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Li C, Cheng K, Zhao Q, Jin L, Wang X, Liufu T, Zhao X, Li X, Wang X, Lyu J, Huang D, Li P, Chen XW, Wang Z, Hu X, Quan L, Chen Z. Diazo-carboxyl Click Derivatization Enables Sensitive Analysis of Carboxylic Acid Metabolites in Biosamples. Anal Chem 2023; 95:16976-16986. [PMID: 37943785 DOI: 10.1021/acs.analchem.3c03277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Carboxylic acids are central metabolites in bioenergetics, signal transduction, and post-translation protein regulation. However, the quantitative analysis of carboxylic acids as an indispensable part of metabolomics is prohibitively challenging, particularly in trace amounts of biosamples. Here we report a diazo-carboxyl/hydroxylamine-ketone double click derivatization method for the sensitive analysis of hydrophilic, low-molecular-weight carboxylic acids. In general, our method renders a 5- to 2000-fold higher response in mass spectrometry along with improved chromatographic separation. With this method, we presented the near-single-cell analysis of carboxylic acid metabolites in 10 mouse egg cells before and after fertilization. Malate, fumarate, and β-hydroxybutyrate were found to decrease after fertilization. We also monitored the isotope labeling kinetics of carboxylic acids inside adherent cells cultured in 96-well plates during drug treatment. Finally, we applied this method to plasma or serum samples (5 μL) collected from mice and humans under pathological and physiological conditions. The double click derivatization method paves a way toward single-cell metabolomics and bedside diagnostics.
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Affiliation(s)
- Cong Li
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kunlun Cheng
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Qijin Zhao
- 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
| | - Li Jin
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xuelian Wang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Tongling Liufu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Xutong Zhao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Xiaochuan Li
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiao Wang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Jia Lyu
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Dong Huang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Pingping 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
| | - Xiao-Wei Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing 100034, China
| | - Xinli Hu
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Li Quan
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Beijing 100871, China
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2
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Zhang J, Jiang X, Yang Y, Yang L, Lu B, Ji Y, Guo L, Zhang F, Xue J, Zhi X. Peptidome analysis reveals critical roles for peptides in a rat model of intestinal ischemia/reperfusion injury. Aging (Albany NY) 2023; 15:12852-12872. [PMID: 37955663 DOI: 10.18632/aging.205200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/15/2023] [Indexed: 11/14/2023]
Abstract
Intestinal ischemia/reperfusion injury (IIRI) has the potential to be life threatening and is associated with significant morbidity and serious damage to distant sites in the body on account of disruption of the intestinal mucosal barrier. In the present study, we have explored this line of research by comparing and identifying peptides that originated from the intestinal segments of IIRI model rats by using liquid chromatography-mass spectrometry (LC-MS). We also analyzed the basic characteristics, cleavage patterns, and functional domains of differentially expressed peptides (DEPs) between the IIRI model rats and control (sham-operated) rats and identified bioactive peptides that are potentially associated with ischemia reperfusion injury. We also performed bioinformatics analyses in order to identify the biological roles of the DEPs based on their precursor proteins. Enrichment analysis demonstrated the role of several DEPs in impairment of the intestinal mucosal barrier caused by IIRI. Based on the results of comprehensive ingenuity pathway analysis, we identified the DEPs that were significantly correlated with IIRI. We identified a candidate precursor protein (Actg2) and seven of its peptides, and we found that Actg2-6 had a more significant difference in its expression, a longer half-life, and better lipophilicity, hydrophobicity, and stability than the other candidate Actg2 peptides examined. Furthermore, we observed that Actg2-6 might play critical roles in the protection of the intestinal mucosal barrier during IIRI. In summary, our study provides a better understanding of the peptidomics profile of IIRI, and the results indicate that Actg2-6 could be a useful target in the treatment of IIRI.
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Affiliation(s)
- Jiaxuan Zhang
- Department of Trauma Center, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xiaoqi Jiang
- Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yang Yang
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Lei Yang
- Department of Clinical Biobank and Institute of Oncology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Bing Lu
- Department of Clinical Biobank and Institute of Oncology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yannan Ji
- Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Leijun Guo
- Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Fan Zhang
- Department of Pediatrics, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong 226001, China
| | - Jianhua Xue
- Department of Trauma Center, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xiaofei Zhi
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
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3
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Bao Q, Wang Z, Cheng S, Zhang J, Liu Q, Zhang Y, Cheng D, Guo X, Wang X, Han B, Sun P. Peptidomic Analysis Reveals that Novel Peptide LDP2 Protects Against Hepatic Ischemia/Reperfusion Injury. J Clin Transl Hepatol 2023; 11:405-415. [PMID: 36643038 PMCID: PMC9817043 DOI: 10.14218/jcth.2022.00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/12/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND AND AIMS Hepatic ischemia/reperfusion (I/R) injury has become an inevitable issue during liver transplantation, with no effective treatments available. However, peptide drugs provide promising regimens for the treatment of this injury and peptidomics has gradually attracted increasing attention. This study was designed to analyze the spectrum of peptides in injured livers and explore the potential beneficial peptides involved in I/R injury. METHODS C57BL/6 mice were used to establish a liver I/R injury animal model. Changes in peptide profiles in I/R-injured livers were analyzed by mass spectrometry, and the functions of the identified peptides were predicted by bioinformatics. AML12 cells were used to simulate hepatic I/R injury in vitro. After treatment with candidate liver-derived peptides (LDPs) 1-10, the cells were collected at various reperfusion times for further study. RESULTS Our preliminary study demonstrated that 6 h of reperfusion caused the most liver I/R injury. Peptidomic results suggested that 10 down-regulated peptides were most likely to alleviate I/R injury by supporting mitochondrial function. Most importantly, a novel peptide, LDP2, was identified that alleviated I/R injury of AML12 cells. It increased cell viability and reduced the expression of inflammation- and apoptosis-related proteins. In addition, LDP2 inhibited the expression of proteins related to autophagy. CONCLUSIONS Investigation of changes in the profiles of peptides in I/R-injured livers led to identification of a novel peptide, LDP2 with potential function in liver protection by inhibiting inflammation, apoptosis, and autophagy.
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Affiliation(s)
- Qun Bao
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengxin Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Sheng Cheng
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Zhang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuli Liu
- Department of Anesthesiology and SICU, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunpeng Zhang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daqing Cheng
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xirong Guo
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingyun Wang
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Han
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Correspondence to: Peng Sun, Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China. ORCID: https://orcid.org/0000-0003-4031-6889. Tel: +86-18121225835, Fax: +86-21- 52039999, E-mail: ; Bo Han, Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 720 XianXia Road, Shanghai 200336, China. ORCID: https://orcid.org/0000-0002-9882-7166. Tel: +86-18017337189, Fax: +86-21- 52039999, E-mail:
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Correspondence to: Peng Sun, Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China. ORCID: https://orcid.org/0000-0003-4031-6889. Tel: +86-18121225835, Fax: +86-21- 52039999, E-mail: ; Bo Han, Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal Oncology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 720 XianXia Road, Shanghai 200336, China. ORCID: https://orcid.org/0000-0002-9882-7166. Tel: +86-18017337189, Fax: +86-21- 52039999, E-mail:
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Vu NQ, Yen HC, Fields L, Cao W, Li L. HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search. J Proteome Res 2023; 22:420-431. [PMID: 36696582 PMCID: PMC10160011 DOI: 10.1021/acs.jproteome.2c00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases are typically experimentally built and comprised of short sequences with high sequence similarity to each other, we developed a novel database searching tool, HyPep, which utilizes sequence homology searching for peptide identification. HyPep aligns de novo sequenced peptides, generated through PEAKS software, with neuropeptide database sequences and identifies neuropeptides based on the alignment score. HyPep performance was optimized using LC-MS/MS measurements of peptide extracts from various Callinectes sapidus neuronal tissue types and compared with a commercial database searching software, PEAKS DB. HyPep identified more neuropeptides from each tissue type than PEAKS DB at 1% false discovery rate, and the false match rate from both programs was 2%. In addition to identification, this report describes how HyPep can aid in the discovery of novel neuropeptides.
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Affiliation(s)
- Nhu Q Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Hsu-Ching Yen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Weifeng Cao
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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Zhang GN, Xu YJ, Jin L. Peptidomics analysis of plasma in patients with ankylosing spondylitis. Front Immunol 2023; 14:1104351. [PMID: 36798127 PMCID: PMC9927206 DOI: 10.3389/fimmu.2023.1104351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Background This study aimed to explore the differential expression of peptides associated with ankylosing spondylitis (AS) patients, enabling identification of potential functional peptides to provide the basis for the novel intervention targets for AS. Material and Methods 3 AS patients and 3 healthy volunteers were enrolled in this study. The expression profiles for peptides present in the plasma of AS patients and the healthy individual were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The physicochemical properties and biological functions of identified peptides were further analyzed by bioinformatics. The results of peptide identification were verified by cell viability analysis, using CCK8 and Edu staining assay, and the differential peptides relevant to the disease were screened. Results 52 differential peptides were successfully identified using mass spectrometry. 44 peptides were up-regulated, while eight were down-regulated. FGA-peptide (sequences: DSGEGDFLAEGGGVRGPR), C4A-peptide (sequences: NGFKSHAL), and TUBB-peptide (sequences: ISEQFTAMFR) were screened out that could significantly promote the proliferation of fibroblasts in AS patients. Bioinformatics analysis showed these differentially expressed peptides might be associated with "MHC class I protein binding" and "pathogenic Escherichia coli infection" pathways, which might further affect the progression of AS. Conclusion This pilot study shows 3 differentially expressed peptides may have the potential function for the occurrence and development of AS, may provide novel insights into the underlying molecular mechanisms of AS based on peptide omics.
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Affiliation(s)
- Guo-Ning Zhang
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Jia Xu
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Jin
- Department of Rheumatology and Immunology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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7
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Xu Z, Ding J, Zhang L, Feng X, Zhou J, Shen X, Lu H, Qian L, Li X. Peptidomics analysis revealed that a novel peptide VMP‑19 protects against Ang II‑induced injury in human umbilical vein endothelial cells. Mol Med Rep 2021; 23:298. [PMID: 33649860 PMCID: PMC7930926 DOI: 10.3892/mmr.2021.11937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/02/2021] [Indexed: 11/06/2022] Open
Abstract
Vascular endothelial dysfunction is a vital pathological change in hypertension, which is mainly caused by apoptosis and oxidative stress injury of vascular endothelial cells. Peptidomics is a method for the direct analysis of small bioactive peptides in various biological samples using liquid chromatography‑mass spectrometry (MS)/MS. Given the advantages of the low molecular weight, optimum targeting and easy access to cells, peptides have attracted extensive attention in the field of drug research. However, to the best of our knowledge, little is currently known regarding the role of peptides in vascular endothelial injury. In order to investigate the peptides involved in vascular endothelial protection, MS was used to analyze the peptide profiles in the supernatant of human umbilical vein endothelial cells (HUVECs) stimulated by Ang II. The results revealed that 211 peptides were identified, of which six were upregulated and 13 were downregulated when compared with the control group. Subsequently, the present study analyzed the physical and chemical properties and biological functions of identified peptides by bioinformatics, and successfully screened a peptide (LLQDSVDFSLADAINTEFK) named VMP‑19 that could alleviate the apoptosis and oxidative stress injury of HUVECs induced by Ang II. In conclusion, to the best of our knowledge, the present study was the first to use peptidomics to analyze the peptide profiles of supernatant secreted by HUVECs, and revealed that the novel peptide VMP‑19 could protect HUVECs from apoptosis and oxidative stress injury. The results of the present study could provide novel insights into treatment strategies for hypertension.
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Affiliation(s)
- Zhongqing Xu
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jingjing Ding
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Li Zhang
- Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Xianzhen Feng
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Jun Zhou
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Xiaoyi Shen
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Hong Lu
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Lingmei Qian
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China
| | - Xun Li
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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8
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Peptidomics Analysis Reveals Peptide PDCryab1 Inhibits Doxorubicin-Induced Cardiotoxicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7182428. [PMID: 33110475 PMCID: PMC7582065 DOI: 10.1155/2020/7182428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 12/14/2022]
Abstract
Doxorubicin (DOX) is limited due to dose-dependent cardiotoxicity. Peptidomics is an emerging field of proteomics that has attracted much attention because it can be used to study the composition and content of endogenous peptides in various organisms. Endogenous peptides participate in various biological processes and are important sources of candidates for drug development. To explore peptide changes related to DOX-induced cardiotoxicity and to find peptides with cardioprotective function, we compared the expression profiles of peptides in the hearts of DOX-treated and control mice by mass spectrometry. The results showed that 236 differential peptides were identified upon DOX treatment, of which 22 were upregulated and 214 were downregulated. Next, we predicted that 31 peptides may have cardioprotective function by conducting bioinformatics analysis on the domains of each precursor protein, the predicted score of peptide biological activity, and the correlation of each peptide with cardiac events. Finally, we verified that a peptide (SPFYLRPPSF) from Cryab can inhibit cardiomyocyte apoptosis, reduce the production of reactive oxygen species, improve cardiac function, and ameliorate myocardial fibrosis in vitro and vivo. In conclusion, our results showed that the expression profiles of peptides in cardiac tissue change significantly upon DOX treatment and that these differentially expressed peptides have potential cardioprotective functions. Our study suggests a new direction for the treatment of DOX-induced cardiotoxicity.
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9
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Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR. Linked optical and gene expression profiling of single cells at high-throughput. Genome Biol 2020; 21:49. [PMID: 32093753 PMCID: PMC7041248 DOI: 10.1186/s13059-020-01958-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through changes in gene expression. Linking sequencing with optical analysis has provided insight into the molecular basis of cellular function, but current approaches have limited throughput. Here, we present a high-throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements on thousands of cells in a single experiment. We use the platform to characterize DNA and RNA changes through the cell cycle and correlate antibody fluorescence with gene expression. The platform's ability to isolate rare cell subsets and perform multiple measurements, including fluorescence and sequencing-based analysis, holds potential for scalable multi-modal single-cell analysis.
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Affiliation(s)
- Jesse Q Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Christian A Siltanen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angew Chem Int Ed Engl 2019; 58:9348-9364. [PMID: 30500998 PMCID: PMC6542728 DOI: 10.1002/anie.201811951] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 01/14/2023]
Abstract
Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non-targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non-targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high-throughput single-cell profiling data. Single-cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry, 1420 Circle Drive, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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11
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Erforschung der fundamentalen Strukturen des Lebens: Nicht zielgerichtete chemische Analyse von Einzelzellen und subzellulären Strukturen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Thanh D. Do
- Department of ChemistryUniversity of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
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12
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Abstract
Metabolomics, the characterization of metabolites and their changes within biological systems, has seen great technological and methodological progress over the past decade. Most metabolomic experiments involve the characterization of the small-molecule content of fluids or tissue homogenates. While these microliter and larger volume metabolomic measurements can characterize hundreds to thousands of compounds, the coverage of molecular content decreases as sample sizes are reduced to the nanoliter and even to the picoliter volume range. Recent progress has enabled the ability to characterize the major molecules found within specific individual cells. Especially within the brain, a myriad of cell types are colocalized, and oftentimes only a subset of these cells undergo changes in both healthy and pathological states. Here we highlight recent progress in mass spectrometry-based approaches used for single cell metabolomics, emphasizing their application to neuroscience research. Single cell studies can be directed to measuring differences between members of populations of similar cells (e.g., oligodendrocytes), as well as characterizing differences between cell types (e.g., neurons and astrocytes), and are especially useful for measuring changes occurring during different behavior states, exposure to diets and drugs, neuronal activity, and disease. When combined with other omics approaches such as transcriptomics, and with morphological and physiological measurements, single cell metabolomics aids fundamental neurochemical studies, has great potential in pharmaceutical development, and should improve the diagnosis and treatment of brain diseases.
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Affiliation(s)
- Meng Qi
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Marina C Philip
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ning Yang
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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13
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Konop CJ, Knickelbine JJ, Sygulla MS, Wruck CD, Vestling MM, Stretton AOW. Mass Spectrometry of Single GABAergic Somatic Motorneurons Identifies a Novel Inhibitory Peptide, As-NLP-22, in the Nematode Ascaris suum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2009-2023. [PMID: 26174364 PMCID: PMC4654748 DOI: 10.1007/s13361-015-1177-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 06/04/2023]
Abstract
Neuromodulators have become an increasingly important component of functional circuits, dramatically changing the properties of both neurons and synapses to affect behavior. To explore the role of neuropeptides in Ascaris suum behavior, we devised an improved method for cleanly dissecting single motorneuronal cell bodies from the many other cell processes and hypodermal tissue in the ventral nerve cord. We determined their peptide content using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). The reduced complexity of the peptide mixture greatly aided the detection of peptides; peptide levels were sufficient to permit sequencing by tandem MS from single cells. Inhibitory motorneurons, known to be GABAergic, contain a novel neuropeptide, As-NLP-22 (SLASGRWGLRPamide). From this sequence and information from the A. suum expressed sequence tag (EST) database, we cloned the transcript (As-nlp-22) and synthesized a riboprobe for in situ hybridization, which labeled the inhibitory motorneurons; this validates the integrity of the dissection method, showing that the peptides detected originate from the cells themselves and not from adhering processes from other cells (e.g., synaptic terminals). Synthetic As-NLP-22 has potent inhibitory activity on acetylcholine-induced muscle contraction as well as on basal muscle tone. Both of these effects are dose-dependent: the inhibitory effect on ACh contraction has an IC50 of 8.3 × 10(-9) M. When injected into whole worms, As-NLP-22 produces a dose-dependent inhibition of locomotory movements and, at higher levels, complete paralysis. These experiments demonstrate the utility of MALDI TOF/TOF MS in identifying novel neuromodulators at the single-cell level. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher J Konop
- Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jennifer J Knickelbine
- Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Parasitology and Vector Biology Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Molly S Sygulla
- Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Colin D Wruck
- Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Martha M Vestling
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Antony O W Stretton
- Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Parasitology and Vector Biology Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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14
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Ong TH, Kissick DJ, Jansson ET, Comi TJ, Romanova EV, Rubakhin SS, Sweedler JV. Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Anal Chem 2015; 87:7036-42. [PMID: 26076060 PMCID: PMC4511976 DOI: 10.1021/acs.analchem.5b01557] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cell-to-cell variability and functional heterogeneity are integral features of multicellular organisms. Chemical classification of cells into cell type is important for understanding cellular specialization as well as organismal function and organization. Assays to elucidate these chemical variations are best performed with single cell samples because tissue homogenates average the biochemical composition of many different cells and oftentimes include extracellular components. Several single cell microanalysis techniques have been developed but tend to be low throughput or require preselection of molecular probes that limit the information obtained. Mass spectrometry (MS) is an untargeted, multiplexed, and sensitive analytical method that is well-suited for studying chemically complex individual cells that have low analyte content. In this work, populations of cells from the rat pituitary, the rat pancreatic islets of Langerhans, and from the Aplysia californica nervous system, are classified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) MS by their peptide content. Cells were dispersed onto a microscope slide to generate a sample where hundreds to thousands of cells were separately located. Optical imaging was used to determine the cell coordinates on the slide, and these locations were used to automate the MS measurements to targeted cells. Principal component analysis was used to classify cellular subpopulations. The method was modified to focus on the signals described by the lower principal components to explore rare cells having a unique peptide content. This approach efficiently uncovers and classifies cellular subtypes as well as discovers rare cells from large cellular populations.
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Affiliation(s)
- Ta-Hsuan Ong
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - David J Kissick
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Erik T Jansson
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Troy J Comi
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Konop CJ, Knickelbine JJ, Sygulla MS, Vestling MM, Stretton AOW. Different neuropeptides are expressed in different functional subsets of cholinergic excitatory motorneurons in the nematode Ascaris suum. ACS Chem Neurosci 2015; 6:855-70. [PMID: 25812635 DOI: 10.1021/cn5003623] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Neuropeptides are known to have dramatic effects on neurons and synapses; however, despite extensive studies of the motorneurons in the parasitic nematode Ascaris suum, their peptide content had not yet been described. We determined the peptide content of single excitatory motorneurons by mass spectrometry and tandem mass spectrometry. There are two subsets of ventral cord excitatory motorneurons, each with neuromuscular output either anterior or posterior to their cell body, mediating forward or backward locomotion, respectively. Strikingly, the two sets of neurons contain different neuropeptides, with AF9 and six novel peptides (As-NLP-21.1-6) in anterior projectors, and the six afp-1 peptides in addition to AF2 in posterior projectors. In situ hybridization confirmed the expression of these peptides, validating the integrity of the dissection technique. This work identifies new components of the functional behavioral circuit, as well as potential targets for antiparasitic drug development.
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Affiliation(s)
- Christopher J. Konop
- Department of Zoology, ‡Parasitology and Vector Biology
Training Program, §Department of Chemistry, ∥Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jennifer J. Knickelbine
- Department of Zoology, ‡Parasitology and Vector Biology
Training Program, §Department of Chemistry, ∥Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Molly S. Sygulla
- Department of Zoology, ‡Parasitology and Vector Biology
Training Program, §Department of Chemistry, ∥Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martha M. Vestling
- Department of Zoology, ‡Parasitology and Vector Biology
Training Program, §Department of Chemistry, ∥Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Antony O. W. Stretton
- Department of Zoology, ‡Parasitology and Vector Biology
Training Program, §Department of Chemistry, ∥Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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16
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Ong TH, Tillmaand EG, Makurath M, Rubakhin SS, Sweedler JV. Mass spectrometry-based characterization of endogenous peptides and metabolites in small volume samples. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:732-40. [PMID: 25617659 DOI: 10.1016/j.bbapap.2015.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/22/2014] [Accepted: 01/16/2015] [Indexed: 12/22/2022]
Abstract
Technologies to assay single cells and their extracellular microenvironments are valuable in elucidating biological function, but there are challenges. Sample volumes are low, the physicochemical parameters of the analytes vary widely, and the cellular environment is chemically complex. In addition, the inherent difficulty of isolating individual cells and handling small volume samples complicates many experimental protocols. Here we highlight a number of mass spectrometry (MS)-based measurement approaches for characterizing the chemical content of small volume analytes, with a focus on methods used to detect intracellular and extracellular metabolites and peptides from samples as small as individual cells. MS has become one of the most effective means for analyzing small biological samples due to its high sensitivity, low analyte consumption, compatibility with a wide array of sampling approaches, and ability to detect a large number of analytes with different properties without preselection. Having access to a flexible portfolio of MS-based methods allows quantitative, qualitative, untargeted, targeted, multiplexed, and spatially resolved investigations of single cells and their similarly scaled extracellular environments. Combining MS with on-line and off-line sample conditioning tools, such as microfluidic and capillary electrophoresis systems, significantly increases the analytical coverage of the sample's metabolome and peptidome, and improves individual analyte characterization/identification. Small volume assays help to reveal the causes and manifestations of biological and pathological variability, as well as the functional heterogeneity of individual cells within their microenvironments and within cellular populations. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ta-Hsuan Ong
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Emily G Tillmaand
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Monika Makurath
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Stanislav S Rubakhin
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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17
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Gemperline E, Li L. MALDI-MS-assisted molecular imaging of metabolites in legume plants. Methods Mol Biol 2015; 1203:29-40. [PMID: 25361664 DOI: 10.1007/978-1-4939-1357-2_4] [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] [Indexed: 06/04/2023]
Abstract
Mass spectrometric imaging (MSI) is a powerful analytical tool that provides spatial information of several compounds in a single experiment. This technique has been used extensively to study proteins, peptides, and lipids, and is becoming more common for studying small molecules such as endogenous metabolites. With matrix-assisted laser desorption/ionization (MALDI)-MSI, spatial distributions of multiple metabolites can be simultaneously detected within a biological tissue section. Herein, we present a method developed specifically for imaging metabolites in legume plant roots and root nodules which can be adapted for studying metabolites in other legume organs and even other biological tissue samples. We focus on essential steps such as sample preparation and matrix application, comparing several useful techniques, and present a standard workflow that can be easily modified for different tissue types and instrumentation.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison, 5232 Rennebohm Hall, 777 Highland Avenue, Madison, WI, 53705-2222, USA
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18
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Chen R, Ouyang C, Xiao M, Li L. In situ identification and mapping of neuropeptides from the stomatogastric nervous system of Cancer borealis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2437-2444. [PMID: 25303472 PMCID: PMC4216564 DOI: 10.1002/rcm.7037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/26/2014] [Accepted: 08/31/2014] [Indexed: 06/02/2023]
Abstract
RATIONALE The crustacean stomatogastric nervous system (STNS) is a classic experimental model to derive basic knowledge about neuronal functions and how they coordinate with each other to generate neural circuits. To investigate the components of the neuromodulators and how they are distributed in such a system is essential to understand the underlying mechanism. In this study, in situ mass spectrometry based techniques were employed to fulfill this goal. METHODS Offline high-performance liquid chromatography (HPLC) separation was coupled with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) to analyze the neuropeptides in the stomatogastric ganglion (STG) tissue extract from the Jonah crab Cancer borealis. Direct tissue analysis was employed to investigate the neuropeptides present in the STNS. MALDI imaging was also applied to map the localization of multiple neuropeptide families in the STG and the upstream nerve fibers. RESULTS Fifty-seven neuropeptides were detected from a single desheathed STG using direct tissue analysis, and they were from eleven different neuropeptide families, including FaRP, AST-A, AST-B, etc. Differential neuropeptide profiles from three different types of ganglia and two types of nerve fiber tissues from the STNS were documented. The direct tissue analysis was shown better for studying neuropeptides from small neural organs like the STG as compared to the large-scale HPLC/MALDI analysis. MALDI images were also acquired to study the distribution of neuropeptides in the STG. CONCLUSIONS In this study, the components and distribution of neuropeptides have been analyzed in the STNS from C. borealis using direct tissue profiling and MALDI imaging. The results show that the direct tissue analysis of desheathed neural tissues can provide higher sensitivity for neuropeptide study compared to large-scale HPLC/MALDI analysis of pooled tissues. The results are valuable for understanding the functions of neuropeptides in neural network generation.
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Affiliation(s)
- Ruibing Chen
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chuanzi Ouyang
- Department of Chemistry and Pharmacy School, University of Wisconsin at Madison, WI 53705, USA
| | - Mingming Xiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lingjun Li
- Department of Chemistry and Pharmacy School, University of Wisconsin at Madison, WI 53705, USA
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19
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Gemperline E, Li L. MALDI-mass spectrometric imaging for the investigation of metabolites in Medicago truncatula root nodules. J Vis Exp 2014. [PMID: 24637669 DOI: 10.3791/51434] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Most techniques used to study small molecules, such as pharmaceutical drugs or endogenous metabolites, employ tissue extracts which require the homogenization of the tissue of interest that could potentially cause changes in the metabolic pathways being studied(1). Mass spectrometric imaging (MSI) is a powerful analytical tool that can provide spatial information of analytes within intact slices of biological tissue samples(1-5). This technique has been used extensively to study various types of compounds including proteins, peptides, lipids, and small molecules such as endogenous metabolites. With matrix-assisted laser desorption/ionization (MALDI)-MSI, spatial distributions of multiple metabolites can be simultaneously detected. Herein, a method developed specifically for conducting untargeted metabolomics MSI experiments on legume roots and root nodules is presented which could reveal insights into the biological processes taking place. The method presented here shows a typical MSI workflow, from sample preparation to image acquisition, and focuses on the matrix application step, demonstrating several matrix application techniques that are useful for detecting small molecules. Once the MS images are generated, the analysis and identification of metabolites of interest is discussed and demonstrated. The standard workflow presented here can be easily modified for different tissue types, molecular species, and instrumentation.
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Affiliation(s)
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin- Madison; School of Pharmacy, University of Wisconsin- Madison;
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20
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Romanova EV, Aerts JT, Croushore CA, Sweedler JV. Small-volume analysis of cell-cell signaling molecules in the brain. Neuropsychopharmacology 2014; 39:50-64. [PMID: 23748227 PMCID: PMC3857641 DOI: 10.1038/npp.2013.145] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/26/2013] [Accepted: 05/06/2013] [Indexed: 12/19/2022]
Abstract
Modern science is characterized by integration and synergy between research fields. Accordingly, as technological advances allow new and more ambitious quests in scientific inquiry, numerous analytical and engineering techniques have become useful tools in biological research. The focus of this review is on cutting edge technologies that aid direct measurement of bioactive compounds in the nervous system to facilitate fundamental research, diagnostics, and drug discovery. We discuss challenges associated with measurement of cell-to-cell signaling molecules in the nervous system, and advocate for a decrease of sample volumes to the nanoliter volume regimen for improved analysis outcomes. We highlight effective approaches for the collection, separation, and detection of such small-volume samples, present strategies for targeted and discovery-oriented research, and describe the required technology advances that will empower future translational science.
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Affiliation(s)
- Elena V Romanova
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jordan T Aerts
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Callie A Croushore
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Beckman Institute for Advanced Science and Technology and the Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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21
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Unal M, Alapan Y, Jia H, Varga AG, Angelino K, Aslan M, Sayin I, Han C, Jiang Y, Zhang Z, Gurkan UA. Micro and Nano-Scale Technologies for Cell Mechanics. Nanobiomedicine (Rij) 2014; 1:5. [PMID: 30023016 PMCID: PMC6029242 DOI: 10.5772/59379] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/18/2014] [Indexed: 01/09/2023] Open
Abstract
Cell mechanics is a multidisciplinary field that bridges cell biology, fundamental mechanics, and micro and nanotechnology, which synergize to help us better understand the intricacies and the complex nature of cells in their native environment. With recent advances in nanotechnology, microfabrication methods and micro-electro-mechanical-systems (MEMS), we are now well situated to tap into the complex micro world of cells. The field that brings biology and MEMS together is known as Biological MEMS (BioMEMS). BioMEMS take advantage of systematic design and fabrication methods to create platforms that allow us to study cells like never before. These new technologies have been rapidly advancing the study of cell mechanics. This review article provides a succinct overview of cell mechanics and comprehensively surveys micro and nano-scale technologies that have been specifically developed for and are relevant to the mechanics of cells. Here we focus on micro and nano-scale technologies, and their applications in biology and medicine, including imaging, single cell analysis, cancer cell mechanics, organ-on-a-chip systems, pathogen detection, implantable devices, neuroscience and neurophysiology. We also provide a perspective on the future directions and challenges of technologies that relate to the mechanics of cells.
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Affiliation(s)
- Mustafa Unal
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, USA
| | - Yunus Alapan
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, USA
- Case Biomanufacturing and Microfabrication Laboratory, Case Western Reserve University, Cleveland, USA
| | - Hao Jia
- Department of Biology, Case Western Reserve University, Cleveland, USA
| | - Adrienn G. Varga
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, USA
| | - Keith Angelino
- Department of Civil Engineering, Case Western Reserve University, Cleveland, USA
| | - Mahmut Aslan
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, USA
- Case Biomanufacturing and Microfabrication Laboratory, Case Western Reserve University, Cleveland, USA
| | - Ismail Sayin
- Case Biomanufacturing and Microfabrication Laboratory, Case Western Reserve University, Cleveland, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, USA
| | - Chanjuan Han
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, USA
| | - Yanxia Jiang
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, USA
| | - Zhehao Zhang
- Department of Civil Engineering, Case Western Reserve University, Cleveland, USA
| | - Umut A. Gurkan
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, USA
- Case Biomanufacturing and Microfabrication Laboratory, Case Western Reserve University, Cleveland, USA
- Department of Orthopaedics, Case Western Reserve University, Cleveland, USA
- Advanced Platform Technology Center, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, USA
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22
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Passarelli MK, Ewing AG. Single-cell imaging mass spectrometry. Curr Opin Chem Biol 2013; 17:854-9. [PMID: 23948695 DOI: 10.1016/j.cbpa.2013.07.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
Abstract
Single-cell imaging mass spectrometry (IMS) is a powerful technique used to map the distributions of endogenous biomolecules with subcellular resolution. Currently, secondary ion mass spectrometry is the predominant technique for single-cell IMS, thanks to its submicron lateral resolution and surface sensitivity. However, recent methodological and technological developments aimed at improving the spatial resolution of matrix assisted laser desorption ionization (MALDI) have made this technique a potential platform of single-cell IMS. MALDI opens the field of single-cell IMS to new possibilities, including single cell proteomic imaging and atmospheric pressure analyses; however, sensitivity is a challenge. In this report, we estimate the availability of proteins and lipids in a single cell and discuss strategies employed to improve sensitivity at the single-cell level.
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23
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Nemes P, Rubakhin SS, Aerts JT, Sweedler JV. Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry. Nat Protoc 2013; 8:783-99. [PMID: 23538882 PMCID: PMC3655804 DOI: 10.1038/nprot.2013.035] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Single-cell mass spectrometry (MS) empowers metabolomic investigations by decreasing analytical dimensions to the size of individual cells and subcellular structures. We describe a protocol for investigating and quantifying metabolites in individual isolated neurons using single-cell capillary electrophoresis (CE) coupled to electrospray ionization (ESI) time-of-flight (TOF) MS. The protocol requires ∼2 h for sample preparation, neuron isolation and metabolite extraction, and 1 h for metabolic measurement. We used the approach to detect more than 300 distinct compounds in the mass range of typical metabolites in various individual neurons (25-500 μm in diameter) isolated from the sea slug (Aplysia californica) central and rat (Rattus norvegicus) peripheral nervous systems. We found that a subset of identified compounds was sufficient to reveal metabolic differences among freshly isolated neurons of different types and changes in the metabolite profiles of cultured neurons. The protocol can be applied to the characterization of the metabolome in a variety of smaller cells and/or subcellular domains.
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Affiliation(s)
- Peter Nemes
- 1] Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2]
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Gelman JS, Dasgupta S, Berezniuk I, Fricker LD. Analysis of peptides secreted from cultured mouse brain tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2408-17. [PMID: 23402728 DOI: 10.1016/j.bbapap.2013.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 01/02/2023]
Abstract
Peptides represent a major class of cell-cell signaling molecules. Most peptidomic studies have focused on peptides present in brain or other tissues. For a peptide to function in intercellular signaling, it must be secreted. The present study was undertaken to identify the major peptides secreted from mouse brain slices that were cultured in oxygenated buffer for 3-4h. Approximately 75% of the peptides identified in extracts of cultured slices matched the previously reported peptide content of heat-inactivated mouse brain tissue, whereas only 2% matched the peptide content of unheated brain tissue; the latter showed a large number of postmortem changes. As found with extracts of heat-inactivated mouse brain, the extracts of cultured brain slices represented secretory pathway peptides as well as peptides derived from intracellular proteins such as those present in the cytosol and mitochondria. A subset of the peptides detected in the extracts of the cultured slices was detected in the culture media. The vast majority of secreted peptides arose from intracellular proteins and not secretory pathway proteins. The peptide RVD-hemopressin, a CB1 cannabinoid receptor agonist, was detected in culture media, which is consistent with a role for RVD-hemopressin as a non-classical neuropeptide. Taken together with previous studies, the present results show that short-term culture of mouse brain slices is an appropriate system to study peptide secretion, especially the non-conventional pathway(s) by which peptides produced from intracellular proteins are secreted. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Julia S Gelman
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Gelman JS, Sironi J, Berezniuk I, Dasgupta S, Castro LM, Gozzo FC, Ferro ES, Fricker LD. Alterations of the intracellular peptidome in response to the proteasome inhibitor bortezomib. PLoS One 2013; 8:e53263. [PMID: 23308178 PMCID: PMC3538785 DOI: 10.1371/journal.pone.0053263] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/27/2012] [Indexed: 01/07/2023] Open
Abstract
Bortezomib is an antitumor drug that competitively inhibits proteasome beta-1 and beta-5 subunits. While the impact of bortezomib on protein stability is known, the effect of this drug on intracellular peptides has not been previously explored. A quantitative peptidomics technique was used to examine the effect of treating human embryonic kidney 293T (HEK293T) cells with 5-500 nM bortezomib for various lengths of time (30 minutes to 16 hours), and human neuroblastoma SH-SY5Y cells with 500 nM bortezomib for 1 hour. Although bortezomib treatment decreased the levels of some intracellular peptides, the majority of peptides were increased by 50-500 nM bortezomib. Peptides requiring cleavage at acidic and hydrophobic sites, which involve beta-1 and -5 proteasome subunits, were among those elevated by bortezomib. In contrast, the proteasome inhibitor epoxomicin caused a decrease in the levels of many of these peptides. Although bortezomib can induce autophagy under certain conditions, the rapid bortezomib-mediated increase in peptide levels did not correlate with the induction of autophagy. Taken together, the present data indicate that bortezomib alters the balance of intracellular peptides, which may contribute to the biological effects of this drug.
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Affiliation(s)
- Julia S. Gelman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juan Sironi
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Iryna Berezniuk
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Leandro M. Castro
- Department of Cell Biology and Development, University of São Paulo, São Paulo, Brazil
| | - Fabio C. Gozzo
- Chemistry Institute, State University of Campinas, São Paulo, Brazil
| | - Emer S. Ferro
- Department of Cell Biology and Development, University of São Paulo, São Paulo, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
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26
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Ouedraogo R, Textoris J, Daumas A, Capo C, Mege JL. Whole-cell MALDI-TOF mass spectrometry: a tool for immune cell analysis and characterization. Methods Mol Biol 2013; 1061:197-209. [PMID: 23963939 DOI: 10.1007/978-1-62703-589-7_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used in proteomics. It has been recently demonstrated that MALDI-TOF MS can be used to identify and classify numerous bacterial species or subspecies. We applied MALDI-TOF MS directly to intact mammalian cells, and we found that this method is valuable to identify human circulating cells and cells involved in the immune response including macrophages. As macrophages are characterized by a high degree of plasticity in response to their microenvironment, we stimulated human macrophages with cytokines, bacterial products, and a variety of bacteria. We found that MALDI-TOF MS discriminated unstimulated and stimulated macrophages, and also detected multifaceted activation of macrophages. We conclude that whole-cell MALDI-TOF MS is an accurate method to identify various cell types and to detect subtle modifications in cell activity.
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Affiliation(s)
- Richard Ouedraogo
- Unité de Recherche sur les Maladies Infectieuses Tropicales et Emergentes, Aix Marseille Université, Marseille, France
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Tucker KR, Li Z, Rubakhin SS, Sweedler JV. Secondary ion mass spectrometry imaging of molecular distributions in cultured neurons and their processes: comparative analysis of sample preparation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1931-8. [PMID: 22930440 PMCID: PMC3475608 DOI: 10.1007/s13361-012-0472-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 05/24/2023]
Abstract
Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200 Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied; the approaches evaluated included rinsing with water and cell stabilization with glycerol and 4 % paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast.
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Affiliation(s)
| | | | | | - Jonathan V. Sweedler
- Contact author: Jonathan Sweedler, 600 S. Mathews Ave. 63-5, Urbana IL 61801 USA, , 217 244 7359
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TARGETED MASS spectrometry Imaging: Specific Targeting Mass Spectrometry imaging technologies from history to perspective. ACTA ACUST UNITED AC 2012; 47:133-74. [DOI: 10.1016/j.proghi.2012.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2012] [Indexed: 12/28/2022]
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29
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Ketola RA, Mauriala T. Mass spectrometric tools for cell and tissue studies. Eur J Pharm Sci 2012; 46:293-314. [DOI: 10.1016/j.ejps.2012.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/14/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
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30
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Direct detection of peptides and proteins on a microfluidic platform with MALDI mass spectrometry. Anal Bioanal Chem 2012; 404:1681-9. [DOI: 10.1007/s00216-012-6257-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/03/2012] [Accepted: 07/09/2012] [Indexed: 12/27/2022]
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31
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Murphy D, Konopacka A, Hindmarch C, Paton JFR, Sweedler JV, Gillette MU, Ueta Y, Grinevich V, Lozic M, Japundzic-Zigon N. The hypothalamic-neurohypophyseal system: from genome to physiology. J Neuroendocrinol 2012; 24:539-53. [PMID: 22448850 PMCID: PMC3315060 DOI: 10.1111/j.1365-2826.2011.02241.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The elucidation of the genomes of a large number of mammalian species has produced a huge amount of data on which to base physiological studies. These endeavours have also produced surprises, not least of which has been the revelation that the number of protein coding genes needed to make a mammal is only 22 333 (give or take). However, this small number belies an unanticipated complexity that has only recently been revealed as a result of genomic studies. This complexity is evident at a number of levels: (i) cis-regulatory sequences; (ii) noncoding and antisense mRNAs, most of which have no known function; (iii) alternative splicing that results in the generation of multiple, subtly different mature mRNAs from the precursor transcript encoded by a single gene; and (iv) post-translational processing and modification. In this review, we examine the steps being taken to decipher genome complexity in the context of gene expression, regulation and function in the hypothalamic-neurohypophyseal system (HNS). Five unique stories explain: (i) the use of transcriptomics to identify genes involved in the response to physiological (dehydration) and pathological (hypertension) cues; (ii) the use of mass spectrometry for single-cell level identification of biological active peptides in the HNS, and to measure in vitro release; (iii) the use of transgenic lines that express fusion transgenes enabling (by cross-breeding) the generation of double transgenic lines that can be used to study vasopressin (AVP) and oxytocin (OXT) neurones in the HNS, as well as their neuroanatomy, electrophysiology and activation upon exposure to any given stimulus; (iv) the use of viral vectors to demonstrate that somato-dendritically released AVP plays an important role in cardiovascular homeostasis by binding to V1a receptors on local somata and dendrites; and (v) the use of virally-mediated optogenetics to dissect the role of OXT and AVP in the modulation of a wide variety of behaviours.
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Affiliation(s)
- D Murphy
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK.
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32
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Lanni EJ, Rubakhin SS, Sweedler JV. Mass spectrometry imaging and profiling of single cells. J Proteomics 2012; 75:5036-5051. [PMID: 22498881 DOI: 10.1016/j.jprot.2012.03.017] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/08/2012] [Accepted: 03/13/2012] [Indexed: 11/25/2022]
Abstract
Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies-secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption/ionization mass spectrometry (MALDI MS)-are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enables new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling.
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Affiliation(s)
- Eric J Lanni
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA.
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33
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Yang HJ, Sugiura Y, Ikegami K, Konishi Y, Setou M. Axonal gradient of arachidonic acid-containing phosphatidylcholine and its dependence on actin dynamics. J Biol Chem 2011; 287:5290-300. [PMID: 22207757 DOI: 10.1074/jbc.m111.316877] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylcholine (PC) is the most abundant component of lipid bilayers and exists in various molecular forms, through combinations of two acylated fatty acids. Arachidonic acid (AA)-containing PC (AA-PC) can be a source of AA, which is a crucial mediator of synaptic transmission and intracellular signaling. However, the distribution of AA-PC within neurons has not been indicated. In the present study, we used imaging mass spectrometry to characterize the distribution of PC species in cultured neurons of superior cervical ganglia. Intriguingly, PC species exhibited a unique distribution that was dependent on the acyl chains at the sn-2 position. In particular, we found that AA-PC is enriched within the axon and is distributed across a proximal-to-distal gradient. Inhibitors of actin dynamics (cytochalasin D and phallacidin) disrupted this gradient. This is the first report of the gradual distribution of AA-PC along the axon and its association with actin dynamics.
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Affiliation(s)
- Hyun-Jeong Yang
- Department of Cell Biology and Anatomy, Hamamatsu University School of Medicine, 1-20-1, Handayama, Hamamatsu 431-3192, Japan
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34
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Yin P, Bousquet-Moore D, Annangudi SP, Southey BR, Mains RE, Eipper BA, Sweedler JV. Probing the production of amidated peptides following genetic and dietary copper manipulations. PLoS One 2011; 6:e28679. [PMID: 22194882 PMCID: PMC3241674 DOI: 10.1371/journal.pone.0028679] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/13/2011] [Indexed: 11/23/2022] Open
Abstract
Amidated neuropeptides play essential roles throughout the nervous and endocrine systems. Mice lacking peptidylglycine α-amidating monooxygenase (PAM), the only enzyme capable of producing amidated peptides, are not viable. In the amidation reaction, the reactant (glycine-extended peptide) is converted into a reaction intermediate (hydroxyglycine-extended peptide) by the copper-dependent peptidylglycine-α-hydroxylating monooxygenase (PHM) domain of PAM. The hydroxyglycine-extended peptide is then converted into amidated product by the peptidyl-α-hydroxyglycine α-amidating lyase (PAL) domain of PAM. PHM and PAL are stitched together in vertebrates, but separated in some invertebrates such as Drosophila and Hydra. In addition to its luminal catalytic domains, PAM includes a cytosolic domain that can enter the nucleus following release from the membrane by γ-secretase. In this work, several glycine- and hydroxyglycine-extended peptides as well as amidated peptides were qualitatively and quantitatively assessed from pituitaries of wild-type mice and mice with a single copy of the Pam gene (PAM+/−) via liquid chromatography-mass spectrometry-based methods. We provide the first evidence for the presence of a peptidyl-α-hydroxyglycine in vivo, indicating that the reaction intermediate becomes free and is not handed directly from PHM to PAL in vertebrates. Wild-type mice fed a copper deficient diet and PAM+/− mice exhibit similar behavioral deficits. While glycine-extended reaction intermediates accumulated in the PAM+/− mice and reflected dietary copper availability, amidated products were far more prevalent under the conditions examined, suggesting that the behavioral deficits observed do not simply reflect a lack of amidated peptides.
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Affiliation(s)
- Ping Yin
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Danielle Bousquet-Moore
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Suresh P. Annangudi
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bruce R. Southey
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Richard E. Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Betty A. Eipper
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- * E-mail: (JVS); (BAE)
| | - Jonathan V. Sweedler
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (JVS); (BAE)
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35
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Yamada M, Yao I, Hayasaka T, Ushijima M, Matsuura M, Takada H, Shikata N, Setou M, Kwon AH, Ito S. Identification of oligosaccharides from histopathological sections by MALDI imaging mass spectrometry. Anal Bioanal Chem 2011; 402:1921-30. [DOI: 10.1007/s00216-011-5622-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/28/2011] [Accepted: 11/28/2011] [Indexed: 02/06/2023]
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36
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Yin H, Marshall D. Microfluidics for single cell analysis. Curr Opin Biotechnol 2011; 23:110-9. [PMID: 22133547 DOI: 10.1016/j.copbio.2011.11.002] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/30/2011] [Accepted: 11/02/2011] [Indexed: 01/23/2023]
Abstract
Substantial evidence shows that the heterogeneity of individual cells within a genetically identical population can be critical to their chance of survival. Methods that use average responses from a population often mask the difference from individual cells. To fully understand cell-to-cell variability, a complete analysis of an individual cell, from its live state to cell lysates, is essential. Highly sensitive detection of multiple components and high throughput analysis of a large number of individual cells remain the key challenges to realise this aim. In this context, microfluidics and lab-on-a-chip technology have emerged as the most promising avenue to address these challenges. In this review, we will focus on the recent development in microfluidics that are aimed at total single cell analysis on chip, that is, from an individual live cell to its gene and proteins. We also discuss the opportunities that microfluidic based single cell analysis can bring into the drug discovery process.
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Affiliation(s)
- Huabing Yin
- Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, UK.
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37
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Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
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Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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38
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Samir P, Link AJ. Analyzing the cryptome: uncovering secret sequences. AAPS JOURNAL 2011; 13:152-8. [PMID: 21327597 DOI: 10.1208/s12248-011-9252-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 12/23/2010] [Indexed: 12/21/2022]
Abstract
The mammalian cryptome consists of bioactive peptides generated by the proteolysis of precursor proteins. It is speculated that the cryptide repertoire increases the complexity of the proteome by an order of magnitude. Cryptides have been found to function in a wide range of processes including neuronal signaling, antigen presentation, and the inflammatory response. Due to their potential as therapeutic agents, there has been an increasing interest in studying cryptides. In this review, we discuss different approaches for discovering these hidden peptides and how proteomic tools can be utilized to aid in their identification and characterization.
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Affiliation(s)
- Parimal Samir
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2363, USA
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39
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Jarecki JL, Andersen K, Konop CJ, Knickelbine JJ, Vestling MM, Stretton AO. Mapping neuropeptide expression by mass spectrometry in single dissected identified neurons from the dorsal ganglion of the nematode Ascaris suum. ACS Chem Neurosci 2010; 1:505-519. [PMID: 20806053 PMCID: PMC2929024 DOI: 10.1021/cn1000217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 04/18/2010] [Indexed: 11/30/2022] Open
Abstract
We have developed a method for dissecting single neurons from the nematode Ascaris suum, in order to determine their peptide content by mass spectrometry (MS). In this paper, we use MALDI-TOF MS and tandem MS to enumerate and sequence the peptides present in the two neurons, ALA and RID, that comprise the dorsal ganglion. We compare the peptide content determined by MS with the results of immunocytochemistry and in situ hybridization of previously isolated peptides AF2, AF8 and 6 peptides encoded by the afp-1 transcript. We find complete agreement between the three techniques, which validates single neuron MS as a method for peptide localization. We also discovered and sequenced 6 novel peptides in the ALA neuron. Cloning of cDNAs and database searching of Genomic Survey Sequences showed that transcript afp-12 encodes peptide AF36 (VPSAADMMIRFamide), and afp-13 encodes AF19 (AEGLSSPLIRFamide), AF34 (DSKLMDPLIRFamide), AF35 (DPQQRIVTDETVLRFamide), and 3 non-amidated peptides (PepTT, PepTL, and PepGE). We have found no similarities with reported peptide expression in the nematode Caenorhabditis elegans. This method promises to be ideally suited for determining the peptide content of each of the 298 neurons in the nervous system of this nematode.
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Affiliation(s)
| | - Kari Andersen
- Department of Zoology, University of Wisconsin-Madison
| | | | | | | | - Antony O. Stretton
- Neuroscience Training Program, University of Wisconsin-Madison
- Department of Zoology, University of Wisconsin-Madison
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40
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Bioanalytical tools for single-cell study of exocytosis. Anal Bioanal Chem 2010; 397:3281-304. [PMID: 20521141 DOI: 10.1007/s00216-010-3843-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/08/2010] [Accepted: 05/11/2010] [Indexed: 10/19/2022]
Abstract
Regulated exocytosis is a fundamental biological process used to deliver chemical messengers for cell-cell communication via membrane fusion and content secretion. A plethora of cell types employ this chemical-based communication to achieve crucial functions in many biological systems. Neurons in the brain and platelets in the circulatory system are representative examples utilizing exocytosis for neurotransmission and blood clotting. Single-cell studies of regulated exocytosis in the past several decades have greatly expanded our knowledge of this critical process, from vesicle/granule transport and docking at the early stages of exocytosis to membrane fusion and to eventual chemical messenger secretion. Herein, four main approaches that have been widely used to study single-cell exocytosis will be highlighted, including total internal reflection fluorescence microscopy, capillary electrophoresis, single-cell mass spectrometry, and microelectrochemistry. These techniques are arranged in the order following the route of a vesicle/granule destined for secretion. Within each section, the basic principles and experimental strategies are reviewed and representative examples are given revealing critical spatial, temporal, and chemical information of a secretory vesicle/granule at different stages of its lifetime. Lastly, an analytical chemist's perspective on potential future developments in this exciting field is discussed.
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41
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Brown RB, Hewel JA, Emili A, Audet J. Single amino acid resolution of proteolytic fragments generated in individual cells. Cytometry A 2010; 77:347-55. [DOI: 10.1002/cyto.a.20880] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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42
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Mellors JS, Jorabchi K, Smith LM, Ramsey JM. Integrated microfluidic device for automated single cell analysis using electrophoretic separation and electrospray ionization mass spectrometry. Anal Chem 2010; 82:967-73. [PMID: 20058879 PMCID: PMC2836921 DOI: 10.1021/ac902218y] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microfabricated fluidic device was developed for the automated real-time analysis of individual cells using capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS). The microfluidic structure incorporates a means for rapid lysis of single cells within a free solution electrophoresis channel, where cellular constituents were separated, and an integrated electrospray emitter for ionization of separated components. The eluent was characterized using mass spectrometry. Human erythrocytes were used as a model system for this study. In this monolithically integrated device, cell lysis occurs at a channel intersection using a combination of rapid buffer exchange and an increase in electric field strength. An electroosmotic pump is incorporated at the end of the electrophoretic separation channel to direct eluent to the integrated electrospray emitter. The dissociated heme group and the alpha and beta subunits of hemoglobin from individual erythrocytes were detected as cells continuously flowed through the device. The average analysis throughput was approximately 12 cells per minute, demonstrating the potential of this method for high-throughput single cell analysis.
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Affiliation(s)
- J Scott Mellors
- Department of Chemistry, Chapman Hall Room 251, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3216, USA
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Millet LJ, Bora A, Sweedler JV, Gillette MU. Direct cellular peptidomics of supraoptic magnocellular and hippocampal neurons in low-density co-cultures. ACS Chem Neurosci 2010; 1:36-48. [PMID: 20401326 DOI: 10.1021/cn9000022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genomic and proteomic studies of brain regions of specialized function provide evidence that communication among neurons is mediated by systems of diverse chemical messengers. These analyses are largely tissue- or population-based, whereas the actual communication is from cell-to-cell. To understand the complement of intercellular signals produced by individual neurons, new methods are required. We have developed a novel neuron-to-neuron, serum-free, co-culture approach that was used to determine the higher-level cellular peptidome of individual primary mammalian neurons. We isolated magnocellular neurons from the supraoptic nucleus of early postnatal rat and maintained them in serum-free low density cultures without glial support layers; under these conditions they required low-density co-cultured neurons. Co-culturing magnocellular neurons with hippocampal neurons permitted local access to individual neurons within the culture for mass spectrometry. Using direct sampling, peptide profiles were obtained for spatially distinct, identifiable neurons within the co-culture. We repeatedly detected 10 peaks that we assign to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enables the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides.
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Affiliation(s)
- Larry J. Millet
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Adriana Bora
- Neuroscience Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
- Neuroscience Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Martha U. Gillette
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
- Neuroscience Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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Annangudi SP, Luszpak AE, Kim SH, Ren S, Hatcher NG, Weiler IJ, Thornley KT, Kile BM, Wightman RM, Greenough WT, Sweedler JV. Neuropeptide Release is Impaired in a Mouse Model of Fragile X Mental Retardation Syndrome. ACS Chem Neurosci 2010; 1:306-314. [PMID: 20495672 PMCID: PMC2873207 DOI: 10.1021/cn900036x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 12/17/2009] [Indexed: 02/05/2023] Open
Abstract
Fragile X syndrome (FXS), an inherited disorder characterized by mental retardation and autismlike behaviors, is caused by the failure to transcribe the gene for fragile X mental retardation protein (FMRP), a translational regulator and transporter of select mRNAs. FXS model mice (Fmr1 KO mice) exhibit impaired neuropeptide release. Release of biogenic amines does not differ between wild-type (WT) and Fmr1 KO mice. Rab3A, an mRNA cargo of FMRP involved in the recruitment of vesicles, is decreased by ∼50% in synaptoneurosomes of Fmr1 KO mice; however, the number of dense-core vesicles (DCVs) does not differ between WT and Fmr1 KO mice. Therefore, deficits associated with FXS may reflect this aberrant vesicle release, specifically involving docking and fusion of peptidergic DCVs, and may lead to defective maturation/maintenance of synaptic connections.
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Affiliation(s)
| | | | | | | | | | | | - Keith T. Thornley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Brian M. Kile
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - R. Mark Wightman
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - William T. Greenough
- Beckman Institute
- Neuroscience Program
- Departments of Psychology, Psychiatry, and Cell and Structural Biology
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45
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Single cell analytics: an overview. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 124:99-122. [PMID: 21072695 DOI: 10.1007/10_2010_96] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The research field of single cell analysis is rapidly expanding, driven by developments in flow cytometry, microscopy, lab-on-a-chip devices, and many other fields. The promises of these developments include deciphering cellular mechanisms and the quantification of cell-to-cell differences, ideally with spatio-temporal resolution. However, these promises are challenging as the analytical techniques have to cope with minute analyte amounts and concentrations. We formulate first these challenges and then present state-of-the-art analytical techniques available to investigate the different cellular hierarchies--from the genome to the phenome, i.e., the sum of all phenotypes.
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Chen R, Cape SS, Sturm RM, Li L. Mass spectrometric imaging of neuropeptides in decapod crustacean neuronal tissues. Methods Mol Biol 2010; 656:451-463. [PMID: 20680607 DOI: 10.1007/978-1-60761-746-4_26] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The emerging technology mass spectrometric imaging (MSI) provides an attractive opportunity to detect and probe the molecular content of tissues in an anatomical context. This powerful methodology has been applied extensively to the localization of proteins, peptides, pharmaceuticals, metabolites, lipids, and other biological and chemical compounds in tissues. Herein, we present a method developed specifically for mapping neuropeptides in crustacean neuronal tissues. Both cryostat tissue sectioning and whole-mount tissue blotting techniques are highlighted. Careful sample preparation is essential for obtaining sufficient analyte/matrix mixing while retaining the spatial localization of the neuropeptides. Several matrix application apparatus and techniques are described and compared. Furthermore, three-dimensional (3D) imaging has been developed to provide detailed information about the distribution of neuropeptides within 3D structure of a crustacean brain.
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Affiliation(s)
- Ruibing Chen
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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Zimmerman TA, Rubakhin SS, Romanova EV, Tucker KR, Sweedler JV. MALDI mass spectrometric imaging using the stretched sample method to reveal neuropeptide distributions in aplysia nervous tissue. Anal Chem 2009; 81:9402-9. [PMID: 19835365 PMCID: PMC2837479 DOI: 10.1021/ac901820v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuropeptides are a diverse set of complex cell-cell signaling molecules that modulate behavior, learning, and memory. Their spatially heterogeneous distributions, large number of post-translational modifications, and wide range of physiologically active concentrations make their characterization challenging. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging is well-suited to characterizing and mapping neuropeptides in the central nervous system. Because matrix application can cause peptide migration within tissue samples, application parameters for MALDI typically represent a compromise between attaining the highest signal quality and preserving native spatial distributions. The stretched sample approach minimizes this trade-off by fragmenting the tissue section into thousands of spatially isolated islands, each approximately 40 mum in size. This inhibits analyte migration between the pieces and, at the same time, reduces analyte-salt adduct formation. Here, we present methodological improvements that enable the imaging of stretched tissues and reveal neuropeptide distributions in nervous tissue from Aplysia californica. The distributions of known neuropeptides are shown to correspond with previous immunohistochemical results, demonstrating that the stretched imaging method is well-suited for working with easily redistributed molecules and heterogeneous tissues and reduces adducts from physiological salts.
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Affiliation(s)
- Tyler A. Zimmerman
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Stanislav S. Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Elena V. Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Kevin R. Tucker
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801
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Niepel M, Spencer SL, Sorger PK. Non-genetic cell-to-cell variability and the consequences for pharmacology. Curr Opin Chem Biol 2009; 13:556-61. [PMID: 19833543 DOI: 10.1016/j.cbpa.2009.09.015] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 09/03/2009] [Indexed: 10/20/2022]
Abstract
Recent advances in single-cell assays have focused attention on the fact that even members of a genetically identical group of cells or organisms in identical environments can exhibit variability in drug sensitivity, cellular response, and phenotype. Underlying much of this variability is stochasticity in gene expression, which can produce unique proteomes even in genetically identical cells. Here we discuss the consequences of non-genetic cell-to-cell variability in the cellular response to drugs and its potential impact for the treatment of human disease.
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Affiliation(s)
- Mario Niepel
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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Franck J, El Ayed M, Wisztorski M, Salzet M, Fournier I. On-Tissue N-Terminal Peptide Derivatizations for Enhancing Protein Identification in MALDI Mass Spectrometric Imaging Strategies. Anal Chem 2009; 81:8305-17. [DOI: 10.1021/ac901043n] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Franck
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. El Ayed
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Wisztorski
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Salzet
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - I. Fournier
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
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Franck J, Arafah K, Barnes A, Wisztorski M, Salzet M, Fournier I. Improving Tissue Preparation for Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging. Part 1: Using Microspotting. Anal Chem 2009; 81:8193-202. [DOI: 10.1021/ac901328p] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Franck
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
| | - Karim Arafah
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
| | - Alan Barnes
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
| | - Maxence Wisztorski
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
| | - Michel Salzet
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
| | - Isabelle Fournier
- Université de Lille1, CNRS, Team, Laboratoire de Neuroimmunologie des Annélides, MALDI Imaging, F-59655 Villeneuve d’Ascq Cedex, France, and Shimadzu Corporation, Wharfside, Trafford Wharf Road, Manchester, U.K
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