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Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients
Kim, Taeoh,Kim, Sang Jin,Kim, Kyunggon,Kang, Un-Beom,Lee, Cheolju,Park, Kyong Soo,Yu, Hyeong Gon,Kim, Youngsoo WILEY-VCH 2007 Proteomics Vol. No.
<P>Diabetes can lead to serious microvascular complications like proliferative diabetic retinopathy (PDR), which is the leading cause of blindness in adults. The proteomic changes that occur during PDR cannot be measured in the human retina for ethical reasons, but could be reflected by proteomic changes in vitreous humor. Thus, we considered that comparisons between the proteome profiles of the vitreous humors of PDR and nondiabetic controls could lead to the discovery of novel pathogenic proteins and clinical biomarkers. In this study, the authors used several proteomic methods to comprehensively examine vitreous humor proteomes of PDR patients and nondiabetic controls. These methods included immunoaffinity subtraction (IS)/2-DE/MALDI-MS, nano-LC-MALDI-MS/MS, and nano-LC-ESI-MS/MS. The identified proteins were subjected to the Trans-Proteomic Pipeline validation process. Resultantly, 531 proteins were identified, i.e., 415 and 346 proteins were identified in PDR and nondiabetic control vitreous humor samples, respectively, and of these 531 proteins, 240 were identified for the first time in this study. The PDR vitreous proteome was also found to contain many proteins possibly involved in the pathogenesis of PDR. The proteins described provide the most comprehensive proteome listing in the vitreous humor samples of PDR and nondiabetic control patients.</P>
Kim Na Hyun,Choi Bo-Yun,Kim Eun Sil,Kim Su Jung,Hong Jeong Yeon,Heo Sun-Hee,Jeong Jin-Yong,Kim Kyunggon,Yoo Hyun Ju,Sul Woo Jun,Lee Sei Won 생화학분자생물학회 2023 Experimental and molecular medicine Vol.55 No.-
The interaction between the microbial environment and the host is important for immune homeostasis. Recent research suggests that microbiota dysbiosis can be involved in respiratory diseases. Emphysema is a chronic inflammatory disease, but it is unclear whether dysbiosis caused by antibiotics can affect disease progression. Here, we tried to elucidate the effect of systemic antibiotics on smoking-exposed emphysema models. In this study, the antibiotic mixture caused more alveolar destruction and airspace expansion in the smoking group than in the smoking only or control groups. This emphysema aggravation as a result of antibiotic exposure was associated with increased levels of inflammatory cells, IL-6, IFNγ and protein concentrations in bronchoalveolar lavage fluid. Proteomics analysis indicated that autophagy could be involved in antibiotic-associated emphysema aggravation, and increased protein levels of LC3B, atg3, and atg7 were identified by Western blotting. In microbiome and metabolome analyses, the composition of the gut microbiota was different with smoking and antibiotic exposure, and the levels of short-chain fatty acids (SCFAs), including acetate and propionate, were reduced by antibiotic exposure. SCFA administration restored emphysema development with reduced inflammatory cells, IL-6, and IFNγ and decreased LC3B, atg3, and atg7 levels. In conclusion, antibiotics can aggravate emphysema, and inflammation and autophagy may be associated with this aggravation. This study provides important insight into the systemic impact of microbial dysbiosis and the therapeutic potential of utilizing the gut microbiota in emphysema.
NEDD4L limits cAMP signaling through ubiquitination of CREB‐regulated transcription coactivator 3
Kim, Yo‐,Han,Yoo, Hanju,Hong, A‐,Reum,Kwon, Minseo,Kang, Sang‐,Wook,Kim, Kyunggon,Song, Youngsup Federation of American Society for Experimental Bi 2018 The FASEB Journal Vol.32 No.7
<P>The transcription factor cAMP-responsive element-binding protein (CREB) is involved in a variety of physiologic processes. Although its activity appears to be largely correlated with its phosphorylation status, cAMP-mediated dephosphorylation and the subsequent nuclear migration of the CREB-regulated transcription factors (CRTCs) are required to stimulate CREB transcriptional activity. Among the 3 identified mammalian homologs of CRTCs, CRTC3 has been shown to be expressed predominantly in adipose tissues in response to catecholamine signals that regulate lipid metabolism. Here, we show that prolonged cAMP signaling down-regulates CRTC3 in a proteasome-dependent manner and that neural precursor cell-expressed developmentally down-regulated gene 4-like (NEDD4L), a specific ubiquitin ligase for CRTC3, is responsible for this process. By recognizing the PY motif of CRTC3, NEDD4L interacts with CRTC3 and promotes its polyubiquitination. Interaction between NEDD4L and CRTC3 is further boosted by cAMP signaling, and this enhanced interaction appears to be dependent on the cAMP-mediated phosphorylation of NEDD4L at the Ser448 site. Furthermore, we show that food withdrawal stimulates NEDD4L phosphorylation in mice, which then show a decrease of adipose tissue CRTC3 protein levels. Together, these results suggest that NEDD4L plays a key role in the feedback regulation of cAMP signaling by limiting CRTC3 protein levels.Kim, Y.-H., Yoo, H., Hong, A.-R., Kwon, M., Kang, S.-W., Kim, K., Song, Y. NEDD4L limits cAMP signaling through ubiquitination of CREB-regulated transcription coactivator 3.</P>
Kim, Kyunggon,Kim, Sang Jin,Han, Dohyun,Jin, Jonghwa,Yu, Jiyoung,Park, Kyong Soo,Yu, Hyeong Gon,Kim, Youngsoo American Chemical Society 2013 Journal of proteome research Vol.12 No.3
<P>Diabetic retinopathy (DR) is a complication of diabetes and 80% of diabetes mellitus (DM) patients whose DM duration is over 10 years can be expected to suffer with DR. The diagnosis of DR depends on an ophthalmological examination, and no molecular methods of screening DR status exist. Nonproliferative diabetic retinopathy (NPDR) is the early DR which is hard to be noticed in early NPDR, showing significant cause of adult blindness in type 2 diabetes patients. Protein biomarkers have been valuable in the diagnosis of disease and the use of multiple biomarkers has been suggested to overcome the low specificity of single ones. For biomarker development, multiple reaction monitoring (MRM) has been spotlighted as an alternative method to quantify target proteins with no need for immunoassay. In this study, 54 candidate DR marker proteins from a previous study were verified by MRM in plasma samples from NPDR patients in 3 stages (mild, moderate and severe; 15 cases each) and diabetic patients without retinopathy (15 cases) as a control. Notably, 27 candidate markers distinguished moderate NPDR from type 2 diabetic patients with no diabetic retinopathy, generating AUC values (>0.7). Specifically, 28 candidate proteins underwent changes in expression as type 2 diabetic patients with no diabetic retinopathy progressed to mild and moderate NPDR. Further, a combination of 4 markers from these 28 candidates had the improved specificity in distinguishing moderate NPDR from type 2 diabetic patients with no diabetic retinopathy, yielding a merged AUC value of nearly 1.0. We concluded that MRM is a fast, robust approach of multimarker panel determination and an assay platform that provides improved specificity compared with single biomarker assay systems.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jprobs/2013/jprobs.2013.12.issue-3/pr3012073/production/images/medium/pr-2012-012073_0008.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/pr3012073'>ACS Electronic Supporting Info</A></P>
A Highly Linear Two-Stage Amplifier Integrated Circuit Using InGaP/GaAs HBT
Kyunggon Choi,Minsu Kim,Hyungchul Kim,Sungchan Jung,Jaeyong Cho,Sungchul Yoo,Yong Hwan Kim,Hyungmo Yoo,Youngoo Yang IEEE 2010 IEEE journal of solid-state circuits Vol.45 No.10
<P>This paper presents a linearized two-stage amplifier integrated circuit (IC), having an output power level of about 1 Watt, used for general purpose applications. A predistortion method, based on alignment of the nonlinear characteristics between the first- and the second-stage amplifiers, has been proposed and analyzed in order to enhance the linearization aspects. The resistors in the active bias circuits of both the stages are optimized to achieve the best cancellation conditions for the third-order intermodulation components. The two-stage amplifier IC, which is based on an InGaP/GaAs hetero-junction bipolar transistor (HBT) technology, has been designed and implemented for the 900 MHz band. An output 1 dB compression point (P1dB) of 29.6 dBm, a maximum third-order output intercept point (OIP3) of as high as 48.7 dBm at a two-tone average output power of 21 dBm have been obtained while having a quiescent current of 375 mA and a single bias supply of 5.5 V. The implemented amplifier is able to maintain its IMD3 performance below -60 dBc up to an output power of 21 dBm.</P>
Jin, Jonghwa,Min, Hophil,Kim, Sang Jin,Oh, Sohee,Kim, Kyunggon,Yu, Hyeong Gon,Park, Taesung,Kim, Youngsoo Hindawi Publishing Corporation 2016 Journal of diabetes research Vol.2016 No.-
<P>Diabetic retinopathy (DR) is a common microvascular complication caused by diabetes mellitus (DM) and is a leading cause of vision impairment and loss among adults. Here, we performed a comprehensive proteomic analysis to discover biomarkers for DR. First, to identify biomarker candidates that are specifically expressed in human vitreous, we performed data-mining on both previously published DR-related studies and our experimental data; 96 proteins were then selected. To confirm and validate the selected biomarker candidates, candidates were selected, confirmed, and validated using plasma from diabetic patients without DR (No DR) and diabetics with mild or moderate nonproliferative diabetic retinopathy (Mi or Mo NPDR) using semiquantitative multiple reaction monitoring (SQ-MRM) and stable-isotope dilution multiple reaction monitoring (SID-MRM). Additionally, we performed a multiplex assay using 15 biomarker candidates identified in the SID-MRM analysis, which resulted in merged AUC values of 0.99 (No DR versus Mo NPDR) and 0.93 (No DR versus Mi and Mo NPDR). Although further validation with a larger sample size is needed, the 4-protein marker panel (APO4, C7, CLU, and ITIH2) could represent a useful multibiomarker model for detecting the early stages of DR.</P>
Han, Dohyun,Moon, Sungyoon,Kim, Yikwon,Ho, Won-Kyung,Kim, Kyunggon,Kang, Yup,Jun, Heesook,Kim, Youngsoo American ChemicalSociety 2012 JOURNAL OF PROTEOME RESEARCH Vol.11 No.4
<P>Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examined extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive analytical strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, we attempted to generate data on a large-scale phosphoproteome from the INS-1 rat pancreatic beta-cell line using linear ion trap MS/MS. To profile the phosphoproteome in-depth, we used comprehensive phosphoproteomic strategies, including detergent-based protein extraction (SDS and SDC), differential sample preparation (in-gel, in-solution digestion, and FASP), TiO2 enrichment, and MS replicate analyses (MS2-only and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. We identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of INS-1 cell lysate in 24 LC-MS/MS runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologues. Our informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathology of type 2 diabetes, such as Pdx-1, Nkx2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies.</P>