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Kim JH, Lee SK, Yoo YC, Park NH, Park DB, Yoo JS, An HJ, Park YM, Cho KG. Proteome analysis of human cerebrospinal fluid as a diagnostic biomarker in patients with meningioma. Med Sci Monit 2013; 18:BR450-60. [PMID: 23111736 PMCID: PMC3560610 DOI: 10.12659/msm.883538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND To identify meningioma-specific proteins, cerebrospinal fluid (CSF) from 4 patients with a meningioma and 4 patients with a non-brain tumorous lesion were analyzed. MATERIAL/METHODS Two-dimensional electrophoresis and electrospray quadrupole time-of-flight tandem mass spectrometry analyses revealed 10 unique spots, containing 11 independent proteins (spot #2 and #4 each contained 2 proteins and spot #3 was not identified) were evident in CSF associated with human meningioma: serum albumin precursor (3 different isoforms), Apolipoprotein E (Apo E), Apolipoprotein J precursor (Apo J), Transthyretin precursor (TTR), Prostaglandin D2 synthase 21 kDa (PTGDS), proapolipoprotein, Chain D hemoglobin Ypsilanti, alpha-1-antitrypsin (AAT), and beta-2-microglobulin precursor (β2M). RESULTS The contents of Apo E, Apo J and AAT were increased, while PTGDS, TTR and β2M were decreased. CONCLUSIONS The results observed by 2-dimensional electrophoresis were verified by Western blot analysis. The unique proteins may represent possible candidate biomarkers of meningioma.
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Kim JY, Lee JR, Choi S, Kim EM, Jung NK, Kim YH, Yoo JS, Lee SW. Quantitative pattern analysis of the N-terminally processed isoforms of platelet factor-4 in serum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:521-530. [PMID: 23322658 DOI: 10.1002/rcm.6480] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 11/20/2012] [Accepted: 11/28/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Platelet factor 4 (PF4) is a small cytokine belonging to the CXC chemokine family which has been shown to play a role in inflammation and in the regulation of angiogenesis. In general, chemokines are susceptible to proteolytic cleavage in amino and carboxy terminal regions, which usually results in dramatic changes to the chemokine bioactivity. The purpose of this study was to identify various platelet factor-4 (PF4) isoforms caused by proteolytic processing and to quantify their levels in normal serum. METHODS First, we identified the N-terminally truncated PF4 isoforms from a standard purified PF4 protein sample by using mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analysis. Then, we used high-performance liquid chromatography (HPLC) to semi-purify PF4 from serum samples, and the levels of the four most abundant PF4 isoforms were quantitatively determined using selected reaction monitoring (SRM) assays on a nano-LC/triple-quadrupole mass spectrometer. RESULTS We have identified seven N-terminally processed PF4 isoforms and compared the levels of major PF4 isoforms from nine serum samples. Pro-p1 (EAEEDGDLQCLCVK-; average MW, 7765.2) is the major PF4 isoform in serum whereas the PF4 isoforms, designated Prot-p4 (FASAEAEEDGDLQCLCVK-;average MW, 8141.5), Prot-p3 (SAEAEEDGDLQCLCVK-; average MW, 7923.3), and Prot-p2 (AEEDGDLQCLCVK- ; average MW, 7836.3), are at about 16%, 3%, and 2% levels of the major one, respectively. CONCLUSIONS This study is the first report on the levels of N-terminally processed PF4 isoforms in serum. Also, this study shows the usefulness of SRM in determining concentrations of protein isoform variants, which can be often overlooked in immunoassay analysis.
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Lee HJ, Jeong SK, Na K, Lee MJ, Lee SH, Lim JS, Cha HJ, Cho JY, Kwon JY, Kim H, Song SY, Yoo JS, Park YM, Kim H, Hancock WS, Paik YK. Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project. J Proteome Res 2013; 12:2458-66. [DOI: 10.1021/pr301040g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Kwon KH, Kim JY, Kim SY, Min HK, Lee HJ, Ji IJ, Kang T, Park GW, An HJ, Lee B, Ravid R, Ferrer I, Chung CK, Paik YK, Hancock WS, Park YM, Yoo JS. Chromosome 11-Centric Human Proteome Analysis of Human Brain Hippocampus Tissue. J Proteome Res 2013; 12:97-105. [DOI: 10.1021/pr3008368] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jeong SK, Lee HJ, Na K, Cho JY, Lee MJ, Kwon JY, Kim H, Park YM, Yoo JS, Hancock WS, Paik YK. GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J Proteome Res 2012; 12:106-11. [PMID: 23252913 DOI: 10.1021/pr3009447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an effort to map the human proteome, the Chromosome-centric Human Proteome Project (C-HPP) was recently initiated. As a member of the international consortium working on this project, our laboratory developed a gene-centric proteomic database called GenomewidePDB, which integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. As an example case, we chose chromosome 13, which is the largest acrocentric human chromosome with the lowest gene density and contains 326 predicted proteins. All proteins stored in GenomewidePDB are linked to other resources, including neXtProt and Ensembl for protein and gene information, respectively. The Global Proteome Machine database (GPMdb) and the PeptideAtlas are also accessed for observed mass spectrometry (MS) information, while Human Protein Atlas is used for information regarding antibody availability and tissue expression, respectively. Gene ontology disease information is also included. As a pilot work, we constructed this GenomewidePDB with the identified 3615 proteins including 53 chromosome 13-origin proteins that are present in normal human placenta tissue. Thus, developing a comprehensive database containing actual experimental proteomics data will provide a valuable resource for cross chromosomal comparison in the C-HPP community.
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Byun K, Young Kim J, Bayarsaikhan E, Kim D, Jeong GB, Yun KN, Kyeong Min H, Kim SU, Yoo JS, Lee B. Quantitative proteomic analysis reveals that lipopolysaccharide induces mitogen-activated protein kinase-dependent activation in human microglial cells. Electrophoresis 2012; 33:3756-63. [PMID: 23161002 DOI: 10.1002/elps.201200345] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/18/2012] [Accepted: 08/21/2012] [Indexed: 11/12/2022]
Abstract
Microglial cells act as the first and main form of active immune defense in the central nervous system related to inflammation and neurodegenerative disease. Lipopolysaccharide (LPS) induces many genes encoding inflammatory mediators, including cytokines such as tumor necrosis factor-α, interleukin-1β, (IL-1β), and IL-6, chemokines, and prostaglandins in microglial cells. Quantitative proteomics methods with isobaric chemical labeling using tandem mass tags and 2D-nano LC-ESI-MS/MS were used to systematically analyze proteomic changes in microglia responding to LPS stimulation. As a result, we found that the expression level of 21 proteins in human microglial cells changed after activation. Among those, one of the strong mitogen-activated protein kinase (MAPK) regulator proteins, CMPK1 was highly upregulated after LPS stimulation in human microglial cells. We detected and validated upregulation of MAPK including ERK1/2, p38, and SAPK/JNK by immunohistochemistry and Western blotting. NFκB, strong transcription factor of CMPK1, was translocated to the nucleus from the cytosol by high contents screening after LPS stimulation. Taken together, we conclude that MAPK signaling plays an important role in LPS-induced human microglial activation related to inflammatory response.
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Heo CK, Hwang HM, Ruem A, Yu DY, Lee JY, Yoo JS, Kim IG, Yoo HS, Oh S, Ko JH, Cho EW. Identification of a mimotope for circulating anti-cytokeratin 8/18 antibody and its usage for the diagnosis of breast cancer. Int J Oncol 2012; 42:65-74. [PMID: 23128437 PMCID: PMC3583721 DOI: 10.3892/ijo.2012.1679] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/14/2012] [Indexed: 12/22/2022] Open
Abstract
A novel circulating tumor-associated autoantibody, K94, obtained from a hepatocellular carcinoma (HCC) mouse model was characterized. The target antigen of K94 autoanti-body was expressed in various tumor cell lines including liver cancer, and its secretion was detectable using MCF-7 breast carcinoma cells. Proteomic analysis revealed that the protein bands reactive to K94 included cytokeratin (CK) 8 and 18, which are known to be related to tumorigenesis and form a heterotypic complex with each other. However, K94 showed no activity toward CK8 or CK18 separately. The epitope of the K94 antibody was only presented by a complex between CK8 and CK18, which was confirmed by analysis using recombinant CK8 and CK18 proteins. To formulate an assay for anti-CK8/18 complex autoantibody, a mimotope peptide reactive to K94 was selected from loop-constrained heptapeptide (-CX7C-) display phage library, of which sequence was CISPDAHSC (K94p1). A mimotope enzyme-linked immunosorbent assay (ELISA) using phage-displayed K94p1 peptide as a coating antigen was able to discriminate breast cancer (n=30) patients from normal subjects (n=30) with a sensitivity of 50% and a specificity of 82.61%. CA15.3 was detected at very low levels in the same breast cancer subjects and did not discriminate breast cancer patients from normal subjects, although it is a conventional biomarker of breast cancer. These results suggest that a mimotope ELISA composed of K94p1 peptide may be useful for the diagnosis of breast cancer.
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Kim YS, Ahn YH, Song KJ, Kang JG, Lee JH, Jeon SK, Kim HC, Yoo JS, Ko JH. Overexpression and β-1,6-N-acetylglucosaminylation-initiated aberrant glycosylation of TIMP-1: a "double whammy" strategy in colon cancer progression. J Biol Chem 2012; 287:32467-78. [PMID: 22859303 DOI: 10.1074/jbc.m112.370064] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
There has been ongoing debate over whether tissue inhibitor of metalloproteinase-1 (TIMP-1) is pro- or anti-oncogenic. We confirmed that TIMP-1 reinforced cell proliferation in an αvβ3 integrin-dependent manner and conferred resistance against cytotoxicity triggered by TNF-α and IL-2 in WiDr colon cancer cells. The cell-proliferative effects of TIMP-1 contributed to clonogenicity and tumor growth during the onset and early phase of tumor formation in vivo and in vitro. However, mass-produced TIMP-1 impeded further tumor growth by tightly inhibiting the activities of collagenases, which are critical for tumor growth and malignant transformation. Tumor cells could overcome this impasse by overexpression of N-acetylglucosaminyltransferase V, which deteriorates TIMP-1 into an aberrant glycoform. The aberrant glycoform of TIMP-1 was responsible for the mitigated inhibition of collagenases. The outbalanced activities of collagenases can degrade the basement membrane and the interstitial matrix, which act as a physical barrier for tumor growth and progression more efficiently. The concomitant overexpression of TIMP-1 and N-acetylglucosaminyltransferase V enabled WiDr cells to show a higher tumor growth rate as well as more malignant behaviors in a three-dimensional culture system.
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Ahn YH, Shin PM, Oh NR, Park GW, Kim H, Yoo JS. A lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform for identification of multiple liver cancer biomarkers in human plasma. J Proteomics 2012; 75:5507-15. [PMID: 22789673 DOI: 10.1016/j.jprot.2012.06.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/04/2012] [Accepted: 06/30/2012] [Indexed: 10/28/2022]
Abstract
Aberrantly glycosylated proteins related to liver cancer progression were captured with specific lectin and identified from human plasma by multiple reaction monitoring (MRM) mass spectrometry as multiple biomarkers for hepatocellular carcinoma (HCC). The lectin fractionation for fucosylated protein glycoforms in human plasma was conducted with a fucose-specific aleuria aurantia lectin (AAL). Following tryptic digestion of the lectin-captured fraction, plasma samples from 30 control cases (including 10 healthy, 10 hepatitis B virus [HBV], and 10 cirrhosis cases) and 10 HCC cases were quantitatively analyzed by MRM to identify which glycoproteins are viable HCC biomarkers. A1AG1, AACT, A1AT, and CERU were found to be potent biomarkers to differentiate HCC plasma from control plasmas. The AUROC generated independently from these four biomarker candidates ranged from 0.73 to 0.92. However, the lectin-coupled MRM assay with multiple combinations of biomarker candidates is superior statistically to those generated from the individual candidates with AUROC more than 0.95, which can be an alternative to the immunoassay inevitably requiring tedious development of multiple antibodies against biomarker candidates to be verified. Eventually the lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform was found to be efficient to identify multiple biomarkers from human plasma according to cancer progression.
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Lee H, Song M, Shin N, Shin CH, Min BS, Kim HS, Yoo JS, Kim H. Diagnostic significance of serum HMGB1 in colorectal carcinomas. PLoS One 2012; 7:e34318. [PMID: 22496788 PMCID: PMC3319566 DOI: 10.1371/journal.pone.0034318] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 02/29/2012] [Indexed: 12/13/2022] Open
Abstract
High mobility group box 1 protein (HMGB1), a nuclear protein, can be translocated to the cytoplasm and secreted in colon cancer cells. However, the diagnostic significance of HMGB1 has not been evaluated in colorectal carcinomas. For this purpose, we have screened the expression and secretion of HMGB1 in 10 colon cancer cell lines and 1 control cell line and found that HMGB1 was detected in the culture medium. To evaluate the diagnostic value of HMGB1, we performed an enzyme-linked immunosorbent assay to measure HMGB1 levels and compared them to carcinoembryonic antigen (CEA) levels in the serum samples of 219 colorectal carcinoma patients and 75 healthy control subjects. We found that the serum HMGB1 level was increased by 1.5-fold in patients with colorectal carcinoma compared to those in healthy controls. When HMGB1 and CEA levels were compared, HMGB1 had similar efficacy as CEA regarding cancer detection (the sensitivity was 20.1% for HMGB1 vs. 25.6% for CEA, and the specificity was 96% for HMGB1 vs. 90.7% for CEA). Moreover, the diagnostic accuracy of HMGB1 for stage I cancer was significantly higher than that of CEA (sensitivity: 41.2% vs. 5.9%; specificity: 96% vs. 90.7). When we combined HMGB1 and CEA, the overall diagnostic sensitivity was higher than that of CEA alone (42% vs. 25.6%), and the diagnostic sensitivity for stage I was also elevated (47% vs. 5.9%). However, the prognosis of patients was not related with serum HMGB1 concentrations. Our findings indicate that serum HMGB1 levels are increased in a subset of colorectal carcinomas, suggesting their potential utility as a supportive diagnostic marker for colorectal carcinomas.
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Kwak D, Choi S, Jeong H, Jang JH, Lee Y, Jeon H, Lee MN, Noh J, Cho K, Yoo JS, Hwang D, Suh PG, Ryu SH. Osmotic stress regulates mammalian target of rapamycin (mTOR) complex 1 via c-Jun N-terminal Kinase (JNK)-mediated Raptor protein phosphorylation. J Biol Chem 2012; 287:18398-407. [PMID: 22493283 DOI: 10.1074/jbc.m111.326538] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mTOR complex 1 (mTORC1) is a multiprotein complex that integrates diverse signals including growth factors, nutrients, and stress to control cell growth. Raptor is an essential component of mTORC1 that functions to recruit specific substrates. Recently, Raptor was suggested to be a key target of regulation of mTORC1. Here, we show that Raptor is phosphorylated by JNK upon osmotic stress. We identified that osmotic stress induces the phosphorylation of Raptor at Ser-696, Thr-706, and Ser-863 using liquid chromatography-tandem mass spectrometry. We found that JNK is responsible for the phosphorylation. The inhibition of JNK abolishes the phosphorylation of Raptor induced by osmotic stress in cells. Furthermore, JNK physically associates with Raptor and phosphorylates Raptor in vitro, implying that JNK is responsible for the phosphorylation of Raptor. Finally, we found that osmotic stress activates mTORC1 kinase activity in a JNK-dependent manner. Our findings suggest that the molecular link between JNK and Raptor is a potential mechanism by which stress regulates the mTORC1 signaling pathway.
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Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, Keown P, Baker MS, Yoo JS, Garin J, Archakov A, Bergeron J, Salekdeh GH, Hancock WS. Standard Guidelines for the Chromosome-Centric Human Proteome Project. J Proteome Res 2012; 11:2005-13. [DOI: 10.1021/pr200824a] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Sung HJ, Jeon SA, Ahn JM, Seul KJ, Kim JY, Lee JY, Yoo JS, Lee SY, Kim H, Cho JY. Large-scale isotype-specific quantification of Serum amyloid A 1/2 by multiple reaction monitoring in crude sera. J Proteomics 2012; 75:2170-80. [PMID: 22300576 DOI: 10.1016/j.jprot.2012.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/09/2012] [Accepted: 01/14/2012] [Indexed: 12/19/2022]
Abstract
Quantification is an essential step in biomarker development. Multiple reaction monitoring (MRM) is a new modified mass spectrometry-based quantification technology that does not require antibody development. Serum amyloid A (SAA) is a positive acute-phase protein identified as a lung cancer biomarker in our previous study. Acute SAA exists in two isoforms with highly similar (92%) amino acid sequences. Until now, studies of SAA have been unable to distinguish between SAA1 and SAA2. To overcome the unavailability of a SAA2-specific antibody, we developed MRM methodology for the verification of SAA1 and SAA2 in clinical crude serum samples from 99 healthy controls and 100 lung adenocarcinoma patients. Differential measurement of SAA1 and SAA2 was made possible for the first time with the developed isotype-specific MRM method. Most healthy control samples had small or no MS/MS peaks of the targeted peptides otherwise, higher peak areas with 10- to 34-fold increase over controls were detected in lung cancer samples. In addition, our SAA1 MRM data demonstrated good agreement with the SAA1 enzyme-linked immunosorbent assay (ELISA) data. Finally, successful quantification of SAA2 in crude serum by MRM, for the first time, shows that SAA2 can be a good biomarker for the detection of lung cancers.
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Ahn YH, Kim KH, Shin PM, Ji ES, Kim H, Yoo JS. Identification of low-abundance cancer biomarker candidate TIMP1 from serum with lectin fractionation and peptide affinity enrichment by ultrahigh-resolution mass spectrometry. Anal Chem 2012; 84:1425-31. [PMID: 22196688 DOI: 10.1021/ac2024987] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As investigating a proteolytic target peptide originating from the tissue inhibitor of metalloproteinase 1 (TIMP1) known to be aberrantly glycosylated in patients with colorectal cancer (CRC), we first confirmed that TIMP1 is to be a CRC biomarker candidate in human serum. For this, we utilized matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) showing ultrahigh-resolution and high mass accuracy. This investigation used phytohemagglutinin-L(4) (L-PHA) lectin, which shows binding affinity to the β-1,6-N-acetylglucosamine moiety of N-linked glycan on a protein, to compare fractionated aberrant protein glycoforms from both noncancerous control and CRC serum. Each lectin-captured fraction containing aberrant glycoforms of TIMP1 was digested by trypsin, resulting in the tryptic target peptide, representative of the serum glycoprotein TIMP1. The resulting target peptide was enriched using a stable isotope standard and capture by the antipeptide antibody (SISCAPA) technique and analyzed by a 15 T MALDI FTICR mass spectrometer with high mass accuracy (Δ < 0.5 ppm to the theoretical mass value of the target peptide). Since exact measurement of multiplex isotopic peaks of the target peptide could be accomplished by virtue of high mass resolution (Rs > 400,000), robust identification of the target peptide is only achievable with 15 T FTICR MS. Also, MALDI data obtained in this study showed that the L-PHA-captured glycoforms of TIMP1 were measured in the pooled CRC serum with about 5 times higher abundance than that in the noncancerous serum, and were further proved by MRM mass analysis. These results confirm that TIMP1 in human serum is a potent CRC biomarker candidate, demonstrating that ultrahigh-resolution MS can be a powerful tool toward identifying and verifying potential protein biomarker candidates.
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Ahn YH, Shin PM, Ji ES, Kim H, Yoo JS. A lectin-coupled, multiple reaction monitoring based quantitative analysis of human plasma glycoproteins by mass spectrometry. Anal Bioanal Chem 2012; 402:2101-12. [DOI: 10.1007/s00216-011-5646-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/01/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
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Ahn YH, Kim KH, Shin PM, Ji ES, Yoo JS. Mass Spectrometry for Analysis of Cancer Biomarker from Human Plasma. J Anal Sci Technol 2011. [DOI: 10.5355/jast.2011.a135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Ahn YH, Ji ES, Shin PM, Kim KH, Kim YS, Ko JH, Yoo JS. A multiplex lectin-channel monitoring method for human serum glycoproteins by quantitative mass spectrometry. Analyst 2011; 137:691-703. [PMID: 22158852 DOI: 10.1039/c1an15775b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A mass profiling method and multiple reaction monitoring (MRM)-based quantitative approach were used to analyze multiple lectin-captured fractions of human serum using different lectins such as aleuria aurantia lectin (AAL), phytohemagglutinin-L(4) (L-PHA), concanavalin A (Con A), and Datura stramonium agglutinin (DSA) to quantitatively monitor protein glycosylation diversity. Each fraction, prepared by multiple lectin-fractionation and tryptic digestion, was analyzed by 1-D LC-MS/MS. Semi-quantitative profiling showed that the list of glycoproteins identified from each lectin-captured fraction is significantly different according to the used lectin. Thus, it was confirmed that the multiplex lectin-channel monitoring (LCM) using multiple lectins is useful for investigating protein glycosylation diversity in a proteome sample. Based on the semi-quantitative mass profiling, target proteins showing lectin-specificity among each lectin-captured fraction were selected and analyzed by the MRM-based method in triplicate using each lectin-captured fraction (average CV 7.9%). The MRM-based analysis for each lectin-captured fraction was similar to those obtained by the profiling experiments. The abundance of each target protein measured varied dramatically, based on the lectin-specificity. The multiplex LCM approach using MRM-based analyses is useful for quantitatively monitoring target protein glycoforms selectively fractionated by multiple lectins. Thus through multiplex LCM rather than single, we could inquire minutely into protein glycosylation states.
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Lee JY, Kim JY, Park GW, Cheon MH, Kwon KH, Ahn YH, Moon MH, Lee HJ, Paik YK, Yoo JS. Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. Mol Cell Proteomics 2011; 10:M111.009290. [PMID: 21940909 DOI: 10.1074/mcp.m111.009290] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A simple mass spectrometric approach for the discovery and validation of biomarkers in human plasma was developed by targeting nonglycosylated tryptic peptides adjacent to glycosylation sites in an N-linked glycoprotein, one of the most important biomarkers for early detection, prognoses, and disease therapies. The discovery and validation of novel biomarkers requires complex sample pretreatment steps, such as depletion of highly abundant proteins, enrichment of desired proteins, or the development of new antibodies. The current study exploited the steric hindrance of glycan units in N-linked glycoproteins, which significantly affects the efficiency of proteolytic digestion if an enzymatically active amino acid is adjacent to the N-linked glycosylation site. Proteolytic digestion then results in quantitatively different peptide products in accordance with the degree of glycosylation. The effect of glycan steric hindrance on tryptic digestion was first demonstrated using alpha-1-acid glycoprotein (AGP) as a model compound versus deglycosylated alpha-1-acid glycoprotein. Second, nonglycosylated tryptic peptide biomarkers, which generally show much higher sensitivity in mass spectrometric analyses than their glycosylated counterparts, were quantified in human hepatocellular carcinoma plasma using a label-free method with no need for N-linked glycoprotein enrichment. Finally, the method was validated using a multiple reaction monitoring analysis, demonstrating that the newly discovered nonglycosylated tryptic peptide targets were present at different levels in normal and hepatocellular carcinoma plasmas. The area under the receiver operating characteristic curve generated through analyses of nonglycosylated tryptic peptide from vitronectin precursor protein was 0.978, the highest observed in a group of patients with hepatocellular carcinoma. This work provides a targeted means of discovering and validating nonglycosylated tryptic peptides as biomarkers in human plasma, without the need for complex enrichment processes or expensive antibody preparations.
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Yun SH, Park GW, Kim JY, Kwon SO, Choi CW, Leem SH, Kwon KH, Yoo JS, Lee C, Kim S, Kim SI. Proteomic characterization of the Pseudomonas putida KT2440 global response to a monocyclic aromatic compound by iTRAQ analysis and 1DE-MudPIT. J Proteomics 2011; 74:620-8. [DOI: 10.1016/j.jprot.2011.01.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/19/2011] [Accepted: 01/31/2011] [Indexed: 11/28/2022]
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Adare A, Afanasiev S, Aidala C, Ajitanand NN, Akiba Y, Akimoto R, Alexander J, Al-Ta'ani H, Andrews KR, Angerami A, Aoki K, Apadula N, Appelt E, Aramaki Y, Armendariz R, Aschenauer EC, Awes TC, Azmoun B, Babintsev V, Bai M, Bannier B, Barish KN, Bassalleck B, Basye AT, Bathe S, Baublis V, Baumann C, Bazilevsky A, Belmont R, Ben-Benjamin J, Bennett R, Berdnikov A, Berdnikov Y, Blau DS, Bok JS, Boyle K, Brooks ML, Broxmeyer D, Buesching H, Bumazhnov V, Bunce G, Butsyk S, Campbell S, Caringi A, Castera P, Chen CH, Chi CY, Chiu M, Choi IJ, Choi JB, Choudhury RK, Christiansen P, Chujo T, Chvala O, Cianciolo V, Citron Z, Cole BA, Conesa del Valle Z, Connors M, Csanád M, Csörgo T, Dairaku S, Datta A, David G, Dayananda MK, Denisov A, Deshpande A, Desmond EJ, Dharmawardane KV, Dietzsch O, Dion A, Donadelli M, D'Orazio L, Drapier O, Drees A, Drees KA, Durham JM, Durum A, Efremenko YV, Engelmore T, Enokizono A, En'yo H, Esumi S, Fadem B, Fields DE, Finger M, Finger M, Fleuret F, Fokin SL, Frantz JE, Franz A, Frawley AD, Fukao Y, Fusayasu T, Garishvili I, Glenn A, Gong X, Gonin M, Goto Y, Granier de Cassagnac R, Grau N, Greene SV, Grosse Perdekamp M, Gunji T, Guo L, Gustafsson HÅ, Haggerty JS, Hahn KI, Hamagaki H, Hamblen J, Hanks J, Han R, Harper C, Hashimoto K, Haslum E, Hayano R, Hemmick TK, Hester T, He X, Hill JC, Hollis RS, Holzmann W, Homma K, Hong B, Horaguchi T, Hori Y, Hornback D, Huang S, Ichihara T, Ichimiya R, Iinuma H, Ikeda Y, Imai K, Inaba M, Iordanova A, Isenhower D, Ishihara M, Issah M, Isupov A, Ivanischev D, Iwanaga Y, Jacak BV, Jia J, Jiang X, Johnson BM, Jones T, Joo KS, Jouan D, Kamin J, Kaneti S, Kang BH, Kang JH, Kang JS, Kapustinsky J, Karatsu K, Kasai M, Kawall D, Kazantsev AV, Kempel T, Khanzadeev A, Kijima KM, Kim BI, Kim DJ, Kim EJ, Kim YJ, Kim YK, Kinney E, Kiss Á, Kistenev E, Kleinjan D, Kline P, Kochenda L, Komkov B, Konno M, Koster J, Kotov D, Král A, Kunde GJ, Kurita K, Kurosawa M, Kwon Y, Kyle GS, Lacey R, Lai YS, Lajoie JG, Lebedev A, Lee DM, Lee J, Lee KB, Lee KS, Lee SH, Lee SR, Leitch MJ, Leite MAL, Lichtenwalner P, Lim SH, Linden Levy LA, Litvinenko A, Liu H, Liu MX, Li X, Love B, Lynch D, Maguire CF, Makdisi YI, Malakhov A, Manion A, Manko VI, Mannel E, Mao Y, Masui H, McCumber M, McGaughey PL, McGlinchey D, McKinney C, Means N, Mendoza M, Meredith B, Miake Y, Mibe T, Mignerey AC, Miki K, Milov A, Mitchell JT, Miyachi Y, Mohanty AK, Moon HJ, Morino Y, Morreale A, Morrison DP, Motschwiller S, Moukhanova TV, Murakami T, Murata J, Nagamiya S, Nagle JL, Naglis M, Nagy MI, Nakagawa I, Nakamiya Y, Nakamura KR, Nakamura T, Nakano K, Newby J, Nguyen M, Nihashi M, Nouicer R, Nyanin AS, Oakley C, O'Brien E, Ogilvie CA, Okada K, Oka M, Oskarsson A, Ouchida M, Ozawa K, Pak R, Pantuev V, Papavassiliou V, Park BH, Park IH, Park SK, Pate SF, Pei H, Peng JC, Pereira H, Peresedov V, Peressounko DY, Petti R, Pinkenburg C, Pisani RP, Proissl M, Purschke ML, Qu H, Rak J, Ravinovich I, Read KF, Reygers K, Riabov V, Riabov Y, Richardson E, Roach D, Roche G, Rolnick SD, Rosati M, Rosendahl SSE, Rukoyatkin P, Sahlmueller B, Saito N, Sakaguchi T, Samsonov V, Sano S, Sarsour M, Sato T, Savastio M, Sawada S, Sedgwick K, Seidl R, Seto R, Sharma D, Shein I, Shibata TA, Shigaki K, Shim HH, Shimomura M, Shoji K, Shukla P, Sickles A, Silva CL, Silvermyr D, Silvestre C, Sim KS, Singh BK, Singh CP, Singh V, Slunečka M, Sodre T, Soltz RA, Sondheim WE, Sorensen SP, Sourikova IV, Stankus PW, Stenlund E, Stoll SP, Sugitate T, Sukhanov A, Sun J, Sziklai J, Takagui EM, Takahara A, Taketani A, Tanabe R, Tanaka Y, Taneja S, Tanida K, Tannenbaum MJ, Tarafdar S, Taranenko A, Tennant E, Themann H, Thomas D, Togawa M, Tomášek L, Tomášek M, Torii H, Towell RS, Tserruya I, Tsuchimoto Y, Utsunomiya K, Vale C, van Hecke HW, Vazquez-Zambrano E, Veicht A, Velkovska J, Vértesi R, Virius M, Vossen A, Vrba V, Vznuzdaev E, Wang XR, Watanabe D, Watanabe K, Watanabe Y, Watanabe YS, Wei F, Wei R, Wessels J, White SN, Winter D, Woody CL, Wright RM, Wysocki M, Yamaguchi YL, Yang R, Yanovich A, Ying J, Yokkaichi S, Yoo JS, Young GR, Younus I, You Z, Yushmanov IE, Zajc WA, Zelenski A, Zhou S, Zolin L. Cross section and parity-violating spin asymmetries of W± boson production in polarized p + p collisions at sqrt[s] = 500 GeV. PHYSICAL REVIEW LETTERS 2011; 106:062001. [PMID: 21405459 DOI: 10.1103/physrevlett.106.062001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Indexed: 05/30/2023]
Abstract
Large parity-violating longitudinal single-spin asymmetries A(L)(e+) = -0.86(-0.14) (+0.30) and A(L)(e-) = 0.88(-0.71) (+0.12) are observed for inclusive high transverse momentum electrons and positrons in polarized p+p collisions at a center-of-mass energy of sqrt[s] = 500 GeV with the PHENIX detector at RHIC. These e± come mainly from the decay of W± and Z0 bosons, and their asymmetries directly demonstrate parity violation in the couplings of the W± to the light quarks. The observed electron and positron yields were used to estimate W± boson production cross sections for the e± channels of σ(pp → W+ X) × BR(W+ → e+ ν(e)) = 144.1 ± 21.2(stat)(-10.3) (+3.4) (syst) ± 21.6(norm) pb, and σ(pp → W- X) × BR(W- → e- ν[over ¯](e)) = 31.7 ± 12.1(stat)(-8.2) (+10.1) (syst) ± 4.8(norm) pb.
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Wang JP, Yoo JS, Jang HD, Lee JH, Cho JH, Kim IH. Effect of dietary fermented garlic by Weissella koreensis powder on growth performance, blood characteristics, and immune response of growing pigs challenged with Escherichia coli lipopolysaccharide. J Anim Sci 2011; 89:2123-31. [PMID: 21317348 DOI: 10.2527/jas.2010-3186] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two experiments were conducted to investigate the effect of fermented garlic by Weissella koreensis powder (WKG) on pig growth performance and immune responses after an Escherichia coli lipopolysaccharide (LPS) challenge. In Exp. 1, 120 growing barrows (23.5 ± 0.5 kg of BW and 56 d of age) were used in a 35-d experiment to determine the optimal amounts of WKG. Pigs were randomly allotted to 1 of 5 treatments with 6 replicate pens and 4 pigs per pen. Dietary treatments included 1) NC (negative control; basal diet without antibiotics), 2) PC (positive control; basal diet + 1 g of tylosin/kg), 3) WKG1 (basal diet + 1 g of WKG/kg), 4) WKG2 (basal diet + 2 g of WKG/kg), and 5) basal diet + 4 g of WKG/kg. At the end of the feeding period, 12 pigs each were selected from the NC and WKG2 treatment groups, and 6 pigs were injected with LPS (50 μg/kg of BW) and the other 6 pigs with an equivalent amount of sterile saline, resulting in a 2 × 2 factorial arrangement of treatments. Blood samples and rectal temperature data were collected at 0, 2, 4, 6, 8, and 12 h after challenge. The ADG of pigs fed WKG- and antibiotic-supplemented diets was greater (P<0.05) than NC from d 14 to 35 and the overall phase, but no dosage-dependent effects were observed. At the end of the experiment, the fecal E. coli count was linearly reduced by the increasing amounts of WKG at d 35 (P=0.01). Challenge with LPS increased white blood cell counts at 6 and 8 h (P<0.01) and depressed lymphocyte concentration at 4, 8, and 12 h (P<0.01). During challenge, LPS injection increased rectal temperature at 2, 4, 6, and 8 h postchallenge (P<0.05), and WKG2 alleviated (P<0.05) the increase in the temperature at 2 h postchallenge. The LPS injection increased plasma tumor necrosis factor-α and IGF-1 concentrations at 2, 4, 6, 8, and 12 h (P<0.01), whereas an alleviating effect of WKG was observed at 4, 6, and 8 h after LPS challenge (P<0.05). At 2, 4, and 6 h postchallenge, concentration of cluster of differentiation-antigen-4-positive cells and cluster of differentiation-antigen-8-positive cells (CD4(+) and CD8(+), respectively) increased in the LPS treatments (P<0.05), and the WKG2 boosted this effect (P<0.05). In conclusion, dietary supplementation of WKG2 in growing pigs can improve ADG and have a beneficial effect on the immune response during an inflammatory challenge.
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Kim YH, Park KH, Kim SY, Ji ES, Kim JY, Lee SK, Yoo JS, Kim HS, Park YM. Identification of trimethylation at C-terminal lysine of pilin in the cyanobacterium Synechocystis PCC 6803. Biochem Biophys Res Commun 2010; 404:587-92. [PMID: 21130745 DOI: 10.1016/j.bbrc.2010.11.133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 11/24/2010] [Indexed: 12/13/2022]
Abstract
Various post-translational modifications (PTMs) of pilin in Synechocystis sp. PCC 6803 have been proposed. In this study, we investigated previously unidentified PTMs of pilin by mass spectrometry (MS). MALDI-TOF MS and TOF/TOF MS showed that the molecular mass of the C-terminal lysine of pilin was increased by 42Da, which could represent acetylation (ΔM=42.0470) or trimethylation (ΔM=42.0106). To discriminate between these isobaric modifications, the molecular mass of the C-terminal tryptic peptide was measured using 15T Fourier transform ion cyclotron resonance (FT-ICR) MS. The high magnetic field FT-ICR provided sub-ppm mass accuracy, revealing that the C-terminal lysine was modified by trimethylation. We could also detect the existence of mono- and di-methylation of the C-terminal lysine. Cells expressing a pilin point mutant with glutamine replacing the C-terminal lysine showed dramatically reduced motility and short pili. These findings suggest that trimethylation of pilin at the C-terminal lysine may be essential for the biogenesis of functional pili.
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Ahmed A, Cho YJ, No MH, Koh J, Tomczyk N, Giles K, Yoo JS, Kim S. Application of the Mason−Schamp Equation and Ion Mobility Mass Spectrometry To Identify Structurally Related Compounds in Crude Oil. Anal Chem 2010; 83:77-83. [DOI: 10.1021/ac101934q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Yun SH, Choi CW, Kwon SO, Park GW, Cho K, Kwon KH, Kim JY, Yoo JS, Lee JC, Choi JS, Kim S, Kim SI. Quantitative proteomic analysis of cell wall and plasma membrane fractions from multidrug-resistant Acinetobacter baumannii. J Proteome Res 2010; 10:459-69. [PMID: 21053951 DOI: 10.1021/pr101012s] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acinetobacter baumannii is a Gram-negative, nonmotile aerobic bacterium that has emerged as an important nosocomial pathogen. Multidrug-resistant (MDR) A. baumannii is difficult to treat with antibiotics, and treatment failure in infected patients is of great concern in clinical settings. To investigate proteome regulation in A. baumannii under antibiotic stress conditions, quantitative membrane proteomic analyses of a clinical MDR A. baumannii strain cultured in subminimal inhibitory concentrations of tetracycline and imipenem were performed using a combination of label-free (one-dimensional electrophoresis-liquid chromatography-tandem mass spectrometry) and label (isobaric tag for relative and absolute quantitation) approaches. In total, 484 proteins were identified, and 302 were classified as outer membrane, periplasmic, or plasma membrane proteins. The clinical A. baumannii strain DU202 responded specifically and induced different cell wall and membrane protein sets that provided resistance to the antibiotics. The induction of resistance-nodulation-cell division transporters and protein kinases, and the repression of outer membrane proteins were common responses in the presence of tetracycline and imipenem. Induction of a tetracycline resistant pump, ribosomal proteins, and iron-uptake transporters appeared to be dependent on tetracycline conditions, whereas β-lactamase and penicillin-binding proteins appeared to be dependent on imipenem conditions. These results suggest that combined liquid chromatography-based proteomic approaches can be used to identify cell wall and membrane proteins involved in the antibiotic resistance of A. baumannii.
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Kang D, Ji ES, Moon MH, Yoo JS. Lectin-based enrichment method for glycoproteomics using hollow fiber flow field-flow fractionation: application to Streptococcus pyogenes. J Proteome Res 2010; 9:2855-62. [PMID: 20377246 DOI: 10.1021/pr900937w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This paper presents a new application of hollow fiber flow field-flow fractionation (HF5) as a preparative method to preconcentrate high mannose type N-linked glycoproteins from Streptococcus pyogenes by means of the mannose-specific binding affinity between concanavalian A (ConA) and N-linked glycosylated proteins. Prior to fractionation of N-linked glycoproteins from bacterial lysates, it was examined that ConA formed several types of multimers depending on the pH values (4, 6, and 8) of the carrier solution and it was confirmed that the molecular weight (MW) of ConA, spiked with alpha-1 acid glycoprotein (AGP) as a standard glycoprotein, increased due to binding with the mannose moiety of AGP. After adding ConA to bacterial lysates, mannose type N-linked glycoproteins were found to be enriched when the ConA fraction was isolated from whole bacterial lysates through HF5 run. For the identification of glycoproteins, the ConA fraction of HF5 was tryptically digested and followed by two-dimensional nanoflow strong cation exchange-reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry (2D SCX-RPLC-ESI-MS-MS) analysis to identify the N-linked glycoprotein species. From two-dimensional shotgun analyses, 45 proteins that exist on the Asn-Xaa-Ser/Thr sequence were identified as high mannose type N-linked glycoprotein. As a result, it was first demonstrated that HF5 is an alternative tool to enrich high mannose type N-linked glycoproteins using ConA-specific binding affinity.
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