1
|
Nwabufo CK, Aigbogun OP. The Role of Mass Spectrometry Imaging in Pharmacokinetic Studies. Xenobiotica 2022; 52:811-827. [PMID: 36048000 DOI: 10.1080/00498254.2022.2119900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Although liquid chromatography-tandem mass spectrometry is the gold standard analytical platform for the quantification of drugs, metabolites, and biomarkers in biological samples, it cannot localize them in target tissues.The localization and quantification of drugs and/or their associated metabolites in target tissues is a more direct measure of bioavailability, biodistribution, efficacy, and regional toxicity compared to the traditional substitute studies using plasma.Therefore, combining high spatial resolution imaging functionality with the superior selectivity and sensitivity of mass spectrometry into one analytical technique will be a valuable tool for targeted localization and quantification of drugs, metabolites, and biomarkers.Mass spectrometry imaging (MSI) is a tagless analytical technique that allows for the direct localization and quantification of drugs, metabolites, and biomarkers in biological tissues, and has been used extensively in pharmaceutical research.The overall goal of this current review is to provide a detailed description of the working principle of MSI and its application in pharmacokinetic studies encompassing absorption, distribution, metabolism, excretion, and toxicity processes, followed by a discussion of the strategies for addressing the challenges associated with the functional utility of MSI in pharmacokinetic studies that support drug development.
Collapse
Affiliation(s)
- Chukwunonso K Nwabufo
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Omozojie P Aigbogun
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
2
|
Aftab W, Lahiri S, Imhof A. ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data. Mol Cell Proteomics 2022; 21:100242. [PMID: 35569805 PMCID: PMC9194865 DOI: 10.1016/j.mcpro.2022.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/08/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI-IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI-IMS. This is achieved by combining information from IMS and shotgun proteomics (LC-MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC-MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.
Collapse
Affiliation(s)
- Wasim Aftab
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Shibojyoti Lahiri
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Axel Imhof
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| |
Collapse
|
3
|
Kruse ARS, Spraggins JM. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Front Physiol 2022; 13:837773. [PMID: 35222094 PMCID: PMC8874197 DOI: 10.3389/fphys.2022.837773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
The kidney functions through the coordination of approximately one million multifunctional nephrons in 3-dimensional space. Molecular understanding of the kidney has relied on transcriptomic, proteomic, and metabolomic analyses of kidney homogenate, but these approaches do not resolve cellular identity and spatial context. Mass spectrometry analysis of isolated cells retains cellular identity but not information regarding its cellular neighborhood and extracellular matrix. Spatially targeted mass spectrometry is uniquely suited to molecularly characterize kidney tissue while retaining in situ cellular context. This review summarizes advances in methodology and technology for spatially targeted mass spectrometry analysis of kidney tissue. Profiling technologies such as laser capture microdissection (LCM) coupled to liquid chromatography tandem mass spectrometry provide deep molecular coverage of specific tissue regions, while imaging technologies such as matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) molecularly profile regularly spaced tissue regions with greater spatial resolution. These technologies individually have furthered our understanding of heterogeneity in nephron regions such as glomeruli and proximal tubules, and their combination is expected to profoundly expand our knowledge of the kidney in health and disease.
Collapse
Affiliation(s)
- Angela R. S. Kruse
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jeffrey M. Spraggins,
| |
Collapse
|
4
|
Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
Collapse
Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| |
Collapse
|
5
|
Zubair F. MALDI mass Spectrometry based proteomics for drug discovery & development. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:29-35. [PMID: 34916018 DOI: 10.1016/j.ddtec.2021.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Matrix-assisted laser desorption/ ionization (MALDI) is a soft ionization technique for introducing wide range of analytes into a mass spectrometer (MS). MALDI MS is a powerful tool in drug discovery research and development, providing a high-throughput molecular analysis technique in both preclinical and clinical systems. In particular, MALDI MS is invaluable in the study of peptides and proteins that drive all biological functions. This technology is label-free, provides high specificity in molecular identification, and is high-throughput. MALDI MS has been used in biomarker discovery and quantitation in virtually all tissues, serum, plasma, CSF, and urine for diagnostics, patient stratification, and monitoring drug efficacy. Other applications include characterization of biological drugs, spatial mapping of biomarkers and drugs in tissues, drug screening, and toxicological assessment.
Collapse
|
6
|
Innovation in drug toxicology: Application of mass spectrometry imaging technology. Toxicology 2021; 464:153000. [PMID: 34695509 DOI: 10.1016/j.tox.2021.153000] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 01/19/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful molecular imaging technology that can obtain qualitative, quantitative, and location information by simultaneously detecting and mapping endogenous or exogenous molecules in biological tissue slices without specific chemical labeling or complex sample pretreatment. This article reviews the progress made in MSI and its application in drug toxicology research, including the tissue distribution of toxic drugs and their metabolites, the target organs (liver, kidney, lung, eye, and central nervous system) of toxic drugs, the discovery of toxicity-associated biomarkers, and explanations of the mechanisms of drug toxicity when MSI is combined with the cutting-edge omics methodologies. The unique advantages and broad prospects of this technology have been fully demonstrated to further promote its wider use in the field of pharmaceutical toxicology.
Collapse
|
7
|
Abstract
![]()
Previously, we have
demonstrated native mass spectrometry imaging
(native MSI) in which the spatial distribution of proteins maintained
in their native-like, folded conformations was determined using liquid
extraction surface analysis (LESA). While providing an excellent testbed
for proof of principle, the spatial resolution of LESA is currently
limited for imaging primarily by the physical size of the sampling
pipette tip. Here, we report the adoption of nanospray-desorption
electrospray ionization (nano-DESI) for native MSI, delivering substantial
improvements in resolution versus native LESA MSI. In addition, native
nano-DESI may be used for location-targeted top–down proteomics
analysis directly from tissue. Proteins, including a homodimeric complex
not previously detected by native MSI, were identified through a combination
of collisional activation, high-resolution MS and proton transfer
charge reduction.
Collapse
Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| |
Collapse
|
8
|
Awdishu L, Atilano-Roque A, Tuey S, Joy MS. Identification of Novel Biomarkers for Predicting Kidney Injury Due to Drugs Using "Omic" Strategies. Pharmgenomics Pers Med 2020; 13:687-705. [PMID: 33293850 PMCID: PMC7719321 DOI: 10.2147/pgpm.s239471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Drug-induced kidney injury accounts for 20% of community- and hospital-acquired cases of acute kidney injury (AKI). The incidence is higher among older individuals, who often have co-existing morbidities and are exposed to more diagnostic procedures and therapies. While demographic and clinical components have been identified as risk factors, the proposed cellular mechanisms of drug-induced kidney injury are numerous and complicated. There are also limitations recognized in the use of traditional biomarkers, such as serum creatinine and blood urea nitrogen, to provide high sensitivity, specificity, and timeliness to identification of drug-induced kidney injury. Therefore, novel biomarkers are currently being investigated, identified, developed, and validated for their performance over the traditional biomarkers. This review will provide an overview of drug-induced kidney injury and will discuss what is known regarding "omic" (proteomic, genomic, transcriptomic, and metabolomic) biomarker strategies for drugs known to induce nephrotoxicity.
Collapse
Affiliation(s)
- Linda Awdishu
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA, USA
| | - Amandla Atilano-Roque
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Stacey Tuey
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Melanie S Joy
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
- University of Colorado, School of Medicine, Division of Renal Diseases and Hypertension, Aurora, CO, USA
| |
Collapse
|
9
|
Kim SW, Choi JW, Yun JW, Chung IS, Cho HC, Song SE, Im SS, Song DK. Proteomics approach to identify serum biomarkers associated with the progression of diabetes in Korean patients with abdominal obesity. PLoS One 2019; 14:e0222032. [PMID: 31504048 PMCID: PMC6736247 DOI: 10.1371/journal.pone.0222032] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/20/2019] [Indexed: 12/25/2022] Open
Abstract
Type 2 diabetes is a metabolic disease with a group of metabolic derangements and inflammatory reactants in the serum. Despite the substantial public health implications, markers of diabetes progression with abdominal obesity are still needed to facilitate early detection and treatment. In this study, we performed a proteomic approach to identify differential target proteins underlying diabetes progression in patients with abdominal obesity. Proteomic differences were investigated in the serum of controls and patients with prediabetes or diabetes with or without abdominal obesity by 2-DE combined with MALDI-TOF-MS. Proteomics data were validated by western blot analyses and major protein-protein interactions were assessed using a network analysis with String database. Among 245 matched protein spots, 36 exhibited marked differences in normal patients with abdominal obesity, prediabetes, and diabetes compared to levels in normal patients without abdominal obesity. Seven (Alpha-1-antichymotrypsin, Alpha-1-antitrypsin, Apolipoprotein A-I, haptoglobin, retinol-binding protein 4, transthyretin, and zinc-alpha2-glycoprotein) of these spots exhibited significant differences between normal and prediabetes/diabetes patients. After a network analysis, functional annotation using Gene Ontology indicated that most of the identified proteins were involved in lipid transport, lipid localization, and the regulation of serum lipoprotein particle levels. Our results indicated that variation in the levels of these identified protein biomarkers has been reported in normal, prediabetes and diabetic Assessment of the levels of these biomarkers may contribute to the development of biomarkers for not only early diagnosis but also in prognosis of diabetes mellitus type 2.
Collapse
Affiliation(s)
- Sang Woo Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jung-Won Choi
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jong Won Yun
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk, South Korea
| | - In-Sung Chung
- Division of Occupational and Environmental Medicine and Department of Preventive Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Ho Chan Cho
- Department of Internal Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Eun Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Soon Im
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
| | - Dae-Kyu Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
| |
Collapse
|
10
|
Lee MC, Cheng KJ, Chen SM, Li YC, Imai K, Lee CM, Lee JA. A novel preventive mechanism of gentamicin-induced nephrotoxicity by atorvastatin. Biomed Chromatogr 2019; 33:e4639. [PMID: 31256419 DOI: 10.1002/bmc.4639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 11/05/2022]
Abstract
Atorvastatin (ATO) inhibits the synthesis of nonsteroidal isoprenoid compounds and possesses a pleiotropic effect. However, the detailed mechanism of ATO in preventing gentamicin (GM)-induced renal injury remains obscure. Although underlying multifaceted mechanisms involving GM-induced nephrotoxicity were well known, further work on elucidating the essential mechanism was needed. Using a fluorogenic derivatization-liquid chromatography tandem mass spectrometry proteomic method (FD-LC-MS/MS method), we investigated the effects and mechanisms of ATO treatment on GM-induced nephrotoxicity in rats. Consequently, 49 differentially expressed proteins were identified. The most significant mechanisms of nephrotoxicity caused by GM were mitochondrial dysfunction, fatty acid metabolism and oxidative stress. Their upstream regulator was found to be PPARα. The proteins involved in GM nephrotoxicity were sodium-hydrogen exchanger regulatory factor (SLC9A3R1), cathepsin V (CTSV), macrophage migration inhibitory factor (MIF) and RhoGDP dissociation inhibitor alpha (ARHGDIA). After ATO intervention, we observed a reversed enrichment pattern of their expression, especially in CTSV and SLC9A3R1 (P-value<0.05). We predicted that ATO may improve abnormal phospholipid metabolism and phospholipidosis caused by GM and also alleviate cell volume homeostasis and reverse the interference of GM with the transporter. Furthermore, proteomic results also provided clues as to GM-induced nephrotoxicity biomarkers such as CTSV and transthyretin.
Collapse
Affiliation(s)
- Mei-Chun Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Pharmacy, MacKay Memorial Hospital, Taipei, Taiwan.,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Kuei-Ju Cheng
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shih-Ming Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chieh Li
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan
| | - Chun-Ming Lee
- Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan.,Department of Internal Medicine, St. Joseph's Hospital, Yunlin County, Taiwan.,Division of Infectious Disease, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan.,MacKay Medical College, New Taipei City, Taiwan
| | - Jen-Ai Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
11
|
Takeo E, Sugiura Y, Uemura T, Nishimoto K, Yasuda M, Sugiyama E, Ohtsuki S, Higashi T, Nishikawa T, Suematsu M, Fukusaki E, Shimma S. Tandem Mass Spectrometry Imaging Reveals Distinct Accumulation Patterns of Steroid Structural Isomers in Human Adrenal Glands. Anal Chem 2019; 91:8918-8925. [PMID: 31204806 DOI: 10.1021/acs.analchem.9b00619] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Visualizing tissue distribution of steroid hormones is a promising application of MALDI mass spectrometry imaging (MSI). On-tissue chemical derivatization using Girard's T reagent has enhanced the ionization efficiency of steroids. However, discriminating between structural isomers with distinct bioactivities remains a challenge. Herein, we used ion trap MS/tandem MS (MS3) to distinguish a mineralcorticoid aldosterone (Aldo) and a glucocorticoid cortisol (F), from their structural isomers. Our method is also useful to detect hybrid steroids (18-hydroxycortisol [18-OHF] and 18-oxocortisol) with sufficient signal-to-noise ratio. The clinical applicability of the tandem MS method was evaluated by analyzing F, Aldo, and 18-OHF distributions in human adrenal glands. In such clinical specimens, small Aldo-producing cell clusters (APCCs) were identified and were first found to produce a high level of Aldo and not to contain F. Moreover, a part of APCCs produced 18-OHF, presumably converted from F by APCC-specific CYP11B2 activity. Catecholamine species were also visualized with another derivatization reagent (TAHS), and those profiling successfully discriminated pheochromocytoma species. These tandem MSI-methods, coupled with on-tissue chemical derivatization has proven to be useful for detecting low-abundance steroids, including Aldo and hybrid steroids and thus identifying steroid hormone-producing lesions.
Collapse
Affiliation(s)
- Emi Takeo
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Yuki Sugiura
- Department of Biochemistry , Keio University School of Medicine , 35 Shinanomachi , Shinjuku-ku, Tokyo 160-8582 , Japan
| | - Tatsuki Uemura
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences , Kumamoto University , 5-1 Oe-honmachi , Chuo-ku, Kumamoto 862-0973 , Japan
| | - Koshiro Nishimoto
- Department of Biochemistry , Keio University School of Medicine , 35 Shinanomachi , Shinjuku-ku, Tokyo 160-8582 , Japan.,Department of Uro-Oncology , Saitama Medical University International Medical Center , 1397-1 Yamane , Hidaka , Saitama 350-1298 , Japan
| | - Masanori Yasuda
- Department of Pathology , Saitama Medical University International Medical Center , 1397-1 Yamane , Hidaka , Saitama 350-1298 , Japan
| | - Eiji Sugiyama
- Department of Biochemistry , Keio University School of Medicine , 35 Shinanomachi , Shinjuku-ku, Tokyo 160-8582 , Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences , Kumamoto University , 5-1 Oe-honmachi , Chuo-ku, Kumamoto 862-0973 , Japan
| | - Tatsuya Higashi
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Tetsuo Nishikawa
- Endocrinology and Diabetes Center , Yokohama Rosai Hospital , 3211 Kozukuecho , Kohoku-ku, Yokohama , Kanagawa 222-0036 , Japan
| | - Makoto Suematsu
- Department of Biochemistry , Keio University School of Medicine , 35 Shinanomachi , Shinjuku-ku, Tokyo 160-8582 , Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| |
Collapse
|
12
|
Moreno-Gordaliza E, Esteban-Fernández D, Lázaro A, Aboulmagd S, Humanes B, Tejedor A, Linscheid MW, Gómez-Gómez MM. Lipid imaging for visualizing cilastatin amelioration of cisplatin-induced nephrotoxicity. J Lipid Res 2018; 59:1561-1574. [PMID: 30049708 PMCID: PMC6121926 DOI: 10.1194/jlr.m080465] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/12/2018] [Indexed: 12/26/2022] Open
Abstract
Nephrotoxicity is a major limitation to cisplatin antitumor therapies. Cilastatin, an inhibitor of renal dehydropeptidase-I, was recently proposed as a promising nephroprotector against cisplatin toxicity, preventing apoptotic cell death. In this work, cilastatin nephroprotection was further investigated in a rat model, with a focus on its effect on 76 renal lipids altered by cisplatin, including 13 new cisplatin-altered mitochondrial cardiolipin species. Lipid imaging was performed with MALDI mass spectrometry imaging (MALDI-MSI) in kidney sections from treated rats. Cilastatin was proved to significantly diminish the lipid distribution alterations caused by cisplatin, lipid levels being almost completely recovered to those of control samples. The extent of recovery of cisplatin-altered lipids by cilastatin turned out to be relevant for discriminating direct or secondary lipid alterations driven by cisplatin. Lipid peroxidation induced by cisplatin was also shown to be reduced when cilastatin was administered. Importantly, significant groups separation was achieved during multivariate analysis of cortex and outer-medullary lipids, indicating that damaged kidney can be discerned from the nephroprotected and healthy groups and classified according to lipid distribution. Therefore, we propose MALDI-MSI as a powerful potential tool offering multimolecule detection possibilities to visualize and evaluate nephrotoxicity and nephroprotection based on lipid analysis.
Collapse
Affiliation(s)
- Estefanía Moreno-Gordaliza
- Department of Analytical Chemistry, Faculty of Chemistry, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Diego Esteban-Fernández
- Department of Chemistry, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Alberto Lázaro
- Humboldt Universität zu Berlin, 12489 Berlin, Germany; and Renal Pathophysiology Laboratory, Department of Nephrology, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; Department of Physiology, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Sarah Aboulmagd
- Department of Chemistry, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Blanca Humanes
- Humboldt Universität zu Berlin, 12489 Berlin, Germany; and Renal Pathophysiology Laboratory, Department of Nephrology, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Alberto Tejedor
- Humboldt Universität zu Berlin, 12489 Berlin, Germany; and Renal Pathophysiology Laboratory, Department of Nephrology, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Michael W Linscheid
- Department of Chemistry, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - M Milagros Gómez-Gómez
- Department of Analytical Chemistry, Faculty of Chemistry, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
13
|
Maronpot RR, Nyska A, Troth SP, Gabrielson K, Sysa-Shah P, Kalchenko V, Kuznetsov Y, Harmelin A, Schiffenbauer YS, Bonnel D, Stauber J, Ramot Y. Regulatory Forum Opinion Piece*: Imaging Applications in Toxicologic Pathology-Recommendations for Use in Regulated Nonclinical Toxicity Studies. Toxicol Pathol 2018. [PMID: 28641506 DOI: 10.1177/0192623317710014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Available imaging systems for use in preclinical toxicology studies increasingly show utility as important tools in the toxicologic pathologist's armamentarium, permit longitudinal evaluation of functional and morphological changes in tissues, and provide important information such as organ and lesion volume not obtained by conventional toxicology study parameters. Representative examples of practical imaging applications in toxicology research and preclinical studies are presented for ultrasound, positron emission tomography/single-photon emission computed tomography, optical, magnetic resonance imaging, and matrix-assisted laser desorption ionization-imaging mass spectrometry imaging. Some of the challenges for making imaging systems good laboratory practice-compliant for regulatory submission are presented. Use of imaging data on a case-by-case basis as part of safety evaluation in regulatory submissions is encouraged.
Collapse
Affiliation(s)
| | - Abraham Nyska
- 2 Toxicologic Pathology, Sackler School of Medicine, Tel Aviv University, Timrat, Israel
| | - Sean P Troth
- 3 Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Kathleen Gabrielson
- 4 Department of Molecular and Comparative Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Polina Sysa-Shah
- 4 Department of Molecular and Comparative Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vyacheslav Kalchenko
- 5 Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri Kuznetsov
- 5 Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- 5 Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Yuval Ramot
- 8 Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| |
Collapse
|
14
|
Schmit PO, Vialaret J, Wessels HJ, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics 2018; 175:12-26. [DOI: 10.1016/j.jprot.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
|
15
|
Prentice BM, Caprioli RM, Vuiblet V. Label-free molecular imaging of the kidney. Kidney Int 2017; 92:580-598. [PMID: 28750926 PMCID: PMC6193761 DOI: 10.1016/j.kint.2017.03.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/25/2022]
Abstract
In this review, we will highlight technologies that enable scientists to study the molecular characteristics of tissues and/or cells without the need for antibodies or other labeling techniques. Specifically, we will focus on matrix-assisted laser desorption/ionization imaging mass spectrometry, infrared spectroscopy, and Raman spectroscopy.
Collapse
Affiliation(s)
- Boone M Prentice
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Departments of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.
| | - Vincent Vuiblet
- Biophotonic Laboratory, UMR CNRS 7369 URCA, Reims, France; Nephropathology, Department of Biopathology Laboratory, CHU de Reims, Reims, France; Nephrology and Renal Transplantation department, CHU de Reims, Reims, France.
| |
Collapse
|
16
|
Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection. Biochim Biophys Acta Gen Subj 2017; 1861:1702-1714. [PMID: 28300637 DOI: 10.1016/j.bbagen.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection. Subjecting the dissected pieces to the modified Folch method allows to separate the metabolites from proteins. The proteins can then be subjected to digestion under controlled conditions to improve protein identification yields. RESULTS The proof of concept experiment on rat brain generated 162 and 140 metabolite assignments from three ROIs (cerebellum, hippocampus and midbrain/hypothalamus) in positive and negative modes, respectively, and 890, 1303 and 1059 unique proteins. Integrated metabolite and protein overrepresentation analysis identified pathways associated with the biological functions of each ROI, most of which were not identified when looking at the protein and metabolite lists individually. CONCLUSIONS This combined MALDI MS imaging and multi-omics approach further extends the amount of information that can be generated from single tissue sections. GENERAL SIGNIFICANCE To the best of our knowledge, this is the first report combining both imaging and multi-omics analyses in the same workflow and on the same tissue section.
Collapse
Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| |
Collapse
|
17
|
MALDI-LTQ-Orbitrap mass spectrometry imaging for lipidomic analysis in kidney under cisplatin chemotherapy. Talanta 2017; 164:16-26. [DOI: 10.1016/j.talanta.2016.11.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/06/2016] [Accepted: 11/12/2016] [Indexed: 01/06/2023]
|
18
|
Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:795-816. [PMID: 28087424 DOI: 10.1016/j.bbapap.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation. MALDI-IMS has evolved rapidly over the last decade and has been successfully used in both medical and basic research by scientists worldwide. In this review, we explore the clinical applications of MALDI-IMS, focusing on the major cancer types and neurodegenerative diseases. In particular, we re-emphasize the diagnostic potential of IMS and the challenges that must be confronted when conducting MALDI-IMS in clinical settings. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
Collapse
Affiliation(s)
- Yasemin Ucal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Zeynep Aslıhan Durer
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Hakan Atak
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Elif Kadioglu
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Abdurrahman Coskun
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Aysel Ozpinar
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey.
| |
Collapse
|
19
|
Abstract
Over the last decade mass spectrometry imaging (MSI) has been integrated in to many areas of drug discovery and development. It can have significant impact in oncology drug discovery as it allows efficacy and safety of compounds to be assessed against the backdrop of the complex tumour microenvironment. We will discuss the roles of MSI in investigating compound and metabolite biodistribution and defining pharmacokinetic -pharmacodynamic relationships, analysis that is applicable to all drug discovery projects. We will then look more specifically at how MSI can be used to understand tumour metabolism and other applications specific to oncology research. This will all be described alongside the challenges of applying MSI to industry research with increased use of metrology for MSI.
Collapse
|
20
|
Karlsson O, Hanrieder J. Imaging mass spectrometry in drug development and toxicology. Arch Toxicol 2016; 91:2283-2294. [PMID: 27933369 PMCID: PMC5429351 DOI: 10.1007/s00204-016-1905-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/24/2016] [Indexed: 11/25/2022]
Abstract
During the last decades, imaging mass spectrometry has gained significant relevance in biomedical research. Recent advances in imaging mass spectrometry have paved the way for in situ studies on drug development, metabolism and toxicology. In contrast to whole-body autoradiography that images the localization of radiolabeled compounds, imaging mass spectrometry provides the possibility to simultaneously determine the discrete tissue distribution of the parent compound and its metabolites. In addition, imaging mass spectrometry features high molecular specificity and allows comprehensive, multiplexed detection and localization of hundreds of proteins, peptides and lipids directly in tissues. Toxicologists traditionally screen for adverse findings by histopathological examination. However, studies of the molecular and cellular processes underpinning toxicological and pathologic findings induced by candidate drugs or toxins are important to reach a mechanistic understanding and an effective risk assessment strategy. One of IMS strengths is the ability to directly overlay the molecular information from the mass spectrometric analysis with the tissue section and allow correlative comparisons of molecular and histologic information. Imaging mass spectrometry could therefore be a powerful tool for omics profiling of pharmacological/toxicological effects of drug candidates and toxicants in discrete tissue regions. The aim of the present review is to provide an overview of imaging mass spectrometry, with particular focus on MALDI imaging mass spectrometry, and its use in drug development and toxicology in general.
Collapse
Affiliation(s)
- Oskar Karlsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institute, 171 76, Stockholm, Sweden.
- Department of Pharmaceutical Biosciences, Drug Safety and Toxicology, Uppsala University, 751 24, Uppsala, Sweden.
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V, 431 80, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London, WC1N, UK
| |
Collapse
|
21
|
Potential of MALDI imaging for the toxicological evaluation of environmental pollutants. J Proteomics 2016; 144:133-9. [PMID: 27178109 DOI: 10.1016/j.jprot.2016.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/13/2016] [Accepted: 05/08/2016] [Indexed: 01/02/2023]
Abstract
Risk assessment related to the exposure of humans to chemicals released into the environment is a major concern of our modern societies. In this context, toxicology plays a crucial role to characterize the effects of this exposure on health and identify the targets of these molecules. MALDI imaging mass spectrometry (IMS) is an enabling technology for biodistribution studies of chemicals. Although the majority of published studies are presented in a pharmacological context, the concepts discussed in this review can be applied to the toxicological evaluation of chemicals released into the environment. The major asset of IMS is the simultaneous localization and identification of a parent molecule and its metabolites without labeling and without any prior knowledge. Quantification methods developed in IMS are presented with application to an environmental pollutant. IMS is effective in the localization of chemicals and endogenous species. This opens unique perspectives for the discovery of molecular alterations in metabolites and protein biomarkers that could help for a better understanding of toxicity mechanisms. Distribution studies of agrochemicals in plants by IMS can contribute to a better understanding of their mode of action and to a more effective use of these chemicals, avoiding the current concern of environmental damage.
Collapse
|
22
|
Shi F, Archer JJ, Levis RJ. Nonresonant, femtosecond laser vaporization and electrospray post-ionization mass spectrometry as a tool for biological tissue imaging. Methods 2016; 104:79-85. [PMID: 26931651 DOI: 10.1016/j.ymeth.2016.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 12/30/2022] Open
Abstract
An ambient mass spectrometry imaging (MSI) source is demonstrated with both high spatial and mass resolution that enables measurement of the compositional heterogeneity within a biological tissue sample. The source is based on nonresonant, femtosecond laser electrospray mass spectrometry (LEMS) coupled to a quadrupole time-of-flight (QTOF) mass analyzer. No matrix deposition and minimal sample preparation is necessary for the source. The laser, translation stage, and mass spectrometer are synchronized and controlled using a customized user interface. Single or multiple laser shots may be applied to each pixel. A scanning rate of 2.0s per pixel is achieved. Measurement of a patterned ink film indicates the potential of LEMS for ambient imaging with a lateral resolution of ∼60μm. Metabolites including sugar, anthocyanins and other small metabolites were successfully mapped from plant samples without oversampling using a spot size of 60×70μm(2). Molecular identification of the detected analytes from the tissue was enabled by accurate mass measurement in conjunction with tandem mass spectrometry. Statistical analysis, non-negative matrix factorization and principle component analysis, were applied to the imaging data to extract regions with distinct and/or correlated spectral profiles.
Collapse
Affiliation(s)
- Fengjian Shi
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, United States
| | - Jieutonne J Archer
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, United States
| | - Robert J Levis
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, United States.
| |
Collapse
|
23
|
OuYang C, Chen B, Li L. High Throughput In Situ DDA Analysis of Neuropeptides by Coupling Novel Multiplex Mass Spectrometric Imaging (MSI) with Gas-Phase Fractionation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1992-2001. [PMID: 26438126 PMCID: PMC4837696 DOI: 10.1007/s13361-015-1265-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 05/05/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging (MSI) is a powerful tool to map the spatial distribution of biomolecules on tissue sections. Recent developments of hybrid MS instruments allow combination of different types of data acquisition by various mass analyzers into a single MSI analysis, which reduces experimental time and sample consumptions. Here, using the well-characterized crustacean nervous system as a test-bed, we explore the utility of high resolution and accurate mass (HRAM) MALDI Orbitrap platform for enhanced in situ characterization of the neuropeptidome with improved chemical information. Specifically, we report on a multiplex-MSI method, which combines HRAM MSI with data dependent acquisition (DDA) tandem MS analysis in a single experiment. This method enables simultaneous mapping of neuropeptide distribution, sequence validation, and novel neuropeptide discovery in crustacean neuronal tissues. To enhance the dynamic range and efficiency of in situ DDA, we introduced a novel approach of fractionating full m/z range into several sub-mass ranges and embedding the setup using the multiplex-DDA-MSI scan events to generate pseudo fractionation before MS/MS scans. The division of entire m/z into multiple segments of m/z sub-ranges for MS interrogation greatly decreased the complexity of molecular species from tissue samples and the heterogeneity of the distribution and variation of intensities of m/z peaks. By carefully optimizing the experimental conditions such as the dynamic exclusion, the multiplex-DDA-MSI approach demonstrates better performance with broader precursor coverage, less biased MS/MS scans towards high abundance molecules, and improved quality of tandem mass spectra for low intensity molecular species. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Chuanzi OuYang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53705, USA.
| |
Collapse
|
24
|
Abstract
MALDI MS imaging (MALDI-MSI) offers a capability to not only evaluate the distribution, localization and metabolism of drugs within tissues but also allow correlative tissue measurement of the effect of the drug on biomolecules in the targeted pathway. Particularly for MALDI-MSI, lipid molecules are readily detectable within tissues. Case study examples are provided for two different drugs targeting the sphingosine-1-phosphate/ceramide nexus in tumor xenograft tissues. A workflow combining high-resolution MALDI-MSI with on-tissue confirmation of targeted compounds using a structural library and on-tissue enzymatic digestion strategy is described. Representative images of drug metabolite distribution that correlate to an increase or decrease in sphingosine-1-phosphate or ceramide species are provided.
Collapse
|
25
|
Nilsson A, Goodwin RJA, Shariatgorji M, Vallianatou T, Webborn PJH, Andrén PE. Mass Spectrometry Imaging in Drug Development. Anal Chem 2015; 87:1437-55. [DOI: 10.1021/ac504734s] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anna Nilsson
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Richard J. A. Goodwin
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Mohammadreza Shariatgorji
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Theodosia Vallianatou
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Peter J. H. Webborn
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Per E. Andrén
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| |
Collapse
|
26
|
Challenges and recent advances in mass spectrometric imaging of neurotransmitters. Bioanalysis 2014; 6:525-40. [PMID: 24568355 DOI: 10.4155/bio.13.341] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometric imaging (MSI) is a powerful tool that grants the ability to investigate a broad mass range of molecules, from small molecules to large proteins, by creating detailed distribution maps of selected compounds. To date, MSI has demonstrated its versatility in the study of neurotransmitters and neuropeptides of different classes toward investigation of neurobiological functions and diseases. These studies have provided significant insight in neurobiology over the years and current technical advances are facilitating further improvements in this field. Herein, we briefly review new MSI studies of neurotransmitters, focusing specifically on the challenges and recent advances of MSI of neurotransmitters.
Collapse
|
27
|
Abstract
To fully understand the drug mechanism of action of new chemical entities, pharmacologists need to acquire confident and precise data in pharmacokinetics and in pharmacodynamics and build strong pharmacokinetic/pharmacodynamic relationships. Target engagement in evaluating new chemical entities provides the basis for treatment efficacy. Classical technologies are sometimes limited or inefficient to provide these precise data; however, label-free MS imaging technology is able to provide these molecular features, spatial distributions, quantification and metabolomics data. Important considerations for imaging biological sections are described. Various applications in pharmacology are presented across different therapeutic areas, where MS imaging answers crucial drug discovery and preclinical development needs.
Collapse
|
28
|
Grove KJ, Voziyan PA, Spraggins JM, Wang S, Paueksakon P, Harris RC, Hudson BG, Caprioli RM. Diabetic nephropathy induces alterations in the glomerular and tubule lipid profiles. J Lipid Res 2014; 55:1375-85. [PMID: 24864273 DOI: 10.1194/jlr.m049189] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/19/2022] Open
Abstract
Diabetic nephropathy (DN) is a major life-threatening complication of diabetes. Renal lesions affect glomeruli and tubules, but the pathogenesis is not completely understood. Phospholipids and glycolipids are molecules that carry out multiple cell functions in health and disease, and their role in DN pathogenesis is unknown. We employed high spatial resolution MALDI imaging MS to determine lipid changes in kidneys of eNOS(-/-) db/db mice, a robust model of DN. Phospholipid and glycolipid structures, localization patterns, and relative tissue levels were determined in individual renal glomeruli and tubules without disturbing tissue morphology. A significant increase in the levels of specific glomerular and tubular lipid species from four different classes, i.e., gangliosides, sulfoglycosphingolipids, lysophospholipids, and phosphatidylethanolamines, was detected in diabetic kidneys compared with nondiabetic controls. Inhibition of nonenzymatic oxidative and glycoxidative pathways attenuated the increase in lipid levels and ameliorated renal pathology, even though blood glucose levels remained unchanged. Our data demonstrate that the levels of specific phospho- and glycolipids in glomeruli and/or tubules are associated with diabetic renal pathology. We suggest that hyperglycemia-induced DN pathogenic mechanisms require intermediate oxidative steps that involve specific phospholipid and glycolipid species.
Collapse
Affiliation(s)
- Kerri J Grove
- Departments of Chemistry, Vanderbilt University Medical Center, Nashville, TN 37232 Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232 Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Paul A Voziyan
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232 Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232 Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232 Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Suwan Wang
- Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232 Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Paisit Paueksakon
- Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Raymond C Harris
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232 Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232 Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Billy G Hudson
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232 Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232 Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Richard M Caprioli
- Departments of Chemistry, Vanderbilt University Medical Center, Nashville, TN 37232 Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232 Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232
| |
Collapse
|
29
|
Ye H, Mandal R, Catherman A, Thomas PM, Kelleher NL, Ikonomidou C, Li L. Top-down proteomics with mass spectrometry imaging: a pilot study towards discovery of biomarkers for neurodevelopmental disorders. PLoS One 2014; 9:e92831. [PMID: 24710523 PMCID: PMC3978070 DOI: 10.1371/journal.pone.0092831] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 02/27/2014] [Indexed: 11/19/2022] Open
Abstract
In the developing mammalian brain, inhibition of NMDA receptor can induce widespread neuroapoptosis, inhibit neurogenesis and cause impairment of learning and memory. Although some mechanistic insights into adverse neurological actions of these NMDA receptor antagonists exist, our understanding of the full spectrum of developmental events affected by early exposure to these chemical agents in the brain is still limited. Here we attempt to gain insights into the impact of pharmacologically induced excitatory/inhibitory imbalance in infancy on the brain proteome using mass spectrometric imaging (MSI). Our goal was to study changes in protein expression in postnatal day 10 (P10) rat brains following neonatal exposure to the NMDA receptor antagonist dizocilpine (MK801). Analysis of rat brains exposed to vehicle or MK801 and comparison of their MALDI MS images revealed differential relative abundances of several proteins. We then identified these markers such as ubiquitin, purkinje cell protein 4 (PEP-19), cytochrome c oxidase subunits and calmodulin, by a combination of reversed-phase (RP) HPLC fractionation and top-down tandem MS platform. More in-depth large scale study along with validation experiments will be carried out in the future. Overall, our findings indicate that a brief neonatal exposure to a compound that alters excitatory/inhibitory balance in the brain has a long term effect on protein expression patterns during subsequent development, highlighting the utility of MALDI-MSI as a discovery tool for potential biomarkers.
Collapse
Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, PR China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, PR China
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Rakesh Mandal
- Department of Neurology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Adam Catherman
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Paul M. Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Chrysanthy Ikonomidou
- Department of Neurology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail: (CI); (LL)
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail: (CI); (LL)
| |
Collapse
|
30
|
Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
Collapse
Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | |
Collapse
|
31
|
Wong SCC, Chan CML, Ma BBY, Lam MYY, Choi GCG, Au TCC, Chan ASK, Chan ATC. Advanced proteomic technologies for cancer biomarker discovery. Expert Rev Proteomics 2014; 6:123-34. [DOI: 10.1586/epr.09.1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
32
|
Karlsson O, Bergquist J, Andersson M. Quality measures of imaging mass spectrometry aids in revealing long-term striatal protein changes induced by neonatal exposure to the cyanobacterial toxin β-N-methylamino-L-alanine (BMAA). Mol Cell Proteomics 2013; 13:93-104. [PMID: 24126143 PMCID: PMC3879633 DOI: 10.1074/mcp.m113.031435] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many pathological processes are not directly correlated to dramatic alterations in protein levels. The changes in local concentrations of important proteins in a subset of cells or at specific loci are likely to play a significant role in disease etiologies, but the precise location might be unknown, or the concentration might be too small to be adequately sampled for traditional proteomic techniques. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a unique analytical method that combines analysis of multiple molecular species and of their distribution in a single platform. As reproducibility is essential for successful biomarker discovery, it is important to systematically assess data quality in biologically relevant MALDI IMS experiments. In the present study, we applied four simple tools to study the reproducibility for individual sections, within-group variation, and between-group variation of data acquired from brain sections of 21 animals divided into three treatment groups. We also characterized protein changes in distinct regions of the striatum from six-month-old rats treated neonatally (postnatal days 9–10) with the cyanobacterial toxin β-N-methylamino-l-alanine (BMAA), which has been implicated in neurodegenerative diseases. The results showed that optimized experimental settings can yield high-quality MALDI IMS data with relatively low variation (14% to 15% coefficient of variance) that allow the characterization of subtle changes in protein expression in various subregions of the brain. This was further exemplified by the dose-dependent reduction of myelin basic protein in the caudate putamen and the nucleus accumbens of adult rats neonatally treated with BMAA (150 and 460 mg/kg). The reduction in myelin basic protein was confirmed through immunohistochemistry and indicates that developmental exposure to BMAA may induce structural effects on axonal growth and/or directly on the proliferation of oligodendrocytes and myelination, which might be important for the previously shown BMAA-induced long-term cognitive impairments.
Collapse
Affiliation(s)
- Oskar Karlsson
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
| | | | | |
Collapse
|
33
|
Norris JL, Caprioli RM. Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research. Chem Rev 2013; 113:2309-42. [PMID: 23394164 PMCID: PMC3624074 DOI: 10.1021/cr3004295] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeremy L. Norris
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
| | - Richard M. Caprioli
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
| |
Collapse
|
34
|
Lalowski M, Magni F, Mainini V, Monogioudi E, Gotsopoulos A, Soliymani R, Chinello C, Baumann M. Imaging mass spectrometry: a new tool for kidney disease investigations. Nephrol Dial Transplant 2013; 28:1648-56. [PMID: 23553250 DOI: 10.1093/ndt/gft008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Matrix-assisted laser desorption ionization (MALDI)-profiling and imaging mass spectrometry are promising technologies for measuring hundreds of different molecules directly on tissues. For instance, small molecules, drugs and their metabolites, endogenous lipids, carbohydrates and complex peptides/proteins can be measured at the same time without significant disruption of sample integrity. In this review, the potential of MALDI-profiling/imaging technologies in disease proteomics, drug action and studies of cellular processes in the context of kidney tissue is described. Spatial and sequence information obtained in tissue MALDI-profiling/imaging studies can be correlated with other mass spectrometry-based techniques, auxiliary imaging technologies and routine (immuno) histochemical staining.
Collapse
Affiliation(s)
- Maciej Lalowski
- Meilahti Clinical Proteomics Core Facility, Biochemistry and Developmental Biology, Institute of Biomedicine, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Hanrieder J, Ekegren T, Andersson M, Bergquist J. MALDI imaging of post-mortem human spinal cord in amyotrophic lateral sclerosis. J Neurochem 2013; 124:695-707. [PMID: 22994484 DOI: 10.1111/jnc.12019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 07/02/2012] [Accepted: 08/28/2012] [Indexed: 12/14/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating, rapidly progressing disease of the central nervous system that is characterized by motor neuron degeneration in the brainstem and the spinal cord. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry is an emerging powerful technique that allows for spatially resolved, comprehensive, and specific characterization of molecular species in situ. In this study, we report for the first time the MALDI imaging-based spatial protein profiling and relative quantification of post-mortem human spinal cord samples obtained from ALS patients and controls. In normal spinal cord, protein distribution patterns were well in line with histological features. For example, thymosin beta 4, ubiquitin, histone proteins, acyl-CoA-binding protein, and macrophage inhibitory factor were predominantly localized to the gray matter. Furthermore, unsupervised statistics revealed a significant reduction of two protein species in ALS gray matter. One of these proteins (m/z 8451) corresponds to an endogenous truncated form of ubiquitin (Ubc 1-76), with both C-terminal glycine residues removed (Ubc-T/Ubc 1-74). This region-specific ubiquitin processing suggests a disease-related change in protease activity. These results highlight the importance of MALDI mass spectrometry as a versatile approach to elucidate molecular mechanisms of neurodegenerative diseases.
Collapse
Affiliation(s)
- Jörg Hanrieder
- Department of Chemical and Biological Engineering, Analytical Chemistry, Chalmers University of Technology, Gothenburg, Sweden.
| | | | | | | |
Collapse
|
36
|
Abstract
MALDI (Matrix-Assisted Laser Desorption/Ionization) Imaging mass spectrometry is a powerful new method for analyzing the spatial distribution of molecules in tissues. Several different classes of cellular constituents such as proteins, peptides, lipids, and small molecules can be analyzed in situ while maintaining the morphological integrity of the tissue. This allows a correlation of the morphology with the previously acquired molecular patterns. By this, specific molecules can be clearly assigned to their cellular origin. Here, we will present a protocol for the analysis of proteins in tissues which are either native or alcohol-fixed and paraffin-embedded.
Collapse
Affiliation(s)
- Stephan Meding
- Institute of Pathology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
| | | |
Collapse
|
37
|
|
38
|
|
39
|
Imaging and Identification of Phospholipids in Mouse Liver Tissue by Matrix Assisted Laser Desorption Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Imaging. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.3724/sp.j.1096.2011.00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
40
|
Grüner BM, Hahne H, Mazur PK, Trajkovic-Arsic M, Maier S, Esposito I, Kalideris E, Michalski CW, Kleeff J, Rauser S, Schmid RM, Küster B, Walch A, Siveke JT. MALDI imaging mass spectrometry for in situ proteomic analysis of preneoplastic lesions in pancreatic cancer. PLoS One 2012; 7:e39424. [PMID: 22761793 PMCID: PMC3383687 DOI: 10.1371/journal.pone.0039424] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 05/20/2012] [Indexed: 01/07/2023] Open
Abstract
The identification of new biomarkers for preneoplastic pancreatic lesions (PanINs, IPMNs) and early pancreatic ductal adenocarcinoma (PDAC) is crucial due to the diseases high mortality rate upon late detection. To address this task we used the novel technique of matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on genetically engineered mouse models (GEM) of pancreatic cancer. Various GEM were analyzed with MALDI IMS to investigate the peptide/protein-expression pattern of precursor lesions in comparison to normal pancreas and PDAC with cellular resolution. Statistical analysis revealed several discriminative m/z-species between normal and diseased tissue. Intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN) could be distinguished from normal pancreatic tissue and PDAC by 26 significant m/z-species. Among these m/z-species, we identified Albumin and Thymosin-beta 4 by liquid chromatography and tandem mass spectrometry (LC-MS/MS), which were further validated by immunohistochemistry, western blot, quantitative RT-PCR and ELISA in both murine and human tissue. Thymosin-beta 4 was found significantly increased in sera of mice with PanIN lesions. Upregulated PanIN expression of Albumin was accompanied by increased expression of liver-restricted genes suggesting a hepatic transdifferentiation program of preneoplastic cells. In conclusion we show that GEM of endogenous PDAC are a suitable model system for MALDI-IMS and subsequent LC-MS/MS analysis, allowing in situ analysis of small precursor lesions and identification of differentially expressed peptides and proteins.
Collapse
Affiliation(s)
- Barbara M. Grüner
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
| | - Pawel K. Mazur
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | | | - Stefan Maier
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Esposito
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Evdokia Kalideris
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | | | - Jörg Kleeff
- Department of Surgery, Technische Universität München, Munich, Germany
| | - Sandra Rauser
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Roland M. Schmid
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Axel Walch
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jens T. Siveke
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
- * E-mail:
| |
Collapse
|
41
|
Clemis EJ, Smith DS, Camenzind AG, Danell RM, Parker CE, Borchers CH. Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging. Anal Chem 2012; 84:3514-22. [PMID: 22356211 DOI: 10.1021/ac202875d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MALDI imaging allows the creation of a "molecular image" of a tissue slice. This image is reconstructed from the ion abundances in spectra obtained while rastering the laser over the tissue. These images can then be correlated with tissue histology to detect potential biomarkers of, for example, aberrant cell types. MALDI, however, is known to have problems with ion suppression, making it difficult to correlate measured ion abundance with concentration. It would be advantageous to have a method which could provide more accurate protein concentration measurements, particularly for screening applications or for precise comparisons between samples. In this paper, we report the development of a novel MALDI imaging method for the localization and accurate quantitation of proteins in tissues. This method involves optimization of in situ tryptic digestion, followed by reproducible and uniform deposition of an isotopically labeled standard peptide from a target protein onto the tissue, using an aerosol-generating device. Data is acquired by MALDI multiple reaction monitoring (MRM) mass spectrometry (MS), and accurate peptide quantitation is determined from the ratio of MRM transitions for the endogenous unlabeled proteolytic peptides to the corresponding transitions from the applied isotopically labeled standard peptides. In a parallel experiment, the quantity of the labeled peptide applied to the tissue was determined using a standard curve generated from MALDI time-of-flight (TOF) MS data. This external calibration curve was then used to determine the quantity of endogenous peptide in a given area. All standard curves generate by this method had coefficients of determination greater than 0.97. These proof-of-concept experiments using MALDI MRM-based imaging show the feasibility for the precise and accurate quantitation of tissue protein concentrations over 2 orders of magnitude, while maintaining the spatial localization information for the proteins.
Collapse
Affiliation(s)
- Elizabeth J Clemis
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Two frontline MS technologies, which have recently gained much attention, are discussed within the scope of this review. Besides a brief summary on the contemporary state of lung cancer and chronic obstructive pulmonary disease, the principles of multiple reaction monitoring and matrix assisted laser desorption ionization (MALDI) MS imaging are presented. A comprehensive overview of quantitative mass spectrometry applications is provided, covering multiple reaction monitoring assay developments for analysis of proteins (biomarkers) and low-molecular-weight compounds (drugs) with a special focus on the disease areas of lung cancer and chronic obstructive pulmonary disease. The MALDI-MS imaging applications are discussed similarly, providing references to studies conducted on lung tissues in order to localize drug compounds and protein biomarkers.
Collapse
|
43
|
|
44
|
Calligaris D, Villard C, Lafitte D. Advances in top-down proteomics for disease biomarker discovery. J Proteomics 2011; 74:920-34. [DOI: 10.1016/j.jprot.2011.03.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/01/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
|
45
|
Li S, Liu X, Wei L, Wang H, Zhang J, Wei H, Qian X, Jiang Y, He F. Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy. SCIENCE CHINA-LIFE SCIENCES 2011; 54:393-402. [PMID: 21574042 PMCID: PMC7088802 DOI: 10.1007/s11427-011-4165-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 02/22/2011] [Indexed: 02/08/2023]
Abstract
A non-invasive diagnostic approach is crucial for the evaluation of severity of liver disease, treatment decisions, and assessing drug efficacy. This study evaluated plasma proteomic profiling via an N-terminal isotope tagging strategy coupled with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry measurement to detect liver fibrosis staging. Pooled plasma from different liver fibrosis stages, which were assessed in advance by the current gold-standard of liver biopsy, was quantitatively analyzed. A total of 72 plasma proteins were found to be dysregulated during the fibrogenesis process, and this finding constituted a valuable candidate plasma biomarker bank for follow-up analysis. Validation results of fibronectin by Western blotting reconfirmed the mass-based data. Ingenuity Pathways Analysis showed four types of metabolic networks for the functional effect of liver fibrosis disease in chronic hepatitis B patients. Consequently, quantitative proteomics via the N-terminal acetyl isotope labeling technique provides an effective and useful tool for screening plasma candidate biomarkers for liver fibrosis. We quantitatively monitored the fibrogenesis process in CHB patients. We discovered many new valuable candidate biomarkers for the diagnosis of liver fibrosis and also partly identified the mechanism involved in liver fibrosis disease. These results provide a clearer understanding of liver fibrosis pathophysiology and will also hopefully lead to improvement of clinical diagnosis and treatment.
Collapse
Affiliation(s)
- ShuLong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Rauser S, Deininger SO, Suckau D, Höfler H, Walch A. Approaching MALDI molecular imaging for clinical proteomic research: current state and fields of application. Expert Rev Proteomics 2011; 7:927-41. [PMID: 21142893 DOI: 10.1586/epr.10.83] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MALDI imaging mass spectrometry ('MALDI imaging') is an increasingly recognized technique for biomarker research. After years of method development in the scientific community, the technique is now increasingly applied in clinical research. In this article, we discuss the use of MALDI imaging in clinical proteomics and put it in context with classical proteomics techniques. We also highlight a number of upcoming challenges for personalized medicine, development of targeted therapies and diagnostic molecular pathology where MALDI imaging could help.
Collapse
Affiliation(s)
- Sandra Rauser
- Institute of Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg, Germany
| | | | | | | | | |
Collapse
|
47
|
LIU H, CHEN GQ, WANG YY, LI ZL. Imaging and Identification of Phospholipids in Mouse Liver Tissue by Matrix-Assisted Laser Desorption Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1016/s1872-2040(10)60409-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Reidel B, Thompson JW, Farsiu S, Moseley MA, Skiba NP, Arshavsky VY. Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. Mol Cell Proteomics 2010; 10:M110.002469. [PMID: 21173383 DOI: 10.1074/mcp.m110.002469] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The retina is a highly ordered tissue whose outermost layers are formed by subcellular compartments of photoreceptors generating light-evoked electrical responses. We studied protein distributions among individual photoreceptor compartments by separating the entire photoreceptor layer of a flat-mounted frozen retina into a series of thin tangential cryosections and analyzing protein compositions of each section by label-free quantitative mass spectrometry. Based on 5038 confidently identified peptides assigned to 896 protein database entries, we generated a quantitative proteomic database (a "map") correlating the distribution profiles of identified proteins with the profiles of marker proteins representing individual compartments of photoreceptors and adjacent cells. We evaluated the applicability of several common peptide-to-protein quantification algorithms in the context of our database and found that the highest reliability was obtained by summing the intensities of all peptides representing a given protein, using at least the 5-6 most intense peptides when applicable. We used this proteome map to investigate the distribution of glycolytic enzymes, critical in fulfilling the extremely high metabolic demands of photoreceptor cells, and obtained two major findings. First, unlike the majority of neurons rich in hexokinase I, but similar to other highly metabolically active cells, photoreceptors express hexokinase II. Hexokinase II has a very high catalytic activity when associated with mitochondria, and indeed we found it colocalized with mitochondria in photoreceptors. Second, photoreceptors contain very little triosephosphate isomerase, an enzyme converting dihydroxyacetone phosphate into glyceraldehyde-3-phosphate. This may serve as a functional adaptation because dihydroxyacetone phosphate is a major precursor in phospholipid biosynthesis, a process particularly active in photoreceptors because of the constant renewal of their light-sensitive membrane disc stacks. Overall, our approach for proteomic profiling of very small tissue amounts at a resolution of a few microns, combining cryosectioning and liquid chromatography-tandem MS, can be applied for quantitative investigation of proteomes where spatial resolution is paramount.
Collapse
Affiliation(s)
- Boris Reidel
- Albert Eye Research Institute, 2310 Erwin Road, Durham NC 27710, USA
| | | | | | | | | | | |
Collapse
|
49
|
Matrix-assisted laser desorption/ionization imaging mass spectrometry. Int J Mol Sci 2010; 11:5040-55. [PMID: 21614190 PMCID: PMC3100838 DOI: 10.3390/ijms11125040] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 11/25/2010] [Accepted: 11/27/2010] [Indexed: 12/24/2022] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-mass spectrometric technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation, or labeling of biological samples. MALDI-IMS has revealed the characteristic distribution of several biomolecules, including proteins, peptides, amino acids, lipids, carbohydrates, and nucleotides, in various tissues. The versatility of MALDI-IMS has opened a new frontier in several fields such as medicine, agriculture, biology, pharmacology, and pathology. MALDI-IMS has a great potential for discovery of unknown biomarkers. In this review, we describe the methodology and applications of MALDI-IMS for biological samples.
Collapse
|
50
|
Molecular mass spectrometry imaging in biomedical and life science research. Histochem Cell Biol 2010; 134:423-43. [DOI: 10.1007/s00418-010-0753-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
|