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Department of Biochemistry and Molecular Biology

Department of Biochemistry and Molecular Biology
:::
簡昆鎰老

Kun-Yi Chien

JobTitle： Professor

CurrentJob： Chang Chung University

E-mail： kychien@mail.cgu.edu.tw

Phone： 5971

Education： Ph.D., National Tsing Hua University

Expertise： Biochemistry, Proteomics, Protein Chemistry, and Spectroscopy Research

Research Directions and Laboratory Features

Proteomics is the comprehensive study of protein expression levels. In the biomedical field, proteomics research usually focuses on identifying proteins that are differentially expressed between two samples. Due to the rapid advancement of analytical technologies, the coverage of proteomic analysis has gradually caught up with that of genomic research. The two most important technologies in this field are mass spectrometry and peptide separation techniques.

The main research interest of our laboratory is to develop and improve these two technologies in order to enhance the breadth, sensitivity, reliability, and automation of proteomic data analysis. Therefore, our laboratory focuses on the development and improvement of the following three proteomic analysis technologies:

1. Establishment of High-Depth Proteome and Phosphoproteome Analysis Technologies

We have established multiple nanoliter-scale multidimensional liquid-phase separation systems, enabling general whole-proteome and phosphoproteome analyses to achieve a depth of more than 10,000 proteins and 30,000 phosphorylated peptides.

2. Establishment of Sensitive Technologies for Simultaneous Detection of Dozens of Target Proteins

By combining chemical modification and chromatographic separation techniques, we remove peptide populations that are unsuitable for quantification. This allows for increased sample loading, and, together with multiple reaction monitoring mass spectrometry, enables simultaneous quantitative analysis of dozens of proteins.

3. Establishment of Analytical Technologies for Ultra-Low-Input Samples

We have established an ultra-low-flow liquid chromatography system to increase the concentration of samples entering the mass spectrometer, thereby improving detection sensitivity. This technology will be applied to single-cell proteomic analysis.

Publication

  1. Chang PK, Chien KY, Chen JC.Dopamine transporter is downregulated and its association with chaperone protein Hsc70 is enhanced by activation of dopamine D3 receptor. Brain Res Bull. 2020 Dec;165:263-271
  2. Chakraborty A, Lin WC, Lin YT, Huang KJ, Wang PY, Chang IY, Wang HI, Ma KT, Wang CY, Huang XR, Lee YH, Chen BC, Hsieh YJ, Chien KY, Lin TY, Liu JL, Sung LY, Yu JS, Chang YS, Pai LM. SNAP29 mediates the assembly of histidine-induced CTP synthase filaments in proximity to the cytokeratin network. J Cell Sci. 2020 May 11;133(9):jcs240200. doi: 10.1242/jcs.240200.
  3. Hsiao TF, Wang CL, Wu YC, Feng HP, Chiu YC, Lin HY, Liu KJ, Chang GC, Chien KY, Yu JS, Yu CJ. Integrative omics analysis reveals soluble cadherin-3 as a survival predictor and an early monitoring marker of EGFR tyrosine kinase inhibitor therapy in lung cancer. Clin Cancer Res. 2020 Jul 1;26(13):3220-3229. doi: 10.1158/1078-0432.CCR-19-3972.
  4. Cheng ML, Chien KY, Lai CH, Li GJ, Lin JF, Ho HY. Metabolic Reprogramming of Host Cells in Response to Enteroviral Infection. Cells. 2020 Feb 18;9(2). pii: E473. doi: 10.3390/cells9020473.
  5. Hsiao YC, Lin SY, Chien KY, Chen SF, Wu CC, Chang YT, Chi LM, , Chiang WF, Chien CY, Chang KP, Chang YS, Yu JS. An immuno-MALDI mass spectrometry assay for the oral cancer biomarker, matrix metalloproteinase-1, in dried saliva spot samples. Anal Chim Acta. 2020 Mar 1;1100:118-130.
  6. Chi LM, Hsiao YC, Chien KY, Chen SF, Chuang YN, Lin SY, Wang WS, Chang IY, Yang C, , Chiang WF, Chien CY, Chang YS, Chang KP, Yu JS. Assessment of candidate biomarkers in paired saliva and plasma samples from oral cancer patients by targeted mass spectrometry. J Proteomics. 2020 Jan 16;211:103571.
  7. Tang WF, Huang RT, Chien KY, Tang P, Horng JT. A large-scale proteomic identification of targets of cellular miR-197 downregulated by enterovirus A71. J Proteome Res. 2019 Jan 4; 18(1):449-460
  8. Lin WC, Chakraborty A, Huang SC, Wang PY, Hsieh YJ, Chien KY, Lee YH, Chang CC, Tang HY, Lin YT, Tung CS, Luo JD, Chen TW, Lin TY, Cheng ML, Chen YT, Yeh CT, Liu JL, Sung LY, Shiao MS, Yu JS, Chang YS, Pai LM. Histidine-Dependent Protein Methylation Is Required for Compartmentalization of CTP Synthase. Cell Rep. 2018 Sep 4;24(10):2733-2745.e7. doi: 10.1016/j.celrep.2018.08.007.
  9. Huang TY, Chi LM, Chien KY. Size-exclusion chromatography using reverse-phase columns for protein separation. J Chromatogr A. 2018 Oct 12;1571:201-212. doi: 10.1016/j.chroma.2018.08.020. Epub 2018 Aug 10.
  10. He JP, Hou PP, Chen QT, Wang WJ, Sun XY, Yang PB, Li YP, Yao LM, Li X, Jiang XD, Chien KY, Zhang ZM, Wu QW, Cowin AJ, Wu Q, Chen HZ. Flightless-I Blocks p62-Mediated Recognition of LC3 to Impede Selective Autophagy and Promote Breast Cancer Progression. Cancer Res. 2018 Sep 1;78(17):4853-4864. doi: 10.1158/0008-5472.CAN-17-3835. Epub 2018 Jun 13.
  11. Chuang CF, King CE, Ho BW, Chien KY, Chang YC. Unbiased Proteomic Study of the Axons of Cultured Rat Cortical Neurons. J Proteome Res. 2018 May 4;17(5):1953-1966. doi: 10.1021/acs.jproteome.8b00069. Epub 2018 Apr 19.
  12. Li XX, Wang ZJ, Zheng Y, Guan YF, Yang PB, Chen X, Peng C, He JP, Ai YL, Wu SF, Chien KY, Wu Q, Chen HZ. Nuclear Receptor Nur77 Facilitates Melanoma Cell Survival under Metabolic Stress by Protecting Fatty Acid Oxidation. Mol Cell. 2018 Feb 1;69(3):480-492.e7.
  13. Hsiao YC, , Chen YT, Chi LM, Chien KY, Chiang WF, Chang YT, Chen SF, Wang WS, Chuang YN, Lin SY, Chien CY, Chang KP, Chang YS, Yu JS. Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring-Mass Spectrometry. Proteomics Clin Appl. 2018 Mar;12(2). doi: 10.1002/prca.201700039
  14. Chen HY, Chang JT, Chien KY, Lee YS, You GR, Cheng AJ. The Endogenous GRP78 Interactome in Human Head and Neck Cancers: A Deterministic Role of Cell Surface GRP Cancer Stemness. Sci Rep. 2018 Jan 11;8(1):536.
  15. Tsai HJ, Chien KY, Liao HR, Shih MS, Lin YC, Chang YW, Cheng JC, Tseng CP. Functional links between Disabled-2 Ser723 phosphorylation and thrombin signaling in human platelets. J Thromb Haemost. 2017 Oct;15(10):2029-2044.
  16. Chen TW, Gan RC, Fang YK, Chien KY, Liao WC, Chen CC, Wu TH, Chang IY, Yang C, Huang PJ, Yeh YM, Chiu CH, Huang TW, Tang P. FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci Rep. 2017 Sep 5;7(1):10430.
  17. Hsiao YC, Chi LM, Chien KY, Chiang WF, Chen SF, Chuang YN, Lin SY, Wu CC, Chang YT, , Chen YT, Chia SL, Chien CY, Chang KP, Chang YS, Yu JS. Development of a Multiplexed Assay for Oral Cancer Candidate Biomarkers Using Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry. Mol Cell Proteomics. 2017 Oct;16(10):1829-1849.
  18. Hsieh YJ, Chien KY, Yang IF, Lee IN, Wu CC, Huang TY, Yu JS. Oxidation of protein-bound methionine in Photofrin-photodynamic therapy-treated human tumor cells explored by methionine-containing peptide enrichment and quantitative proteomics approach. Sci Rep. 2017 May 2;7(1):1370.
  19. Bian XL, Chen HZ, Yang PB, Li YP, Zhang FN, Zhang JY, Wang WJ, Zhao WX, Zhang S, Chen QT, Zheng Y, Sun XY, Wang XM, Chien KY, Wu Q. Nur77 suppresses hepatocellular carcinoma via switching glucose metabolism toward gluconeogenesis through attenuating phosphoenolpyruvate carboxykinase sumoylation. Nat Commun. 2017 Feb 27;8:14420.
  20. Lin YH, Zhen YY, Chien KY, Lee IC, Lin WC, Chen MY, Pai LM. LIMCH1 regulates nonmuscle myosin-II activity and suppresses cell migration. Mol Biol Cell. 2017 Apr 15;28(8):1054-1065.
  21. Lin YT, Chien KY, Wu CC, Chang WY, , Chen MC, Yeh CT, Yu JS. Super-SILAC mix coupled with SIM/AIMS assays for targeted verification of phosphopeptides discovered in a large-scale phosphoproteome analysis of hepatocellular carcinoma. J Proteomics. 2017 Mar 22;157:40-51.
  22. Kung YA, Hung CT, Chien KY, Shih SR. Control of the negative IRES trans-acting factor KHSRP by ubiquitination. Nucleic Acids Res. 2017 Jan 9;45(1):271-287.