• Mass Spectrometry Letters
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• v.9 no.2
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• pp.51-55
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• 2018

Capture of non-glycoproteins during lectin affinity chromatography is frequently observed, although it would seem to be anomalous. In actuality, lectin affinity chromatography works at post-translational modification (PTM) sites on a glycoprotein which is not involved in protein-protein interactions (PPIs). In this study, serial affinity column set (SACS) using lectins followed by proteomics methods was used to identify PPI mechanisms of captured proteins in human plasma. MetaCore, STRING, Ingenuity Pathway Analysis (IPA), and IntAct were individually used to elucidate the interactions of the identified abundant proteins and to obtain the corresponding interaction maps. The abundant non-glycoproteins were captured with the binding to the selected glycoproteins. Therefore, depletion process in sample pretreatment for abundant protein removal should be considered with more caution because it may lose precious disease-related low abundant proteins through PPIs of the removed abundant proteins in human plasma during the depletion process in biomarker discovery. Glycoproteins bearing specific glycans are frequently associated with cancer and can be specifically isolated by lectin affinity chromatography. Therefore, SACS using Lycopersicon esculentum lectin (LEL) can also be used to study disease interactomes.

• BMB Reports
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• v.45 no.6
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• pp.323-330
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• 2012

The glycome consists of all glycans (or carbohydrates) within a biological system, and modulates a wide range of important biological activities, from protein folding to cellular communications. The mining of the glycome for disease markers represents a new paradigm for biomarker discovery; however, this effort is severely complicated by the vast complexity and structural diversity of glycans. This review summarizes recent developments in analytical technology and methodology as applied to the fields of glycomics and glycoproteomics. Mass spectrometric strategies for glycan compositional profiling are described, as are potential refinements which allow structure-specific profiling. Analytical methods that can discern protein glycosylation at a specific site of modification are also discussed in detail. Biomarker discovery applications are shown at each level of analysis, highlighting the key role that glycoscience can play in helping scientists understand disease biology.

• BMB Reports
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• v.56 no.6
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• pp.341-346
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• 2023

Acute myocardial infarction (AMI) is a multifaceted syndrome influenced by the functions of various extrinsic and intrinsic pathways and pathological processes, which can be detected in circulation using biomarkers. In this study, we investigated the secretome protein profile of induced-hypertrophy cardiomyocytes to identify next-generation biomarkers for AMI diagnosis and management. Hypertrophy was successfully induced in immortalized human cardiomyocytes (T0445) by 200 nM ET-1 and 1 μM Ang II. The protein profiles of hypertrophied cardiomyocyte secretomes were analyzed by nano-liquid chromatography with tandem mass spectrometry and differentially expressed proteins that have been identified by Ingenuity Pathway Analysis. The levels of 32 proteins increased significantly (>1.4 fold), whereas 17 proteins (<0.5 fold) showed a rapid decrease in expression. Proteomic analysis showed significant upregulation of six 14-3-3 protein isoforms in hypertrophied cardiomyocytes compared to those in control cells. Multi-reaction monitoring results of human plasma samples showed that 14-3-3 protein-zeta levels were significantly elevated in patients with AMI compared to those of healthy controls. These findings elucidated the role of 14-3-3 protein-zeta in cardiac hypertrophy and cardiovascular disorders and demonstrated its potential as a novel biomarker and therapeutic strategy.

• Genomics & Informatics
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• v.14 no.1
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• pp.2-11
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• 2016

The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins. Recently, it has been addressed that cellular pathways can provide better indications of disease states than individual molecules and also network analysis of the DEPs enables effective identification of cellular pathways altered in disease conditions and key molecules representing the altered cellular pathways. Accordingly, a number of network-based approaches to identify disease-related pathways and representative molecules of such pathways have been developed. In this review, we summarize analytical platforms for network-based protein biomarker discovery and key components in the platforms.

• Journal of Microbiology and Biotechnology
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• v.22 no.5
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• pp.654-658
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• 2012

Osteoarthritis (OA) is the most common rheumatic pathology. One of the major objectives of OA research is the development of early diagnostic strategies such as those using proteomic technology. Synovial fluid (SF) in OA patients is a potential source of biomarkers for OA. The efficient and reliable preparation of SF proteomes is a critical step towards biomarker discovery. In this study, we have optimized a pretreatment method for twodimensional gel electrophoresis (2DE) separation of the SF proteome, by enriching low-abundance proteins and simultaneously removing hyaluronic acid, albumin, and IgG. SF samples pretreated using this optimized method were then evaluated by 1DE and 2DE separation followed by immunodetection of cartilage oligomeric matrix protein (COMP), a known OA biomarker, and by the identification of 3 proteins (apolipoprotein, haptoglobin precursor, and fibrinogen D fragment) that are related to joint diseases.

• KSBB Journal
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• v.26 no.4
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• pp.352-356
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• 2011

The detection of biomarkers is an important issue for disease diagnosis. However, many systems are not suitable to detect the biomarker itself directly. For direct detection of biomarker proteins in human serum, a new affinity-capture method using aptamers combined with the mass spectrometry was suggested. Since signals from protein samples cannot be amplified, modified chromatin immunoprecipitation (ChIP) and subsequent cross-linking with formaldehyde between aptamers and target proteins were used not to lose the captured target proteins, which allowed us to perform a harsh washing step to remove the non-specifically bound proteins. As a model system, a thrombin aptamer was used as a bait and thrombin as a target protein. Using our modified ChIP and affinity-capture method, non-specific binding proteins on the beads decreased significantly, suggesting that our new method is efficient and can be applied to developing diagnosis systems for various biomarkers.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2297-2299
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• 2016

Background: Early detection of malignant transformation with expression biomarkers has significant potential to improve the survival rate of patients as such biomarkers enable prediction of progression and assess sensitivity to chemotherapy. The expression of interferon inducible transmembrane protein 1 (IFITM1) has been associated with early invasion events in several carcinomas, including head and neck cancers, and hence has been proposed as a novel candidate biomarker. As the incidence of oral squamous cell carcinoma (OSCC) is highest in the Indian population, we sought to investigate: 1) the expression pattern of IFITM1 in OSCC tissue samples obtained from Indian patients of Dravidian origin; and 2) the possibility of using IFITM1 expression as a potential biomarker. Materials and Methods: Total RNA extracted from thirty eight OSCC biopsy samples was subjected to semi-quantitative RT-PCR with IFITM1 and GAPDH specific primers. Results: Of the thirty eight OSCC samples that were analyzed, IFITM1 overexpression was identified in fifteen (39%). Seven expressed a low level, while the remainder expressed high level of IFITM1. Conclusions: The overexpression of IFITM1 in OSCC samples indicates that IFITM1 may be explored for the possibility of use as a high confidence diagnostic biomarker in oral cancers. To the best of our knowledge, this is the first time that IFITM1 overexpression is being reported in Indian OSCC samples.

• Applied Chemistry for Engineering
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• v.30 no.3
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• pp.379-383
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• 2019

The capability of detecting amyloid beta 42 ($A{\beta}42$), a biomarker of Alzheimer's disease, using a thiolated protein A-functionalized bimetallic surface plasmon resonance (SPR) chip was investigated. An optimized configuration of a bimetallic chip containing gold and silver was obtained through calculations in the intensity measurement mode. The surface of the SPR bimetallic chip was functionalized with thiolated protein A for the immobilization of $A{\beta}42$ antibody. The response of the thiolated protein A-functionalized bimetallic chip to $A{\beta}42$ in the concentration range of 50 to 1,000 pg/mL was linear. Compared to protein A without thiolation, the thiolated protein A resulted in greater sensitivity. Therefore, the thiolated protein A-functionalized bimetallic SPR chip can be used to detect very low concentrations of the biomarker for Alzheimer's disease.

• Proceedings of the Korean Society of Soil Zoology Conference
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• 2005.09a
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• pp.25-25
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• 2005

• The Journal of Korean Medicine
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• v.43 no.3
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• pp.106-121
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• 2022

Objectives: The purpose of this study was to investigate the anti-inflammatory effect of Cornus Officinalis fruit extract(CE) and Cornus Officinalis Fruit Cheonghyeol Plus(CCP) in Human Umbilical Vein Endothelial Cell. Methods: We measured cell viability of CE, CCP and treated HUVEC with TNF-α. We measured the mRNA expression levels of KLF2, eNOS, MCP-1, ICAM-1, VCAM-1, the protein expression levels of KLF2, eNOS, MCP-1, ICAM-1, VCAM-1, and the protein phosphorylation level of ERK, JNK, p38 and the biomarker expression levels of MCP-1, ICAM-1, VCAM-1. Results: 1.CE incresed the mRNA, protein expression levels of KLF2, eNOS at concentrations of 100㎍/㎖ compared to the control group. CE decresed the mRNA, protein and biomarker expression levels of MCP-1,ICAM-1,VCAM-1 at concentrations of 100㎍/㎖ compared to the control group. CE decresed the protein phosphorylation level of p38 at concentrations of 100㎍/㎖ compared to the control group. 2. CCP incresed the mRNA, protein expression levels of KLF2, eNOS at concentrations of 100㎍/㎖ or more compared to the control group. CCP decresed the mRNA, protein and biomarker expression levels of MCP-1, ICAM-1, VCAM-1 at concentrations of 100㎍/㎖ or more compared to the control group. CCP decresed the protein phosphorylation level of ERK at concentrations of 100㎍/㎖ or more, p38 at concentrations of 200㎍/㎖ or more, and JNK at concentrations of 400㎍/㎖ compared to the control group. Conclusions: These results present that CE and CCP has anti-inflammatory effect in HUVEC. So, it could help treat or prevent inflammation in vein caused by dyslipidemia and contribute prevention of cardiovascular and cerebrovascular cerebrovascular diseases.