學歷
學校 系所 學位
國立清華大學 生物資訊與結構生物研究所(中央研究院國際研究生學程之化學生物與生物物理學程) 博士
國立陽明大學 遺傳所 碩士
國立台灣大學 動物學系 學士
經歷
期間 單位 部門 職稱
2022.02 – 迄今 輔仁大學 醫學系 副教授
2012.02 – 2022.01 輔仁大學 醫學系 助理教授
2010.11 – 2012.01 日本京都大學 藥學系 博士後研究
2010.04 – 2010.10 日本慶應義塾大學 尖端生命科學研究所 博士後研究
2009.08 – 2010.03 中央研究院 化學所 博士後研究
專長
蛋白質體學分析
轉譯後修飾蛋白質體學分析
臨床治療藥物監測之技術開發
學術著作
期刊論文
期間 內容
Updated: 2025/12/31
1. Lee YC, Ku WC, Hung YL, Chen YC, Hung CF, Wang JT, and Liu WL*. (2025) Factors associated with beyond-therapeutic serum voriconazole trough level among critically ill patients with invasive fungal infections. BMC Infect Dis 25(1): 1807. PMID: 41275081.
2. Ku WC, Phan NN, Liu CY, Huang CJ, Liao CC, Huang YC, Kong PH, Tseng LM*, and Huang CC*. (2025) Collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes by functional proteomics from core needle biopsy samples of Taiwanese breast cancer. Biophys Rep 44: 102210. PMID: 40927672.
3. Ku WC, Liu CY, Huang CJ, Liao CC, Huang YC, Kong PH, Hsieh CC, H, Tseng LM*, and Huang CC*. (2025) Integrating functional proteomics and next generation sequencing reveals potential therapeutic targets for Taiwanese breast cancer. Clin Proteomics 22(1): 4. PMID: 39844043.
4. Pan PY, Ke CC, Wang YY, Lin YH, Ku WC, Au CF, Chan CC, Huang CY, and Lin YH*. (2024) Proteomic profiling of TBC1 domain family member 21-null sperms reveals the critical roles of TEKT 1 in their tail defects, Dev Dyn 253(11): 1024-1035. PMID: 38822685.
5. Wang, YY, Lin, YH, Wu, VC, Lin, YH, Huang, CY, Ku, WC, and Sun, CY*. (2023) Decreased Klotho expression causes accelerated decline of male fecundity through oxidative injury in murine testis. Antioxidants (Basel) 12(9). PMID: 37759974.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. Chen CC, Ku WC, Chiu SK, and Tzeng CM*. (2006) Deoxyribonucleic acid hybridization acceleration by photovoltaic effect. Appl Phys Lett 89(23), 233902.
45. 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.
46. 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.
47. 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.
研討會論文
期間 內容
1. Wei-Chi Ku, Chi-Jung Huang, Shao-Kuan Chen, and Yen-Chieh Wang. (2025) Phosphoproteomics Identifies CDK18 as a Key Driver in ccRCC Progression and Potential Therapeutic Target. Asia Oceania Mass Spectrometry Conference 2025 (AOMSC 2025)
2. 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)
3. 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).
4. 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.
5. 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.
6. 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).
7. 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.
8. 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.
9. 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)
10. 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.
11. 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.
12. 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.
實務研究
實務研究內容
期間 內容
研究簡介 (Research Interest)

With recent advances in high-resolution instrumentation and analytical workflows, mass spectrometry (MS) has become indispensable in both clinical chemistry, such as therapeutic drug monitoring (TDM), and biomedical research, including quantitative proteomics. Leveraging state-of-the-art MS platforms, our laboratory conducts several major research programs, summarized below.

Precision Medicine in Renal Cell Carcinoma
Renal cell carcinoma (RCC) represents approximately 1.26% of annual cancer cases in Taiwan and exhibits marked inter-patient heterogeneity in signaling pathways that shape therapeutic response and prognosis. The rapid emergence of resistance to targeted therapies further complicates treatment sequencing. To address these challenges, we apply quantitative phosphoproteomics to build a Taiwan-specific, patient-derived RCC “phospho-barcode” that enables mechanistic tumor stratification and identification of actionable signaling vulnerabilities. Current efforts focus on defining subtype-specific phosphor-signatures, including alterations in kinases such as CDK18, to advance precision therapeutic strategies.
In parallel, our work has shown that estrogen suppresses RCC growth through intracellular signaling mechanisms and modulates resistance to the first-line agent sunitinib. We identified estrogen-associated pathways capable of counteracting sunitinib resistance and demonstrated that activation of the nonclassical receptor GPER1 by its agonist G-1 inhibits the growth and migration of sunitinib-resistant RCC cells. Building on these findings, we are now exploring the repurposing of selective estrogen receptor modulators (SERMs), originally developed for osteoporosis, as potential therapeutic agents in RCC. Collectively, these studies aim to elucidate key mechanisms driving RCC progression and resistance, ultimately informing new treatment strategies and prognostic approaches.

Development and Application of LC–MS-Based Therapeutic Drug Monitoring
Over the past decade, LC–MS has gained substantial recognition as a robust platform for TDM across a wide spectrum of clinical applications. Using selected-reaction monitoring (SRM) strategies, LC–MS enables highly sensitive and selective quantification of therapeutics in complex biological matrices, including whole blood, serum, and tissue homogenates. In collaboration with an internationally recognized clinical chemistry laboratory, we developed multiplexed TDM assays for five widely prescribed antifungal agents, as well as time-resolved quantification of busulfan used in hematopoietic stem cell transplantation conditioning.
Building on these successes, our current efforts extend TDM methodology to biologics. Specifically, we aim to accurately quantify the pharmacologically active forms of monoclonal antibody therapeutics in patient samples. Ongoing work focuses on agents used in the management of rheumatoid arthritis, with the goal of developing MS-based assays that complement or surpass existing immunochemical methods in specificity, precision, and clinical interpretability.
研究計畫
期間 主持人 計畫名稱 贊助單位 贊助金額 職稱
近三年國科會計畫
1. 利用多層次蛋白質體學技術解析益生菌短鏈脂肪酸對腎細胞癌細胞增殖的影響及其分子機制(114-2113-M-030-012-), 計畫主持人, 2025/08 – 2026/07.
2. 後縱韌帶骨化症: 組織病理機轉，病人生物標誌，及後縱韌帶細胞培養之研究與應用(113-2314-B-A49-084-MY3), 共同主持人, 2024/08 – 2027/07.
3. 解析人蔘皂甘和產生丁酸腸道益生菌的三生元調控大腸直腸癌肝轉移的分子機制：從脂肪肝微環境到外泌體介導的訊號通路(113-2314-B-281-004-), 共同主持人, 2024/08 – 2025/07.
4. 研究電刺激對視網膜神經節細胞中粒線體之影響並研究其對治療青光眼之臨床潛力(112-2314-B-281-002-), 共同主持人, 2023/08 – 2024/07.
近三年其他計畫
1. 運用非數據依賴擷取之無標記定量蛋白體學以及同量異位標記定量磷酸蛋白體學技術，探討丁酸鹽對亮細胞腎細胞癌生長調控作用 (國泰醫院), 計畫主持人, 2024/08 – 2025/07.
2. 運用鄰近標記與磷酸化蛋白質體學剖析CDK18在腎明亮細胞癌之生長及貼附遷移調控機制 (輔仁大學), 計畫主持人, 2024/08 – 2025/07.
3. 探討類風溼性關節炎生物製劑Certolizumab pegol血中有效濃度與藥物持續使用比率之關係 (台北病理中心), 計畫主持人, 2023/02 – 2024/01.
其他教學經驗
其他教學經驗
期間 內容
醫學一/普通生物學、普通暨分析化學、生物化學(一)
醫學二/生物化學(二)、生物化學實驗、遺傳學、細胞生物學
醫學三/胃腸單元組長
職治一/普通生物學
生醫藥學所碩士班/專題討論、論文研究法、細胞生物技術學、基因蛋白體學與藥物開發
通識課程/健康與生活
校內服務
校內服務內容
期間 內容
2024.09 – 迄今 輔仁大學醫學院研發助理執行長