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Ya-Wen Chen

Title(s)Assistant Professor of Medicine
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    Collapse Biography 
    Collapse Education and Training
    Columbia University Medical Center, New YorkPostdoctoral Training12/2018Stem Cell Biology, Pulmonary
    University of Maryland, Baltimore, BaltimorePh.D.07/2012Molecular Medicine
    Georgetown University, Washington DCM.S.05/2007Tumor Biology
    Tunghai University, Taichung, TaiwanB.S.06/2003Biology
    Collapse Awards and Honors
    Francis Family Foundation2018Parker B. Francis Fellowship
    International Society for Stem Cell Research2017Travel Award
    NHLBI Progenitor Cell Biology Consortium2017Training Award-human pluripotent stem cell biology and gene editing
    NHLBI Progenitor Cell Biology Consortium2017Training Award-Multiplexed in situ hybridzation
    International Society for Stem Cell Research2015Travel Award
    Columbia University Medical Center2015Samuel Bard Young Investigator Awards
    Journal of Investigative Dermatology2014Profile December: Meet the Investigator
    University of Maryland, Baltimore2010Travel Award
    Gordon Research Conference2010Winner of Biochemical Journal Poster Prize
    Gordon Research Conference20102nd place, Student Category of Plasminogen Activation & Extracellular Proteolysis
    Taiwan1999Masterpiece of Biology of National Science & Experiment Competition
    Asia-Pacific Economic Cooperation (APEC)1998Young Scientist Award of the 1st APEC Youth Science Festival
    Taiwan1998The third Award of the 38th National Private and high schools Science Fair

    Collapse Overview 
    Collapse Overview
    Currently, the only way to replace lung tissue is to perform lung transplantation, which is an complicate procedure that achieves only 10 to 20% survival at 10 years and is hampered by a severe shortage of donor organs. The ability to reconstruct lung tissue from hPSCs would fundamentally change the outlook of pulmonary medicine. In vitro generated lung tissue could be used for regenerative purposes. Alternatively, postnatal lung stem cells could be generated in sufficient quantities from hPSCs and used for stem-cell therapies and regenerative medicine. Over the past few years, lung progenitor populations have been identified in mouse models. It has become clear that many types of differentiated epithelial cells in the lung, such as club and ATII cells, can function as stem cells in steady state and following injury. Our research interests are applying human pluripotent stem cells (hPSCs, including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)) as a model to study the mechanisms of lung injury repair and ultimately apply the hPSC-derived lung stem/progenitor or mature airway/lung epithelial cells to facilitate lung injury repair, stem-cell therapy, and regenerative medicine.

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. de Carvalho ALRT, Strikoudis A, Liu HY, Chen YW, Dantas TJ, Vallee RB, Correia-Pinto J, Snoeck HW. Glycogen synthase kinase 3 induces multilineage maturation of human pluripotent stem cell-derived lung progenitors in 3D culture. Development. 2019 01 22; 146(2). PMID: 30578291.
      View in: PubMed
    2. Guenthart BA, Chen YW, Bacchetta M. New insights and therapeutic targets: Lung injury and disease. J Thorac Cardiovasc Surg. 2019 01; 157(1):416-420. PMID: 30557958.
      View in: PubMed
    3. Zhang Y, Yang Y, Jiang M, Huang SX, Zhang W, Al Alam D, Danopoulos S, Mori M, Chen YW, Balasubramanian R, Chuva de Sousa Lopes SM, Serra C, Bialecka M, Kim E, Lin S, Toste de Carvalho ALR, Riccio PN, Cardoso WV, Zhang X, Snoeck HW, Que J. 3D Modeling of Esophageal Development using Human PSC-Derived Basal Progenitors Reveals a Critical Role for Notch Signaling. Cell Stem Cell. 2018 10 04; 23(4):516-529.e5. PMID: 30244870.
      View in: PubMed
    4. Dorrello NV, Guenthart BA, O'Neill JD, Kim J, Cunningham K, Chen YW, Biscotti M, Swayne T, Wobma HM, Huang SXL, Snoeck HW, Bacchetta M, Vunjak-Novakovic G. Functional vascularized lung grafts for lung bioengineering. Sci Adv. 2017 08; 3(8):e1700521. PMID: 28875163.
      View in: PubMed
    5. Lai YH, Ding YJ, Moses D, Chen YH. Teratogenic Effects of Topiramate in a Zebrafish Model. Int J Mol Sci. 2017 Aug 07; 18(8). PMID: 28783116.
      View in: PubMed
    6. Chen YW, Huang SX, de Carvalho ALRT, Ho SH, Islam MN, Volpi S, Notarangelo LD, Ciancanelli M, Casanova JL, Bhattacharya J, Liang AF, Palermo LM, Porotto M, Moscona A, Snoeck HW. A three-dimensional model of human lung development and disease from pluripotent stem cells. Nat Cell Biol. 2017 May; 19(5):542-549. PMID: 28436965.
      View in: PubMed
    7. O’Neill, J. D., Guenthart, B. A., Kim, J., Chicotka, S., Queen, D., Fung, K., Marboe, C., Romanov, A., Huang, S. X. L., Chen, Y.-W., Snoeck, H.-W., Bacchetta, M., & Vunjak-Novakovic, G.Cross-circulation for extracorporeal support and recovery of the lung. Nature Biomedical Engineering. 2017.
    8. Chen, Y.-W., Ahmed, A., & Snoeck, H.-W.Generation of three-dimensional lung bud organoid and its derived branching colonies. Protocol Exchange. 2017.
    9. Chang CF, Hsu LS, Weng CY, Chen CK, Wang SY, Chou YH, Liu YY, Yuan ZX, Huang WY, Lin H, Chen YH, Tsai JN. N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability. Int J Mol Sci. 2016 Jun 14; 17(6). PMID: 27314333.
      View in: PubMed
    10. Chen YW, Yin S, Lai YJ, Johnson MD, Lin CY. Plasminogen-Dependent Matriptase Activation Accelerates Plasmin Generation by Differentiating Primary Human Keratinocytes. J Invest Dermatol. 2016 06; 136(6):1210-1218. PMID: 26872599.
      View in: PubMed
    11. Wu YC, Chang CY, Kao A, Hsi B, Lee SH, Chen YH, Wang IJ. Hypoxia-induced retinal neovascularization in zebrafish embryos: a potential model of retinopathy of prematurity. PLoS One. 2015; 10(5):e0126750. PMID: 25978439.
      View in: PubMed
    12. Huang SX, Green MD, de Carvalho AT, Mumau M, Chen YW, D'Souza SL, Snoeck HW. The in vitro generation of lung and airway progenitor cells from human pluripotent stem cells. Nat Protoc. 2015 Mar; 10(3):413-25. PMID: 25654758.
      View in: PubMed
    13. Huang SX, Islam MN, O'Neill J, Hu Z, Yang YG, Chen YW, Mumau M, Green MD, Vunjak-Novakovic G, Bhattacharya J, Snoeck HW. Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nat Biotechnol. 2014 Jan; 32(1):84-91. PMID: 24291815.
      View in: PubMed
    14. Chou FP, Chen YW, Zhao XF, Xu-Monette ZY, Young KH, Gartenhaus RB, Wang JK, Kataoka H, Zuo AH, Barndt RJ, Johnson M, Lin CY. Imbalanced matriptase pericellular proteolysis contributes to the pathogenesis of malignant B-cell lymphomas. Am J Pathol. 2013 Oct; 183(4):1306-17. PMID: 24070417.
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    15. Wu BY, Lee SP, Hsiao HC, Chiu H, Chen CY, Yeo YH, Lee HS, Chen YW, Kaul M, Kataoka H, Johnson MD, Wang JK, Lin CY. Matriptase expression and zymogen activation in human pilosebaceous unit. J Histochem Cytochem. 2014 Jan; 62(1):50-9. PMID: 24004857.
      View in: PubMed
    16. Chen YW, Wang JK, Chou FP, Wu BY, Hsiao HC, Chiu H, Xu Z, Baksh ANH, Shi G, Kaul M, Barndt R, Shanmugam VK, Johnson MD, Lin CY. Matriptase regulates proliferation and early, but not terminal, differentiation of human keratinocytes. J Invest Dermatol. 2014 Feb; 134(2):405-414. PMID: 23900022.
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    17. Chen YW, Xu Z, Baksh AN, Wang JK, Chen CY, Swanson R, Olson ST, Kataoka H, Johnson MD, Lin CY. Antithrombin regulates matriptase activity involved in plasmin generation, syndecan shedding, and HGF activation in keratinocytes. PLoS One. 2013; 8(5):e62826. PMID: 23675430.
      View in: PubMed
    18. Tsai IT, Chen YH, Chen YH, Wang YH. Amikacin-induced Fin Reduction is Mediated by Autophagy. J Toxicol Pathol. 2013 Mar; 26(1):79-82. PMID: 23723573.
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    19. Lin, CY., Chen, YW., Xu, ZH., Johnson, MD.Handbook of Proteolytic Enzymes (Third edition). MS. 681|Matriptase. 2012.
    20. Wu CK, Huang YT, Lee JK, Chiang LT, Chiang FT, Huang SW, Lin JL, Tseng CD, Chen YH, Tsai CT. Cardiac myosin binding protein C and MAP-kinase activating death domain-containing gene polymorphisms and diastolic heart failure. PLoS One. 2012; 7(4):e35242. PMID: 22529996.
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    21. Chen, YW., Eckert, RL., Johnson, M., Lin, CY.The transmembrane serine protease matriptase: implications for cellular biology and human diseases. J Med Sci. 2012.
    22. Xu H, Xu Z, Tseng IC, Chou FP, Chen YW, Wang JK, Johnson MD, Kataoka H, Lin CY. Mechanisms for the control of matriptase activity in the absence of sufficient HAI-1. Am J Physiol Cell Physiol. 2012 Jan 15; 302(2):C453-62. PMID: 22031598.
      View in: PubMed
    23. Xu Z, Chen YW, Battu A, Wilder P, Weber D, Yu W, Mackerell AD, Chen LM, Chai KX, Johnson MD, Lin CY. Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade. J Med Chem. 2011 Nov 10; 54(21):7567-78. PMID: 21966950.
      View in: PubMed
    24. Chiu YJ, Huang TH, Chiu CS, Lu TC, Chen YW, Peng WH, Chen CY. Analgesic and Antiinflammatory Activities of the Aqueous Extract from Plectranthus amboinicus (Lour.) Spreng. Both In Vitro and In Vivo. Evid Based Complement Alternat Med. 2012; 2012:508137. PMID: 21915187.
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    25. Chou FP, Xu H, Lee MS, Chen YW, Richards OX, Swanson R, Olson ST, Johnson MD, Lin CY. Matriptase is inhibited by extravascular antithrombin in epithelial cells but not in most carcinoma cells. Am J Physiol Cell Physiol. 2011 Nov; 301(5):C1093-103. PMID: 21795523.
      View in: PubMed
    26. Ho MY, Chiou ML, Du WS, Chang FY, Chen YH, Weng YJ, Cheng CC. Inductive properties of polypyridyl ruthenium complexes significantly regulate various protein distributions in Escherichia coli. J Inorg Biochem. 2011 Jun; 105(6):902-10. PMID: 21513691.
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    27. Lee GH, Chang MY, Hsu CH, Chen YH. Essential roles of basic helix-loop-helix transcription factors, Capsulin and Musculin, during craniofacial myogenesis of zebrafish. Cell Mol Life Sci. 2011 Dec; 68(24):4065-78. PMID: 21347725.
      View in: PubMed
    28. Chen CJ, Wu BY, Tsao PI, Chen CY, Wu MH, Chan YL, Lee HS, Johnson MD, Eckert RL, Chen YW, Chou F, Wang JK, Lin CY. Increased matriptase zymogen activation in inflammatory skin disorders. Am J Physiol Cell Physiol. 2011 Mar; 300(3):C406-15. PMID: 21123732.
      View in: PubMed
    29. Chen YW, Wang JK, Chou FP, Chen CY, Rorke EA, Chen LM, Chai KX, Eckert RL, Johnson MD, Lin CY. Regulation of the matriptase-prostasin cell surface proteolytic cascade by hepatocyte growth factor activator inhibitor-1 during epidermal differentiation. J Biol Chem. 2010 Oct 08; 285(41):31755-62. PMID: 20696767.
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    30. Jiang H, Jans R, Xu W, Rorke EA, Lin CY, Chen YW, Fang S, Zhong Y, Eckert RL. Type I transglutaminase accumulation in the endoplasmic reticulum may be an underlying cause of autosomal recessive congenital ichthyosis. J Biol Chem. 2010 Oct 08; 285(41):31634-46. PMID: 20663883.
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    31. Chou CY, Hsu CH, Wang YH, Chang MY, Chen LC, Cheng SC, Chen YH. Biochemical and structural properties of zebrafish Capsulin produced by Escherichia coli. Protein Expr Purif. 2011 Jan; 75(1):21-7. PMID: 20627128.
      View in: PubMed
    32. Chen YW, Lee MS, Lucht A, Chou FP, Huang W, Havighurst TC, Kim K, Wang JK, Antalis TM, Johnson MD, Lin CY. TMPRSS2, a serine protease expressed in the prostate on the apical surface of luminal epithelial cells and released into semen in prostasomes, is misregulated in prostate cancer cells. Am J Pathol. 2010 Jun; 176(6):2986-96. PMID: 20382709.
      View in: PubMed
    33. Ho MY, Chiou ML, Chang RC, Chen YH, Cheng CC. Outer membrane protein OmpF involved in the transportation of polypyridyl ruthenium complexes into Escherichia coli. J Inorg Biochem. 2010 May; 104(5):614-7. PMID: 20176402.
      View in: PubMed
    34. Wang YH, Cheng CC, Lee WJ, Chiou ML, Pai CW, Wen CC, Chen WL, Chen YH. A novel phenotype-based approach for systematically screening antiproliferation metallodrugs. Chem Biol Interact. 2009 Nov 10; 182(1):84-91. PMID: 19682442.
      View in: PubMed
    35. Wang JK, Lee MS, Tseng IC, Chou FP, Chen YW, Fulton A, Lee HS, Chen CJ, Johnson MD, Lin CY. Polarized epithelial cells secrete matriptase as a consequence of zymogen activation and HAI-1-mediated inhibition. Am J Physiol Cell Physiol. 2009 Aug; 297(2):C459-70. PMID: 19535514.
      View in: PubMed
    36. Chen YH, Wang YH, Yu TH, Wu HJ, Pai CW. Transgenic zebrafish line with over-expression of Hedgehog on the skin: a useful tool to screen Hedgehog-inhibiting compounds. Transgenic Res. 2009 Dec; 18(6):855-64. PMID: 19412740.
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    37. Chen YH, Huang YH, Wen CC, Wang YH, Chen WL, Chen LC, Tsay HJ. Movement disorder and neuromuscular change in zebrafish embryos after exposure to caffeine. Neurotoxicol Teratol. 2008 Sep-Oct; 30(5):440-7. PMID: 18508234.
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    38. Lin CY, Tseng IC, Chou FP, Su SF, Chen YW, Johnson MD, Dickson RB. Zymogen activation, inhibition, and ectodomain shedding of matriptase. Front Biosci. 2008 Jan 01; 13:621-35. PMID: 17981575.
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    39. Lin CY, Yung RF, Lee HC, Chen WT, Chen YH, Tsai HJ. Myogenic regulatory factors Myf5 and Myod function distinctly during craniofacial myogenesis of zebrafish. Dev Biol. 2006 Nov 15; 299(2):594-608. PMID: 17007832.
      View in: PubMed
    40. Wang YH, Chen YH, Lin YJ, Tsai HJ. Spatiotemporal expression of zebrafish keratin 18 during early embryogenesis and the establishment of a keratin 18:RFP transgenic line. Gene Expr Patterns. 2006 Apr; 6(4):335-9. PMID: 16446122.
      View in: PubMed
    41. Wang YH, Chen YH, Wu TN, Lin YJ, Tsai HJ. A keratin 18 transgenic zebrafish Tg(k18(2.9):RFP) treated with inorganic arsenite reveals visible overproliferation of epithelial cells. Toxicol Lett. 2006 Jun 01; 163(3):191-7. PMID: 16376500.
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    42. Lee HC, Huang HY, Lin CY, Chen YH, Tsai HJ. Foxd3 mediates zebrafish myf5 expression during early somitogenesis. Dev Biol. 2006 Feb 15; 290(2):359-72. PMID: 16386728.
      View in: PubMed
    43. Chen YH, Liang CT, Tsai HJ. Expression, purification and DNA-binding activity of tilapia muscle-specific transcription factor, MyoD, produced in Escherichia coli. Comp Biochem Physiol B Biochem Mol Biol. 2002 Apr; 131(4):795-805. PMID: 11923092.
      View in: PubMed
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