1
|
Mallah K, Zibara K, Kerbaj C, Eid A, Khoshman N, Ousseily Z, Kobeissy A, Cardon T, Cizkova D, Kobeissy F, Fournier I, Salzet M. Neurotrauma investigation through spatial omics guided by mass spectrometry imaging: Target identification and clinical applications. MASS SPECTROMETRY REVIEWS 2023; 42:189-205. [PMID: 34323300 DOI: 10.1002/mas.21719] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Traumatic brain injury (TBI) represents one of the major public health concerns worldwide due to the increase in TBI incidence as a result of injuries from daily life accidents such as sports and motor vehicle transportation as well as military-related practices. This type of central nervous system trauma is known to predispose patients to several neurological disorders such as Parkinson's disease, Alzheimer's disease, chronic trauamatic encephalopathy, and age-related Dementia. Recently, several proteomic and lipidomic platforms have been applied on different TBI studies to investigate TBI-related mechanisms that have broadened our understanding of its distinct neuropathological complications. In this study, we provide an updated comprehensive overview of the current knowledge and novel perspectives of the spatially resolved microproteomics and microlipidomics approaches guided by mass spectrometry imaging used in TBI studies and its applications in the neurotrauma field. In this regard, we will discuss the use of the spatially resolved microproteomics and assess the different microproteomic sampling methods such as laser capture microdissection, parafilm assisted microdissection, and liquid microjunction extraction as accurate and precise techniques in the field of neuroproteomics. Additionally, we will highlight lipid profiling applications and their prospective potentials in characterizing molecular processes involved in the field of TBI. Specifically, we will discuss the phospholipid metabolism acting as a precursor for proinflammatory molecules such as eicosanoids. Finally, we will survey the current state of spatial neuroproteomics and microproteomics applications and present the various studies highlighting their findings in these fields.
Collapse
Affiliation(s)
- Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- PRASE, Lebanese University, Beirut, Lebanon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Coline Kerbaj
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Ali Eid
- Department of Basic Medical Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nour Khoshman
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Zahraa Ousseily
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Abir Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Dasa Cizkova
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Center for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| |
Collapse
|
2
|
Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study. Cancers (Basel) 2022; 14:cancers14082001. [PMID: 35454907 PMCID: PMC9031064 DOI: 10.3390/cancers14082001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is one of the most common cancers. Due to the limited and invasive approaches for PCa diagnosis, it is crucial to identify more accurate and non-invasive biomarkers for its detection. The aim of our study was to non-invasively uncover new protein targets for detecting PCa using a proteomics and proteogenomics approach. This work identified several dysregulated mutant protein isoforms in urine from PCa patients, some of them predicted to have a protective or an adverse role in these patients. These results are promising given urine’s non-invasive nature and offers an auspicious opportunity for research and development of PCa biomarkers. Abstract To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein isoforms. Statistical analysis revealed 6 differentially abundant mutant protein isoforms in PCa patients. Analysis of the likely effects of mutations on protein function and PPIs involving the dysregulated mutant protein isoforms suggests a protective role of mutations HSPG2*Q1062H and VASN*R161Q and an adverse role of AMBP*A286G and CD55*S162L in PCa patients. This work originally characterized the urinary proteome, focusing on the proteogenome profile of PCa patients, which is usually overlooked in the analysis of PCa and body fluids. Combined analysis of mass spectrometry data using two different software packages was performed for the first time in the context of PCa, which increased the robustness of the data analysis. The application of proteogenomics to urine proteomic analysis can be very enriching in mutation-related diseases such as cancer.
Collapse
|
3
|
Drelich L, Aboulouard S, Franck J, Salzet M, Fournier I, Wisztorski M. Toward High Spatially Resolved Proteomics Using Expansion Microscopy. Anal Chem 2021; 93:12195-12203. [PMID: 34449217 DOI: 10.1021/acs.analchem.0c05372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Expansion microscopy (EM) is an emerging approach for morphological examination of biological specimens at nanoscale resolution using conventional optical microscopy. To achieve physical separation of cell structures, tissues are embedded in a swellable polymer and expanded several fold in an isotropic manner. This work shows the development and optimization of physical tissue expansion as a new method for spatially resolved large-scale proteomics. Herein we established a novel method to enlarge the tissue section to be compatible with manual microdissection on regions of interest and MS-based proteomic analysis. A major issue in expansion microscopy is the loss of protein information during the mechanical homogenization phase due to the use of proteinase K. For isotropic expansion, different homogenization agents were investigated, both to maximize protein identification and to minimize protein diffusion. Best results were obtained with SDS for homogenization. Using our modified protocol, we were able to enlarge a tissue section more than 3-fold and identified up to 655 proteins from 1 mm in size after expansion, equivalent to 330 μm in their real size corresponding thus to an average of 260 cells. This approach can be performed easily without any expensive sampling instrument. We demonstrated the compatibility of sample preparation for expansion microscopy and proteomic study in a spatial context.
Collapse
Affiliation(s)
- Lauranne Drelich
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Soulaimane Aboulouard
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Julien Franck
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Maxence Wisztorski
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| |
Collapse
|
4
|
Pulukkody AC, Yung YP, Donnarumma F, Murray KK, Carlson RP, Hanley L. Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer. PLoS One 2021; 16:e0250911. [PMID: 34292966 PMCID: PMC8297752 DOI: 10.1371/journal.pone.0250911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Heterogeneity in the distribution of nutrients and oxygen gradients during biofilm growth gives rise to changes in phenotype. There has been long term interest in identifying spatial differences during biofilm development including clues that identify chemical heterogeneity. Laser ablation sample transfer (LAST) allows site-specific sampling combined with label free proteomics to distinguish radially and axially resolved proteomes for Pseudomonas aeruginosa biofilms. Specifically, differential protein abundances on oxic vs. anoxic regions of a biofilm were observed by combining LAST with bottom up proteomics. This study reveals a more active metabolism in the anoxic region of the biofilm with respect to the oxic region for this clinical strain of P. aeruginosa, despite this organism being considered an aerobe by nature. Protein abundance data related to cellular acclimations to chemical gradients include identification of glucose catabolizing proteins, high abundance of proteins from arginine and polyamine metabolism, and proteins that could also support virulence and environmental stress mediation in the anoxic region. Finally, the LAST methodology requires only a few mm2 of biofilm area to identify hundreds of proteins.
Collapse
Affiliation(s)
- Aruni Chathurya Pulukkody
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yeni P. Yung
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kermit K. Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ross P. Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
5
|
Wang K, Donnarumma F, Pettit ME, Szot CW, Solouki T, Murray KK. MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4475. [PMID: 31726477 DOI: 10.1002/jms.4475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI). The captured material was processed using a single-pot solid-phase-enhanced sample preparation (SP3) method and analyzed by LC-MS/MS using ion mobility (IM) enhanced data independent acquisition (DIA) to identify and quantify proteins; more than 600 proteins were identified. Using a modified database that included isoform and the post-translational modifications chain, loss of the initial methionine, and acetylation, 14 MALDI MSI peaks were identified. Comparison of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the identified proteins was achieved through an evolutionary relationships classification system.
Collapse
Affiliation(s)
- Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Michael E Pettit
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Carson W Szot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| |
Collapse
|
6
|
Pagliusi Jr. M, Brandão A, Zanetti G, Bonet I, Sartori C, Vieira A. Using the Parafilm-assisted Microdissection (PAM) Method to Sample Rodent Nucleus Accumbens. Bio Protoc 2020; 10:e3836. [DOI: 10.21769/bioprotoc.3836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/28/2020] [Accepted: 10/12/2020] [Indexed: 11/02/2022] Open
|
7
|
Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
Collapse
Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| |
Collapse
|
8
|
Pettit ME, Donnarumma F, Murray KK, Solouki T. Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis. Anal Chim Acta 2018; 1034:102-109. [DOI: 10.1016/j.aca.2018.06.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 12/30/2022]
|
9
|
Delcourt V, Franck J, Quanico J, Gimeno JP, Wisztorski M, Raffo-Romero A, Kobeissy F, Roucou X, Salzet M, Fournier I. Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions. Mol Cell Proteomics 2017; 17:357-372. [PMID: 29122912 PMCID: PMC5795397 DOI: 10.1074/mcp.m116.065755] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Tissue spatially-resolved proteomics was performed on 3 brain regions, leading to the characterization of 123 reference proteins. Moreover, 8 alternative proteins from alternative open reading frames (AltORF) were identified. Some proteins display specific post-translational modification profiles or truncation linked to the brain regions and their functions. Systems biology analysis performed on the proteome identified in each region allowed to associate sub-networks with the functional physiology of each brain region. Back correlation of the proteins identified by spatially-resolved proteomics at a given tissue localization with the MALDI MS imaging data, was then performed. As an example, mapping of the distribution of the matrix metallopeptidase 3-cleaved C-terminal fragment of α-synuclein (aa 95–140) identified its specific distribution along the hippocampal dentate gyrus. Taken together, we established the molecular physiome of 3 rat brain regions through reference and hidden proteome characterization.
Collapse
Affiliation(s)
- Vivian Delcourt
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France.,§Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jusal Quanico
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jean-Pascal Gimeno
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Maxence Wisztorski
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Antonella Raffo-Romero
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Firas Kobeissy
- ¶Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Xavier Roucou
- §Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
| | - Isabelle Fournier
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
| |
Collapse
|
10
|
Delcourt V, Franck J, Leblanc E, Narducci F, Robin YM, Gimeno JP, Quanico J, Wisztorski M, Kobeissy F, Jacques JF, Roucou X, Salzet M, Fournier I. Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine 2017; 21:55-64. [PMID: 28629911 PMCID: PMC5514399 DOI: 10.1016/j.ebiom.2017.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recently, it was demonstrated that proteins can be translated from alternative open reading frames (altORFs), increasing the size of the actual proteome. Top-down mass spectrometry-based proteomics allows the identification of intact proteins containing post-translational modifications (PTMs) as well as truncated forms translated from reference ORFs or altORFs. METHODS Top-down tissue microproteomics was applied on benign, tumor and necrotic-fibrotic regions of serous ovarian cancer biopsies, identifying proteins exhibiting region-specific cellular localization and PTMs. The regions of interest (ROIs) were determined by MALDI mass spectrometry imaging and spatial segmentation. FINDINGS Analysis with a customized protein sequence database containing reference and alternative proteins (altprots) identified 15 altprots, including alternative G protein nucleolar 1 (AltGNL1) found in the tumor, and translated from an altORF nested within the GNL1 canonical coding sequence. Co-expression of GNL1 and altGNL1 was validated by transfection in HEK293 and HeLa cells with an expression plasmid containing a GNL1-FLAG(V5) construct. Western blot and immunofluorescence experiments confirmed constitutive co-expression of altGNL1-V5 with GNL1-FLAG. CONCLUSIONS Taken together, our approach provides means to evaluate protein changes in the case of serous ovarian cancer, allowing the detection of potential markers that have never been considered.
Collapse
Affiliation(s)
- Vivian Delcourt
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Eric Leblanc
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Fabrice Narducci
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Yves-Marie Robin
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Jean-Pascal Gimeno
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; ONCOLille, Maison Régionale de la Recherche Clinique, Lille, France
| | - Jusal Quanico
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Jean-François Jacques
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| |
Collapse
|
11
|
Systematic assessment of surfactants for matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Chim Acta 2017; 963:76-82. [DOI: 10.1016/j.aca.2017.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
|
12
|
Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection. Biochim Biophys Acta Gen Subj 2017; 1861:1702-1714. [PMID: 28300637 DOI: 10.1016/j.bbagen.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection. Subjecting the dissected pieces to the modified Folch method allows to separate the metabolites from proteins. The proteins can then be subjected to digestion under controlled conditions to improve protein identification yields. RESULTS The proof of concept experiment on rat brain generated 162 and 140 metabolite assignments from three ROIs (cerebellum, hippocampus and midbrain/hypothalamus) in positive and negative modes, respectively, and 890, 1303 and 1059 unique proteins. Integrated metabolite and protein overrepresentation analysis identified pathways associated with the biological functions of each ROI, most of which were not identified when looking at the protein and metabolite lists individually. CONCLUSIONS This combined MALDI MS imaging and multi-omics approach further extends the amount of information that can be generated from single tissue sections. GENERAL SIGNIFICANCE To the best of our knowledge, this is the first report combining both imaging and multi-omics analyses in the same workflow and on the same tissue section.
Collapse
Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| |
Collapse
|
13
|
Wisztorski M, Quanico J, Franck J, Fatou B, Salzet M, Fournier I. Droplet-Based Liquid Extraction for Spatially-Resolved Microproteomics Analysis of Tissue Sections. Methods Mol Biol 2017; 1618:49-63. [PMID: 28523499 DOI: 10.1007/978-1-4939-7051-3_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Obtaining information on protein content while keeping their localization on tissue or organ is of importance in different domains to understand pathophysiological processes. There is increasing interest in studying the microenvironment and heterogeneity of tumors, which currently is difficult with existing proteomics techniques. The advent of new techniques, like MALDI Mass Spectrometry Imaging, made a significant progress in the last decade but is characterized by a number of inherent drawbacks. One of these is the limited identification of proteins. New alternative approaches such as spatially-resolved liquid microextraction have recently been proposed to overcome this limitation. In this chapter, we describe strategies using liquid microjunction to perform extraction of previously digested peptides or of intact proteins from tissue section in a localized manner.
Collapse
Affiliation(s)
- Maxence Wisztorski
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France.
| | - Jusal Quanico
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Julien Franck
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Benoit Fatou
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Michel Salzet
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| |
Collapse
|
14
|
Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Combined MALDI Mass Spectrometry Imaging and Parafilm-Assisted Microdissection-Based LC-MS/MS Workflows in the Study of the Brain. Methods Mol Biol 2017; 1598:269-283. [PMID: 28508367 DOI: 10.1007/978-1-4939-6952-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins and other biomolecules such as lipids are significant players in the central nervous system and are implicated in various neurological disorders. Their identification, quantification, and distribution are thus important not only in understanding the disease but also in developing treatments. A combined workflow allowing the localized microextraction of discrete regions identified by a matrix-assisted laser desorption/ionization mass spectrometry (MSI) imaging experiment for proteomics analysis by liquid chromatography/tandem mass spectrometry (LC MS/MS) is described in this chapter. MSI was initially used to map lipid distributions allowing for the identification of regions of interest (ROIs) that are then subjected to microextraction in a consecutive tissue section. Mounting of consecutive tissue on parafilm allows microdissection of the ROIs, where proteins can then be recovered for processing and LC MS/MS analysis. The PAM method provides a fast and cheap means to perform further downstream analysis after an MSI experiment.
Collapse
Affiliation(s)
- Jusal Quanico
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Julien Franck
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
| |
Collapse
|
15
|
Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Progress and Potential of Imaging Mass Spectrometry Applied to Biomarker Discovery. Methods Mol Biol 2017; 1598:21-43. [PMID: 28508356 DOI: 10.1007/978-1-4939-6952-4_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis. A decade of developments focused on improving and standardizing MSI so that the technique can be translated into the clinical setting. This review describes the progress made in addressing the technological development that allows to bridge local protein detection by MSI to its identification and to illustrate its potential in studying various aspects of cancer biomarker discovery.
Collapse
Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France.
| |
Collapse
|
16
|
Murray KK, Seneviratne CA, Ghorai S. High resolution laser mass spectrometry bioimaging. Methods 2016; 104:118-26. [PMID: 26972785 PMCID: PMC4937799 DOI: 10.1016/j.ymeth.2016.03.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/23/2016] [Accepted: 03/08/2016] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry imaging (MSI) was introduced more than five decades ago with secondary ion mass spectrometry (SIMS) and a decade later with laser desorption/ionization (LDI) mass spectrometry (MS). Large biomolecule imaging by matrix-assisted laser desorption/ionization (MALDI) was developed in the 1990s and ambient laser MS a decade ago. Although SIMS has been capable of imaging with a moderate mass range at sub-micrometer lateral resolution from its inception, laser MS requires additional effort to achieve a lateral resolution of 10μm or below which is required to image at the size scale of single mammalian cells. This review covers untargeted large biomolecule MSI using lasers for desorption/ionization or laser desorption and post-ionization. These methods include laser microprobe (LDI) MSI, MALDI MSI, laser ambient and atmospheric pressure MSI, and near-field laser ablation MS. Novel approaches to improving lateral resolution are discussed, including oversampling, beam shaping, transmission geometry, reflective and through-hole objectives, microscope mode, and near-field optics.
Collapse
Affiliation(s)
- Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | - Suman Ghorai
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
17
|
In vivo Real-Time Mass Spectrometry for Guided Surgery Application. Sci Rep 2016; 6:25919. [PMID: 27189490 PMCID: PMC4870577 DOI: 10.1038/srep25919] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/25/2016] [Indexed: 12/18/2022] Open
Abstract
Here we describe a new instrument (SpiderMass) designed for in vivo and real-time analysis. In this instrument ion production is performed remotely from the MS instrument and the generated ions are transported in real-time to the MS analyzer. Ion production is promoted by Resonant Infrared Laser Ablation (RIR-LA) based on the highly effective excitation of O-H bonds in water molecules naturally present in most biological samples. The retrieved molecular patterns are specific to the cell phenotypes and benign versus cancer regions of patient biopsies can be easily differentiated. We also demonstrate by analysis of human skin that SpiderMass can be used under in vivo conditions with minimal damage and pain. Furthermore SpiderMass can also be used for real-time drug metabolism and pharmacokinetic (DMPK) analysis or food safety topics. SpiderMass is thus the first MS based system designed for in vivo real-time analysis under minimally invasive conditions.
Collapse
|