1
|
Nisa KU, Tarfeen N, Humaira, Wani S, Nisa Q, Ali S, Wali AF. Proteomic approaches in the study of cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
2
|
Applications of mass spectroscopy in understanding cancer proteomics. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
3
|
Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
Collapse
|
4
|
Garg T, Weiss CR, Sheth RA. Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology. Cancers (Basel) 2022; 14:3628. [PMID: 35892890 PMCID: PMC9332307 DOI: 10.3390/cancers14153628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years there has been increased interest in using the immune contexture of the primary tumors to predict the patient's prognosis. The tumor microenvironment of patients with cancers consists of different types of lymphocytes, tumor-infiltrating leukocytes, dendritic cells, and others. Different technologies can be used for the evaluation of the tumor microenvironment, all of which require a tissue or cell sample. Image-guided tissue sampling is a cornerstone in the diagnosis, stratification, and longitudinal evaluation of therapeutic efficacy for cancer patients receiving immunotherapies. Therefore, interventional radiologists (IRs) play an essential role in the evaluation of patients treated with systemically administered immunotherapies. This review provides a detailed description of different technologies used for immune assessment and analysis of the data collected from the use of these technologies. The detailed approach provided herein is intended to provide the reader with the knowledge necessary to not only interpret studies containing such data but also design and apply these tools for clinical practice and future research studies.
Collapse
Affiliation(s)
- Tushar Garg
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Clifford R. Weiss
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Rahul A. Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
5
|
Hajjaji N, Aboulouard S, Cardon T, Bertin D, Robin YM, Fournier I, Salzet M. Path to Clonal Theranostics in Luminal Breast Cancers. Front Oncol 2022; 11:802177. [PMID: 35096604 PMCID: PMC8793283 DOI: 10.3389/fonc.2021.802177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Integrating tumor heterogeneity in the drug discovery process is a key challenge to tackle breast cancer resistance. Identifying protein targets for functionally distinct tumor clones is particularly important to tailor therapy to the heterogeneous tumor subpopulations and achieve clonal theranostics. For this purpose, we performed an unsupervised, label-free, spatially resolved shotgun proteomics guided by MALDI mass spectrometry imaging (MSI) on 124 selected tumor clonal areas from early luminal breast cancers, tumor stroma, and breast cancer metastases. 2868 proteins were identified. The main protein classes found in the clonal proteome dataset were enzymes, cytoskeletal proteins, membrane-traffic, translational or scaffold proteins, or transporters. As a comparison, gene-specific transcriptional regulators, chromatin related proteins or transmembrane signal receptor were more abundant in the TCGA dataset. Moreover, 26 mutated proteins have been identified. Similarly, expanding the search to alternative proteins databases retrieved 126 alternative proteins in the clonal proteome dataset. Most of these alternative proteins were coded mainly from non-coding RNA. To fully understand the molecular information brought by our approach and its relevance to drug target discovery, the clonal proteomic dataset was further compared to the TCGA breast cancer database and two transcriptomic panels, BC360 (nanoString®) and CDx (Foundation One®). We retrieved 139 pathways in the clonal proteome dataset. Only 55% of these pathways were also present in the TCGA dataset, 68% in BC360 and 50% in CDx. Seven of these pathways have been suggested as candidate for drug targeting, 22 have been associated with breast cancer in experimental or clinical reports, the remaining 19 pathways have been understudied in breast cancer. Among the anticancer drugs, 35 drugs matched uniquely with the clonal proteome dataset, with only 7 of them already approved in breast cancer. The number of target and drug interactions with non-anticancer drugs (such as agents targeting the cardiovascular system, metabolism, the musculoskeletal or the nervous systems) was higher in the clonal proteome dataset (540 interactions) compared to TCGA (83 interactions), BC360 (419 interactions), or CDx (172 interactions). Many of the protein targets identified and drugs screened were clinically relevant to breast cancer and are in clinical trials. Thus, we described the non-redundant knowledge brought by this clone-tailored approach compared to TCGA or transcriptomic panels, the targetable proteins identified in the clonal proteome dataset, and the potential of this approach for drug discovery and repurposing through drug interactions with antineoplastic agents and non-anticancer drugs.
Collapse
Affiliation(s)
- Nawale Hajjaji
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Delphine Bertin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Yves-Marie Robin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - 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
|
6
|
Guo Y, Dong X, Jin J, He Y. The Expression Patterns and Prognostic Value of the Proteasome Activator Subunit Gene Family in Gastric Cancer Based on Integrated Analysis. Front Cell Dev Biol 2021; 9:663001. [PMID: 34650966 PMCID: PMC8505534 DOI: 10.3389/fcell.2021.663001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence supports that proteasome activator subunit (PSME) genes play an indispensable role in multiple tumors. The diverse expression patterns, prognostic value, underlying mechanism, and the role in the immunotherapy of PSME genes in gastric cancer (GC) have yet to be fully elucidated. We systematically demonstrated the functions of these genes in GC using various large databases, unbiased in silico approaches, and experimental validation. We found that the median expression levels of all PSME genes were significantly higher in GC tissues than in normal tissues. Our findings showed that up-regulated PSME1 and PSME2 expression significantly correlated with favorable overall survival, post-progression survival, and first progression survival in GC patients. The expression of PSME1 and PSME2 was positively correlated with the infiltration of most immune cells and the activation of anti-cancer immunity cycle steps. Moreover, GC patients with high PSME1 and PSME2 expression have higher immunophenoscore and tumor mutational burden. In addition, a receiver operating characteristic analysis suggested that PSME3 and PSME4 had high diagnostic performance for distinguishing GC patients from healthy individuals. Moreover, our further analysis indicated that PSME genes exert an essential role in GC, and the present study indicated that PSME1 and PSME2 may be potential prognostic markers for enhancing survival and prognostic accuracy in GC patients and may even act as potential biomarkers for GC patients indicating a response to immunotherapy. PSME3 may serve as an oncogene in tumorigenesis and may be a promising therapeutic target for GC. PSME4 had excellent diagnostic performance and could serve as a good diagnostic indicator for GC.
Collapse
Affiliation(s)
- Yongdong Guo
- Cancer Institute, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoping Dong
- Cancer Institute, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jing Jin
- Cancer Institute, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yutong He
- Cancer Institute, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
7
|
Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
Collapse
Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| |
Collapse
|
8
|
Li K, Pei Y, Wu Y, Guo Y, Cui W. Performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in diagnosis of ovarian cancer: a systematic review and meta-analysis. J Ovarian Res 2020; 13:6. [PMID: 31924227 PMCID: PMC6954560 DOI: 10.1186/s13048-019-0605-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND To evaluate the diagnostic performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for ovarian cancer. PATIENTS AND METHODS A thorough research was conducted in PubMed, Web of Science and Embase (until November 2018) to identify studies evaluating the accuracy of MALDI-TOF-MS for ovarian cancer. Using Meta-Disc1.4, Review Manager 5.3 and Stata 15.1 software to analyze the pooled results: sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and 95% confidence intervals (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) show the overall performance of MALDI-TOF-MS. RESULTS Eighteen studies were included in the meta-analysis. Methodological quality analysis of the included studies showed that these articles were at low risk of bias and applicability concerns in total. Summary estimates of the diagnostic parameters were as follows: sensitivity, 0.77 (95% CI: 0.73-0.80); specificity, 0.72 (95% CI: 0.70-0.74), PLR, 2.80 (95% CI: 2.41-3.24); NLR, 0.30 (95% CI: 0.22-0.40) and DOR, 10.71 (95% CI: 7.81-14.68). And the AUC was 0.8336. Egger's test showed no significant publication bias in this meta-analysis. CONCLUSION In conclusion, MALDI-TOF-MS shows a good ability for diagnosing ovarian cancer. Further evaluation and optimization of standardized procedures are necessary for complete relying on MALDI-TOF-MS to diagnose ovarian cancer.
Collapse
Affiliation(s)
- Kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuqing Pei
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Wu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi Guo
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wei Cui
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
9
|
Bonifácio VDB. Ovarian Cancer Biomarkers: Moving Forward in Early Detection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:355-363. [PMID: 32130708 DOI: 10.1007/978-3-030-34025-4_18] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ovarian cancer is a silent cancer which rate survival mainly relays in early stage detection. The discovery of reliable ovarian cancer biomarkers plays a crucial role in the disease management and strongly impact in patient's prognosis and survival. Although having many limitations CA125 is a classical ovarian cancer biomarker, but current research using proteomic or metabolomic methodologies struggles to find alternative biomarkers, using non-invasive our relatively non-invasive sources such as urine, serum, plasma, tissue, ascites or exosomes. Metabolism and metabolites are key players in cancer biology and its importance in biomarkers discovery cannot be neglected. In this chapter we overview the state of art and the challenges facing the use and discovery of biomarkers and focus on ovarian cancer early detection.
Collapse
Affiliation(s)
- Vasco D B Bonifácio
- IBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
10
|
Morozov AV, Karpov VL. Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer. Front Oncol 2019; 9:761. [PMID: 31456945 PMCID: PMC6700291 DOI: 10.3389/fonc.2019.00761] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 01/19/2023] Open
Abstract
The life of every organism is dependent on the fine-tuned mechanisms of protein synthesis and breakdown. The degradation of most intracellular proteins is performed by the ubiquitin proteasome system (UPS). Proteasomes are central elements of the UPS and represent large multisubunit protein complexes directly responsible for the protein degradation. Accumulating data indicate that there is an intriguing diversity of cellular proteasomes. Different proteasome forms, containing different subunits and attached regulators have been described. In addition, proteasomes specific for a particular tissue were identified. Cancer cells are highly dependent on the proper functioning of the UPS in general, and proteasomes in particular. At the same time, the information regarding the role of different proteasome forms in cancer is limited. This review describes the functional and structural heterogeneity of proteasomes, their association with cancer as well as several established and novel proteasome-directed therapeutic strategies.
Collapse
Affiliation(s)
- Alexey V Morozov
- Laboratory of Regulation of Intracellular Proteolysis, W.A. Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
| | - Vadim L Karpov
- Laboratory of Regulation of Intracellular Proteolysis, W.A. Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
| |
Collapse
|
11
|
Seccia V, Navari E, Donadio E, Boldrini C, Ciregia F, Ronci M, Aceto A, Dallan I, Lucacchini A, Casani AP, Mazzoni MR, Giusti L. Proteomic Investigation of Malignant Major Salivary Gland Tumors. Head Neck Pathol 2019; 14:362-373. [PMID: 31098787 PMCID: PMC7235111 DOI: 10.1007/s12105-019-01040-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/07/2019] [Indexed: 12/25/2022]
Abstract
The purpose of this study was to define the proteome profile of fine needle aspiration (FNA) samples of malignant major salivary gland tumors (MSGT) compared to benign counterparts, and to evaluate potential clinical correlations and future applications. Patients affected by MSGT (n = 20), pleomorphic adenoma (PA) (n = 37) and Warthin's tumor (WT) (n = 14) were enrolled. Demographic, clinical and histopathological data were registered for all patients. FNA samples were processed to obtain the protein extracts. Protein separation was obtained by two-dimensional electrophoresis (2-DE) and proteins were identified by mass spectrometry. Western blot analysis was performed to validate the 2-DE results. Statistical differences between groups were calculated by the Mann-Whitney U test for non-normal data. Spearman's rank correlation coefficient was calculated to evaluate correlations among suggested protein biomarkers and clinical parameters. Twelve and 27 differentially expressed spots were found for MSGT versus PA and MSGT versus WT, respectively. Among these, annexin-5, cofilin-1, peptidyl-prolyl-cis-trans-isomerase-A and F-actin-capping-alpha-1 were able to differentiate MSGT from PA, WT, and healthy samples. Moreover, STRING analysis suggested cofilin-1 as a key node of protein interactions. Some of the overexpressed proteins are related to some clinical factors of our cohort, such as survival and outcome. Our results suggest potential protein biomarkers of MSGT, which could allow for more appropriate treatment plans, as well as shedding light on the molecular pathways involved.
Collapse
Affiliation(s)
- Veronica Seccia
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, ENT Section, University of Pisa, Pisa, Italy
| | - Elena Navari
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, ENT Section, University of Pisa, Pisa, Italy
| | - Elena Donadio
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | - Federica Ciregia
- Department of Rheumatology, GIGA Research, Centre Hospitalier Universitaire (CHU) de Liège, University of Liège, Liège, Belgium
| | - Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, University G. d’Annunzio of Chieti-Pescara, Chieti, Italy
| | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences, University G. d’Annunzio of Chieti-Pescara, Chieti, Italy
| | - Iacopo Dallan
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, ENT Section, University of Pisa, Pisa, Italy
| | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Augusto Pietro Casani
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, ENT Section, University of Pisa, Pisa, Italy
| | | | - Laura Giusti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy ,School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
| |
Collapse
|
12
|
Inglese P, Correia G, Pruski P, Glen RC, Takats Z. Colocalization Features for Classification of Tumors Using Desorption Electrospray Ionization Mass Spectrometry Imaging. Anal Chem 2019; 91:6530-6540. [PMID: 31013058 PMCID: PMC6533599 DOI: 10.1021/acs.analchem.8b05598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Supervised modeling of mass spectrometry imaging (MSI) data is a crucial component for the detection of the distinct molecular characteristics of cancerous tissues. Currently, two types of supervised analyses are mainly used on MSI data: pixel-wise segmentation of sample images and whole-sample-based classification. A large number of mass spectra associated with each MSI sample can represent a challenge for designing models that simultaneously preserve the overall molecular content while capturing valuable information contained in the MSI data. Furthermore, intensity-related batch effects can introduce biases in the statistical models. Here we introduce a method based on ion colocalization features that allows the classification of whole tissue specimens using MSI data, which naturally preserves the spatial information associated the with the mass spectra and is less sensitive to possible batch effects. Finally, we propose data visualization strategies for the inspection of the derived networks, which can be used to assess whether the correlation differences are related to coexpression/suppression or disjoint spatial localization patterns and can suggest hypotheses based on the underlying mechanisms associated with the different classes of analyzed samples.
Collapse
Affiliation(s)
- Paolo Inglese
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London SW7 2AZ , United Kingdom
| | - Gonçalo Correia
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London SW7 2AZ , United Kingdom
| | - Pamela Pruski
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London SW7 2AZ , United Kingdom
| | - Robert C Glen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London SW7 2AZ , United Kingdom
| | - Zoltan Takats
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London SW7 2AZ , United Kingdom
| |
Collapse
|
13
|
Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
Collapse
Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
| |
Collapse
|
14
|
Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
Collapse
Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| |
Collapse
|
15
|
Swiatly A, Plewa S, Matysiak J, Kokot ZJ. Mass spectrometry-based proteomics techniques and their application in ovarian cancer research. J Ovarian Res 2018; 11:88. [PMID: 30270814 PMCID: PMC6166298 DOI: 10.1186/s13048-018-0460-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/20/2018] [Indexed: 12/26/2022] Open
Abstract
Ovarian cancer has emerged as one of the leading cause of gynecological malignancies. So far, the measurement of CA125 and HE4 concentrations in blood and transvaginal ultrasound examination are essential ovarian cancer diagnostic methods. However, their sensitivity and specificity are still not sufficient to detect disease at the early stage. Moreover, applied treatment may appear to be ineffective due to drug-resistance. Because of a high mortality rate of ovarian cancer, there is a pressing need to develop innovative strategies leading to a full understanding of complicated molecular pathways related to cancerogenesis. Recent studies have shown the great potential of clinical proteomics in the characterization of many diseases, including ovarian cancer. Therefore, in this review, we summarized achievements of proteomics in ovarian cancer management. Since the development of mass spectrometry has caused a breakthrough in systems biology, we decided to focus on studies based on this technique. According to PubMed engine, in the years 2008-2010 the number of studies concerning OC proteomics was increasing, and since 2010 it has reached a plateau. Proteomics as a rapidly evolving branch of science may be essential in novel biomarkers discovery, therapy decisions, progression predication, monitoring of drug response or resistance. Despite the fact that proteomics has many to offer, we also discussed some limitations occur in ovarian cancer studies. Main difficulties concern both complexity and heterogeneity of ovarian cancer and drawbacks of the mass spectrometry strategies. This review summarizes challenges, capabilities, and promises of the mass spectrometry-based proteomics techniques in ovarian cancer management.
Collapse
Affiliation(s)
- Agata Swiatly
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Szymon Plewa
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Zenon J. Kokot
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| |
Collapse
|
16
|
Lou S, Balluff B, de Graaff MA, Cleven AHG, Briaire-de Bruijn I, Bovée JVMG, McDonnell LA. High-grade sarcoma diagnosis and prognosis: Biomarker discovery by mass spectrometry imaging. Proteomics 2017; 16:1802-13. [PMID: 27174013 DOI: 10.1002/pmic.201500514] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022]
Abstract
The combination of high heterogeneity, both intratumoral and intertumoral, with their rarity has made diagnosis, prognosis of high-grade sarcomas difficult. There is an urgent need for more objective molecular biomarkers, to differentiate between the many different subtypes, and to also provide new treatment targets. Mass spectrometry imaging (MSI) has amply demonstrated its ability to identify potential new markers for patient diagnosis, survival, metastasis and response to therapy in cancer research. In this study, we investigated the ability of MALDI-MSI of proteins to distinguish between high-grade osteosarcoma (OS), leiomyosarcoma (LMS), myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) (Ntotal = 53). We also investigated if there are individual proteins or protein signatures that are statistically associated with patient survival. Twenty diagnostic protein signals were found characteristic for specific tumors (p ≤ 0.05), amongst them acyl-CoA-binding protein (m/z 11 162), macrophage migration inhibitory factor (m/z 12 350), thioredoxin (m/z 11 608) and galectin-1 (m/z 14 633) were assigned. Another nine protein signals were found to be associated with overall survival (p ≤ 0.05), including proteasome activator complex subunit 1 (m/z 9753), indicative for non-OS patients with poor survival; and two histone H4 variants (m/z 11 314 and 11 355), indicative of poor survival for LMS patients.
Collapse
Affiliation(s)
- Sha Lou
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Marieke A de Graaff
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | | | - Judith V M G Bovée
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| |
Collapse
|
17
|
Applications of Mass Spectrometry Imaging for Safety Evaluation. Methods Mol Biol 2017. [PMID: 28748461 DOI: 10.1007/978-1-4939-7172-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mass spectrometry imaging (MSI) was first derived from techniques used in physics, which were then incorporated into chemistry followed by application in biology. Developed over 50 years ago, and with different principles to detect and map compounds on a sample surface, MSI supports modern biology questions by detecting biological compounds within tissue sections. MALDI (matrix-assisted laser desorption/ionization) imaging trend analysis in this field shows an important increase in the number of publications since 2005, especially with the development of the MALDI imaging technique and its applications in biomarker discovery and drug distribution. With recent improvements of statistical tools, absolute and relative quantification protocols, as well as quality and reproducibility evaluations, MALDI imaging has become one of the most reliable MSI techniques to support drug discovery and development phases. MSI allows to potentially address important questions in drug development such as "What is the localization of the drug and its metabolites in the tissues?", "What is the pharmacological effect of the drug in this particular region of interest?", or "Is the drug and its metabolites related to an atypical finding?" However, prior to addressing these questions using MSI techniques, expertise needs to be developed to become proficient at histological procedures (tissue preparation with frozen of fixed tissues), analytical chemistry, matrix application, instrumentation, informatics, and mathematics for data analysis and interpretation.
Collapse
|
18
|
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
|
19
|
Dehghan-Nayeri N, Eshghi P, Pour KG, Rezaei-Tavirani M, Omrani MD, Gharehbaghian A. Differential expression pattern of protein markers for predicting chemosensitivity of dexamethasone-based chemotherapy of B cell acute lymphoblastic leukemia. Cancer Chemother Pharmacol 2017; 80:177-185. [PMID: 28585036 DOI: 10.1007/s00280-017-3347-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/29/2017] [Indexed: 02/06/2023]
Abstract
Dexamethasone is considered as a direct chemotherapeutic agent in the treatment of pediatric acute lymphoblastic leukemia (ALL). Beside the advantages of the drug, some problems arising from the dose-related side effects are challenging issues during the treatment. Accordingly, the classification of patients to dexamethasone sensitive and resistance groups can help to select optimizing the therapeutic dose with the lowest adverse effects particularly in sensitive cases. For this purpose, we investigated inhibited proliferation and induced cytotoxicity in NALM-6 cells, as sensitive cells, after dexamethasone treatment. In addition, comparative protein expression analysis using the 2DE-MALDI-TOF MS technique was performed to identify the specific altered proteins. In addition, we evaluated mRNA expression levels of the identified proteins in bone-marrow samples from pediatric ALL patients using the real-time q-PCR method. Eventually, proteomic analysis revealed a combination of biomarkers, including capping proteins (CAPZA1 and CAPZB), chloride channel (CLIC1), purine nucleoside phosphorylase (PNP), and proteasome activator (PSME1), in response to the dexamethasone treatment. In addition, our results indicated low expression of identified proteins at both the mRNA and protein expression levels after drug treatment. Moreover, quantitative real-time PCR data analysis indicated that independent of the molecular subtypes of the leukemia, CAPZA1, CAPZB, CLIC1, and PNP expression levels were lower in ALL samples than normal samples, although PSME1 expression level was higher in ALL samples than normal samples. Furthermore, the expression level of all proteins (except PSME1) was different between high-risk and standard-risk patients that suggesting the prognostic value of them. In conclusion, our study suggests a panel of biomarkers comprising CAPZA1, CAPZB, CLIC1, PNP, and PSME1 as early diagnosis and treatment evaluation markers that may differentiate cancer cells which are presumably to benefit from dexamethasone-based chemotherapy and may facilitate the prediction of clinical outcome.
Collapse
MESH Headings
- Antineoplastic Agents, Hormonal/administration & dosage
- Antineoplastic Agents, Hormonal/pharmacology
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Child
- Child, Preschool
- Dexamethasone/administration & dosage
- Dexamethasone/pharmacology
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Infant
- Male
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Prognosis
- Proteomics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Collapse
Affiliation(s)
- Nasrin Dehghan-Nayeri
- Proteomics Research Center, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Peyman Eshghi
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kourosh Goudarzi Pour
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Gharehbaghian
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Hematology and Blood Bank, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
20
|
MALDI imaging: beyond classic diagnosis. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:212-218. [PMID: 29382489 DOI: 10.1016/j.bmhimx.2017.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry has been the focus of technology development and application for imaging for several decades. Imaging mass spectrometry using matrix-assisted laser desorption ionization is a new and effective tool for molecular studies of complex biological samples such as tissue sections. As histological features remain intact throughout the analysis of a section, distribution maps of multiple analytes can be correlated with histological and clinical features. Spatial molecular arrangements can be assessed without the need for target-specific reagents, allowing the discovery of diagnostic and prognostic markers of different cancer types and enabling the determination of effective therapies.
Collapse
|
21
|
Lavine BK, White CG, DeNoyer L, Mechref Y. Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recognition analysis of MALDI-TOF mass spectra of serum N-linked glycans. Microchem J 2017. [DOI: 10.1016/j.microc.2016.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
22
|
Rizzo DG, Prentice BM, Moore JL, Norris JL, Caprioli RM. Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion. Anal Chem 2017; 89:2948-2955. [DOI: 10.1021/acs.analchem.6b04395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David G. Rizzo
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boone M. Prentice
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jessica L. Moore
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeremy L. Norris
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
23
|
Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:795-816. [PMID: 28087424 DOI: 10.1016/j.bbapap.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation. MALDI-IMS has evolved rapidly over the last decade and has been successfully used in both medical and basic research by scientists worldwide. In this review, we explore the clinical applications of MALDI-IMS, focusing on the major cancer types and neurodegenerative diseases. In particular, we re-emphasize the diagnostic potential of IMS and the challenges that must be confronted when conducting MALDI-IMS in clinical settings. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Yasemin Ucal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Zeynep Aslıhan Durer
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Hakan Atak
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Elif Kadioglu
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Abdurrahman Coskun
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Aysel Ozpinar
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey.
| |
Collapse
|
24
|
Arentz G, Mittal P, Zhang C, Ho YY, Briggs M, Winderbaum L, Hoffmann MK, Hoffmann P. Applications of Mass Spectrometry Imaging to Cancer. Adv Cancer Res 2017; 134:27-66. [PMID: 28110654 DOI: 10.1016/bs.acr.2016.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.
Collapse
Affiliation(s)
- G Arentz
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - C Zhang
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - Y-Y Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia; ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA, Australia
| | - L Winderbaum
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M K Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia.
| |
Collapse
|
25
|
Nazari M, Muddiman DC. Polarity switching mass spectrometry imaging of healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). Analyst 2017; 141:595-605. [PMID: 26402586 DOI: 10.1039/c5an01513h] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry imaging (MSI) is a rapidly evolving field for monitoring the spatial distribution and abundance of analytes in biological tissue sections. It allows for direct and simultaneous analysis of hundreds of different compounds in a label-free manner. In order to obtain a comprehensive metabolite and lipid data, a polarity switching MSI method using infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) was developed and optimized where the electrospray polarity was alternated from one voxel to the next. Healthy and cancerous ovarian hen tissue sections were analyzed using this method. Distribution and relative abundance of different metabolites and lipids within each tissue section were discerned, and differences between the two were revealed. Additionally, the utility of using mass spectrometry concepts such as spectral accuracy and sulfur counting for confident identification of analytes in an untargeted method are discussed.
Collapse
Affiliation(s)
- Milad Nazari
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| | - David C Muddiman
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| |
Collapse
|
26
|
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
|
27
|
Wang X, Han J, Hardie DB, Yang J, Pan J, Borchers CH. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:755-767. [PMID: 28017863 DOI: 10.1016/j.bbapap.2016.12.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022]
Abstract
In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jingxi Pan
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
| |
Collapse
|
28
|
Electrospray deposition device used to precisely control the matrix crystal to improve the performance of MALDI MSI. Sci Rep 2016; 6:37903. [PMID: 27885266 PMCID: PMC5122855 DOI: 10.1038/srep37903] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/02/2016] [Indexed: 01/15/2023] Open
Abstract
MALDI MSI has been recently applied as an innovative tool for detection of molecular distribution within a specific tissue. MALDI MSI requires deposition of an organic compound, known as matrix, on the tissue of interest to assist analyte desorption and ionization, in which the matrix crystal homogeneity and size greatly influence the imaging reproducibility and spatial resolution in MALDI MSI. In this work, a homemade electrospray deposition device was developed for deposition of matrix in MALDI MSI. The device could be used to achieve 1 μm homogeneous matrix crystals in MALDI MSI analysis. Moreover, it was found, for the first time, that the electrospray deposition device could be used to precisely control the matrix crystal size, and the imaging spatial resolution was increased greatly as the matrix crystals size becoming smaller. In addition, the easily-built electrospray deposition device was durable for acid, base or organic solvent, and even could be used for deposition of nanoparticles matrix, which made it unparalleled for MALDI MSI analysis. The feasibility of the electrospray deposition device was investigated by combination with MALDI FTICR MSI to analyze the distributions of lipids in mouse brain and liver cancer tissue section.
Collapse
|
29
|
Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry - From bench to bedside. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:776-783. [PMID: 27810414 DOI: 10.1016/j.bbapap.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Today, pathologists face many challenges in defining the precise morphomolecular diagnosis and in guiding clinicians to the optimal patients' treatment. To achieve this goal, increasingly, classical histomorphological methods have to be supplemented by high throughput molecular assays. Since MALDI imaging mass spectrometry (IMS) enables the assessment of spatial molecular arrangements in tissue sections, it goes far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. Thus, this technology has the potential to uncover new markers for diagnostic purposes or markers that correlate with disease severity as well as prognosis and therapeutic response. Additionally, in the future MALDI IMS based classifiers measured with this technology in real time in the diagnostic setting might be applicable in the routine diagnostic setting. In this review, recently published studies that show the usefulness, advantages, and applicability of MALDI IMS in different fields of pathology (diagnosis, prognosis and treatment response) are highlighted. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Kristina Schwamborn
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany.
| | - Mark Kriegsmann
- University of Heidelberg, Department of Pathology, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany
| |
Collapse
|
30
|
High nuclear expression of proteasome activator complex subunit 1 predicts poor survival in soft tissue leiomyosarcomas. Clin Sarcoma Res 2016; 6:17. [PMID: 27733900 PMCID: PMC5045577 DOI: 10.1186/s13569-016-0057-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/13/2016] [Indexed: 11/29/2022] Open
Abstract
Background Previous studies on high grade sarcomas using mass spectrometry imaging showed proteasome activator complex subunit 1 (PSME1) to be associated with poor survival in soft tissue sarcoma patients. PSME1 is involved in immunoproteasome assembly for generating tumor antigens presented by MHC class I molecules. In this study, we aimed to validate PSME1 as a prognostic biomarker in an independent and larger series of soft tissue sarcomas by immunohistochemistry. Methods Tissue microarrays containing leiomyosarcomas (n = 34), myxofibrosarcomas (n = 14), undifferentiated pleomorphic sarcomas (n = 15), undifferentiated spindle cell sarcomas (n = 4), pleomorphic liposarcomas (n = 4), pleomorphic rhabdomyosarcomas (n = 2), and uterine leiomyomas (n = 7) were analyzed for protein expression of PSME1 using immunohistochemistry. Survival times were compared between high and low expression groups using Kaplan–Meier analysis. Cox regression models as multivariate analysis were performed to evaluate whether the associations were independent of other important clinical covariates. Results PSME1 expression was variable among soft tissue sarcomas. In leiomyosarcomas, high expression was associated with overall poor survival (p = 0.034), decreased metastasis-free survival (p = 0.002) and lower event-free survival (p = 0.007). Using multivariate analysis, the association between PSME1 expression and metastasis-free survival was still significant (p = 0.025) and independent of the histological grade. Conclusions High expression of PSME1 is associated with poor metastasis-free survival in soft tissue leiomyosarcoma patients, and might be used as an independent prognostic biomarker. Electronic supplementary material The online version of this article (doi:10.1186/s13569-016-0057-z) contains supplementary material, which is available to authorized users.
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Potential of MALDI imaging for the toxicological evaluation of environmental pollutants. J Proteomics 2016; 144:133-9. [PMID: 27178109 DOI: 10.1016/j.jprot.2016.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/13/2016] [Accepted: 05/08/2016] [Indexed: 01/02/2023]
Abstract
Risk assessment related to the exposure of humans to chemicals released into the environment is a major concern of our modern societies. In this context, toxicology plays a crucial role to characterize the effects of this exposure on health and identify the targets of these molecules. MALDI imaging mass spectrometry (IMS) is an enabling technology for biodistribution studies of chemicals. Although the majority of published studies are presented in a pharmacological context, the concepts discussed in this review can be applied to the toxicological evaluation of chemicals released into the environment. The major asset of IMS is the simultaneous localization and identification of a parent molecule and its metabolites without labeling and without any prior knowledge. Quantification methods developed in IMS are presented with application to an environmental pollutant. IMS is effective in the localization of chemicals and endogenous species. This opens unique perspectives for the discovery of molecular alterations in metabolites and protein biomarkers that could help for a better understanding of toxicity mechanisms. Distribution studies of agrochemicals in plants by IMS can contribute to a better understanding of their mode of action and to a more effective use of these chemicals, avoiding the current concern of environmental damage.
Collapse
|
33
|
Feng X, Jiang Y, Xie L, Jiang L, Li J, Sun C, Xu H, Wang R, Zhou M, Zhou Y, Dan H, Wang Z, Ji N, Deng P, Liao G, Geng N, Wang Y, Zhang D, Lin Y, Ye L, Liang X, Li L, Luo G, Feng M, Fang J, Zeng X, Wang Z, Chen Q. Overexpression of proteasomal activator PA28α serves as a prognostic factor in oral squamous cell carcinoma. J Exp Clin Cancer Res 2016; 35:35. [PMID: 26892607 PMCID: PMC4759779 DOI: 10.1186/s13046-016-0309-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/11/2016] [Indexed: 02/05/2023] Open
Abstract
Background Despite recent advances in oral squamous cell carcinoma (OSCC) diagnosis and therapy, disease recurrence remains common and is strongly associated with mortality. It is therefore critical to identify new targets for both treatment and diagnostic purposes. We aimed at investigating the role of PA28α, a proteasomal activator in OSCC. Methods The expression of PA28α was examined in a panel of OSCC cell lines and tissues, associated with oncomine analysis. In a large OSCC patient cohort, the prognostic value of PA28α expression was evaluated. Primary clinical end points were recurrence-free and overall survival rate. Functional involvement of PA28α in OSCC was examined in both in vitro and in vivo models upon specific siRNA knockdown. Results PA28α was found to be overexpressed in OSCC cell lines and tumor tissues. High expression of PA28α was significantly associated with recurrence and poorer overall survival. Specific knockdown of PA28α inhibited OSCC cell proliferation, migration, invasion in vitro and reduced the growth of OSCC xenografts in vivo. Multivariate Cox regression analyses revealed PA28α as independent prognostic predictors. Conclusions These results suggest that PA28α is involved in OSCC oncogenesis and may serve as a potential prognostic factor. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0309-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaodong Feng
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Yuchen Jiang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Liang Xie
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Lu Jiang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Jing Li
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Chongkui Sun
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Hao Xu
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.
| | - Ruinan Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Min Zhou
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Hongxia Dan
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Zhiyong Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Ning Ji
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Peng Deng
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Ga Liao
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Ning Geng
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Yun Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Dunfang Zhang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Ling Ye
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Xinhua Liang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Longjiang Li
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Gang Luo
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Mingye Feng
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Juan Fang
- Guangdong Provincial Key Laboratory of Oral Diseases, Stomatological Hospital, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, China.
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| | - Zhi Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China. .,Guangdong Provincial Key Laboratory of Oral Diseases, Stomatological Hospital, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, China.
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
34
|
Wang X, Han J, Hardie DB, Yang J, Borchers CH. The use of matrix coating assisted by an electric field (MCAEF) to enhance mass spectrometric imaging of human prostate cancer biomarkers. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:86-95. [PMID: 26757076 DOI: 10.1002/jms.3728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
In this work, we combined a newly developed matrix coating technique - matrix coating assisted by an electric field (MCAEF) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to enhance the imaging of peptides and proteins in tissue specimens of human prostate cancer. MCAEF increased the signal-to-noise ratios of the detected proteins by a factor of 2 to 5, and 232 signals were detected within the m/z 3500-37500 mass range on a time-of-flight mass spectrometer and with the sinapinic acid MALDI matrix. Among these species, three proteins (S100-A9, S100-A10, and S100-A12) were only observed in the cancerous cell region and 14 proteins, including a fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2, a fragment of cAMP-regulated phosphoprotein 19, 3 apolipoproteins (C-I, A-I, and A-II), 2 S100 proteins (A6 and A8), β-microseminoprotein, tumor protein D52, α-1-acid glycoprotein 1, heat shock protein β-1, prostate-specific antigen, and 2 unidentified large peptides at m/z 5002.2 and 6704.2, showed significantly differential distributions at the p < 0.05 (t-test) level between the cancerous and the noncancerous regions of the tissue. Among these 17 species, the distributions of apolipoprotein C-I, S100-A6, and S100-A8 were verified by immunohistological staining. In summary, this study resulted in the imaging of the largest group of proteins in prostate cancer tissues by MALDI-MS reported thus far, and is the first to show a correlation between S100 proteins and prostate cancer in a MS imaging study. The successful imaging of the three proteins only found in the cancerous tissues, as well as those showing differential expressions demonstrated the potential of MCAEF-MALDI/MS for the in situ detection of potential cancer biomarkers. Copyright © 2015 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada
| |
Collapse
|
35
|
Harn YC, Powers MJ, Shank EA, Jojic V. Deconvolving molecular signatures of interactions between microbial colonies. Bioinformatics 2015; 31:i142-50. [PMID: 26072476 PMCID: PMC4765860 DOI: 10.1093/bioinformatics/btv251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Motivation: The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies’ molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret. Results: Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning (MOLDL). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies. Availability and implementation: The code used in this paper is available at: https://github.com/frizfealer/IMS_project. Contact:vjojic@cs.unc.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Y-C Harn
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - M J Powers
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - E A Shank
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - V Jojic
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
36
|
Cole LM, Selvan AN, Partridge R, Reed H, Wright C, Clench MR. Communication of medical images to diverse audiences using multimodal imaging. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40679-015-0012-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractA study has been completed examining design issues concerning the interpretation of and dissemination of multimodal medical imaging data sets to diverse audiences. To create a model data set mouse fibrosarcoma tissue was visualised via magnetic resonance imaging (MRI), Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry (MALDI-MSI) and histology. MRI images were acquired using the 0.25T Esaote GScan; MALDI images were acquired using a Q-Star Pulsar I mass spectrometer. Histological staining of the same tissue sections used for MALDI-MSI was then carried out. Areas assigned to hemosiderin deposits due to haemorrhaging could be visualised via MRI. In the MALDI-MSI data obtained the distribution sphingomyelin species could be used to identify regions of viable tumour. Mathematical ‘up sampling’ using hierarchical clustering-based segmentation provided a sophisticated image enhancement tool for both MRI and MALDI-MS and assisted in the correlation of images.
Collapse
|
37
|
Cobice DF, Goodwin RJA, Andren PE, Nilsson A, Mackay CL, Andrew R. Future technology insight: mass spectrometry imaging as a tool in drug research and development. Br J Pharmacol 2015; 172:3266-83. [PMID: 25766375 DOI: 10.1111/bph.13135] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 02/09/2015] [Accepted: 03/03/2015] [Indexed: 12/14/2022] Open
Abstract
In pharmaceutical research, understanding the biodistribution, accumulation and metabolism of drugs in tissue plays a key role during drug discovery and development. In particular, information regarding pharmacokinetics, pharmacodynamics and transport properties of compounds in tissues is crucial during early screening. Historically, the abundance and distribution of drugs have been assessed by well-established techniques such as quantitative whole-body autoradiography (WBA) or tissue homogenization with LC/MS analysis. However, WBA does not distinguish active drug from its metabolites and LC/MS, while highly sensitive, does not report spatial distribution. Mass spectrometry imaging (MSI) can discriminate drug and its metabolites and endogenous compounds, while simultaneously reporting their distribution. MSI data are influencing drug development and currently used in investigational studies in areas such as compound toxicity. In in vivo studies MSI results may soon be used to support new drug regulatory applications, although clinical trial MSI data will take longer to be validated for incorporation into submissions. We review the current and future applications of MSI, focussing on applications for drug discovery and development, with examples to highlight the impact of this promising technique in early drug screening. Recent sample preparation and analysis methods that enable effective MSI, including quantitative analysis of drugs from tissue sections will be summarized and key aspects of methodological protocols to increase the effectiveness of MSI analysis for previously undetectable targets addressed. These examples highlight how MSI has become a powerful tool in drug research and development and offers great potential in streamlining the drug discovery process.
Collapse
Affiliation(s)
- D F Cobice
- University/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - R J A Goodwin
- Drug Metabolism and Distribution, Mass Spectrometry Imaging, AstraZeneca R&D, Macclesfield, UK
| | - P E Andren
- Biomolecular Imaging and Proteomics, National Center for Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - A Nilsson
- Biomolecular Imaging and Proteomics, National Center for Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - C L Mackay
- SIRCAMS, School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - R Andrew
- University/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
38
|
Kang MG, Byun K, Kim JH, Park NH, Heinsen H, Ravid R, Steinbusch HW, Lee B, Park YM. Proteogenomics of the human hippocampus: The road ahead. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:788-97. [PMID: 25770686 DOI: 10.1016/j.bbapap.2015.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 12/26/2022]
Abstract
The hippocampus is one of the most essential components of the human brain and plays an important role in learning and memory. The hippocampus has drawn great attention from scientists and clinicians due to its clinical importance in diseases such as Alzheimer's disease (AD), non-AD dementia, and epilepsy. Understanding the function of the hippocampus and related disease mechanisms requires comprehensive knowledge of the orchestration of the genome, epigenome, transcriptome, proteome, and post-translational modifications (PTMs) of proteins. The past decade has seen remarkable advances in the high-throughput sequencing techniques that are collectively called next generation sequencing (NGS). NGS enables the precise analysis of gene expression profiles in cells and tissues, allowing powerful and more feasible integration of expression data from the gene level to the protein level, even allowing "-omic" level assessment of PTMs. In addition, improved bioinformatics algorithms coupled with NGS technology are finally opening a new era for scientists to discover previously unidentified and elusive proteins. In the present review, we will focus mainly on the proteomics of the human hippocampus with an emphasis on the integrated analysis of genomics, epigenomics, transcriptomics, and proteomics. Finally, we will discuss our perspectives on the potential and future of proteomics in the field of hippocampal biology. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Myoung-Goo Kang
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-840, Republic of Korea
| | - Jae Ho Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Nam Hyun Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Helmut Heinsen
- Morphological Brain Research Unit, Department of Psychiatry, Universität of Würzburg, Würzburg, Germany
| | - Rivka Ravid
- Brain Bank Consultant, Amsterdam, The Netherlands
| | - Harry W Steinbusch
- School for Mental Health and Neuroscience, Department of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Bonghee Lee
- Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea.
| |
Collapse
|
39
|
Mainini V, Lalowski M, Gotsopoulos A, Bitsika V, Baumann M, Magni F. MALDI-imaging mass spectrometry on tissues. Methods Mol Biol 2015; 1243:139-64. [PMID: 25384744 DOI: 10.1007/978-1-4939-1872-0_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-profiling and imaging mass spectrometry (MSI) are promising technologies for measuring hundreds of different molecules directly on tissues. For instance, small molecules, drugs and their metabolites, endogenous lipids, carbohydrates and complex peptides/proteins can be measured at the same time. In the most advanced instruments, it is achieved without significant disruption of sample integrity. MSI is a unique approach for assessing the spatial distribution of molecules using graphical multidimensional maps of their constituent analytes, which may for instance be correlated with histopathological alterations in patient tissues. MALDI-TOF-MSI technology has been implemented in hospitals of several countries, where it is routinely used for quick pathogen(s) identification, a task formerly accomplished by laborious and expensive DNA/RNA-based PCR (polymerase chain reaction) screening.In this chapter, we describe how MSI is performed, what is required from the researcher, the instrument vendors and finally what can be achieved with MSI. We restrict our descriptions only to MALDI-MSI although several other MS techniques of ionization can easily be linked to MSI.
Collapse
Affiliation(s)
- Veronica Mainini
- Department of Health Sciences, University Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
| | | | | | | | | | | |
Collapse
|
40
|
Kriegsmann J, Kriegsmann M, Casadonte R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). Int J Oncol 2014; 46:893-906. [PMID: 25482502 DOI: 10.3892/ijo.2014.2788] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 11/06/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.
Collapse
Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - Mark Kriegsmann
- Institute for Pathology, University of Heidelberg, Heidelberg, Germany
| | | |
Collapse
|
41
|
Cui Y, Irudayaraj J. Inside single cells: quantitative analysis with advanced optics and nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:387-407. [PMID: 25430077 DOI: 10.1002/wnan.1321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.
Collapse
Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
| | | |
Collapse
|
42
|
Aichler M, Luber B, Lordick F, Walch A. Proteomic and metabolic prediction of response to therapy in gastric cancer. World J Gastroenterol 2014; 20:13648-13657. [PMID: 25320503 PMCID: PMC4194549 DOI: 10.3748/wjg.v20.i38.13648] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
Several new treatment options for gastric cancer have been introduced but the prognosis of patients diagnosed with gastric cancer is still poor. Disease prognosis could be improved for high-risk individuals by implementing earlier screenings. Because many patients are asymptomatic during the early stages of gastric cancer, the diagnosis is often delayed and patients present with unresectable locally advanced or metastatic disease. Cytotoxic treatment has been shown to prolong survival in general, but not all patients are responders. The application of targeted therapies and multimodal treatment has improved prognosis for those with advanced disease. However, these new therapeutic strategies do not uniformly benefit all patients. Predicting whether patients will respond to specific therapies would be of particular value and would allow for stratifying patients for personalized treatment strategies. Metabolic imaging by positron emission tomography was the first technique with the potential to predict the response of esophago-gastric cancer to neoadjuvant therapy. Exploring and validating tissue-based biomarkers are ongoing processes. In this review, we discuss the status of several targeted therapies for gastric cancer, as well as proteomic and metabolic methods for investigating biomarkers for therapy response prediction in gastric cancer.
Collapse
|
43
|
Min KW, Bang JY, Kim KP, Kim WS, Lee SH, Shanta SR, Lee JH, Hong JH, Lim SD, Yoo YB, Na CH. Imaging mass spectrometry in papillary thyroid carcinoma for the identification and validation of biomarker proteins. J Korean Med Sci 2014; 29:934-40. [PMID: 25045225 PMCID: PMC4101781 DOI: 10.3346/jkms.2014.29.7.934] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/24/2014] [Indexed: 01/09/2023] Open
Abstract
Direct tissue imaging mass spectrometry (IMS) by matrix-assisted laser desorption ionization and time-of-flight (MALDI-TOF) mass spectrometry has become increasingly important in biology and medicine, because this technology can detect the relative abundance and spatial distribution of interesting proteins in tissues. Five thyroid cancer samples, along with normal tissue, were sliced and transferred onto conductive glass slides. After laser scanning by MALDI-TOF equipped with a smart beam laser, images were created for individual masses and proteins were classified at 200-µm spatial resolution. Based on the spatial distribution, region-specific proteins on a tumor lesion could be identified by protein extraction from tumor tissue and analysis using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using all the spectral data at each spot, various intensities of a specific peak were detected in the tumor and normal regions of the thyroid. Differences in the molecular weights of expressed proteins between tumor and normal regions were analyzed using unsupervised and supervised clustering. To verify the presence of discovered proteins through IMS, we identified ribosomal protein P2, which is specific for cancer. We have demonstrated the feasibility of IMS as a useful tool for the analysis of tissue sections, and identified the tumor-specific protein ribosomal protein P2.
Collapse
Affiliation(s)
- Kyueng-Whan Min
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Joo-Young Bang
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
- SMART Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Kwang Pyo Kim
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
- SMART Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- The Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea
| | - Sang Hwa Lee
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Selina Rahman Shanta
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
| | - Jeong Hwa Lee
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
| | - Ji Hye Hong
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
| | - So Dug Lim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Young-Bum Yoo
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea
| | - Chan-Hyun Na
- Department of Molecular Biotechnology, WCU Program, Konkuk University, Seoul, Korea
| |
Collapse
|
44
|
Cole LM, Bluff JE, Carolan VA, Paley MN, Tozer GM, Clench MR. MALDI-MSI and label-free LC-ESI-MS/MS shotgun proteomics to investigate protein induction in a murine fibrosarcoma model following treatment with a vascular disrupting agent. Proteomics 2014; 14:890-903. [DOI: 10.1002/pmic.201300429] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/05/2013] [Accepted: 12/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Laura M. Cole
- Biomedical Research Centre; Sheffield Hallam University; Sheffield UK
| | - Joanne E. Bluff
- Tumour Microcirculation Group; Department of Oncology; CR-UK/YCR Sheffield Cancer Research Centre; University of Sheffield; Sheffield UK
| | - Vikki A. Carolan
- Biomedical Research Centre; Sheffield Hallam University; Sheffield UK
| | - Martyn N. Paley
- Department of Cardiovascular Science; University of Sheffield; Sheffield UK
| | - Gillian M. Tozer
- Tumour Microcirculation Group; Department of Oncology; CR-UK/YCR Sheffield Cancer Research Centre; University of Sheffield; Sheffield UK
| | - Malcolm R. Clench
- Biomedical Research Centre; Sheffield Hallam University; Sheffield UK
| |
Collapse
|
45
|
Chatterji B, Pich A. MALDI imaging mass spectrometry and analysis of endogenous peptides. Expert Rev Proteomics 2014; 10:381-8. [PMID: 23992420 DOI: 10.1586/14789450.2013.814939] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, MALDI imaging mass spectrometry (MALDI-IMS) has developed as a promising tool to investigate the spatial distribution of biomolecules in intact tissue specimens. Ion densities of various molecules can be displayed as heat maps while preserving anatomical structures. In this short review, an overview of different biomolecules that can be analyzed by MALDI-IMS is given. Many reviews have covered imaging of lipids, small metabolites, whole proteins and enzymatically digested proteins in the past. However, little is known about imaging of endogenous peptides, for example, in the rat brain, and this will therefore be highlighted in this review. Furthermore, sample preparation of frozen or formalin-fixed, paraffin-embedded (FFPE) tissue is crucial for imaging experiments. Therefore, some aspects of sample preparation will be addressed, including washing and desalting, the choice of MALDI matrix and its deposition. Apart from mapping endogenous peptides, their reliable identification in situ still remains challenging and will be discussed as well.
Collapse
Affiliation(s)
- Bijon Chatterji
- Hannover Medical School, Institute of Toxicology, Core Unit Mass Spectrometry - Proteomics, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | | |
Collapse
|
46
|
Lin G, Chung YL. Current opportunities and challenges of magnetic resonance spectroscopy, positron emission tomography, and mass spectrometry imaging for mapping cancer metabolism in vivo. BIOMED RESEARCH INTERNATIONAL 2014; 2014:625095. [PMID: 24724090 PMCID: PMC3958648 DOI: 10.1155/2014/625095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/06/2014] [Accepted: 01/19/2014] [Indexed: 12/18/2022]
Abstract
Cancer is known to have unique metabolic features such as Warburg effect. Current cancer therapy has moved forward from cytotoxic treatment to personalized, targeted therapies, with some that could lead to specific metabolic changes, potentially monitored by imaging methods. In this paper we addressed the important aspects to study cancer metabolism by using image techniques, focusing on opportunities and challenges of magnetic resonance spectroscopy (MRS), dynamic nuclear polarization (DNP)-MRS, positron emission tomography (PET), and mass spectrometry imaging (MSI) for mapping cancer metabolism. Finally, we highlighted the future possibilities of an integrated in vivo PET/MR imaging systems, together with an in situ MSI tissue analytical platform, may become the ultimate technologies for unraveling and understanding the molecular complexities in some aspects of cancer metabolism. Such comprehensive imaging investigations might provide information on pharmacometabolomics, biomarker discovery, and disease diagnosis, prognosis, and treatment response monitoring for clinical medicine.
Collapse
Affiliation(s)
- Gigin Lin
- Department of Radiology, Chang Gung Memorial Hospital at Linkou, Chang Gung University, 5 Fuhsing Street, Guishan, Taoyuan 333, Taiwan
- Molecular Imaging Center, Chang Gung Memorial Hospital at Linkou, Chang Gung University, 5 Fuhsing Street, Guishan, Taoyuan 333, Taiwan
- Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Chang Gung University, 5 Fuhsing Street, Guishan, Taoyuan 333, Taiwan
| | - Yuen-Li Chung
- The Institute of Cancer Research and Royal Marsden Hospital, CRUK Cancer Imaging Centre, Downs Road, Sutton, Surrey SM2 5PT, UK
| |
Collapse
|
47
|
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
| |
Collapse
|
48
|
Karsani SA, Saihen NA, Zain RB, Cheong SC, Abdul Rahman M. Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins. Proteome Sci 2014; 12:3. [PMID: 24422745 PMCID: PMC3974152 DOI: 10.1186/1477-5956-12-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 01/07/2014] [Indexed: 12/03/2022] Open
Abstract
Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins.
Collapse
Affiliation(s)
- Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | | | | | | | | |
Collapse
|
49
|
Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
Collapse
Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | |
Collapse
|
50
|
Neubert P, Walch A. Current frontiers in clinical research application of MALDI imaging mass spectrometry. Expert Rev Proteomics 2014; 10:259-73. [DOI: 10.1586/epr.13.19] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|