1
|
Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
Collapse
Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
2
|
DeHoog RJ, King ME, Keating MF, Zhang J, Sans M, Feider CL, Garza KY, Bensussan A, Krieger A, Lin JQ, Badal S, Alore E, Pirko C, Brahmbhatt K, Yu W, Grogan R, Eberlin LS, Suliburk J. Intraoperative Identification of Thyroid and Parathyroid Tissues During Human Endocrine Surgery Using the MasSpec Pen. JAMA Surg 2023; 158:1050-1059. [PMID: 37531134 PMCID: PMC10398548 DOI: 10.1001/jamasurg.2023.3229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/08/2023] [Indexed: 08/03/2023]
Abstract
Importance Intraoperative identification of tissues through gross inspection during thyroid and parathyroid surgery is challenging yet essential for preserving healthy tissue and improving outcomes for patients. Objective To evaluate the performance and clinical applicability of the MasSpec Pen (MSPen) technology for discriminating thyroid, parathyroid, and lymph node tissues intraoperatively. Design, Setting, and Participants In this diagnostic/prognostic study, the MSPen was used to analyze 184 fresh-frozen thyroid, parathyroid, and lymph node tissues in the laboratory and translated to the operating room to enable in vivo and ex vivo tissue analysis by endocrine surgeons in 102 patients undergoing thyroidectomy and parathyroidectomy procedures. This diagnostic study was conducted between August 2017 and March 2020. Fresh-frozen tissues were analyzed in a laboratory. Clinical analyses occurred in an operating room at an academic medical center. Of the analyses performed on 184 fresh-frozen tissues, 131 were included based on sufficient signal and postanalysis pathologic diagnosis. From clinical tests, 102 patients undergoing surgery were included. A total of 1015 intraoperative analyses were performed, with 269 analyses subject to statistical classification. Statistical classifiers for discriminating thyroid, parathyroid, and lymph node tissues were generated using training sets comprising both laboratory and intraoperative data and evaluated on an independent test set of intraoperative data. Data were analyzed from July to December 2022. Main Outcomes and Measures Accuracy for each tissue type was measured for classification models discriminating thyroid, parathyroid, and lymph node tissues using MSPen data compared to gross analysis and final pathology results. Results Of the 102 patients in the intraoperative study, 80 were female (78%) and the median (IQR) age was 52 (42-66) years. For discriminating thyroid and parathyroid tissues, an overall accuracy, defined as agreement with pathology, of 92.4% (95% CI, 87.7-95.4) was achieved using MSPen data, with 82.6% (95% CI, 76.5-87.4) accuracy achieved for the independent test set. For distinguishing thyroid from lymph node and parathyroid from lymph node, overall training set accuracies of 97.5% (95% CI, 92.8-99.1) and 96.1% (95% CI, 91.2-98.3), respectively, were achieved. Conclusions and Relevance In this study, the MSPen showed high performance for discriminating thyroid, parathyroid, and lymph node tissues intraoperatively, suggesting this technology may be useful for providing near real-time feedback on tissue type to aid in surgical decision-making.
Collapse
Affiliation(s)
- Rachel J. DeHoog
- Department of Surgery, Baylor College of Medicine, Houston, Texas
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Mary E. King
- Department of Surgery, Baylor College of Medicine, Houston, Texas
- Department of Chemistry, The University of Texas at Austin, Austin
| | | | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Marta Sans
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Clara L. Feider
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Kyana Y. Garza
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Alena Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Anna Krieger
- Department of Chemistry, The University of Texas at Austin, Austin
| | - John Q. Lin
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Sunil Badal
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Elizabeth Alore
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | | | | | - Wendong Yu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Raymon Grogan
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Livia S. Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - James Suliburk
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
3
|
Ozulumba T, Montalbine AN, Ortiz-Cárdenas JE, Pompano RR. New tools for immunologists: models of lymph node function from cells to tissues. Front Immunol 2023; 14:1183286. [PMID: 37234163 PMCID: PMC10206051 DOI: 10.3389/fimmu.2023.1183286] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
The lymph node is a highly structured organ that mediates the body's adaptive immune response to antigens and other foreign particles. Central to its function is the distinct spatial assortment of lymphocytes and stromal cells, as well as chemokines that drive the signaling cascades which underpin immune responses. Investigations of lymph node biology were historically explored in vivo in animal models, using technologies that were breakthroughs in their time such as immunofluorescence with monoclonal antibodies, genetic reporters, in vivo two-photon imaging, and, more recently spatial biology techniques. However, new approaches are needed to enable tests of cell behavior and spatiotemporal dynamics under well controlled experimental perturbation, particularly for human immunity. This review presents a suite of technologies, comprising in vitro, ex vivo and in silico models, developed to study the lymph node or its components. We discuss the use of these tools to model cell behaviors in increasing order of complexity, from cell motility, to cell-cell interactions, to organ-level functions such as vaccination. Next, we identify current challenges regarding cell sourcing and culture, real time measurements of lymph node behavior in vivo and tool development for analysis and control of engineered cultures. Finally, we propose new research directions and offer our perspective on the future of this rapidly growing field. We anticipate that this review will be especially beneficial to immunologists looking to expand their toolkit for probing lymph node structure and function.
Collapse
Affiliation(s)
- Tochukwu Ozulumba
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Alyssa N. Montalbine
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer E. Ortiz-Cárdenas
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Rebecca R. Pompano
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
- Carter Immunology Center and University of Virginia (UVA) Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, United States
| |
Collapse
|
4
|
Soudah T, Zoabi A, Margulis K. Desorption electrospray ionization mass spectrometry imaging in discovery and development of novel therapies. MASS SPECTROMETRY REVIEWS 2023; 42:751-778. [PMID: 34642958 DOI: 10.1002/mas.21736] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) is one of the least specimen destructive ambient ionization mass spectrometry tissue imaging methods. It enables rapid simultaneous mapping, measurement, and identification of hundreds of molecules from an unmodified tissue sample. Over the years, since its first introduction as an imaging technique in 2005, DESI-MSI has been extensively developed as a tool for separating tissue regions of various histopathologic classes for diagnostic applications. Recently, DESI-MSI has also emerged as a versatile technique that enables drug discovery and can guide the efficient development of drug delivery systems. For example, it has been increasingly employed for uncovering unique patterns of in vivo drug distribution, the discovery of potentially treatable biochemical pathways, revealing novel druggable targets, predicting therapeutic sensitivity of diseased tissues, and identifying early tissue response to pharmacological treatment. These and other recent advances in implementing DESI-MSI as the tool for the development of novel therapies are highlighted in this review.
Collapse
Affiliation(s)
- Terese Soudah
- The Faculty of Medicine, The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amani Zoabi
- The Faculty of Medicine, The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Katherine Margulis
- The Faculty of Medicine, The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
5
|
Short WD, Olutoye OO, Padon BW, Parikh UM, Colchado D, Vangapandu H, Shams S, Chi T, Jung JP, Balaji S. Advances in non-invasive biosensing measures to monitor wound healing progression. Front Bioeng Biotechnol 2022; 10:952198. [PMID: 36213059 PMCID: PMC9539744 DOI: 10.3389/fbioe.2022.952198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 01/09/2023] Open
Abstract
Impaired wound healing is a significant financial and medical burden. The synthesis and deposition of extracellular matrix (ECM) in a new wound is a dynamic process that is constantly changing and adapting to the biochemical and biomechanical signaling from the extracellular microenvironments of the wound. This drives either a regenerative or fibrotic and scar-forming healing outcome. Disruptions in ECM deposition, structure, and composition lead to impaired healing in diseased states, such as in diabetes. Valid measures of the principal determinants of successful ECM deposition and wound healing include lack of bacterial contamination, good tissue perfusion, and reduced mechanical injury and strain. These measures are used by wound-care providers to intervene upon the healing wound to steer healing toward a more functional phenotype with improved structural integrity and healing outcomes and to prevent adverse wound developments. In this review, we discuss bioengineering advances in 1) non-invasive detection of biologic and physiologic factors of the healing wound, 2) visualizing and modeling the ECM, and 3) computational tools that efficiently evaluate the complex data acquired from the wounds based on basic science, preclinical, translational and clinical studies, that would allow us to prognosticate healing outcomes and intervene effectively. We focus on bioelectronics and biologic interfaces of the sensors and actuators for real time biosensing and actuation of the tissues. We also discuss high-resolution, advanced imaging techniques, which go beyond traditional confocal and fluorescence microscopy to visualize microscopic details of the composition of the wound matrix, linearity of collagen, and live tracking of components within the wound microenvironment. Computational modeling of the wound matrix, including partial differential equation datasets as well as machine learning models that can serve as powerful tools for physicians to guide their decision-making process are discussed.
Collapse
Affiliation(s)
- Walker D. Short
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Oluyinka O. Olutoye
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Benjamin W. Padon
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Umang M. Parikh
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Daniel Colchado
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Hima Vangapandu
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Shayan Shams
- Department of Applied Data Science, San Jose State University, San Jose, CA, United States
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, United States
| | - Taiyun Chi
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States
| | - Jangwook P. Jung
- Department of Biological Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Swathi Balaji
- Laboratory for Regenerative Tissue Repair, Division of Pediatric Surgery, Department of Surgery, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Swathi Balaji,
| |
Collapse
|
6
|
Non-Invasive Differential Diagnosis of Cervical Neoplastic Lesions by the Lipid Profile Analysis of Cervical Scrapings. Metabolites 2022; 12:metabo12090883. [PMID: 36144287 PMCID: PMC9506087 DOI: 10.3390/metabo12090883] [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: 08/22/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cervical cancer is one of the most common cancers in women with pronounced stages of precancerous lesions. Accurate differential diagnosis of such lesions is one of the primary challenges of medical specialists, which is vital to improving patient survival. The aim of this study was to develop and test an algorithm for the differential diagnosis of cervical lesions based on lipid levels in scrapings from the cervical epithelium and cervicovaginal canal. The lipid composition of the samples was analyzed by high-performance chromato-mass spectrometry. Lipid markers were selected using the Mann–Whitney test with a cutoff value of 0.05 and by projections to latent structures discriminant analysis, where a projection threshold of one was chosen. The final selection of variables for binomial logistic regressions was carried out using the Akaike information criterion. As a result, a final neoplasia classification method, based on 20 logistic regression sub-models, has an accuracy of 79% for discrimination NILM/cervicitis/LSIL/HSIL/cancer. The model has a sensitivity of 83% and a specificity of 88% for discrimination of several lesions (HSIL and cancer). This allows us to discuss the prospective viability of further validation of the developed non-invasive method of differential diagnosis.
Collapse
|
7
|
Huang L, Mao X, Sun C, Li T, Song X, Li J, Gao S, Zhang R, Chen J, He J, Abliz Z. Molecular Pathological Diagnosis of Thyroid Tumors Using Spatially Resolved Metabolomics. Molecules 2022; 27:molecules27041390. [PMID: 35209182 PMCID: PMC8876246 DOI: 10.3390/molecules27041390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
The pathological diagnosis of benign and malignant follicular thyroid tumors remains a major challenge using the current histopathological technique. To improve diagnosis accuracy, spatially resolved metabolomics analysis based on air flow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI) technique was used to establish a molecular diagnostic strategy for discriminating four pathological types of thyroid tumor. Without any specific labels, numerous metabolite features with their spatial distribution information can be acquired by AFADESI-MSI. The underlying metabolic heterogeneity can be visualized in line with the cellular heterogeneity in native tumor tissue. Through micro-regional feature extraction and in situ metabolomics analysis, three sets of metabolic biomarkers for the visual discrimination of benign follicular adenoma and differentiated thyroid carcinomas were discovered. Additionally, the automated prediction of tumor foci was supported by a diagnostic model based on the metabolic profile of 65 thyroid nodules. The model prediction accuracy was 83.3% when a test set of 12 independent samples was used. This diagnostic strategy presents a new way of performing in situ pathological examinations using small molecular biomarkers and provides a model diagnosis for clinically indeterminate thyroid tumor cases.
Collapse
Affiliation(s)
- Luojiao Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Xinxin Mao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China;
| | - Chenglong Sun
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Tiegang Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Xiaowei Song
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Jiangshuo Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Shanshan Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Chen
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China;
- Correspondence: (J.C.); (J.H.)
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Correspondence: (J.C.); (J.H.)
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (L.H.); (C.S.); (T.L.); (X.S.); (J.L.); (S.G.); (R.Z.); (Z.A.)
- Center for Imaging and Systems Biology, School of Pharmacy, Minzu University of China, Beijing 100081, China
| |
Collapse
|
8
|
Hou Y, Gao Y, Guo S, Zhang Z, Chen R, Zhang X. Applications of spatially resolved omics in the field of endocrine tumors. Front Endocrinol (Lausanne) 2022; 13:993081. [PMID: 36704039 PMCID: PMC9873308 DOI: 10.3389/fendo.2022.993081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.
Collapse
Affiliation(s)
- Yinuo Hou
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Shudi Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- General Surgery, Tianjin First Center Hospital, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| |
Collapse
|
9
|
Goriainov SV, Esparza C, Zhilyaev DI, Polovkov NY, Borisov RS, Zaikin VG. Ion-Molecular Reactions of Esters of Carbocyclic Alcohols in a Direct Analysis in Real Time (DART) Mass Spectrometer. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821140057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Isberg OG, Xiang Y, Bodvarsdottir SK, Jonasson JG, Thorsteinsdottir M, Takats Z. The effect of sample age on the metabolic information extracted from formalin-fixed and paraffin embedded tissue samples using desorption electrospray ionization mass spectrometry imaging. J Mass Spectrom Adv Clin Lab 2021; 22:50-55. [PMID: 34939055 PMCID: PMC8662337 DOI: 10.1016/j.jmsacl.2021.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Metabolites, especially lipids, have been shown to be promising therapeutic targets. In conjugation with genes and proteins they can be used to identify phenotypes of disease and support the development of targeted treatments. The majority of clinically collected tissue samples are stored in formalin-fixed and paraffin embedded (FFPE) blocks due to their tissue conservation ability and indefinite storage capacity. For metabolic analysis, however, fresh frozen (FF) samples are currently preferred over FFPE samples due to concerns of metabolic information being lost when preparing the samples. With little or no sample preparation, desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) allows for the study of spatial as well as spectral information. Methods: DESI-MSI analysis was performed on FFPE breast cancer tissue microarray samples from 213 patients collected between the years 1935-2013. Logistic regression (LR) models were built to classify samples based on age and FF samples were used for feature validation. Results: LR models developed on the FFPE samples achieved an average classification accuracy of 96% when predicting their age with a 10-year grouping. Closer examination of the metabolic change over time revealed that the mean signal intensities for the lower mass range (100 - 500 m/z) linearly decrease over time, while the mean intensities for the higher mass range (500 - 900 m/z), remained relatively constant. Conclusions: In our samples, which span over 70 years, sample age has a weak yet quantifiable impact on metabolite content in FFPE samples, while the higher mass range is seemingly unaffected. FFPE samples thus provide an alternative avenue for metabolic analysis of lipids.
Collapse
Affiliation(s)
- Olof Gerdur Isberg
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Jon Gunnlaugur Jonasson
- Pathology, Landspitali-National University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Margret Thorsteinsdottir
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
11
|
|
12
|
Lee S, Chintalapudi K, Badu-Tawiah AK. Clinical Chemistry for Developing Countries: Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:437-465. [PMID: 33979544 PMCID: PMC8932337 DOI: 10.1146/annurev-anchem-091520-085936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Early disease diagnosis is necessary to enable timely interventions. Implementation of this vital task in the developing world is challenging owing to limited resources. Diagnostic approaches developed for resource-limited settings have often involved colorimetric tests (based on immunoassays) due to their low cost. Unfortunately, the performance/sensitivity of such simplistic tests are often limited and significantly hinder opportunities for early disease detection. A new criterion for selecting diagnostic tests in low- and middle-income countries is proposed here that is based on performance-to-cost ratio. For example, modern mass spectrometry (MS) now involves analysis of the native sample in the open laboratory environment, enabling applications in many fields, including clinical research, forensic science, environmental analysis, and agriculture. In this critical review, we summarize recent developments in chemistry that enable MS to be applied effectively in developing countries. In particular, we argue that closed automated analytical systems may not offer the analytical flexibility needed in resource-limited settings. Alternative strategies proposed here have potential to be widely accepted in low- and middle-income countries through the utilization of the open-source ambient MS platform that enables microsampling techniques such as dried blood spot to be coupled with miniature mass spectrometers in a centralized analytical platform. Consequently, costs associated with sample handling and maintenance can be reduced by >50% of the total ownership cost, permitting analytical measurements to be operated at high performance-to-cost ratios in the developing world.
Collapse
Affiliation(s)
- Suji Lee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
| | - Kavyasree Chintalapudi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
| |
Collapse
|
13
|
Otsuka Y. Direct Liquid Extraction and Ionization Techniques for Understanding Multimolecular Environments in Biological Systems (Secondary Publication). Mass Spectrom (Tokyo) 2021; 10:A0095. [PMID: 34249586 PMCID: PMC8246329 DOI: 10.5702/massspectrometry.a0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
A combination of direct liquid extraction using a small volume of solvent and electrospray ionization allows the rapid measurement of complex chemical components in biological samples and visualization of their distribution in tissue sections. This review describes the development of such techniques and their application to biological research since the first reports in the early 2000s. An overview of electrospray ionization, ion suppression in samples, and the acceleration of specific chemical reactions in charged droplets is also presented. Potential future applications for visualizing multimolecular environments in biological systems are discussed.
Collapse
Affiliation(s)
- Yoichi Otsuka
- Graduate School of Science, Osaka University, 1–1 Machikaneyama-cho, Toyonaka, Osaka 560–0043, Japan
- JST, PRESTO, 4–1–8 Honcho, Kawaguchi, Saitama 332–0012, Japan
| |
Collapse
|
14
|
Millner A, Atilla-Gokcumen GE. Solving the enigma: Mass spectrometry and small molecule probes to study sphingolipid function. Curr Opin Chem Biol 2021; 65:49-56. [PMID: 34175552 DOI: 10.1016/j.cbpa.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
Sphingolipids are highly bioactive lipids. Sphingolipid metabolism produces key membrane components (e.g. sphingomyelin) and a variety of signaling lipids with different biological functions (e.g. ceramide, sphingosine-1-phosphate). The coordinated activity of tens of different enzymes maintains proper levels and localization of these lipids with key roles in cellular processes. In this review, we highlight the signaling roles of sphingolipids in cell death and survival. We discuss recent findings on the role of specific sphingolipids during these processes, enabled by the use of lipidomics to study compositional and spatial regulation of these lipids and synthetic sphingolipid probes to study subcellular localization and interaction partners of sphingolipids to understand the function of these lipids.
Collapse
Affiliation(s)
- Alec Millner
- Department of Chemistry, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, 14260, USA
| | - G Ekin Atilla-Gokcumen
- Department of Chemistry, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, 14260, USA.
| |
Collapse
|
15
|
Basu SS, Agar NYR. Bringing Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging to the Clinics. Clin Lab Med 2021; 41:309-324. [PMID: 34020766 DOI: 10.1016/j.cll.2021.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is an emerging analytical technique that promises to change tissue-based diagnostics. This article provides a brief introduction to MALDI MSI as well as clinical diagnostic workflows and opportunities to apply this powerful approach. It describes various MALDI MSI applications, from more clinically mature applications such as cancer to emerging applications such as infectious diseases and drug distribution. In addition, it discusses the analytical considerations that need to be considered when bringing these approaches to different diagnostic problems and settings.
Collapse
Affiliation(s)
- Sankha S Basu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
16
|
Nabi MM, Mamun MA, Islam A, Hasan MM, Waliullah ASM, Tamannaa Z, Sato T, Kahyo T, Setou M. Mass spectrometry in the lipid study of cancer. Expert Rev Proteomics 2021; 18:201-219. [PMID: 33793353 DOI: 10.1080/14789450.2021.1912602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cancer is a heterogeneous disease that exploits various metabolic pathways to meet the demand for increased energy and structural components. Lipids are biomolecules that play essential roles as high energy sources, mediators, and structural components of biological membranes. Accumulating evidence has established that altered lipid metabolism is a hallmark of cancer.Areas covered: Mass spectrometry (MS) is a label-free analytical tool that can simultaneously identify and quantify hundreds of analytes. To date, comprehensive lipid studies exclusively rely on this technique. Here, we reviewed the use of MS in the study of lipids in various cancers and discuss its instrumental limitations and challenges.Expert opinion: MS and MS imaging have significantly contributed to revealing altered lipid metabolism in a variety of cancers. Currently, a single MS approach cannot profile the entire lipidome because of its lack of sensitivity and specificity for all lipid classes. For the metabolic pathway investigation, lipid study requires the integration of MS with other molecular approaches. Future developments regarding the high spatial resolution, mass resolution, and sensitivity of MS instruments are warranted.
Collapse
Affiliation(s)
- Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Ganakbari, Savar, Dhaka, Bangladesh
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Tomohito Sato
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Shizuoka, Japan
| |
Collapse
|
17
|
Perez CJ, Ifa DR. Internal standard application strategies in mass spectrometry imaging by desorption electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9053. [PMID: 33474774 DOI: 10.1002/rcm.9053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE We developed a model case study to evaluate three internal standard (IS) application strategies (methods I-III) using the psycholeptic phenobarbital (PB) and the isotopically labelled IS phenobarbital-D5 (PB-D5) from in vitro dosed tissues of the golden apple snail (Pomacea diffusa) by desorption electrospray ionization mass spectrometry imaging (DESI-MSI). METHODS In method I, the IS was deposited as microspots on top of 10 μm thick snail tissues; in method II, a thin IS film was applied; and in method III, the IS was spiked into the DESI solvent spray. DESI-MSI analyses were performed using a Thermo LTQ mass spectrometer equipped with a custom-built DESI source and two-dimensional moving stage. PB (m/z 231) and PB-D5 (m/z 236) were monitored in selected ion monitoring mode between m/z 227 and 239. RESULTS The analytical performance of two IS strategies (methods I and II) in DESI-MSI was evaluated based on an intra- and inter-day precision assay, an accuracy assessment, and statistical analysis. In the inter-day DESI-MSI assay, method I exhibited better precision (6.5%-7.4%) than method II (10.7%-17.6%) between 10 and 100 ng/μL. In the accuracy assessment, PB quality controls of 75 ng/μL were back-calculated as 71 ± 4 and 83 ± 9 ng/μL, resulting in relative errors of -5% and 11% for methods I and II, respectively. Method III did not work under the experimental design and was not evaluated. CONCLUSIONS Three IS application strategies were investigated and compared for a routine quantitative DESI-MSI approach. Methods I and II were not statistically significantly different as shown by a Bland-Altman plot, suggesting that these two methods can be used interchangeably. However, method III requires further research for future quantitative DESI-MSI analyses.
Collapse
Affiliation(s)
- Consuelo J Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| |
Collapse
|
18
|
Wang J, Wang C, Han X. Mass Spectrometry-Based Shotgun Lipidomics for Cancer Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:39-55. [PMID: 33791973 DOI: 10.1007/978-3-030-51652-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Shotgun lipidomics is an analytical approach for large-scale and systematic analysis of the composition, structure, and quantity of cellular lipids directly from lipid extracts of biological samples by mass spectrometry. This approach possesses advantages of high throughput and quantitative accuracy, especially in absolute quantification. As cancer research deepens at the level of quantitative biology and metabolomics, the demand for lipidomics approaches such as shotgun lipidomics is becoming greater. In this chapter, the principles, approaches, and some applications of shotgun lipidomics for cancer research are overviewed.
Collapse
Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA.
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| |
Collapse
|
19
|
Peng Z, Chang Y, Fan J, Ji W, Su C. Phospholipase A2 superfamily in cancer. Cancer Lett 2020; 497:165-177. [PMID: 33080311 DOI: 10.1016/j.canlet.2020.10.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Phospholipase A2 enzymes (PLA2s) comprise a superfamily that is generally divided into six subfamilies known as cytosolic PLA2s (cPLA2s), calcium-independent PLA2s (iPLA2s), secreted PLA2s (sPLA2s), lysosomal PLA2s, platelet-activating factor (PAF) acetylhydrolases, and adipose specific PLA2s. Each subfamily consists of several isozymes that possess PLA2 activity. The first three PLA2 subfamilies play important roles in inflammation-related diseases and cancer. In this review, the roles of well-studied enzymes sPLA2-IIA, cPLA2α and iPLA2β in carcinogenesis and cancer development were discussed. sPLA2-IIA seems to play conflicting roles and can act as a tumor suppressor or a tumor promoter according to the cancer type, but cPLA2α and iPLA2β play protumorigenic role in most cancers. The mechanisms of PLA2-mediated signal transduction and crosstalk between cancer cells and endothelial cells in the tumor microenvironment are described. Moreover, the mechanisms by which PLA2s mediate lipid reprogramming and glycerophospholipid remodeling in cancer cells are illustrated. PLA2s as the upstream regulators of the arachidonic acid cascade are generally high expressed and activated in various cancers. Therefore, they can be considered as potential pharmacological targets and biomarkers in cancer. The detailed information summarized in this review may aid in understanding the roles of PLA2s in cancer, and provide new clues for the development of novel agents and strategies for tumor prevention and treatment.
Collapse
Affiliation(s)
- Zhangxiao Peng
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital & National Center for Liver Cancer, Navy Military Medical University, Shanghai, 200438, China.
| | - Yanxin Chang
- Department of Biliary Tract Surgery IV, Eastern Hepatobiliary Surgical Hospital, Navy Military Medical University, Shanghai, 200438, China.
| | - Jianhui Fan
- Mengchao Hepatobiliary Hospital, Fujian Medical University, Fuzhou, 350025, Fujian Province, China.
| | - Weidan Ji
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital & National Center for Liver Cancer, Navy Military Medical University, Shanghai, 200438, China.
| | - Changqing Su
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital & National Center for Liver Cancer, Navy Military Medical University, Shanghai, 200438, China.
| |
Collapse
|
20
|
Waas M, Kislinger T. Addressing Cellular Heterogeneity in Cancer through Precision Proteomics. J Proteome Res 2020; 19:3607-3619. [PMID: 32697918 DOI: 10.1021/acs.jproteome.0c00338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cells exhibit a broad spectrum of functions driven by differences in molecular phenotype. Understanding the heterogeneity between and within cell types has led to advances in our ability to diagnose and manipulate biological systems. Heterogeneity within and between tumors still poses a challenge to the development and efficacy of therapeutics. In this Perspective we review the toolkit of protein-level experimental approaches for investigating cellular heterogeneity. We describe how innovative approaches and technical developments have supported the advent of bottom-up single-cell proteomic analysis and present opportunities and challenges within cancer research. Finally, we introduce the concept of "precision proteomics" and discuss how the advantages and limitations of various experimental approaches render them suitable for different biological systems and questions.
Collapse
|
21
|
The Potential of Metabolomics in the Diagnosis of Thyroid Cancer. Int J Mol Sci 2020; 21:ijms21155272. [PMID: 32722293 PMCID: PMC7432278 DOI: 10.3390/ijms21155272] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Thyroid cancer is the most common endocrine system malignancy. However, there is still a lack of reliable and specific markers for the detection and staging of this disease. Fine needle aspiration biopsy is the current gold standard for diagnosis of thyroid cancer, but drawbacks to this technique include indeterminate results or an inability to discriminate different carcinomas, thereby requiring additional surgical procedures to obtain a final diagnosis. It is, therefore, necessary to seek more reliable markers to complement and improve current methods. "Omics" approaches have gained much attention in the last decade in the field of biomarker discovery for diagnostic and prognostic characterisation of various pathophysiological conditions. Metabolomics, in particular, has the potential to identify molecular markers of thyroid cancer and identify novel metabolic profiles of the disease, which can, in turn, help in the classification of pathological conditions and lead to a more personalised therapy, assisting in the diagnosis and in the prediction of cancer behaviour. This review considers the current results in thyroid cancer biomarker research with a focus on metabolomics.
Collapse
|
22
|
Guo L, Lai Z, Wang Y, Li Z. In situ probing changes in fatty-acyl chain length and desaturation of lipids in cancerous areas using mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4621. [PMID: 32776652 DOI: 10.1002/jms.4621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Aberrant changes in the expression levels and structure of lipids may shape tumor microenvironment. In this study, we have performed mass spectrometry imaging and profiling analysis of 63 tissues of five types of cancer, namely, breast, colorectal, esophageal, lung, and gastric cancer, using in situ liquid extraction electrosonic spray ionization mass spectrometry imaging. Alteration of fatty-acyl chain length of unsaturated phosphatidylcholines, phosphatidylinositols, and phosphatidylserines and of chain length of (un)saturated fatty acids are associated with different cancerous areas of five types of cancer. The ratios of the same fatty-acyl carbon atom lipids with one double bond difference and the ratios of the same chain-length fatty acids with one double bond difference exhibited significant differences among the cancerous areas of five types of cancer. Our data may reveal that there were different lipid metabolism networks among five types of cancer.
Collapse
Affiliation(s)
- Lei Guo
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanmin Wang
- Department of Clinical Laboratory, Heze Municipal Hospital, Heze, China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
23
|
Li N, Nie H, Jiang L, Ruan G, Du F, Liu H. Recent advances of ambient ionization mass spectrometry imaging in clinical research. J Sep Sci 2020; 43:3146-3163. [PMID: 32573988 DOI: 10.1002/jssc.202000273] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
The structural information and spatial distribution of molecules in biological tissues are closely related to the potential molecular mechanisms of disease origin, transfer, and classification. Ambient ionization mass spectrometry imaging is an effective tool that provides molecular images while describing in situ information of biomolecules in complex samples, in which ionization occurs at atmospheric pressure with the samples being analyzed in the native state. Ambient ionization mass spectrometry imaging can directly analyze tissue samples at a fairly high resolution to obtain molecules in situ information on the tissue surface to identify pathological features associated with a disease, resulting in the wide applications in pharmacy, food science, botanical research, and especially clinical research. Herein, novel ambient ionization techniques, such as techniques based on spray and solid-liquid extraction, techniques based on plasma desorption, techniques based on laser desorption ablation, and techniques based on acoustic desorption were introduced, and the data processing of ambient ionization mass spectrometry imaging was briefly reviewed. Besides, we also highlight recent applications of this imaging technology in clinical researches and discuss the challenges in this imaging technology and the perspectives on the future of the clinical research.
Collapse
Affiliation(s)
- Na Li
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Honggang Nie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Liping Jiang
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
| | - Guihua Ruan
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
| | - Fuyou Du
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
- College of Biological and Environmental Engineering, Changsha University, Changsha, P. R. China
| | - Huwei Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| |
Collapse
|
24
|
Recent advances of ambient mass spectrometry imaging for biological tissues: A review. Anal Chim Acta 2020; 1117:74-88. [DOI: 10.1016/j.aca.2020.01.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
|
25
|
Zhang G, Zhang J, DeHoog RJ, Pennathur S, Anderton CR, Venkatachalam MA, Alexandrov T, Eberlin LS, Sharma K. DESI-MSI and METASPACE indicates lipid abnormalities and altered mitochondrial membrane components in diabetic renal proximal tubules. Metabolomics 2020; 16:11. [PMID: 31925564 PMCID: PMC7301343 DOI: 10.1007/s11306-020-1637-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Diabetic kidney disease (DKD) is the most prevalent complication in diabetic patients, which contributes to high morbidity and mortality. Urine and plasma metabolomics studies have been demonstrated to provide valuable insights for DKD. However, limited information on spatial distributions of metabolites in kidney tissues have been reported. OBJECTIVES In this work, we employed an ambient desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) coupled to a novel bioinformatics platform (METASPACE) to characterize the metabolome in a mouse model of DKD. METHODS DESI-MSI was performed for spatial untargeted metabolomics analysis in kidneys of mouse models (F1 C57BL/6J-Ins2Akita male mice at 17 weeks of age) of type 1 diabetes (T1D, n = 5) and heathy controls (n = 6). RESULTS Multivariate analyses (i.e., PCA and PLS-DA (a 2000 permutation test: P < 0.001)) showed clearly separated clusters for the two groups of mice on the basis of 878 measured m/z's in kidney cortical tissues. Specifically, mice with T1D had increased relative abundances of pseudouridine, accumulation of free polyunsaturated fatty acids (PUFAs), and decreased relative abundances of cardiolipins in cortical proximal tubules when compared with healthy controls. CONCLUSION Results from the current study support potential key roles of pseudouridine and cardiolipins for maintaining normal RNA structure and normal mitochondrial function, respectively, in cortical proximal tubules with DKD. DESI-MSI technology coupled with METASPACE could serve as powerful new tools to provide insight on fundamental pathways in DKD.
Collapse
Affiliation(s)
- Guanshi Zhang
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Rachel J DeHoog
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX, USA.
| |
Collapse
|
26
|
Santoro AL, Drummond RD, Silva IT, Ferreira SS, Juliano L, Vendramini PH, Lemos MBDC, Eberlin MN, Andrade VP. In Situ DESI-MSI Lipidomic Profiles of Breast Cancer Molecular Subtypes and Precursor Lesions. Cancer Res 2020; 80:1246-1257. [PMID: 31911556 DOI: 10.1158/0008-5472.can-18-3574] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022]
Abstract
Clinically meaningful molecular subtypes for classification of breast cancers have been established, however, initiation and progression of these subtypes remain poorly understood. The recent development of desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) facilitates the convergence of analytical chemistry and traditional pathology, allowing chemical profiling with minimal tissue pretreatment in frozen samples. Here, we characterized the chemical composition of molecular subtypes of breast cancer with DESI-MSI. Regions of interest were identified, including invasive breast cancer (IBC), ductal carcinoma in situ (DCIS), and adjacent benign tissue (ABT), and metabolomic profiles at 200 μm elaborated using Biomap software and the Lasso method. Top ions identified in IBC regions included polyunsaturated fatty acids, deprotonated glycerophospholipids, and sphingolipids. Highly saturated lipids, as well as antioxidant molecules [taurine (m/z 124.0068), uric acid (m/z 167.0210), ascorbic acid (m/z 175.0241), and glutathione (m/z 306.0765)], were able to distinguish IBC from ABT. Moreover, luminal B and triple-negative subtypes showed more complex lipid profiles compared with luminal A and HER2 subtypes. DCIS and IBC were distinguished on the basis of cell signaling and apoptosis-related ions [fatty acids (341.2100 and 382.3736 m/z) and glycerophospholipids (PE (P-16:0/22:6, m/z 746.5099, and PS (38:3), m/z 812.5440)]. In summary, DESI-MSI identified distinct lipid composition between DCIS and IBC and across molecular subtypes of breast cancer, with potential implications for breast cancer pathogenesis. SIGNIFICANCE: These findings present the first in situ metabolomic findings of the four molecular subtypes of breast cancer, DCIS, and normal tissue, and add to the understanding of their pathogenesis.
Collapse
Affiliation(s)
| | - Rodrigo D Drummond
- Laboratory of Computational Biology and Bioinformatics, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal Silva
- Laboratory of Computational Biology and Bioinformatics, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Severino S Ferreira
- Department of Surgical Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Luiz Juliano
- Department of Surgical Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Pedro H Vendramini
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Marcos N Eberlin
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil.,Mackenzie Presbyterian University, School of Engineering, São Paulo, Brazil
| | - Victor Piana Andrade
- Department of Surgical Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil.
| |
Collapse
|
27
|
Swiner DJ, Jackson S, Burris BJ, Badu-Tawiah AK. Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time. Anal Chem 2020; 92:183-202. [PMID: 31671262 PMCID: PMC7896279 DOI: 10.1021/acs.analchem.9b04901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.
Collapse
Affiliation(s)
- Devin J. Swiner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Sierra Jackson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Benjamin J. Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Abraham K. Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
28
|
Huang YC, Chung HH, Dutkiewicz EP, Chen CL, Hsieh HY, Chen BR, Wang MY, Hsu CC. Predicting Breast Cancer by Paper Spray Ion Mobility Spectrometry Mass Spectrometry and Machine Learning. Anal Chem 2019; 92:1653-1657. [DOI: 10.1021/acs.analchem.9b03966] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ying-Chen Huang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hua-Yi Hsieh
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Bo-Rong Chen
- Department of Surgery, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
29
|
Holzlechner M, Eugenin E, Prideaux B. Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer. Cancer Rep (Hoboken) 2019; 2:e1229. [PMID: 32729258 PMCID: PMC7941519 DOI: 10.1002/cnr2.1229] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Current methods to identify, classify, and predict tumor behavior mostly rely on histology, immunohistochemistry, and molecular determinants. However, better predictive markers are required for tumor diagnosis and evaluation. Due, in part, to recent technological advancements, metabolomics and lipid biomarkers have become a promising area in cancer research. Therefore, there is a necessity for novel and complementary techniques to identify and visualize these molecular markers within tumors and surrounding tissue. RECENT FINDINGS Since its introduction, mass spectrometry imaging (MSI) has proven to be a powerful tool for mapping analytes in biological tissues. By adding the label-free specificity of mass spectrometry to the detailed spatial information of traditional histology, hundreds of lipids can be imaged simultaneously within a tumor. MSI provides highly detailed lipid maps for comparing intra-tumor, tumor margin, and healthy regions to identify biomarkers, patterns of disease, and potential therapeutic targets. In this manuscript, recent advancement in sample preparation and MSI technologies are discussed with special emphasis on cancer lipid research to identify tumor biomarkers. CONCLUSION MSI offers a unique approach for biomolecular characterization of tumor tissues and provides valuable complementary information to histology for lipid biomarker discovery and tumor classification in clinical and research cancer applications.
Collapse
Affiliation(s)
- Matthias Holzlechner
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Brendan Prideaux
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| |
Collapse
|
30
|
Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform 2019; 20:1957-1971. [PMID: 29304189 PMCID: PMC6954408 DOI: 10.1093/bib/bbx170] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Indexed: 12/14/2022] Open
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
Collapse
Affiliation(s)
| | - Vladimir Shulaev
- Corresponding author: Vladimir Shulaev, Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76210, USA. Tel.: 940-369-5368; Fax: 940-565-3821; E-mail:
| |
Collapse
|
31
|
Lin LE, Chen CL, Huang YC, Chung HH, Lin CW, Chen KC, Peng YJ, Ding ST, Wang MY, Shen TL, Hsu CC. Precision biomarker discovery powered by microscopy image fusion-assisted high spatial resolution ambient ionization mass spectrometry imaging. Anal Chim Acta 2019; 1100:75-87. [PMID: 31987155 DOI: 10.1016/j.aca.2019.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/27/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
Abstract
Mass spectrometry imaging (MSI) using the ambient ionization technique enables a direct chemical investigation of biological samples with minimal sample pretreatment. However, detailed morphological information of the sample is often lost due to its limited spatial resolution. In this study, predictive high-resolution molecular imaging was produced by the fusion of ambient ionization MSI with optical microscopy of routine hematoxylin and eosin (H&E) staining. Specifically, desorption electrospray ionization (DESI) and nanospray desorption electrospray ionization (nanoDESI) mass spectrometry were employed to visualize lipid and protein species on mice tissue sections. The resulting molecular distributions obtained by ambient ionization MSI-microscopy fusion were verified with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MSI and immunohistochemistry (IHC) staining. Label-free molecular imaging with 5-μm spatial resolution can be acquired using DESI and nanoDESI, whereas the typical spatial resolution of ambient ionization MSI was ∼100 μm. In this regard, sharpened molecular histology of tissue sections was achieved, providing complementary references to the pathology. Such a multi-modal integration enables the discovery of potential tumor biomarkers. After image fusion, more than a dozen potential biomarkers on a metastatic mouse lung tissue section and Luminal B breast tumor tissue section were identified.
Collapse
Affiliation(s)
- Li-En Lin
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Ying-Chen Huang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chiao-Wei Lin
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Ko-Chien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Yu-Ju Peng
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Shih-Torng Ding
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Ming-Yang Wang
- National Taiwan University Hospital, No.7, Zhong Shan South Rd., Taipei, 10002, Taiwan
| | - Tang-Long Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| |
Collapse
|
32
|
Preoperative metabolic classification of thyroid nodules using mass spectrometry imaging of fine-needle aspiration biopsies. Proc Natl Acad Sci U S A 2019; 116:21401-21408. [PMID: 31591199 DOI: 10.1073/pnas.1911333116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Thyroid neoplasia is common and requires appropriate clinical workup with imaging and fine-needle aspiration (FNA) biopsy to evaluate for cancer. Yet, up to 20% of thyroid nodule FNA biopsies will be indeterminate in diagnosis based on cytological evaluation. Genomic approaches to characterize the malignant potential of nodules showed initial promise but have provided only modest improvement in diagnosis. Here, we describe a method using metabolic analysis by desorption electrospray ionization mass spectrometry (DESI-MS) imaging for direct analysis and diagnosis of follicular cell-derived neoplasia tissues and FNA biopsies. DESI-MS was used to analyze 178 tissue samples to determine the molecular signatures of normal, benign follicular adenoma (FTA), and malignant follicular carcinoma (FTC) and papillary carcinoma (PTC) thyroid tissues. Statistical classifiers, including benign thyroid versus PTC and benign thyroid versus FTC, were built and validated with 114,125 mass spectra, with accuracy assessed in correlation with clinical pathology. Clinical FNA smears were prospectively collected and analyzed using DESI-MS imaging, and the performance of the statistical classifiers was tested with 69 prospectively collected clinical FNA smears. High performance was achieved for both models when predicting on the FNA test set, which included 24 nodules with indeterminate preoperative cytology, with accuracies of 93% and 89%. Our results strongly suggest that DESI-MS imaging is a valuable technology for identification of malignant potential of thyroid nodules.
Collapse
|
33
|
Perez CJ, Bagga AK, Prova SS, Yousefi Taemeh M, Ifa DR. Review and perspectives on the applications of mass spectrometry imaging under ambient conditions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:27-53. [PMID: 29698560 DOI: 10.1002/rcm.8145] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 05/18/2023]
Abstract
Ambient mass spectrometry (AMS)-based techniques are performed under ambient conditions in which the ionization and desorption occur in the open environment allowing the direct analysis of molecules with minimal or no sample preparation. A selected group of AMS techniques demonstrate imaging capabilities that can provide information about the localization of molecules on complex sample surfaces such as biological tissues. 2D, 3D, and multimodal imaging have unlocked an array of applications to systematically address complex problems in many areas of research such as drug monitoring, natural products, forensics, and cancer diagnostics. In the present review, we summarize recent advances in the field with respect to the implementation of new ambient ionization techniques and current applications in the last 5 years. In more detail, we mainly focus on imaging applications in topics related to animal whole bodies and tissues, single cells, cancer diagnostics and biomarkers, microbial cultures and co-cultures, plant and natural product metabolomics, and forensic applications. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
Collapse
Affiliation(s)
- Consuelo J Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Aafreen K Bagga
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Shamina S Prova
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Maryam Yousefi Taemeh
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| |
Collapse
|
34
|
Ucal Y, Coskun A, Ozpinar A. Quality will determine the future of mass spectrometry imaging in clinical laboratories: the need for standardization. Expert Rev Proteomics 2019; 16:521-532. [DOI: 10.1080/14789450.2019.1624165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yasemin Ucal
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Abdurrahman Coskun
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Aysel Ozpinar
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| |
Collapse
|
35
|
Khatami F, Payab M, Sarvari M, Gilany K, Larijani B, Arjmand B, Tavangar SM. Oncometabolites as biomarkers in thyroid cancer: a systematic review. Cancer Manag Res 2019; 11:1829-1841. [PMID: 30881111 PMCID: PMC6395057 DOI: 10.2147/cmar.s188661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION Thyroid cancer (TC) is an important common endocrine malignancy, and its incidence has increased in the past decades. The current TC diagnosis and classification tools are fine-needle aspiration (FNA) and histological examination following thyroidectomy. The metabolite profile alterations of thyroid cells (oncometabolites) can be considered for current TC diagnosis and management protocols. METHODS This systematic review focuses on metabolite alterations within the plasma, FNA specimens, and tissue of malignant TC contrary to benign, goiter, or healthy TC samples. A systematic search of MEDLINE (PubMed), Scopus, Embase, and Web of Science databases was conducted, and the final 31 studies investigating metabolite biomarkers of TC were included. RESULTS A total of 15 targeted studies and 16 untargeted studies revealed several potential metabolite signatures of TC such as glucose, fructose, galactose, mannose, 2-keto-d-gluconic acid and rhamnose, malonic acid and inosine, cholesterol and arachidonic acid, glycosylation (immunoglobulin G [IgG] Fc-glycosylation), outer mitochondrial membrane 20 (TOMM20), monocarboxylate transporter 4 (MCT4), choline, choline derivatives, myo-/scyllo-inositol, lactate, fatty acids, several amino acids, cell membrane phospholipids, estrogen metabolites such as 16 alpha-OH E1/2-OH E1 and catechol estrogens (2-OH E1), and purine and pyrimidine metabolites, which were suggested as the TC oncometabolite. CONCLUSION Citrate was suggested as the first most significant biomarker and lactate as the second one. Further research is needed to confirm these biomarkers as the TC diagnostic oncometabolite.
Collapse
Affiliation(s)
- Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran,
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Sarvari
- Metabolomics and Genomics Research Center, Endocrinology and Metabolomics Molecular Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Gilany
- Metabolomics and Genomics Research Center, Endocrinology and Metabolomics Molecular Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Reproductive Biotechnology Research Center, Avicenna Research Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, Acercr, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran,
| | - Seyed Mohammad Tavangar
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran,
- Department of Pathology, Dr. Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran,
| |
Collapse
|
36
|
Luberto C, Haley JD, Del Poeta M. Imaging with mass spectrometry, the next frontier in sphingolipid research? A discussion on where we stand and the possibilities ahead. Chem Phys Lipids 2019; 219:1-14. [PMID: 30641043 DOI: 10.1016/j.chemphyslip.2019.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
In the last ten years, mass spectrometry (MS) has become the favored analytical technique for sphingolipid (SPL) analysis and measurements. Indeed MS has the unique ability to both acquire sensitive and quantitative measurements and to resolve the molecular complexity characteristic of SPL molecules, both across the different SPL families and within the same SPL family. Currently, two complementary MS-based approaches are used for lipid research: analysis of lipid extracts, mainly by infusion electrospray ionization (ESI), and mass spectrometry imaging (MSI) from a sample surface (i.e. intact tissue sections, cells, model membranes, thin layer chromatography plates) (Fig. 1). The first allows for sensitive and quantitative information about total lipid molecular species from a given specimen from which lipids have been extracted and chromatographically separated prior to the analysis; the second, albeit generally less quantitative and less specific in the identification of molecular species due to the complexity of the sample, allows for spatial information of lipid molecules from biological specimens. In the field of SPL research, MS analysis of lipid extracts from biological samples has been commonly utilized to implicate the role of these lipids in specific biological functions. On the other hand, the utilization of MSI in SPL research represents a more recent development that has started to provide interesting descriptive observations regarding the distribution of specific classes of SPLs within tissues. Thus, it is the aim of this review to discuss how MSI technology has been employed to extend the study of SPL metabolism and the type of information that has been obtained from model membranes, single cells and tissues. We envision this discussion as a complementary compendium to the excellent technical reviews recently published about the specifics of MSI technologies, including their application to SPL analysis (Fuchs et al., 2010; Berry et al., 2011; Ellis et al., 2013; Eberlin et al., 2011; Kraft and Klitzing, 2014).
Collapse
Affiliation(s)
- Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, United States.
| | - John D Haley
- Department of Pathology, Stony Brook University, Stony Brook, NY, United States
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, United States; Division of Infectious Diseases, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States; Veterans Administrations Medical Center, Northport, NY, United States
| |
Collapse
|
37
|
Assessment of Metabolic Signature for Cancer Diagnosis Using Desorption Electrospray Ionization Mass Spectrometric Imaging. Methods Mol Biol 2019; 1928:275-297. [PMID: 30725461 DOI: 10.1007/978-1-4939-9027-6_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metabolic reprogramming is a hallmark of tumor development. A technique that can map this complex biochemical shift by taking a snapshot of various metabolites in a tissue specimen (biopsy) is of high utility in the context of cancer diagnosis. Desorption electrospray ionization mass spectrometric imaging (DESI-MSI) is such a powerful and emerging analytical technique to simultaneously visualize the distributions of hundreds of metabolites, lipids, and other small molecules in the biological tissue. In DESI-MSI, a fine spray of high-velocity charged microdroplets rapidly extracts molecular species from the tissue surface and subsequently transfers them to the mass spectrometer, while the sample is continuously moved in two dimensions under the impinging spray of microdroplets. This allows a detailed multiplex molecular mapping of the tissue. DESI-MSI enables simultaneous examination of hundreds of putative metabolic biomarkers, an approach that lends much more predictive power than simply evaluating one or a few candidate biomarkers. The speed, versatility, lack of complicated sample preparation, and operation at ambient conditions make DESI-MSI extremely promising as a rapid diagnostic and prognostic tool.
Collapse
|
38
|
Margulis K, Zhou Z, Fang Q, Sievers RE, Lee RJ, Zare RN. Combining Desorption Electrospray Ionization Mass Spectrometry Imaging and Machine Learning for Molecular Recognition of Myocardial Infarction. Anal Chem 2018; 90:12198-12206. [PMID: 30188683 DOI: 10.1021/acs.analchem.8b03410] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lipid profile changes in heart muscle have been previously linked to cardiac ischemia and myocardial infarction, but the spatial distribution of lipids and metabolites in ischemic heart remains to be fully investigated. We performed desorption electrospray ionization mass spectrometry imaging of hearts from in vivo myocardial infarction mouse models. In these mice, myocardial ischemia was induced by blood supply restriction via a permanent ligation of left anterior descending coronary artery. We showed that applying the machine learning algorithm of gradient boosting tree ensemble to the ambient mass spectrometry imaging data allows us to distinguish segments of infarcted myocardium from normally perfused hearts on a pixel by pixel basis. The machine learning algorithm selected 62 molecular ion peaks important for classification of each 200 μm-diameter pixel of the cardiac tissue map as normally perfused or ischemic. This approach achieved very high average accuracy (97.4%), recall (95.8%), and precision (96.8%) at a spatial resolution of ∼200 μm. In addition, we determined the chemical identity of 27 species, mostly small metabolites and lipids, selected by the algorithm as the most significant for cardiac pathology classification. This molecular signature of myocardial infarction may provide new mechanistic insights into cardiac ischemia, assist with infarct size assessment, and point toward novel therapeutic interventions.
Collapse
Affiliation(s)
- Katherine Margulis
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Zhenpeng Zhou
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Qizhi Fang
- Cardiovascular Research Institute and Department of Medicine , University of California San Francisco , San Francisco , California 94131 , United States
| | - Richard E Sievers
- Cardiovascular Research Institute and Department of Medicine , University of California San Francisco , San Francisco , California 94131 , United States
| | - Randall J Lee
- Cardiovascular Research Institute and Department of Medicine , University of California San Francisco , San Francisco , California 94131 , United States
| | - Richard N Zare
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
39
|
Porcari AM, Zhang J, Garza KY, Rodrigues-Peres RM, Lin JQ, Young JH, Tibshirani R, Nagi C, Paiva GR, Carter SA, Sarian LO, Eberlin MN, Eberlin LS. Multicenter Study Using Desorption-Electrospray-Ionization-Mass-Spectrometry Imaging for Breast-Cancer Diagnosis. Anal Chem 2018; 90:11324-11332. [PMID: 30170496 DOI: 10.1021/acs.analchem.8b01961] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The histological and molecular subtypes of breast cancer demand distinct therapeutic approaches. Invasive ductal carcinoma (IDC) is subtyped according to estrogen-receptor (ER), progesterone-receptor (PR), and HER2 status, among other markers. Desorption-electrospray-ionization-mass-spectrometry imaging (DESI-MSI) is an ambient-ionization MS technique that has been previously used to diagnose IDC. Aiming to investigate the robustness of ambient-ionization MS for IDC diagnosis and subtyping over diverse patient populations and interlaboratory use, we report a multicenter study using DESI-MSI to analyze samples from 103 patients independently analyzed in the United States and Brazil. The lipid profiles of IDC and normal breast tissues were consistent across different patient races and were unrelated to country of sample collection. Similar experimental parameters used in both laboratories yielded consistent mass-spectral data in mass-to-charge ratios ( m/ z) above 700, where complex lipids are observed. Statistical classifiers built using data acquired in the United States yielded 97.6% sensitivity, 96.7% specificity, and 97.6% accuracy for cancer diagnosis. Equivalent performance was observed for the intralaboratory validation set (99.2% accuracy) and, most remarkably, for the interlaboratory validation set independently acquired in Brazil (95.3% accuracy). Separate classification models built for ER and PR statuses as well as the status of their combined hormone receptor (HR) provided predictive accuracies (>89.0%), although low classification accuracies were achieved for HER2 status. Altogether, our multicenter study demonstrates that DESI-MSI is a robust and reproducible technology for rapid breast-cancer-tissue diagnosis and therefore is of value for clinical use.
Collapse
Affiliation(s)
- Andreia M Porcari
- Thomson Mass Spectrometry Laboratory, Department of Chemistry , University of Campinas - UNICAMP , Campinas , São Paulo 13083-970 , Brazil.,Laboratory of Multidisciplinary Research , São Francisco University , Bragança Paulista , São Paulo 12916-900 , Brazil
| | - Jialing Zhang
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Kyana Y Garza
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Raquel M Rodrigues-Peres
- Department of Gynecological and Breast Oncology, CAISM Women's Hospital, Faculty of Medical Sciences , University of Campinas , Campinas, São Paulo , 13083-881 , Brazil
| | - John Q Lin
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jonathan H Young
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Robert Tibshirani
- Departments of Biomedical Data Science and Statistics , Stanford University , Stanford , California 94305 , United States
| | - Chandandeep Nagi
- Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Geisilene R Paiva
- Department of Gynecological and Breast Oncology, CAISM Women's Hospital, Faculty of Medical Sciences , University of Campinas , Campinas, São Paulo , 13083-881 , Brazil
| | - Stacey A Carter
- Department of Surgery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Luis Otávio Sarian
- Department of Gynecological and Breast Oncology, CAISM Women's Hospital, Faculty of Medical Sciences , University of Campinas , Campinas, São Paulo , 13083-881 , Brazil
| | - Marcos N Eberlin
- Thomson Mass Spectrometry Laboratory, Department of Chemistry , University of Campinas - UNICAMP , Campinas , São Paulo 13083-970 , Brazil.,Mackenzie Presbiterian University , School of Engineering , São Paulo , SP 01302-907 , Brazil
| | - Livia S Eberlin
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
40
|
Banerjee S. Ambient ionization mass spectrometry imaging for disease diagnosis: Excitements and challenges. J Biosci 2018; 43:731-738. [PMID: 30207318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tissue analysis in histology is extremely important and also considered to be a gold standard to diagnose and prognosticate several diseases including cancer. Intraoperative evaluation of surgical margin of tumor also relies on frozen section histopathology, which is time consuming, challenging and often subjective. Recent development in the ambient ionization mass spectrometry imaging (MSI) technique has enabled us to simultaneously visualize hundreds to thousands of molecules (ion images) in the biopsy specimen, which are strikingly different and more powerful than the single optical tissue image analysis in conventional histopathology. This paper will highlight the emergence of the desorption electrospray ionization MSI (DESI-MSI) technique, which is label-free, requires minimal or no sample preparation and operates under ambient conditions. DESI-MSI can record ion images of lipid/metabolite distributions on biopsy specimens, providing a wealth of diagnostic information based on differential distributions of these molecular species in healthy and unhealthy tissues. Remarkable success of this technology in rapidly evaluating the cancer margin intraoperatively with very high accuracy also promises to bring this imaging technique from bench to bedside.
Collapse
Affiliation(s)
- Shibdas Banerjee
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Karakambadi Road, Tirupati 517 507, India,
| |
Collapse
|
41
|
Banerjee S. Ambient ionization mass spectrometry imaging for disease diagnosis: Excitements and challenges. J Biosci 2018. [DOI: 10.1007/s12038-018-9785-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
42
|
Klein DR, Feider CL, Garza KY, Lin JQ, Eberlin LS, Brodbelt JS. Desorption Electrospray Ionization Coupled with Ultraviolet Photodissociation for Characterization of Phospholipid Isomers in Tissue Sections. Anal Chem 2018; 90:10100-10104. [PMID: 30080398 DOI: 10.1021/acs.analchem.8b03026] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Desorption electrospray ionization (DESI) mass spectrometry imaging has become a powerful strategy for analysis of tissue sections, enabling differentiation of normal and diseased tissue based on changes in the lipid profiles. The most common DESI workflow involves collection of MS1 spectra as the DESI spray is rastered over a tissue section. Relying on MS1 spectra inherently limits the ability to differentiate isobaric and isomeric species or evaluate variations in the relative abundances of key isomeric lipids, such as double-bond positional isomers which may distinguish normal and diseased tissues. Here, 193 nm ultraviolet photodissociation (UVPD), a technique capable of differentiating double-bond positional isomers, is coupled with DESI to map differences in the double-bond isomer composition in tissue sections in a fast, high throughput manner compatible with imaging applications.
Collapse
Affiliation(s)
- Dustin R Klein
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Clara L Feider
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Kyana Y Garza
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - John Q Lin
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Livia S Eberlin
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
43
|
Parrot D, Papazian S, Foil D, Tasdemir D. Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research. PLANTA MEDICA 2018; 84:584-593. [PMID: 29388184 PMCID: PMC6053038 DOI: 10.1055/s-0044-100188] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 05/06/2023]
Abstract
Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.
Collapse
Affiliation(s)
- Delphine Parrot
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Stefano Papazian
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Daniel Foil
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
- Kiel University, Kiel, Germany
| |
Collapse
|
44
|
Cooks RG, Yan X. Mass Spectrometry for Synthesis and Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:1-28. [PMID: 29894228 DOI: 10.1146/annurev-anchem-061417-125820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mass spectrometry is the science and technology of ions. As such, it is concerned with generating ions, measuring their properties, following their reactions, isolating them, and using them to build and transform materials. Instrumentation is an essential element of these activities, and analytical applications are one driving force. Work from the Aston Laboratories at Purdue University's Department of Chemistry is described here, with an emphasis on accelerated reactions of ions in solution and small-scale synthesis; ion/surface collision processes, including surface-induced dissociation (SID) and ion soft landing; and applications to tissue imaging. Our special interest in chirality and the chemistry behind the origins of life is also featured together with the exciting area of tissue diagnostics.
Collapse
Affiliation(s)
- R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA;
| | - Xin Yan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA;
- Current affiliation: Department of Chemistry, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
45
|
Lamont L, Baumert M, Ogrinc Potočnik N, Allen M, Vreeken R, Heeren RMA, Porta T. Integration of Ion Mobility MS E after Fully Automated, Online, High-Resolution Liquid Extraction Surface Analysis Micro-Liquid Chromatography. Anal Chem 2017; 89:11143-11150. [PMID: 28945354 PMCID: PMC5677252 DOI: 10.1021/acs.analchem.7b03512] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Direct
analysis by mass spectrometry (imaging) has become increasingly
deployed in preclinical and clinical research due to its rapid and
accurate readouts. However, when it comes to biomarker discovery or
histopathological diagnostics, more sensitive and in-depth profiling
from localized areas is required. We developed a comprehensive, fully
automated online platform for high-resolution liquid extraction surface
analysis (HR-LESA) followed by micro–liquid chromatography
(LC) separation and a data-independent acquisition strategy for untargeted
and low abundant analyte identification directly from tissue sections.
Applied to tissue sections of rat pituitary, the platform demonstrated
improved spatial resolution, allowing sample areas as small as 400
μm to be studied, a major advantage over conventional LESA.
The platform integrates an online buffer exchange and washing step
for removal of salts and other endogenous contamination that originates
from local tissue extraction. Our carry over–free platform
showed high reproducibility, with an interextraction variability below
30%. Another strength of the platform is the additional selectivity
provided by a postsampling gas-phase ion mobility separation. This
allowed distinguishing coeluted isobaric compounds without requiring
additional separation time. Furthermore, we identified untargeted
and low-abundance analytes, including neuropeptides deriving from
the pro-opiomelanocortin precursor protein and localized a specific
area of the pituitary gland (i.e., adenohypophysis) known to secrete
neuropeptides and other small metabolites related to development,
growth, and metabolism. This platform can thus be applied for the
in-depth study of small samples of complex tissues with histologic
features of ∼400 μm or more, including potential neuropeptide
markers involved in many diseases such as neurodegenerative diseases,
obesity, bulimia, and anorexia nervosa.
Collapse
Affiliation(s)
- Lieke Lamont
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | | | - Nina Ogrinc Potočnik
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | - Mark Allen
- Advion , Harlow CM20 2NQ, United Kingdom
| | - Rob Vreeken
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands.,Janssen Pharmaceutica , Beerse, Belgium
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | - Tiffany Porta
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| |
Collapse
|
46
|
Zhvansky ES, Sorokin AA, Popov IA, Shurkhay VA, Potapov AA, Nikolaev EN. High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:213-216. [PMID: 29028390 DOI: 10.1177/1469066717721484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. Tumor fragments were investigated by the immunohistochemistry method and were identified as necrotic tissue with necrotized vessels, necrotic tissue with tumor stain, tumor with necrosis (tumor tissue as major), tumor, necrotized tumor (necrotic tissues as major), parts of tumor cells, boundary brain tissue, and brain tissue hyperplasia. The technique of classification of tumor tissues based on mass spectrometric profile data processing is suggested in this paper. Classifiers dividing the researched sample to the corresponding tissue type were created as a result of the processing. Classifiers of necrotic and tumor tissues are shown to yield a combined result when the tissue is heterogeneous and consists of both tumor cells and necrotic tissue.
Collapse
Affiliation(s)
- E S Zhvansky
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russian Federation
| | - A A Sorokin
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
| | - I A Popov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
| | - V A Shurkhay
- 3 Federal State Autonomous Institution "N.N. Burdenko National Scientific and Practical Center for Neurosurgery" of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - A A Potapov
- 3 Federal State Autonomous Institution "N.N. Burdenko National Scientific and Practical Center for Neurosurgery" of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - E N Nikolaev
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russian Federation
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russian Federation
| |
Collapse
|