簡易檢索 / 詳目顯示

研究生: 李文心
Lee, Wen-Hsin
論文名稱: 白細胞介素17B受體及中和性抗體D9複合體之蛋白質結晶結構並在其基礎上設計之噬菌體表現抗體資料庫優化抗體
Solving crystal structure of Interleukin-17 receptor B with its neutralizing antibody D9 to guide antibody optimization through phage-displayed library
指導教授: 馬徹
Ma, Che
李文華
Lee, Wen-Hwa
王聖凱
Wang, Sheng-Kai
口試委員: 吳漢忠
Wu, Han-Chung
梁博煌
Liang, Po-Huang
李宗璘
Li, Tsung-Lin
學位類別: 博士
Doctor
系所名稱: 理學院 - 化學系
Department of Chemistry
論文出版年: 2022
畢業學年度: 111
語文別: 英文
論文頁數: 121
中文關鍵詞: 白細胞介素17B受體抗體優化抗體X光繞射結構胰臟癌
外文關鍵詞: Interleukin-17 receptor B, antibody, antibody affinity maturation, X-ray crystal structure, Pancreatic cancer
相關次數: 點閱:2下載:0
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 胰腺癌是一種高度轉移性且惡性的癌症,超過80%的患者在確診時已是癌症末期,因此而錯過了黃金治療時間。此外胰腺癌經常在化療時產生抗藥性反應,以致大多數治療最終無效。因此目前極迫切需要開發新的胰腺腫瘤靶向治療藥物。先前透過IL-17B / IL-17RB訊息傳遞的研究,我們證實了IL-17RB在接受IL-17B的信號下不僅促進胰腺腫瘤生長,更透過下游化學因子訊息活化並聚集巨噬細胞,致使胰臟腫瘤細胞因此有機會滲透與轉移至肺臟。在本論文中,我們發展出了專一識別IL-17RB的小鼠單株抗體D9能辨識蛋白質3D結構並在異種移植小鼠模型中延緩胰腺癌細胞生長速度且顯著延長存活天數。除此之外,我們更解出IL-17RB與D9抗體的複合蛋白質晶體X光繞射結構,從此結構中了解到D9透過與IL-17RB A’-A loop 的結合,使loop產生構造型太改變而阻抗其配體 (ligand) IL-17B的結合,有效使腫瘤生長變遲緩。我們在CDR移植的人類化抗體D9上,透過此複合體結構的資訊設計之噬菌體表現單鏈抗體庫來篩選出應用於人體治療用途的人類化單株抗體1B12,並證實此人類化抗體也在異種移植小鼠模型中延緩胰腺癌細胞生長速度。


    Pancreatic cancer is a highly metastatic cancer with over 80% of the patients are diagnosed in advanced disease stages and are beyond the treatment window for curative resection. Most treatments are ineffective. There is an urgent need to develop targeting therapies for pancreatic cancer. Using both gain- and loss- of-function studies, we previously demonstrated that IL-17B/IL-17RB signaling plays an essential role in supporting pancreatic tumor growth, invasion and metastasis, and mediates downstream cytokine activation and macrophage recruitment. In this thesis, a mouse monoclonal antibody (D9) recognizing IL-17RB on its conformational epitope successfully delays the malignancy of pancreatic cancer cells and significantly extends survival in an orthotropic xenograft mice model. Moreover, clinical data suggests that high-level expression of IL-17RB is associated with shortened progression-free survival in pancreatic cancer patients. Thus, targeting IL-17B/IL-17RB pathway is potentially a new approach for pancreatic cancer treatment. Here, we solved the X-ray crystal structure of the IL-17RB ectodomain in complex with its neutralizing antibody D9. The structure shows that D9 binds to a predicted ligand-binding interface and engages with the A’-A loop of IL-17RB fibronectin III domain 1 in a unique conformational state that was observed for the first time among IL-17 receptors. Moreover, this structure also provides important paratope information to guide the design of antibody humanization and affinity maturation of D9, resulting in a humanized 1B12 antibody with marginal affinity loss and effective neutralization of IL-17B/IL-17RB signaling to impede tumorigenesis in a mouse xenograft model.

    中文摘要………………………………………...………………………………….1 Abstract……………………………………………………………………………...2 Chapter I. Introduction………………….……………………………………...4 Chapter II. Experimental Materials and Methods..…………………………….10 Chapter III. Specific Aims and Results………………………………….……....32 i. Purification of Monoglycosylated and Fully Glycosylated Human Interleukin-17B Receptors………………………………………….……....33 ii. The MG hIL-17RB protein stimulated higher immune response in mice than FG hIL-17RB……………………………………………………….………34 iii. Selection of monoclonal antibodies conformationally recognizing human IL-17RB using hybridoma method from IL-17RBMG ECD immunized mice…………………………………………………….…………………...34 iv. Humanization of Mouse Monoclonal D9 Antibody……………………….36 v. Paratope Mapping of cD9 Antibody……………………………………….39 vi. Structure of Chimeric D9 Antibody Fab…………………………………...40 vii. X-ray crystal structure of bIL-17RBin complex with D9 Fab…..………..42 viii. Structural comparison between solved bIL-17RB and current IL-17RA structures………………………………………………………………...…...44 ix. A unique conformational state of IL-17RB upon D9 binding……….….…..46 x. Detailed Interface between IL-17RB and D9 antibody………………..……48 xi. Affinity Maturation of Humanized D9 Antibody through Structure-based Phage-Displayed Library Design………………………………….….….…..49 xii. Biopanning for phage-displayed hD9 clone selection……………...……...50 xiii. The specificity and neutralization potency of humanized D9 antibody 1B12……………………………………………………………….….….…..52 Chapter IV. Conclusion and Discussion…………………………………….…….54 Chapter V. Reference……………………………..……………………..….……58 Chapter VI. Figure………………………………………..………………...……..69

    Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221. 10.1107/S0907444909052925.
    Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., and Adams, P.D. (2012). Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68, 352-367. 10.1107/S0907444912001308.
    Brochet, X., Lefranc, M.P., and Giudicelli, V. (2008). IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res 36, W503-508. 10.1093/nar/gkn316.
    Cardenes, H.R., Chiorean, E.G., Dewitt, J., Schmidt, M., and Loehrer, P. (2006). Locally advanced pancreatic cancer: current therapeutic approach. Oncologist 11, 612-623. 10.1634/theoncologist.11-6-612.
    Carroll, W.L., Mendel, E., and Levy, S. (1988). Hybridoma fusion cell lines contain an aberrant kappa transcript. Mol Immunol 25, 991-995.
    Chang, S.H., and Dong, C. (2011). Signaling of interleukin-17 family cytokines in immunity and inflammation. Cell Signal 23, 1069-1075. 10.1016/j.cellsig.2010.11.022.
    Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16, 10881-10890. 10.1093/nar/16.22.10881.
    Duan, L., and Pomerantz, R.J. (1994). Elimination of endogenous aberrant kappa chain transcripts from sp2/0-derived hybridoma cells by specific ribozyme cleavage: utility in genetic therapy of HIV-1 infections. Nucleic Acids Res 22, 5433-5438.
    Echols, N., Morshed, N., Afonine, P.V., McCoy, A.J., Miller, M.D., Read, R.J., Richardson, J.S., Terwilliger, T.C., and Adams, P.D. (2014). Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 70, 1104-1114. 10.1107/S1399004714001308.
    Ely, L.K., Fischer, S., and Garcia, K.C. (2009). Structural basis of receptor sharing by interleukin 17 cytokines. Nat Immunol 10, 1245-1251. 10.1038/ni.1813.
    Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132. 10.1107/S0907444904019158.
    Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. (2010). Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501. 10.1107/S0907444910007493.
    Essono, S., Frobert, Y., Grassi, J., Creminon, C., and Boquet, D. (2003). A general method allowing the design of oligonucleotide primers to amplify the variable regions from immunoglobulin cDNA. J Immunol Methods 279, 251-266. 10.1016/s0022-1759(03)00242-4.
    Feig, C., Gopinathan, A., Neesse, A., Chan, D.S., Cook, N., and Tuveson, D.A. (2012). The pancreas cancer microenvironment. Clin Cancer Res 18, 4266-4276. 10.1158/1078-0432.CCR-11-3114.
    Fidler, M.M., Gupta, S., Soerjomataram, I., Ferlay, J., Steliarova-Foucher, E., and Bray, F. (2017). Cancer incidence and mortality among young adults aged 20-39 years worldwide in 2012: a population-based study. Lancet Oncol 18, 1579-1589. 10.1016/S1470-2045(17)30677-0.
    Fossiez, F., Djossou, O., Chomarat, P., Flores-Romo, L., Ait-Yahia, S., Maat, C., Pin, J.J., Garrone, P., Garcia, E., Saeland, S., et al. (1996). T cell interleukin-17 induces stromal cells to produce proinflammatory and hematopoietic cytokines. J Exp Med 183, 2593-2603.
    Furuta, S., Jeng, Y.M., Zhou, L., Huang, L., Kuhn, I., Bissell, M.J., and Lee, W.H. (2011). IL-25 causes apoptosis of IL-25R-expressing breast cancer cells without toxicity to nonmalignant cells. Sci Transl Med 3, 78ra31. 10.1126/scitranslmed.3001374.
    Gaffen, S.L. (2008). An overview of IL-17 function and signaling. Cytokine 43, 402-407. S1043-4666(08)00230-5 [pii]
    10.1016/j.cyto.2008.07.017.
    Giudicelli, V., Brochet, X., and Lefranc, M.P. (2011). IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb Protoc 2011, 695-715. 10.1101/pdb.prot5633.
    Goddard, T.D., Huang, C.C., Meng, E.C., Pettersen, E.F., Couch, G.S., Morris, J.H., and Ferrin, T.E. (2018). UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci 27, 14-25. 10.1002/pro.3235.
    Goepfert, A., Lehmann, S., Wirth, E., and Rondeau, J.M. (2017). The human IL-17A/F heterodimer: a two-faced cytokine with unique receptor recognition properties. Sci Rep 7, 8906. 10.1038/s41598-017-08360-9.
    He, H., Fang, H., Miller, M.D., Phillips, G.N., Jr., and Su, W.P. (2016). Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm. Acta Crystallogr A Found Adv 72, 539-547. 10.1107/S2053273316010731.
    Huang, C.K., Yang, C.Y., Jeng, Y.M., Chen, C.L., Wu, H.H., Chang, Y.C., Ma, C., Kuo, W.H., Chang, K.J., Shew, J.Y., and Lee, W.H. (2014). Autocrine/paracrine mechanism of interleukin-17B receptor promotes breast tumorigenesis through NF-kappa B-mediated antiapoptotic pathway. Oncogene 33, 2968-2977. 10.1038/onc.2013.268.
    Ilic, M., and Ilic, I. (2016). Epidemiology of pancreatic cancer. World J Gastroenterol 22, 9694-9705. 10.3748/wjg.v22.i44.9694.
    Iwakura, Y., Ishigame, H., Saijo, S., and Nakae, S. (2011). Functional specialization of interleukin-17 family members. Immunity 34, 149-162. 10.1016/j.immuni.2011.02.012.
    Jones, P.T., Dear, P.H., Foote, J., Neuberger, M.S., and Winter, G. (1986). Replacing the Complementarity-Determining Regions in a Human-Antibody with Those from a Mouse. Nature 321, 522-525. DOI 10.1038/321522a0.
    Kipps, T.J., Parham, P., Punt, J., and Herzenberg, L.A. (1985). Importance of immunoglobulin isotype in human antibody-dependent, cell-mediated cytotoxicity directed by murine monoclonal antibodies. J Exp Med 161, 1-17.
    Krebber, A., Bornhauser, S., Burmester, J., Honegger, A., Willuda, J., Bosshard, H.R., and Pluckthun, A. (1997). Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system. J Immunol Methods 201, 35-55. 10.1016/s0022-1759(96)00208-6.
    Kunkel, T.A., Roberts, J.D., and Zakour, R.A. (1987). Rapid and Efficient Site-Specific Mutagenesis without Phenotypic Selection. Method Enzymol 154, 367-382.
    Lee, C.V., Liang, W.C., Dennis, M.S., Eigenbrot, C., Sidhu, S.S., and Fuh, G. (2004). High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J Mol Biol 340, 1073-1093. 10.1016/j.jmb.2004.05.051.
    Lefranc, M.P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J., et al. (2009). IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 37, D1006-1012. 10.1093/nar/gkn838.
    Liebschner, D., Afonine, P.V., Baker, M.L., Bunkoczi, G., Chen, V.B., Croll, T.I., Hintze, B., Hung, L.W., Jain, S., McCoy, A.J., et al. (2019a). Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75, 861-877. 10.1107/S2059798319011471.
    Liebschner, D., Afonine, P.V., Baker, M.L., Bunkoczi, G., Chen, V.B., Croll, T.I., Hintze, B., Hung, L.W., Jain, S., McCoy, A.J., et al. (2019b). Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D 75, 861-877. 10.1107/S2059798319011471.
    Liu, S., Desharnais, J., Sahasrabudhe, P.V., Jin, P., Li, W., Oates, B.D., Shanker, S., Banker, M.E., Chrunyk, B.A., Song, X., et al. (2016). Inhibiting complex IL-17A and IL-17RA interactions with a linear peptide. Sci Rep 6, 26071. 10.1038/srep26071.
    Liu, S., Song, X., Chrunyk, B.A., Shanker, S., Hoth, L.R., Marr, E.S., and Griffor, M.C. (2013). Crystal structures of interleukin 17A and its complex with IL-17 receptor A. Nat Commun 4, 1888. 10.1038/ncomms2880.
    McAllister, F., Bailey, J.M., Alsina, J., Nirschl, C.J., Sharma, R., Fan, H., Rattigan, Y., Roeser, J.C., Lankapalli, R.H., Zhang, H., et al. (2014). Oncogenic Kras activates a hematopoietic-to-epithelial IL-17 signaling axis in preinvasive pancreatic neoplasia. Cancer Cell 25, 621-637. 10.1016/j.ccr.2014.03.014.
    Moseley, T.A., Haudenschild, D.R., Rose, L., and Reddi, A.H. (2003). Interleukin-17 family and IL-17 receptors. Cytokine Growth Factor Rev 14, 155-174.
    Ning, B., Tang, Y., Song, H., Yang, S., and Shen, H. (2012). Cloning and sequencing of the light chain variable region from NS-1 myeloma. Oncol Lett 3, 1083-1086. 10.3892/ol.2012.601.
    Pettersen, E.F., Goddard, T.D., Huang, C.C., Meng, E.C., Couch, G.S., Croll, T.I., Morris, J.H., and Ferrin, T.E. (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci 30, 70-82. 10.1002/pro.3943.
    Powell, H.R., Johnson, O., and Leslie, A.G. (2013). Autoindexing diffraction images with iMosflm. Acta Crystallogr D Biol Crystallogr 69, 1195-1203. 10.1107/S0907444912048524.
    Ramsland, P.A., and Farrugia, W. (2002). Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products. J Mol Recognit 15, 248-259. 10.1002/jmr.585.
    Reeves, P.J., Callewaert, N., Contreras, R., and Khorana, H.G. (2002). Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc Natl Acad Sci U S A 99, 13419-13424. 10.1073/pnas.212519299.
    Rouet, R., Dudgeon, K., and Christ, D. (2012). Generation of human single domain antibody repertoires by Kunkel mutagenesis. Methods Mol Biol 907, 195-209. 10.1007/978-1-61779-974-7_10.
    Ryan, D.P., Hong, T.S., and Bardeesy, N. (2014). Pancreatic adenocarcinoma. N Engl J Med 371, 1039-1049. 10.1056/NEJMra1404198.
    Schwede, T., Kopp, J., Guex, N., and Peitsch, M.C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 31, 3381-3385.
    Shen, F., and Gaffen, S.L. (2008). Structure-function relationships in the IL-17 receptor: implications for signal transduction and therapy. Cytokine 41, 92-104.
    Shirai, H., Prades, C., Vita, R., Marcatili, P., Popovic, B., Xu, J., Overington, J.P., Hirayama, K., Soga, S., Tsunoyama, K., et al. (2014). Antibody informatics for drug discovery. Biochim Biophys Acta 1844, 2002-2015. 10.1016/j.bbapap.2014.07.006.
    Sidhu, S.S., Li, B., Chen, Y., Fellouse, F.A., Eigenbrot, C., and Fuh, G. (2004). Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J Mol Biol 338, 299-310. 10.1016/j.jmb.2004.02.050.
    Song, X., and Qian, Y. (2013). IL-17 family cytokines mediated signaling in the pathogenesis of inflammatory diseases. Cell Signal 25, 2335-2347. 10.1016/j.cellsig.2013.07.021.
    Swindells, M.B., Porter, C.T., Couch, M., Hurst, J., Abhinandan, K.R., Nielsen, J.H., Macindoe, G., Hetherington, J., and Martin, A.C. (2017). abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction. J Mol Biol 429, 356-364. 10.1016/j.jmb.2016.08.019.
    Wang, C.C., Chen, J.R., Tseng, Y.C., Hsu, C.H., Hung, Y.F., Chen, S.W., Chen, C.M., Khoo, K.H., Cheng, T.J., Cheng, Y.S., et al. (2009). Glycans on influenza hemagglutinin affect receptor binding and immune response. Proc Natl Acad Sci U S A 106, 18137-18142. 10.1073/pnas.0909696106.
    Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., et al. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46, W296-W303. 10.1093/nar/gky427.
    Wilson, S.C., Caveney, N.A., Yen, M., Pollmann, C., Xiang, X., Jude, K.M., Hafer, M., Tsutsumi, N., Piehler, J., and Garcia, K.C. (2022). Organizing Structural Principles of the Interleukin-17 Ligand-Receptor Axis. Nature. 10.1038/s41586-022-05116-y.
    Wu, H.H., Hwang-Verslues, W.W., Lee, W.H., Huang, C.K., Wei, P.C., Chen, C.L., Shew, J.Y., Lee, E.Y., Jeng, Y.M., Tien, Y.W., et al. (2015). Targeting IL-17B-IL-17RB signaling with an anti-IL-17RB antibody blocks pancreatic cancer metastasis by silencing multiple chemokines. J Exp Med 212, 333-349. 10.1084/jem.20141702.
    Wu, H.H., Tsai, L.H., Huang, C.K., Hsu, P.H., Chen, M.Y., Chen, Y.I., Hu, C.M., Shen, C.N., Lee, C.C., Chang, M.C., et al. (2021). Characterization of initial key steps of IL-17 receptor B oncogenic signaling for targeted therapy of pancreatic cancer. Sci Transl Med 13. 10.1126/scitranslmed.abc2823.
    Zhang, B., Liu, C., Qian, W., Han, Y., Li, X., and Deng, J. (2013). Crystal structure of IL-17 receptor B SEFIR domain. J Immunol 190, 2320-2326. 10.4049/jimmunol.1202922.
    Zwart, P.H., Afonine, P.V., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., McKee, E., Moriarty, N.W., Read, R.J., Sacchettini, J.C., et al. (2008). Automated structure solution with the PHENIX suite. Methods Mol Biol 426, 419-435. 10.1007/978-1-60327-058-8_28.

    QR CODE