A5005537181- Lung Cancer Treatments and Mutations
- Lung Cancer Research Studies
- Lung Cancer Diagnosis and Treatment
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Single-cell and spatial transcriptomics
- Advanced Biosensing Techniques and Applications
- Biosensors and Analytical Detection
- Bacterial Genetics and Biotechnology
- Tuberculosis Research and Epidemiology
- Molecular Biology Techniques and Applications
- Mycobacterium research and diagnosis
- Epigenetics and DNA Methylation
- Peptidase Inhibition and Analysis
- Bacterial biofilms and quorum sensing
- Cell Image Analysis Techniques
- RNA modifications and cancer
- Protein Degradation and Inhibitors
- Metabolomics and Mass Spectrometry Studies
- Health, Environment, Cognitive Aging
- Trace Elements in Health
- Extracellular vesicles in disease
- Corneal surgery and disorders
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Fuel Cells and Bioremediation
Environmental Molecular Sciences Laboratory
2022-2024
Pacific Northwest National Laboratory
2022-2024
Korea Institute of Science and Technology
2017-2024
Seattle University
2024
Battelle
2022
Hanyang University
2016-2021
Seoul Institute
2019
Chungnam National University
2005-2009
Alcon (China)
2008
Samsung (South Korea)
2002
Mesenchymal stem cells (MSCs) have the potential to be a viable therapy against various diseases due their paracrine effects, such as secretion of immunomodulatory, trophic and protective factors. These are known distributed within organs tissues. Although they possess same characteristics, MSCs from different sources believed potentials patterns, which may influence therapeutic effects in disease environments. We characterized protein secretome adipose (AD), bone marrow (BM), placenta (PL),...
Abstract The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 ( IDH ) wild-type glioblastoma (GBM) is currently limited due to high heterogeneity tumors that impedes patient stratification. Here, we describe a distinct binary classification GBM derived from quantitative proteomic analysis 39 GBMs as well mutant low-grade glioma controls. Specifically, cluster 1 (GPC1) exhibit Warburg-like features, neural stem-cell markers,...
Abstract Despite the increased interest in secretomes associated with paracrine/autocrine mechanisms, majority of mass spectrometric cell secretome studies have been performed using serum-free medium (SFM). On other hand, serum-containing (SCM) is not recommended very much because obtained SCM easily contaminated fetal bovine serum (FBS) proteins. In this study, through combination bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed-SILAC (pSILAC), we analyzed differentially...
An improved spatial proteomics platform to quantify >1500 proteins at a high resolution based on hanging-drop arrangement during protein extraction and digestion.
Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling laser microdissection with mass spectrometry-based proteomics has enabled deep unbiased mapping >1000 proteins. However, the throughput is often limited due to tedious two-step procedures, sequential cutting, sample collection. procedure also hinders further improvement resolution <10 μm as needed for subcellular proteomics....
Abstract Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed NSLA, NSLA with these have been well studied can be treated targeted therapies. To provide insights into the molecular profile of without ALK (NENA), we selected 141 tissues performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC...
We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search cell secretomes. is a small supplementary sequence list highly abundant fetal bovine serum proteins added reference database use. The aim behind using prevent contaminant from being misidentified as other database, just we would cRAP Adventitious present either by accident or through unavoidable contacts proteins. expect it be widely used experiments where are obtained serum-free media...
Upon invading target cells, multifunctional autoprocessing repeats-in-toxin (MARTX) toxins secreted by bacterial pathogens release their disease-related modularly structured effector domains. However, it is unclear how a diverse repertoire of domains within these are processed and activated. Here, we report that Makes caterpillars floppy-like (MCF)-containing MARTX require ubiquitous ADP-ribosylation factor (ARF) proteins for processing activation intermediate modules, which localize in...
The field of terminal proteomics is limited in that it optimized for large-scale analysis via multistep processes involving liquid chromatography. Here, we present an integrated N-terminal peptide enrichment method (iNrich) can handle as little 25 μg cell lysate a single-stage encapsulated solid-phase extraction column. iNrich enables simple, rapid, and reproducible sample processing, treatment wide range protein amounts (25 ∼ 1 mg), multiplexed parallel preparation, in-stage...
The role of matrix metalloproteinase-2 (MMP-2) in tumor cell migration has been widely studied, however, the characteristics and effects MMP-2 clinical sample metastatic colorectal cancer (CRC) remain poorly understood. Here, order to unveil perturbed proteomic signal during induced progression, we analyzed plasma proteome CRC patients according disease HCT116 secretome upon knockdown, publicly available tissue data. Collectively, integrative analysis multi-layered proteomes revealed that a...
Phosphorylation is a crucial component of cellular signaling cascades. It controls variety biological functions, including cell growth and apoptosis. Owing to the low stoichiometry phosphorylated proteins, enrichment phosphopeptides prior LC–MS/MS necessary for comprehensive phosphoproteome analysis, quantitative phosphoproteomic workflows are typically limited by amount sample required. To address this issue, we developed an easy-to-establish, widely applicable, reproducible strategy...
GTPase regulator associated with focal adhesion kinase-1 (Graf1) is an essential component of the GPI-enriched endocytic compartment (GEEC) endocytosis pathway. Mutations in human graf1 gene are acute myeloid leukemia (AML), but its normal role cell development remains unclear. We show that Graf, Drosophila ortholog Graf1, expressed and specifically localizes to GEEC membranes macrophage-like plasmatocytes. also find loss Graf impairs endocytosis, enhances EGFR signaling, induces a...
The ferric uptake regulator (Fur) family proteins include sensors of Fe (Fur), Zn (Zur), and peroxide (PerR). Among Fur proteins, Zur are ubiquitous in most prokaryotic organisms, whereas PerR exists mainly Gram positive bacteria as a functional homologue OxyR. such Bacillus subtilis, Listeria monocytogenes Staphylococcus aureus encode three proteins: Fur, Zur, PerR. In this study, we identified five from B. licheniformis: two novel PerR-like (BL00690 BL00950) addition to (BL05249),...
Abstract The distal bronchioles in Idiopathic Pulmonary Fibrosis (IPF) exhibit histopathological abnormalities such as bronchiolization, peribronchiolar fibrosis and honeycomb cysts that contribute to the overall architectural remodeling of lung tissue seen disease. Here we describe an additional histopathologic finding epithelial desquamation patients with IPF, wherein cells detach from basement membrane bronchioles. To understand mechanism driving this pathology, performed spatial...
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
Co-culture system, in which two or more distinct cell types are cultured together, is advantageous that it can mimic the environment of vivo niche cells. In this study, we presented a strategy to analyze secretome specific type under co-culture condition serum-supplemented media. For cell-specific analysis, expressed mouse mutant methionyl-tRNA synthetase for incorporation non-canonical amino acid, azidonorleucine into newly synthesized proteins cells targeted. The azidonorleucine-tagged...
MTB12 protein, also called CFP-2, is a major and early secreted component of Mycobacterium tuberculosis. However, its role during mycobacterial infection has been poorly characterized. In this study, we purified the native protein investigated profile MTB12-induced cytokines [interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha interleukin (IL)-6], in tuberculosis (TB) patients (n = 20) healthy controls 35). The cytokine profiles were compared with those induced by 30-kDa antigen (Ag)....
It is important to identify and test serologically active antigens, so as devise a cocktail of the best antigens or peptides.We searched for that have serodiagnostic utility using two-dimensional fractionation sonic extracts from Mycobacterium tuberculosis probing with pools sera healthy subjects patients (TB).Reactive protein spots patient were identified by tandem mass spectrometry.Three proteins, Rv0652, Rv2626c, Rv3418c, which not previously been described serologic targets,...
One of the most common chemistries used to label primary amines utilizes N-hydroxysuccinimide (NHS), which is also structurally incorporated in various quantitative proteomic reagents such as isobaric tags for relative and absolute quantification (iTRAQ) tandem mass (TMT). In this paper we report detrimental effect hydroxylamine, a widely quenching reagent excess NHS, on phosphopeptides. We found an impairment degree phosphopeptide identification when hydroxylamine-quenched TMT-labeled...