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Kobayashi H, Imai K. Recent Progress in FD-LC-MS/MS Proteomics Method. Front Chem 2021; 9:640336. [PMID: 34178939 PMCID: PMC8220812 DOI: 10.3389/fchem.2021.640336] [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: 12/11/2020] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Through the course of our bio-analytical chemistry studies, we developed a novel proteomics analysis method, FD-LC-MS/MS (fluorogenic derivatization-liquid chromatography-tandem mass spectrometry). This method consists of fluorogenic derivatization (FD), LC separation, and detection/quantification of the derivatized proteins, followed by isolation, tryptic digestion of the isolated proteins, and final identification of the isolated proteins using electrospray ionization nano-LC-MS/MS of the generated peptide mixtures with a probability-based protein identification algorithm. In this review, we will present various examples where this method has been used successfully to identify expressed proteins in individual human cells. FD-LC-MS/MS is also suitable for differential proteomics analysis. Here, two biological samples are treated by the same steps mentioned above, and the two chromatograms obtained are compared to identify peaks with different intensities (variation in protein levels). Associated peak fractions are then isolated, and the differentially expressed proteins between the two samples are identified by LC-MS/MS. Several biomarkers for cancers have been identified by FD-LC-MS/MS. For more efficient separation, nano-flow LC with a phenyl-bonded monolithic silica-based capillary column was adopted for cell-expressed intact protein analysis. The derivatized human cell proteins (K562) and yeast cell (Saccharomyces cerevisiae) proteins as model intact cell proteins were analyzed by nano-flow LC with fluorescence detection. More than 1,300 protein peaks were separated/detected from both cells. For straightforward comparison of multiple peak separation profiles, a novel type of chromatogram display, termed the “spiderweb” chromatogram, was developed. A nano-LC-FD-LC-mass spectrometry trial for molecular weight estimation of FD proteins has also been conducted.
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Affiliation(s)
- Hiroshi Kobayashi
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan.,R&D group, Shinwa Chemical Industries, Ltd., Kyoto, Japan
| | - Kazuhiro Imai
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan
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2
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Kobayashi H, Wada H, Imai K. Phenyl-bonded monolithic silica capillary column liquid chromatographic separation and detection of fluorogenic derivatized intact proteins. Biomed Chromatogr 2021; 35:e5078. [PMID: 33491229 DOI: 10.1002/bmc.5078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/31/2022]
Abstract
Prior to the identification of proteins for proteomics analysis in human cells, separation of fluorogenic derivatized proteins with a fluorogenic reagent, 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, has typically been performed by using a conventional reversed-phase HPLC column. However, the number of proteins in human cells (HepaRG) that are separated by this conventional approach is limited to approximately 500. In this study, a nanoflow liquid chromatography system with an evaluated phenyl-bonded monolithic silica capillary column (0.1 mm i.d., 700 mm length) was used to increase the number of separated fluorogenic derivatized proteins. This system was used to separate derivatized human cell proteins (K562) and yeast (Saccharomyces cerevisiae) proteins as model cell proteomes. More than 1,300 protein peaks were separated/detected from both cell proteomes. We present a straightforward comparison of multiple separation profiles using a novel chromatogram display approach, termed the "spiderweb" chromatogram. In addition, to validate that the detected peaks are derived from proteins, a mass spectrometer was connected to the capillary column and deconvolution of the obtained mass spectra was performed. Furthermore, different molecular weight distribution profiles of the expressed proteins were observed between the two cell proteomes.
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Affiliation(s)
- Hiroshi Kobayashi
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan.,R&D group, Shinwa Chemical Industries Ltd, Kyoto, Japan
| | - Hiroo Wada
- R&D group, Shinwa Chemical Industries Ltd, Kyoto, Japan
| | - Kazuhiro Imai
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan
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Abstract
Multidrug resistance (MDR) is a vital issue in cancer treatment. Drug resistance can be developed through a variety of mechanisms, including increased drug efflux, activation of detoxifying systems and DNA repair mechanisms, and escape of drug-induced apoptosis. Identifying the exact mechanism related in a particular case is a difficult task. Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. In recent years, comparative proteomic methods have been performed to analyze MDR mechanisms in drug-selected model cancer cell lines. In this paper, we review the recent developments and progresses by comparative proteomic approaches to identify potential MDR mechanisms in drug-selected model cancer cell lines, which may help understand and design chemical sensitizers.
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Chen SM, Chen TH, Chang HT, Lin TY, Lin CY, Tsai PY, Imai K, Chen CM, Lee JA. Methylglyoxal and D-lactate in cisplatin-induced acute kidney injury: Investigation of the potential mechanism via fluorogenic derivatization liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS) proteomic analysis. PLoS One 2020; 15:e0235849. [PMID: 32649695 PMCID: PMC7351171 DOI: 10.1371/journal.pone.0235849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023] Open
Abstract
Nephrotoxicity severely limits the chemotherapeutic efficacy of cisplatin (CDDP). Oxidative stress is associated with CDDP-induced acute kidney injury (AKI). Methylglyoxal (MG) forms advanced glycation end products that elevate oxidative stress. We aimed to explore the role of MG and its metabolite D-lactate and identify the proteins involved in CDDP-induced AKI. Six-week-old female BALB/c mice were intraperitoneally administered CDDP (5 mg/kg/day) for 3 or 5 days. Blood urea nitrogen (42.6 ± 7.4 vs. 18.3 ± 2.5; p < 0.05) and urinary N-acetyl-β-D-glucosaminide (NAG; 4.89 ± 0.61 vs. 2.43 ± 0.31 U/L; p < 0.05) were significantly elevated in the CDDP 5-day group compared to control mice. Histological analysis confirmed AKI was successfully induced. Confocal microscopy revealed TNF-α was significantly increased in the CDDP 5-day group. Fluorogenic derivatized liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS) showed the kidney MG (36.25 ± 1.68 vs. 18.95 ± 2.24 mg/g protein, p < 0.05) and D-lactate (1.78 ± 0.29 vs. 1.12 ± 0.06 mol/g protein, p < 0.05) contents were significantly higher in the CDDP 5-day group than control group. FD-LC-MS/MS proteomics identified 33 and nine altered peaks in the CDDP 3-day group and CDDP 5-day group (vs. control group); of the 35 proteins identified using the MOSCOT database, 11 were antioxidant-related. Western blotting confirmed that superoxide dismutase 1 (SOD-1) and parkinson disease protein 7 (DJ-1) are upregulated and may participate with MG in CDDP-induced AKI. This study demonstrates TNF-α, MG, SOD-1 and DJ-1 play crucial roles in CDDP-induced AKI.
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Affiliation(s)
- Shih-Ming Chen
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Hui Chen
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hui-Ting Chang
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Health, Taipei City Government, Taipei, Taiwan
| | - Tzu-Yao Lin
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chia-Yu Lin
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Taipei Medical University Hospital, Taipei, Taiwan
| | - Pei-Yun Tsai
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan-Fang Hospital, Taipei, Taiwan
| | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan
| | - Chien-Ming Chen
- Department of Electro-Optical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Jen-Ai Lee
- Department of Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- * E-mail:
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Kesse S, Boakye-Yiadom KO, Ochete BO, Opoku-Damoah Y, Akhtar F, Filli MS, Asim Farooq M, Aquib M, Maviah Mily BJ, Murtaza G, Wang B. Mesoporous Silica Nanomaterials: Versatile Nanocarriers for Cancer Theranostics and Drug and Gene Delivery. Pharmaceutics 2019; 11:E77. [PMID: 30781850 PMCID: PMC6410079 DOI: 10.3390/pharmaceutics11020077] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Mesoporous silica nanomaterials (MSNs) have made remarkable achievements and are being thought of by researchers as materials that can be used to effect great change in cancer therapies, gene delivery, and drug delivery because of their optically transparent properties, flexible size, functional surface, low toxicity profile, and very good drug loading competence. Mesoporous silica nanoparticles (MSNPs) show a very high loading capacity for therapeutic agents. It is well known that cancer is one of the most severe known medical conditions, characterized by cells that grow and spread rapidly. Thus, curtailing cancer is one of the greatest current challenges for scientists. Nanotechnology is an evolving field of study, encompassing medicine, engineering, and science, and it has evolved over the years with respect to cancer therapy. This review outlines the applications of mesoporous nanomaterials in the field of cancer theranostics, as well as drug and gene delivery. MSNs employed as therapeutic agents, as well as their importance and future prospects in the ensuing generation of cancer theranostics and drug and therapeutic gene delivery, are discussed herein. Thus, the use of mesoporous silica nanomaterials can be seen as using one stone to kill three birds.
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Affiliation(s)
- Samuel Kesse
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Kofi Oti Boakye-Yiadom
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Belynda Owoya Ochete
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Yaw Opoku-Damoah
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
| | - Fahad Akhtar
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Mensura Sied Filli
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Muhammad Asim Farooq
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Md Aquib
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Bazezy Joelle Maviah Mily
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Ghulam Murtaza
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus 54600, Pakistan.
| | - Bo Wang
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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Comparative Proteomic Analysis of Breast Cancer Tissue and the Adjacent Normal Tissue in Iranian Patients with HER2 Negative Ductal Carcinoma of Breast. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2017. [DOI: 10.5812/ijcm.6019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lu M, Whitelegge JP, Whelan SA, He J, Saxton RE, Faull KF, Chang HR. Hydrophobic Fractionation Enhances Novel Protein Detection by Mass Spectrometry in Triple Negative Breast Cancer. ACTA ACUST UNITED AC 2017; 3:1-10. [PMID: 20596302 DOI: 10.4172/jpb.1000118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is widely believed that discovery of specific, sensitive and reliable tumor biomarkers can improve the treatment of cancer. The goal of this study was to develop a novel fractionation protocol targeting hydrophobic proteins as possible cancer cell membrane biomarkers. Hydrophobic proteins of breast cancer tissues and cell lines were enriched by polymeric reverse phase columns. The retained proteins were eluted and digested for peptide identification by nano-liquid chromatography with tandem mass spectrometry using a hybrid linear ion-trap Orbitrap.Hundreds of proteins were identified from each of these three specimens: tumors, normal breast tissue, and breast cancer cell lines. Many of the identified proteins defined key cellular functions. Protein profiles of cancer and normal tissues from the same patient were systematically examined and compared. Stem cell markers were overexpressed in triple negative breast cancer (TNBC) compared with non-TNBC samples. Because breast cancer stem cells are known to be resistant to radiation and chemotherapy, and can be the source of metastasis frequently seen in patients with TNBC, our study may provide evidence of molecules promoting the aggressiveness of TNBC.The initial results obtained using a combination of hydrophobic fractionation and nano-LC mass spectrometry analysis of these proteins appear promising in the discovery of potential cancer biomarkers. When sufficiently refined, this approach may prove useful for early detection and better treatment of breast cancer.
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Affiliation(s)
- Ming Lu
- Gonda/UCLA Breast Cancer Research Laboratory, David Geffen School of Medicine, Los Angeles, California
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8
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Feng Y, Panwar N, Tng DJH, Tjin SC, Wang K, Yong KT. The application of mesoporous silica nanoparticle family in cancer theranostics. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.019] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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Mori M, Ichibangase T, Yamashita S, Kijima-Suda I, Kawahara M, Imai K. Quantification of horse plasma proteins altered by xylazine using the fluorogenic derivatization-liquid chromatography-tandem mass spectrometry. J Equine Sci 2016; 26:141-6. [PMID: 26858580 PMCID: PMC4739145 DOI: 10.1294/jes.26.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/09/2015] [Indexed: 01/10/2023] Open
Abstract
In the doping tests currently used in horse racing, prohibited substances or their metabolites are usually
directly detected in urine or blood samples. However, despite their lasting pharmaceutical effects, some
prohibited substances are rapidly eliminated from horse urine and blood, making them difficult to detect.
Therefore, new indirect biomarkers for doping, such as plasma proteins that are increased by the prohibited
substances, have recently attracted much attention. Here, a fluorogenic derivatization-liquid
chromatography-tandem mass spectrometry (FD-LC-MS/MS) method was adopted for horse plasma proteomics analysis,
in order to identify plasma proteins whose concentrations were altered in response to xylazine in Thoroughbred
horses. Xylazine, which is rapidly absorbed and eliminated and has possibility of the change in the levels of
plasma proteins, was selected as a model drug. Of the ten plasma proteins identified, four proteins, including
three acute phase proteins (haptoglobin, ceruloplasmin, and α-2-macroglobulin-like), were significantly
increased after xylazine administration. Therefore, our present approach might be useful in identifying
indirect biomarkers of drug administration.
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Affiliation(s)
- Miwako Mori
- Laboratory of Bio-analytical Chemistry, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan; Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan; Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Tomoko Ichibangase
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | | | | | - Masahiro Kawahara
- Laboratory of Bio-analytical Chemistry, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
| | - Kazuhiro Imai
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo 202-8585, Japan
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Coumans JVF, Gau D, Poljak A, Wasinger V, Roy P, Moens PDJ. Profilin-1 overexpression in MDA-MB-231 breast cancer cells is associated with alterations in proteomics biomarkers of cell proliferation, survival, and motility as revealed by global proteomics analyses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:778-91. [PMID: 25454514 DOI: 10.1089/omi.2014.0075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite early screening programs and new therapeutic strategies, metastatic breast cancer is still the leading cause of cancer death in women in industrialized countries and regions. There is a need for novel biomarkers of susceptibility, progression, and therapeutic response. Global analyses or systems science approaches with omics technologies offer concrete ways forward in biomarker discovery for breast cancer. Previous studies have shown that expression of profilin-1 (PFN1), a ubiquitously expressed actin-binding protein, is downregulated in invasive and metastatic breast cancer. It has also been reported that PFN1 overexpression can suppress tumorigenic ability and motility/invasiveness of breast cancer cells. To obtain insights into the underlying molecular mechanisms of how elevating PFN1 level induces these phenotypic changes in breast cancer cells, we investigated the alteration in global protein expression profiles of breast cancer cells upon stable overexpression of PFN1 by a combination of three different proteome analysis methods (2-DE, iTRAQ, label-free). Using MDA-MB-231 as a model breast cancer cell line, we provide evidence that PFN1 overexpression is associated with alterations in the expression of proteins that have been functionally linked to cell proliferation (FKPB1A, HDGF, MIF, PRDX1, TXNRD1, LGALS1, STMN1, LASP1, S100A11, S100A6), survival (HSPE1, HSPB1, HSPD1, HSPA5 and PPIA, YWHAZ, CFL1, NME1) and motility (CFL1, CORO1B, PFN2, PLS3, FLNA, FLNB, NME2, ARHGDIB). In view of the pleotropic effects of PFN1 overexpression in breast cancer cells as suggested by these new findings, we propose that PFN1-induced phenotypic changes in cancer cells involve multiple mechanisms. Our data reported here might also offer innovative strategies for identification and validation of novel therapeutic targets and companion diagnostics for persons with, or susceptibility to, breast cancer.
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Affiliation(s)
- Joëlle V F Coumans
- 1 School of Science and Technology, University of New England , Armidale, NSW, Australia
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Ichibangase T, Imai K. [Development and application of FD-LC-MS/MS proteomics analysis revealing protein expression and biochemical events in tissues and cells]. YAKUGAKU ZASSHI 2015; 135:197-203. [PMID: 25747213 DOI: 10.1248/yakushi.14-00213-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is routine to search for and recognized genetic defects in human disorders to provide knowledge for diagnosis, treatment, and protection against diseases. It is also important to investigate and demonstrate the cause of a disease from the proteomic perspective, because intracellular signaling systems depend on protein dynamics. Demonstrating changes in protein levels enables us to understand biochemical events during the initiation and progression of a disease. To understand changes in protein levels in tissues and cells, we have developed a novel proteomics approach, FD-LC-MS/ MS. This consists of fluorogenic derivatization (FD), HPLC separation and detection/quantification of proteins in a biological sample, followed by the isolation and tryptic digestion of target proteins, and then their identification using HPLC and tandem mass spectrometry (MS/MS) with a database-searching algorithm. The method is highly sensitive (femtomole-level detection) through the use of less noisy fluorogenic rather than fluorescence derivatization, and enables precise and comprehensive relative quantitation of protein levels (between-day relative standard deviation of peak heights of ca. 20%) by combining FD with HPLC separation. In this paper, after a simple review of differential profiling using FD-LC-MS/MS, for example the analysis of stimulated vs. unstimulated samples, we introduce the development and application of the FD-LC-MS/MS method for comprehensive differential proteomics of several tissues, including mouse liver, mouse brain, and breast cancer cell lines, to reveal protein levels and biochemical events in tissues and cells.
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12
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Qi BL, Liu P, Wang QY, Cai WJ, Yuan BF, Feng YQ. Derivatization for liquid chromatography-mass spectrometry. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.03.013] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Linge A, Maurya P, Friedrich K, Baretton GB, Kelly S, Henry M, Clynes M, Larkin A, Meleady P. Identification and Functional Validation of RAD23B as a Potential Protein in Human Breast Cancer Progression. J Proteome Res 2014; 13:3212-22. [DOI: 10.1021/pr4012156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Annett Linge
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Priyanka Maurya
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Katrin Friedrich
- Institute
of Pathology, Faculty of Medicine and University Hospital Carl Gustav
Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Gustavo B. Baretton
- Institute
of Pathology, Faculty of Medicine and University Hospital Carl Gustav
Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Shane Kelly
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Michael Henry
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Martin Clynes
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Annemarie Larkin
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
| | - Paula Meleady
- National
Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin
9, Ireland
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Ichibangase T, Imai K. Straightforward proteomic analysis reveals real dynamics of proteins in cells. J Pharm Biomed Anal 2014; 101:31-9. [PMID: 24953415 DOI: 10.1016/j.jpba.2014.05.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 01/23/2023]
Abstract
To reveal real dynamics of proteins in cells, we have developed a novel type of straightforward proteomic analysis named FD-LC-MS/MS. This technique consists of fluorogenic derivatization (FD) of intact proteins, followed by high performance liquid chromatographic (LC) separation, detection and quantification of the derivatized proteins, isolation of the subject proteins, enzymatic digestion of the isolated proteins, and identification of the proteins using HPLC and MS/MS with a database-searching algorithm. The method is uncomplicated, sensitive, reproducible, and easily quantifies and identifies intact proteins in tissues and cells. Additionally, in contrast to other proteomic approaches, our method does not require any pretreatment steps, such as precipitation and clean-up, except for the derivatization, resulting in high reproducibility and the same or higher detectability than that of other methods. In this article, after a brief review of other types of proteomic analyses, we introduce the development and application of the FD-LC-MS/MS method. We also discuss the features and perspectives of this method.
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Affiliation(s)
- Tomoko Ichibangase
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, Japan
| | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, Japan.
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Ichibangase T, Nakata K, Imai K. Improved separation of fluorogenic derivatized intact proteins with high resolution and efficiency using a reversed-phase liquid chromatographic system. Biomed Chromatogr 2014; 28:862-7. [DOI: 10.1002/bmc.3172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoko Ichibangase
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi, Nishitokyo-shi Tokyo Japan
| | - Katsunori Nakata
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi, Nishitokyo-shi Tokyo Japan
| | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi, Nishitokyo-shi Tokyo Japan
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16
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Current applications of chromatographic methods for diagnosis and identification of potential biomarkers in cancer. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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17
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Barrientos G, Freitag N, Tirado-González I, Unverdorben L, Jeschke U, Thijssen VL, Blois SM. Involvement of galectin-1 in reproduction: past, present and future. Hum Reprod Update 2013; 20:175-93. [DOI: 10.1093/humupd/dmt040] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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18
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Ichibangase T, Yazawa I, Imai K. Efficient chromatographic separation of intact proteins derivatized with a fluorogenic reagent for proteomics analysis. Biomed Chromatogr 2013; 27:1520-3. [DOI: 10.1002/bmc.2952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 05/07/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Tomoko Ichibangase
- Research Institute of Pharmaceutical Sciences; Musashino University; Tokyo; Japan
| | | | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences; Musashino University; Tokyo; Japan
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Kabbage M, Trimeche M, Ben Nasr H, Hammann P, Kuhn L, Hamrita B, Chahed K. Tropomyosin-4 correlates with higher SBR grades and tubular differentiation in infiltrating ductal breast carcinomas: an immunohistochemical and proteomics-based study. Tumour Biol 2013; 34:3593-602. [PMID: 23812729 DOI: 10.1007/s13277-013-0939-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/12/2013] [Indexed: 01/16/2023] Open
Abstract
The aim of this study is to evaluate tropomyosin-4 (TM4) expression in infiltrating ductal breast carcinomas (IDCAs), as well as its prognostic significance. Using a 2-DE/MALDI-TOF mass spectrometry investigation coupled with an immunohistochemical approach, we have assessed the expression of TM4 in IDCAs, as well as in other types of breast tumors. Proteomic analyses revealed an increased expression of tropomyosin-4 in IDCA tumors. Using immunohistochemistry, overexpression of tropomyosin-4 was confirmed in 51 additional tumor specimens. Statistical analyses revealed, however, no significant correlations between tropomyosin-4 expression and clinicopathological parameters of the disease including tumor stage, patient age, estrogen and progesterone receptor status, and lymph node metastasis occurrence. A significant association was found, however, with a high Scarf-Bloom-Richardson (SBR) grade, a known marker of tumor severity. Additionally, the SBR component showing a correlation with TM4 expression was the tubular differentiation status. This study demonstrates the upregulation of tropomyosin-4 in IDCA tissues, which may highlight its involvement in breast cancer development. Our findings also support a link between tropomyosin-4 expression and aggressiveness of IDCA tumors.
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Affiliation(s)
- Maria Kabbage
- Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Al Munastir, Tunisia
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Koshiyama A, Ichibangase T, Imai K. Comprehensive fluorogenic derivatization-liquid chromatography/tandem mass spectrometry proteomic analysis of colorectal cancer cell to identify biomarker candidate. Biomed Chromatogr 2012; 27:440-50. [PMID: 22991145 DOI: 10.1002/bmc.2811] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/06/2012] [Accepted: 08/06/2012] [Indexed: 01/28/2023]
Abstract
Existing colorectal cancer biomarkers are insufficient for providing a quick and accurate diagnosis, which is critical for a good prognosis. More appropriate biomarkers are thus needed. To identify new colorectal cancer biomarker candidates, we conducted a comprehensive differential proteomic analysis of six cancer cell lines and a normal cell line, utilizing a fluorogenic derivatization-liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS) approach. Two sets of intracellular biomarker candidates were identified: one for colorectal cancer, and the other for metastatic colorectal cancer. Our results suggest that cooperative expression of FABP5 and cyclophilin A might be linked to Her2 signaling. Upregulation of LDHB and downregulation of GAPDH suggest the existence of a specific nonglycolytic energy production pathway in metastatic colorectal cancer cells. Downregulation of 14-3-3ζ/δ, cystatin-B, Ran and thioredoxin could be a result of their secretion, which then stimulates metastasis via activity in the sera and ascitic fluids. We propose a possible flow scheme to describe the dynamics of protein expression in colorectal cancer cells leading to tumor progression and metastasis via cell proliferation, angiogenesis, disorganization of actin filaments and epithelial-mesenchymal transition. Our results suggest that colorectal tumor progression may be regulated by signaling mediated by Her2, hypoxia, and TGFβ.
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Affiliation(s)
- Akiyo Koshiyama
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, Japan
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Tsai PY, Chen SM, Chen HY, Li YC, Imai K, Hsu KY, Lee JA. Proteome analysis of altered proteins in streptozotocin-induced diabetic rat kidney using the fluorogenic derivatization-liquid chromatography-tandem mass spectrometry method. Biomed Chromatogr 2012; 27:382-9. [PMID: 22972526 DOI: 10.1002/bmc.2803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/25/2012] [Accepted: 07/25/2012] [Indexed: 01/14/2023]
Abstract
To find new molecular markers for early diagnosis of diabetic nephropathy, we applied fluorogenic derivatization-liquid chromatography-tandem mass spectrometry to identify the differentially expressed proteins in the kidney of control and streptozotocin-induced diabetic rats. The Sprague-Dawley rats were injected with the sodium citrate buffer or streptozotocin and then killed after 1, 4, 12 and 24 weeks. The results showed that seven proteins were significantly changed after 1 week of injection. Only one protein had significantly changed after 4 weeks of injection. However, after 12 weeks of injection, the number of altered proteins rose to 10. After 24 weeks of injection, 18 proteins had altered significantly. Five common proteins were significantly altered at week 12 and 24 after injection, respectively. Importantly, these proteins appeared prior to microalbuminuria and may serve as new biomarkers that are able to improve early detection of and new drug development for diabetic-related nephropathy.
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Affiliation(s)
- Pei-Yun Tsai
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing St, Taipei, 11031, Taiwan
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Ichibangase T. Development of Highly Sensitive and Reproducible Analytical System for Biological Macromolecules with Fluorogenic Derivatization. CHROMATOGRAPHY 2012. [DOI: 10.15583/jpchrom.2012.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Fan R, Grignon D, Gulcicek EE, Faught P, Cheng L. Proteomic studies of Anaplasia in Wilms Tumor. PROTEOMICS INSIGHTS 2011. [DOI: 10.4137/pri.s7466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Wilms tumor is the most common malignant tumor in the pediatric kidney. Anaplasia, focal or diffuse as defined by histological criteria, is the most important parameter to guide the clinical treatment plan. We sought to identify and characterize potential useful biomarkers associated with anaplasia and provide insight into the peculiar molecular biology of Wilms tumor with unfavorable histology. Utilizing isobaric tagging technology for relative and absolute quantitation, coupled with tandem mass spectrometry, we identified proteins that are differently regulated in different Wilms tumor histologies. Four Wilms tumor specimens were selected, including two with classic favorable histology, one with focal anaplasia, and one with diffuse anaplasia. A total of 256 proteins with a Protein Score >1.0 are identified from all samples (proteins with >90% confidence). Compared with classic favorable morphology: in the focal anaplasia group, we identified a total of 26 proteins of which six were underexpressed and 20 were overexpressed; in the diffuse anaplasia group, we identified a total of 20 proteins of which eight were underexpressed and 12 were overexpressed. With a total of 39 involved proteins, seven were common to both the focal and diffuse anaplasia cases, and clearly seemed to have a similar regulation. The newly identified potential markers for Wilms tumor with unfavorable histology include ENO1, GAPDH, ALDOA, SLC25A6, LDHA, PGAM1, MIF, RBP1, HBA, HP, COL1A1, CFL1, and FSCN1 etc. In Wilms tumors, though there are unfavorable histology differences (focal or diffuse anaplasia), the protein expression seems to be similarly dysregulated compared with the favorable histology group. The newly identified potential markers may provide insights into the molecular biology of Wilms tumor and may have practical implications.
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Affiliation(s)
- Rong Fan
- Department of Pathology, Indiana University, Indianapolis, IN, USA
| | - David Grignon
- Department of Pathology, Indiana University, Indianapolis, IN, USA
| | - Erol E. Gulcicek
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA
| | - Philip Faught
- Department of Pathology, Indiana University, Indianapolis, IN, USA
| | - Liang Cheng
- Department of Pathology, Indiana University, Indianapolis, IN, USA
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Koshiyama A, Ichibangase T, Moriya K, Koike K, Yazawa I, Imai K. Liquid chromatographic separation of proteins derivatized with a fluorogenic reagent at cysteinyl residues on a non-porous column for differential proteomics analysis. J Chromatogr A 2011; 1218:3447-52. [DOI: 10.1016/j.chroma.2011.03.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/24/2011] [Accepted: 03/26/2011] [Indexed: 11/25/2022]
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25
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Hamrita B, Nasr HB, Kabbage M, Hamann P, Kuhn L, Guillier C, Remadi S, Chaieb A, Khairi H, Chouchane L, Chahed K. [The therapeutic contribution of proteomic approaches in cancers]. GYNECOLOGIE, OBSTETRIQUE & FERTILITE 2011; 39:87-93. [PMID: 21317010 DOI: 10.1016/j.gyobfe.2010.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 09/24/2010] [Indexed: 05/30/2023]
Abstract
Up to now, there are no protein tumor markers with a specificity and sensitivity sufficient to have a utility in prognosis and early diagnosis of cancer. Recent advances in proteomics approaches have led to the identification of novel tumor markers of cancer that may have a utility in screening strategies and treatment. The purpose of the current review is to describe the major advances in cancer proteomics, especially those related to the study of serum biomarkers, immune-related responses (autoantibodies) and alterations in cellular proteins.
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Affiliation(s)
- B Hamrita
- Laboratoire d'immuno-oncologie moléculaire, faculté de médecine de Monastir, 5019 Monastir, Tunisie.
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26
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Imai K, Koshiyama A, Nakata K. Towards clinical proteomics analysis. Biomed Chromatogr 2010; 25:59-64. [DOI: 10.1002/bmc.1541] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Accepted: 09/08/2010] [Indexed: 12/13/2022]
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27
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Bateman NW, Sun M, Hood BL, Flint MS, Conrads TP. Defining central themes in breast cancer biology by differential proteomics: conserved regulation of cell spreading and focal adhesion kinase. J Proteome Res 2010; 9:5311-24. [PMID: 20681588 DOI: 10.1021/pr100580e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Breast cancer is a highly heterogeneous disease, an observation that underscores the importance of elucidating conserved molecular characteristics, such as gene and protein expression, across breast cancer cell types toward providing a greater understanding of context-specific features central to this disease. Motivated by the goal of defining central biological themes across breast cancer cell subtypes, we conducted a global proteomic analysis of three breast cancer cell lines, MCF7, SK-BR-3, and MDA-MB-231, and compared these to a model of nontransformed mammary cells (MCF10A). Our results demonstrate modulation of proteins localized to the extracellular matrix, plasma membrane, and nucleus, along with coordinate decreases in proteins that regulate "cell spreading," a cellular event previously shown to be dysregulated in transformed cells. Protein interaction network analysis revealed the clustering of focal adhesion kinase (FAK), a fundamental regulator of cell spreading, with several proteins identified as mutually, differentially abundant across breast cancer cell lines that impact expression and activity of FAK, such as neprilysin and keratin 19. These analyses provide insights into conservation of protein expression across breast cancer cell subtypes, a subset of which warrants further investigation for their roles in the regulation of cell spreading and FAK in breast cancer.
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Affiliation(s)
- Nicholas W Bateman
- Department of Pharmacology & Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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28
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Ohyama K, Tomonari M, Ichibangase T, To H, Kishikawa N, Nakashima K, Imai K, Kuroda N. A toxicoproteomic study on cardioprotective effects of pre-administration of docetaxel in a mouse model of adriamycin-induced cardiotoxicity. Biochem Pharmacol 2010; 80:540-7. [DOI: 10.1016/j.bcp.2010.04.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 04/30/2010] [Accepted: 04/30/2010] [Indexed: 11/25/2022]
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29
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Koshiyama A, Imai K. Synthesis and evaluation of a fluorogenic reagent for proteomic studies: 7-fluoro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide (DAABD-F). Analyst 2010; 135:2119-24. [PMID: 20539882 DOI: 10.1039/c0an00205d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the successful selection of fluorogenic derivatization reagent 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide (DAABD-Cl) as a component of a novel method (FD-LC-MS/MS method) for proteomics studies, a further reactive reagent has been required to obtain more species of proteins: DAABD-Cl reacts with only thiol moieties of proteins to give fluorescence at 505 nm with excitation at 395 nm. Here, we synthesized reagent 7-fluoro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, DAABD-F, having a 7-fluorine moiety instead of the 7-chlorine moiety in DAABD-Cl, expecting it to exhibit high reactivity to amino moieties of proteins. As expected, the reaction rates of low molecular thiols with DAABD-F were 50 times higher than those with DAABD-Cl. DAABD-F was able to react with the amino moiety of a low molecular amine, beta-alanine, producing fluorescence at 554 nm with excitation at 432 nm. The reaction with DAABD-F of a typical model protein, bovine serum albumin (BSA), needed a lower amount of reagent (DAABD-F) than DAABD-Cl to produce a single fluorescent derivative (fluorescence at 495 nm with excitation at 390 nm) that was demonstrated to be solely a cysteinyl residue modified product. A derivatization reaction with DAABD-F towards a soluble extract of a normal human mammary epithelial cell (HMEC) resulted in the same fluorescent protein profiles as those with DAABD-Cl except one (AHNAK nucleoprotein isoform1) that was produced by the derivatization at a lysinyl residue (4761Lys) and was identified according to the usual procedure of isolation and tryptic digestion of the fluorescent protein peak on the chromatogram and final LC-MS/MS with a database-searching algorithm.
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Affiliation(s)
- Akiyo Koshiyama
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi Tokyo, Japan 202-8585
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Ichibangase T, Imai K. Application of Fluorogenic Derivatization-Liquid Chromatography-Tandem Mass Spectrometric Proteome Method to Skeletal Muscle Proteins in Fast Thoroughbred Horses. J Proteome Res 2009; 8:2129-34. [DOI: 10.1021/pr801004s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tomoko Ichibangase
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi Tokyo, Japan 202-8585
| | - Kazuhiro Imai
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi Tokyo, Japan 202-8585
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