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Assistant Professor

University Department/Institute Degree
National Tsing Hua University, Taiwan Institute of Bioinformatics and Structural Biology (in association with Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica) Ph.D.
National Yang Ming University, Taiwan Institute of Genetics M.Sc.
National Taiwan University, Taiwan Department of Zoology B.Sc

Period Institute Department Position
2010.11 – 2012.01 Kyoto University, Japan Graduate School of Pharmaceutical Sciences Researcher
2010.04 – 2010.10 Keio University, Japan Institute for Advanced Biosciences Researcher
2009.08 – 2010.03 Academia Sinica, Taiwan Institute of Chemistry Post-doctoral Fellow

2.Post-translational modification proteomics
3.Therapeutic drug monitoring

Journal Paper
Updated: 2023/2/28

1. Chen YN, Shih, CY, Guo, SL, Liu, CY, Shen MH, Chang SC, Ku WC, Huang CC*, and Huang CJ*. (2023) Potential prognostic and predictive value of UBE2N, IMPDH1, DYNC1LI1 and HRASLS2 in colorectal cancer stool specimens. Biomed Rep 18(3): 22. PMID: 36846616.

2. Lu ML, Ku WC, Syifa N, Hu SC, Chou CT, Wu YH, Kuo PH, Chen CH, Chen WJ, and Wu TH*. (2022) Developing a sensitive platform to measure 5-methyltetrahydrofolate in subjects with MTHFR and PON1 gene polymorphisms. Nutrients 14(16): 3320. PMID: 36014826.

3. Huang A, Huang SY, Shah P, Ku WC, Huang KT, Liu YF, Su CL, and Huang RS*. (2022) Suboptimal folic acid exposure rewires oncogenic metabolism and proteomics signatures to mediate human breast cancer malignancy. J Nutr Biochem 106109000. PMID: 35460832.

4. Hsu WH, Han DS, Ku WC, Chao YM, Chen CC*, and Lin YL*. (2022) Metabolomic and proteomic characterization of sng and pain phenotypes in fibromyalgia. Eur J Pain 26(2): 445-462. PMID: 34608709.

5. Cheng YC, Huang CJ, Ku WC, Guo SL, Tien LT, Lee YJ*, and Chien, CC*. (2022) Downregulated calcium-binding protein S100A16 and HSP27 in placenta-derived multipotent cells induce functional astrocyte differentiation. Stem Cell Rev Rep, 18(2): 839-852. PMID: 35061207.

6. Chang CC, Kao WY, Liu CY, Su HH, Kan YA, Lin PY, Ku WC, Chang KW, Yang RN, and Huang CJ*. (2022) Butyrate supplementation regulates expression of chromosome segregation 1like protein to reverse the genetic distortion caused by p53 mutations in colorectal cancer. Int J Oncol 60(6), 64. PMID: 35417036.

7. Wang YC, Ku WC, Liu, CY, Cheng, YC, Chien, CC, Chang, KW, and Huang, CJ*. (2021) Supplementation of probiotic Butyricicoccus pullicaecorum mediates anticancer effect on bladder urothelial cells by regulating butyrate-responsive molecular signatures. Diagnostics 11(12): 2270. PMID: 34943506.

8. Liu CY, Huang CS, Huang CC, Ku WC, Shih HY, and Huang CJ*. (2021) Co-occurrence of differentiated thyroid cancer and second primary malignancy: Correlation with expression profiles of mismatch repair protein and cell cycle regulators. Cancers (Basel) 13(21): 5486. PMID: 34771648.

9. Chen RL, Fang LH, Yang XY, El Amrani M, Uijtendaal EV, Chen YF, and Ku WC*. (2021) Therapeutic drug monitoring of busulfan in patients undergoing hematopoietic cell transplantation: A pilot single-center study in Taiwan. Pharmaceuticals 14(7): 613. PMID: 34206798.

10. Chen SK, Wang YC, Lin TY, Wu HJ, Huang CJ, and Ku WC*. (2021) G-Protein-coupled estrogen receptor 1 agonist G-1 perturbs sunitinib resistance-related phosphoproteomic signatures in renal cell carcinoma. Cancer Genom Proteom 18(3): 207-220. PMID: 33893075.

11. Ku WC, Sridharan B, Chen JY, Li JY, Yang SY, and Lee MJ*. (2021) Kaempferitrin-treated HepG2 differentially expressed exosomal markers and affect extracellular vesicle sizes in the secretome. Biomolecules 11(2): 187. PMID: 33572893.

12. Wang YY, Ke CC, Chen YL, Lin YH, Yu IS, Ku WC, O'Bryan MK, and Lin YH*. (2020) Deficiency of the Tbc1d21 gene causes male infertility with morphological abnormalities of the sperm mitochondria and flagellum in mice. PLoS Genet 16(9): e1009020. PMID: 32976492.

13. Lin YH, Huang CY, Ke CC, Wang YY, Lai TH, Liu HC, Ku WC, Chan CC, and Lin YH*. (2020) ACTN4 mediates SEPT14 mutation-induced sperm head defects. Biomedicines 8(11): 518. PMID: 33228246.

14. Cheng YC, Ku WC, Tseng TT, Wu CP, Li MJ, and Lee SC*. (2020) Anchorage independence altered vasculogenic phenotype of melanoma cells through downregulation in aminopeptidase N /syndecan-1/integrin beta4 axis. Aging (Albany NY) 12(17): 16803-16819. PMID: 32756007.

15. Huang KT, Shen YL, Lee CN, Chu KY, Ku WC, Liu CY, and Huang RS*. (2020) Using differential threshold effects of individual and combined periconceptional methyl donor status on maternal genomic LINE-1 and imprinted H19 DNA methylation to predict birth weight variance in the Taiwan Pregnancy-Newborn Epigenetics (TPNE) cohort study. J Nutr 150(1): 108-117. PMID: 31504733.

16. Yeh TT, Ho MY, Chen WY, Hsu YC, Ku WC, Tseng HW, Chen ST, and Chen SF*. (2019) Comparison of different fractionation strategies for in-depth phosphoproteomics by liquid chromatography tandem mass spectrometry. Anal Bioanal Chem 411(15): 3417-3424. PMID: 31011783.

17. Ku WC, Chen SK, Lin CM, Tang C, and Wang YC*. (2019) Label-free quantitative phosphoproteomics reveals the role of beta-estradiol in sunitinib-resistant renal cell carcinoma growth via perturbing transforming growing factor-beta pathway. Urol Sci 30(3): 107-113.

18. Hsu WH, Lee CH, Chao YM, Kuo CH, Ku WC, Chen CC*, and Lin YL*. (2019) ASIC3-dependent metabolomics profiling of serum and urine in a mouse model of fibromyalgia. Sci Rep 9(1): 12123. PMID: 31431652.

19. Hsu WH, Shen YC, Shiao YJ, Kuo CH, Lu CK, Lin TY, Ku WC*, and Lin YL*. (2019) Combined proteomic and metabolomic analyses of cerebrospinal fluid from mice with ischemic stroke reveals the effects of a Buyang Huanwu decoction in neurodegenerative disease. PLoS One 14(1): e0209184. PMID: 30645580.

20. Ke CC, Lin YH, Wang YY, Wu YY, Chen MF, Ku WC, Chiang HS, and Lai TH*. (2018) TBC1D21 potentially interacts with and regulates Rap1 during murine spermatogenesis. Int J Mol Sci 19(11): 3292. PMID: 30360518.

21. Ku WC, Chang YL, Wu SF, Shih HN, Tzeng YM, Kuo HR, Chang KM, Agrawal DC, Liu BL, Chang CA, Huang S, and Lee MJ*. (2017) A comparative proteomic study of secretomes in kaempferitrin-treated CTX TNA2 astrocytic cells. Phytomedicine 36: 137-144. PMID: 29157807.

22. Tsai CF, Ku WC, Chen YJ, and Ishihama Y*. (2017) Absolute phosphorylation stoichiometry analysis by motif-targeting quantitative mass spectrometry. Methods Mol Biol 1636: 313-325. PMID: 28730488.

23. Huang JH, Ku WC, Chen YC, Chang YL, and Chu CY*. (2017) Dual mechanisms regulate the nucleocytoplasmic localization of human DDX6. Sci Rep 7: 42853. PMID: 28216671.

24. Lin YH, Ke CC, Wang YY, Chen MF, Chen TM, Ku WC, Chiang HS, and Yeh CH*. (2017) RAB10 interacts with the male germ cell-specific GTPase-activating protein during mammalian spermiogenesis. Int J Mol Sci 18(1): 97. PMID: 28067790.

25. Wu ST, Ku WC, Huang CJ, Wang YJ, Lin CM, and Chen SK*. (2016) Cellular effects induced by 17-β-estradiol to reduce the survival of renal cell carcinoma cells. J Biomed Sci 23(1): 67. PMID: 27680214.

26. Hirata H, Ku WC, Yip AK, Ursekar CP, Kawauchi K, Roy A, Guo AK, Vedula SR, Harada I, Chiam KH, Ishihama Y, Lim CT, Sawada Y*, and Sokabe M*. (2016) MEKK1-dependent phosphorylation of calponin-3 tunes cell contractility. J Cell Sci 129(19): 3574-3582. PMID: 27528401.

27. Cheng YC, Huang CJ, Lee YJ, Tien LT, Ku WC, Chien R, Lee FK*, and Chien CC*. (2016) Knocking down of heat-shock protein 27 directs differentiation of functional glutamatergic neurons from placenta-derived multipotent cells. Sci Rep 6: 30314. PMID: 27444754.

28. Chen KC, Lin CM, Huang CJ, Chen SK, Wu ST, Chiang HS*, and Ku WC*. (2016) Dual Roles of 17-beta estradiol in estrogen receptor-dependent growth inhibition in renal cell carcinoma. Cancer Genom Proteom 13(3): 219-230. PMID: 27107064.

29. Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC*, and Juan HF*. (2015) Temporal phosphoproteome dynamics induced by an ATP synthase inhibitor citreoviridin. Mol Cell Proteomics 14(12): 3284-3298. PMID: 26503892.

30. Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y*, and Chen YJ*. (2015) Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. Nat Commun 6: 6622. PMID: 25814448.

31. Hu CW, Tseng CW, Chien CW, Huang HC, Ku WC, Lee SJ*, Chen YJ*, and Juan HF*. (2013) Quantitative proteomics reveals diverse roles of miR-148a from gastric cancer progression to neurological development. J Proteome Res 12(9): 3993-4004. PMID: 23869555.

32. Araki Y, Ku WC, Akioka M, May AI, Hayashi Y, Arisaka F, Ishihama Y, and Ohsumi Y*. (2013) Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity. J Cell Biol 203(2): 299-313. PMID: 24165940.

33. Ku WC, and Ishihama Y*. (2013) Proteomic analyses of post-translational modifications. In: Li, S. Y. F., ed. Quantitative Proteome Analysis, pp. 45-66, Pan Stanford Publishing.

34. Hu CW, Lin MH, Huang HC, Ku WC, Yi TH, Tsai CF, Chen YJ, Sugiyama N, Ishihama Y*, Juan HF*, and Wu SH*. (2012) Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production. J Proteome Res 11(11): 5362-5375. PMID: 23030682.

35. Ku WC, Sugiyama N, and Ishihama Y*. (2012) Large-scale protein phosphorylation analysis by mass spectrometry-based phosphoproteomics. In: Mukai, H., ed. Protein Kinase Technologies, pp. 35-46, Humana Press.

36. Chen YJ, Ku WC, Lin PY, Chou HC, Khoo KH, and Chen YJ*. (2010) S-Alkylating labeling strategy for site-specific identification of the S-nitrosoproteome. J Proteome Res 9(12): 6417-6439. PMID: 20925432.

37. Ku WC, Chiu SK, Chen YJ, Huang HH, Wu WG, and Chen YJ*. (2009) Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2. Mol Cell Proteomics 8(9): 2034-2050. PMID: 19505873.

38. Chen YJ, Ku WC, Feng LT, Tsai ML, Hsieh CH, Hsu WH, Liaw WF, Hung CH*, and Chen YJ*. (2008) Nitric oxide physiological responses and delivery mechanisms probed by water-soluble Roussin’s red ester and {Fe(NO)2}10 DNIC. J Am Chem Soc 130(33): 10929-10938. PMID: 18661983.

39. Chen CC, Ku WC, Chiu SK, and Tzeng CM*. (2006) Deoxyribonucleic acid hybridization acceleration by photovoltaic effect. Appl Phys Lett 89(23), 233902.

40. Ku WC, Lau WK, Tseng YT, Tzeng CM, and Chiu SK*. (2004) Dextran sulfate provides a quantitative and quick microarray hybridization reaction. Biochem Biophys Res Commun 315(1): 30-37. PMID: 15013421.

41. Chu SK, Hsu M, Ku WC, Tu CY, Tseng YT, Lau WK, Yan RY, Ma JT, and Tzeng CM*. (2003) Synergistic effects of epoxy- and amine-silanes on microarray DNA immobilization and hybridization. Biochem J 374(Pt 3): 625-632. PMID: 12809552.

42. Ku WC, Cheng AJ, and Wang TC*. (1997) Inhibition of telomerase activity by PKC inhibitors in human nasopharyngeal cancer cells in culture. Biochem Biophys Res Commun 241(3): 730-736. PMID: 9434777.

Conference Paper
1. Li-Hua Fang, Xin-Yi Yang, Wen-Hui Ku, Erik van Maarseveen, Rong-Long Chen, and Wei-Chi Ku. (2018) A pilot, single-center study of busulfan TDM in patients receiving hematopoietic cell transplant in Taiwan. Mass Spectrometry for Clinical Diagnosis 2018 (MSCD 2018)
2. Yu-Heng Hsieh, Shao-Kuan Chen, Yen-Chieh Wang, Teh-Sheng Hsieh, Chih-Jung Huang, and Wei-Chi Ku. (2018) Quantitative Phosphoproteomics Indicates Altered Cell Migration in Prolonged Cabozantinib-Treated Renal Cell Carcinoma Cell Lines. 17th Human Proteome Organization World Congress 2018 (HUPO 2018).
3. Li-Hua Fang, Xin-Yi Yang, Rong-Long Chen, Wen-Hui Ku, Yen-Fu Chen, Erik van Maarseveen, and Wei-Chi Ku. (2017) Pharmacokinetics of Plasma Busulfan using Isotope Dilution Mass Spectrometry: A Pilot Study of Patients Receiving Hematopoietic Cell Transplant in Taiwan. IATDMCT2017.
4. Shao-Kuan Chen, Chi-Jung Huang, Yen-Chieh Wang, Tai-Yuan Lin, and Wei-Chi Ku. (2017) Phospho-barcodes of renal cell carcinoma cell lines reveals differential mechanisms in sunitinib resistance. 65th ASMS Conference on Mass Spectrometry.
5. Shao-Kuan Chen, Chi-Jung Huang, Tai-Yuan Lin, and Wei-Chi Ku. (2016) Early phosphoproteomic dynamics for potential growth-regulating mechanisms in G-1 treated renal cell carcinoma cell line. 15th Human Proteome Organization World Congress 2016 (HUPO 2016).
6. Wei-Chi Ku, Chi‐Jung Huang, Sheng‐Tang Wu, and Shao‐Kuan Chen. (2015) Investigating the Effect of Estrogen on Renal Cell Carcinoma with Different VHL Genetic Backgrounds using Quantitative Proteomics. 63th ASMS Conference on Mass Spectrometry.
7. Wei-Chi Ku, Zhi-Yu Liu, Chi-Jung Huang, Kuo-Chiang Chen, Yen-Chieh Wang, Shao-Kuan Chen, and Chih-Ming Lin. (2014) Temporal phosphoproteomic study on estrogen receptor-dependent cytotoxicity in renal cell carcinoma. 62th ASMS Conference on Mass Spectrometry.
8. Wei-Chi Ku, Sung-Kay Chiu, Yi-Ju Chen, Hsin-Hung Huang, Wen-Guey Wu, and Yu-Ju Chen. (2009) Complementary Quantitative Proteomics Reveals an AP-4 Complex Repressing HDM2 Expression. HUPO2009 World Congress. (Young Investigator Award)
9. Yi-Ju Chen, Wei-Chi Ku, Ming-Li Tsai, Wen-Feng Liaw, and Yu-Ju Chen. (2007) Exploring the Acting Mechanism of Nitric Oxide by Proteomic Study Using in vitro Cell Cultures as a Model System. 55th ASMS Conference on Mass Spectrometry.
10. Wei-Chi Ku, Hsin-Hung Huang, Yi-Ju Chen, and Yu-Ju Chen. (2007) Identification of AP-4 Complex as Potential Transcriptional Regulator of Mdm2 by Quantitative Proteomic Approach. 55th ASMS Conference on Mass Spectrometry.
11. Wei-Chi Ku, Mandy Hsu, Ching-Yu Tu, Jing-Tyan Ma, Sung-Kay Chiu, and Chi-Meng Tzeng. (2001) A microarray slide that efficiently immobilizes biological materials. Chips to Hits 2001.

Research Interest
With recent advances in instrument and analytical strategy, mass spectrometry (MS) has been an indispensable technology in clinical chemistry, ex. therapeutic drug monitoring (TDM), as well as biomedical research, such as quantitative proteomics. By applying state-of-art MS technologies, we explore several research topics as follows:

Precision medicine of renal cell carcinoma
In Taiwan, renal cell carcinoma (RCC) accounts for 1.26% of all cancer cases annually. For each patient with RCC, he or she may carry individualized signaling alteration, which can affect the therapeutic efficacy as well as prognostic results. The sequence of the most optimal therapies still remains highly challenging issue, especially on the quick development of drug resistance in mRCC patients. We take advantage of quantitative phosphoproteomics to construct Taiwan-localized and personalized RCC “phospho-barcode” database, and screen for novel drug targets for managing RCC.

Development and application of TDM methods
In the past decade, there is increased recognition that LC-MS based TDM is important in wide applications in clinical tests. By using selected reaction monitoring (SRM) approach, LC-MS provides highly sensitive and selective detection of drug targets in complex biological samples, such as blood and tissue. We have been cooperated with world-leading clinical chemistry laboratory and developed TDM method for simultaneous quantitation of five commonly-used anti-fungal agents, as well as temporal measurement of busulfan for conditioning of hematopoietic stem cell transplantation. With the success of application in several TDM methods, we take a step forward to develop TDM methods for accurately quantitate active form of monoclonal antibody drug in patient blood samples. Currently, we focus on the drugs for treating rheumatoid arthritis.