decipher the mystery of this disease, improve diagnostic tools, and lead to more effective screening programs.
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Affiliation(s)
- Mohamed A Elzek
- Egybiotech for Research and Biotechnology, Alexandria, Egypt,
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10
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Longuespée R, Alberts D, Pottier C, Smargiasso N, Mazzucchelli G, Baiwir D, Kriegsmann M, Herfs M, Kriegsmann J, Delvenne P, De Pauw E. A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing. Methods 2015; 104:154-62. [PMID: 26690073 DOI: 10.1016/j.ymeth.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/09/2015] [Accepted: 12/12/2015] [Indexed: 11/29/2022] Open
Abstract
Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest.
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Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium; Proteopath GmbH, Trier, Germany.
| | - Deborah Alberts
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | - Charles Pottier
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Michael Herfs
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany; MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany
| | - Philippe Delvenne
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
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11
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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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12
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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: 4.2] [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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13
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Arafah K, Longuespée R, Desmons A, Kerdraon O, Fournier I, Salzet M. Lipidomics for clinical diagnosis: Dye-Assisted Laser Desorption/Ionization (DALDI) method for lipids detection in MALDI mass spectrometry imaging. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:487-98. [PMID: 24905741 DOI: 10.1089/omi.2013.0175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lipid-based biomarkers for research and diagnosis are rapidly emerging to unpack the basis of person-to-person and population variations in disease susceptibility, drug and nutritional responses, to name but a few. Hence, with the advent of MALDI Mass Spectrometry Imaging, lipids have begun to be investigated intensively. However, lipids are highly mobile during tissue preparation, and are soluble in the solvent used for matrix preparation or in the fixing fluid such as formalin, resulting in substantial delocalization. In the present article, we investigated as another alternative, the possibility of using specific dyes that can absorb UV wavelengths, in order to desorb the lipids specifically from tissue sections, and are known to immobilize them in tissues. Indeed, after lipid insolubilization with chromate solution or chemical fixation with osmium tetroxide, heterocyclic-based dyes can be directly used without matrix. Taking into account the fact that some dyes have this matrix-free capability, we identified particular dyes dedicated to histological staining of lipids that could be used with MALDI mass spectrometry imaging. We stained tissue sections with either Sudan Black B, Nile Blue A, or Oil Red O. An important advantage of this assay relies on its compatibility with usual practices of histopathological investigation of lipids. As a new method, DALDI stands for Dye-Assisted Laser Desorption Ionization and allows for future clinical and histopathological applications using routine histological protocols. Additionally, this novel methodology was validated in human ovarian cancer biopsies to demonstrate its use as a suitable procedure, for histological diagnosis in lipidomics field.
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Affiliation(s)
- Karim Arafah
- 1 Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université de Lille 1 , Cité Scientifique, Villeneuve D'Ascq, France
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14
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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: 0.7] [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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15
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Longuespée R, Couture F, Levesque C, Kwiatkowska A, Desjardins R, Gagnon S, Vergara D, Maffia M, Fournier I, Salzet M, Day R. Implications of Proprotein Convertases in Ovarian Cancer Cell Proliferation and Tumor Progression: Insights for PACE4 as a Therapeutic Target. Transl Oncol 2014; 7:S1936-5233(14)00043-6. [PMID: 24818756 PMCID: PMC4145398 DOI: 10.1016/j.tranon.2014.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 11/26/2022] Open
Abstract
Proprotein convertases are a family of kexin-like serine proteases that process proteins at single and multiple basic residues. Among the predicted and identified PC substrates, an increasing number of proteins having functions in cancer progression indicate that PCs may be potential targets for antineoplastic drugs. In support of this notion, we identified PACE4 as a vital PC involved in prostate cancer proliferation and progression, contrasting with the other co-expressed PCs. The aim of the present study was to test the importance of PCs in ovarian cancer cell proliferation and tumor progression. Based on tissue-expression profiles, furin, PACE4, PC5/6 and PC7 all displayed increased expression in primary tumor, ascites cells and metastases. These PCs were also expressed in variable levels in three model ovarian cell lines tested, namely SKOV3, CAOV3 and OVCAR3 cells. Since SKOV3 cells closely represented the PC expression profile of ovarian cancer cells, we chose them to test the effects of PC silencing using stable gene-silencing shRNA strategy to generate knockdown SKOV3 cells for each expressed PC. In vitro and in vivo assays confirmed the role of PACE4 in the sustainment of SKOV3 cell proliferation, which was not observed with the other three PCs. We also tested PACE4 peptide inhibitors on all three cell lines and observed consequent reduced cell proliferation which was correlated with PACE4 expression. Overall, these data support a role of PACE4 in promoting cell proliferation in ovarian cancer and provides further evidence for PACE4 as a potential therapeutic target.
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Affiliation(s)
- Rémi Longuespée
- MALDI Imaging Team, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, Université Nord de France, Cité Scientifique, Université de Lille 1, Villeneuve D'Ascq, France; Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Frédéric Couture
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Christine Levesque
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Anna Kwiatkowska
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Roxane Desjardins
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Sandra Gagnon
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Daniele Vergara
- MALDI Imaging Team, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, Université Nord de France, Cité Scientifique, Université de Lille 1, Villeneuve D'Ascq, France; Laboratory of Clinical Proteomic, "Giovanni Paolo II" Hospital, ASL-Lecce, Italy
| | - Michelle Maffia
- Laboratory of Clinical Proteomic, "Giovanni Paolo II" Hospital, ASL-Lecce, Italy
| | - Isabelle Fournier
- MALDI Imaging Team, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, Université Nord de France, Cité Scientifique, Université de Lille 1, Villeneuve D'Ascq, France
| | - Michel Salzet
- MALDI Imaging Team, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, Université Nord de France, Cité Scientifique, Université de Lille 1, Villeneuve D'Ascq, France.
| | - Robert Day
- Faculté de Médecine et des Sciences de la Santé, Institut de Pharmacologie de Sherbrooke et Département de chirurgie et service d'urologie, Université de Sherbrooke, Sherbrooke, Canada.
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Longuespée R, Boyon C, Desmons A, Kerdraon O, Leblanc E, Farré I, Vinatier D, Day R, Fournier I, Salzet M. Spectroimmunohistochemistry: A Novel Form of MALDI Mass Spectrometry Imaging Coupled to Immunohistochemistry for Tracking Antibodies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:132-41. [DOI: 10.1089/omi.2013.0075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rémi Longuespée
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Institut de Pharmacologie de Sherbrooke, Département de Chirurgie/Urologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Charlotte Boyon
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Hôpital Jeanne de Flandre, Service de Chirurgie Gynécologique, Lille Cedex, France
| | - Annie Desmons
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
| | - Olivier Kerdraon
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Laboratoire d'Anatomie et de Cytologie Pathologiques, CHRU Lille, Lille Cedex, France
| | - Eric Leblanc
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Centre Oscar-Lambret, Département de Cancérologie Gynécologique, Lille Cedex, France
| | - Isabelle Farré
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Centre Oscar-Lambret, Département de Cancérologie Gynécologique, Lille Cedex, France
| | - Denis Vinatier
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Hôpital Jeanne de Flandre, Service de Chirurgie Gynécologique, Lille Cedex, France
| | - Robert Day
- Laboratoire d'Anatomie et de Cytologie Pathologiques, CHRU Lille, Lille Cedex, France
| | - Isabelle Fournier
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
| | - Michel Salzet
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
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Altmäe S, Esteban FJ, Stavreus-Evers A, Simón C, Giudice L, Lessey BA, Horcajadas JA, Macklon NS, D'Hooghe T, Campoy C, Fauser BC, Salamonsen LA, Salumets A. Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update 2014; 20:12-28. [PMID: 24082038 PMCID: PMC3845681 DOI: 10.1093/humupd/dmt048] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 08/04/2013] [Accepted: 08/19/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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Affiliation(s)
- Signe Altmäe
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | | | - Anneli Stavreus-Evers
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185 Uppsala, Sweden
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (FIVI) and Instituto Universitario IVI/INCLIVA, Valencia University, 46021 Valencia, Spain
| | - Linda Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143-0132, USA
| | - Bruce A. Lessey
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University Medical Group, Greenville Hospital System, Greenville, South Carolina, SC 29605, USA
| | - Jose A. Horcajadas
- Araid-Hospital Miguel Servet, 50004 Zaragoza, Spain
- Department of Genetics, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Nick S. Macklon
- Department of Obstetrics and Gynaecology, Division of Developmental Origins of Adult Disease, University of Southampton, Princess Anne Hospital, SO16 5YA Southampton, UK
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Thomas D'Hooghe
- Leuven University Fertility Center, Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven (Leuven University), 3000 Leuven, Belgium
| | - Cristina Campoy
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | - Bart C. Fauser
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Lois A. Salamonsen
- Prince Henry's Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- Department of Obstetrics and Gynaecology, University of Tartu, 51014 Tartu, Estonia
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Franck J, Quanico J, Wisztorski M, Day R, Salzet M, Fournier I. Quantification-Based Mass Spectrometry Imaging of Proteins by Parafilm Assisted Microdissection. Anal Chem 2013; 85:8127-34. [DOI: 10.1021/ac4009397] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Julien Franck
- Laboratoire de Spectrométrie
de Masse Biologique Fondamentale et Appliquée-EA 4550, Université de Lille 1, Bât SN3, 1er étage, F-59655 Villeneuve D′Ascq, France
| | - Jusal Quanico
- Laboratoire de Spectrométrie
de Masse Biologique Fondamentale et Appliquée-EA 4550, Université de Lille 1, Bât SN3, 1er étage, F-59655 Villeneuve D′Ascq, France
- Institut de pharmacologie de
Sherbrooke, Département de chirurgie/service d’urologie,
Faculté de Médicine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec,
J1H 5N4, Canada
| | - Maxence Wisztorski
- Laboratoire de Spectrométrie
de Masse Biologique Fondamentale et Appliquée-EA 4550, Université de Lille 1, Bât SN3, 1er étage, F-59655 Villeneuve D′Ascq, France
| | - Robert Day
- Institut de pharmacologie de
Sherbrooke, Département de chirurgie/service d’urologie,
Faculté de Médicine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec,
J1H 5N4, Canada
| | - Michel Salzet
- Laboratoire de Spectrométrie
de Masse Biologique Fondamentale et Appliquée-EA 4550, Université de Lille 1, Bât SN3, 1er étage, F-59655 Villeneuve D′Ascq, France
| | - Isabelle Fournier
- Laboratoire de Spectrométrie
de Masse Biologique Fondamentale et Appliquée-EA 4550, Université de Lille 1, Bât SN3, 1er étage, F-59655 Villeneuve D′Ascq, France
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