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Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C CDH1 governs mitotic protein stability and cell cycle entry. Nat Commun 2024; 15:3220. [PMID: 38622115 PMCID: PMC11018817 DOI: 10.1038/s41467-024-47427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Induced oncoproteins degradation provides an attractive anti-cancer modality. Activation of anaphase-promoting complex (APC/CCDH1) prevents cell-cycle entry by targeting crucial mitotic proteins for degradation. Phosphorylation of its co-activator CDH1 modulates the E3 ligase activity, but little is known about its regulation after phosphorylation and how to effectively harness APC/CCDH1 activity to treat cancer. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)-catalyzed phosphorylation-dependent cis-trans prolyl isomerization drives tumor malignancy. However, the mechanisms controlling its protein turnover remain elusive. Through proteomic screens and structural characterizations, we identify a reciprocal antagonism of PIN1-APC/CCDH1 mediated by domain-oriented phosphorylation-dependent dual interactions as a fundamental mechanism governing mitotic protein stability and cell-cycle entry. Remarkably, combined PIN1 and cyclin-dependent protein kinases (CDKs) inhibition creates a positive feedback loop of PIN1 inhibition and APC/CCDH1 activation to irreversibly degrade PIN1 and other crucial mitotic proteins, which force permanent cell-cycle exit and trigger anti-tumor immunity, translating into synergistic efficacy against triple-negative breast cancer.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02215, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen, 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Emily Stern Gatof
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Daniela Arango Isaza
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jaymin M Patel
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Xiao Zhen Zhou
- Departments of Pathology and Laboratory Medicine, Biochemistry, and Oncology, and Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
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Ke S, Dang F, Wang L, Chen JY, Naik MT, Thavamani A, Liu Y, Li W, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Wang X, Clohessy JG, Heng YJ, Lahav G, Gray NS, Zho XZ, Wei W, Wulf GM, Lu KP. Reciprocal inhibition of PIN1 and APC/C CDH1 controls timely G1/S transition and creates therapeutic vulnerability. Res Sq 2023:rs.3.rs-2447544. [PMID: 36711754 PMCID: PMC9882653 DOI: 10.21203/rs.3.rs-2447544/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cyclin-dependent kinases (CDKs) mediated phosphorylation inactivates the anaphase-promoting complex (APC/CCDH1), an E3 ubiquitin ligase that contains the co-activator CDH1, to promote G1/S transition. PIN1 is a phosphorylation-directed proline isomerase and a master cancer signaling regulator. However, little are known about APC/CCDH1 regulation after phosphorylation and about PIN1 ubiquitin ligases. Here we uncover a domain-oriented reciprocal inhibition that controls the timely G1/S transition: The non-phosphorylated APC/CCDH1 E3 ligase targets PIN1 for degradation in G1 phase, restraining G1/S transition; APC/CCDH1 itself, after phosphorylation by CDKs, is inactivated by PIN1-catalyzed isomerization, promoting G1/S transition. In cancer, PIN1 overexpression and APC/CCDH1 inactivation reinforce each other to promote uncontrolled proliferation and tumorigenesis. Importantly, combined PIN1- and CDK4/6-inhibition reactivates APC/CCDH1 resulting in PIN1 degradation and an insurmountable G1 arrest that translates into synergistic anti-tumor activity against triple-negative breast cancer in vivo. Reciprocal inhibition of PIN1 and APC/CCDH1 is a novel mechanism to control timely G1/S transition that can be harnessed for synergistic anti-cancer therapy.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Arizona, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yujing Jan Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiao Zhen Zho
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Departments of Biochemistry & Oncology, Schulich School of Medicine and Dentistry, and Robarts Research Institute, Western University, London, ON N6A 3K7, Canada
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kun Ping Lu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Departments of Biochemistry & Oncology, Schulich School of Medicine and Dentistry, and Robarts Research Institute, Western University, London, ON N6A 3K7, Canada
- Lead Contact
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Naik MT, Kang M, Ho CC, Liao PH, Hsieh YL, Naik NM, Wang SH, Chang I, Shih HM, Huang TH. Author Correction: Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction. Sci Rep 2018; 8:5022. [PMID: 29555948 PMCID: PMC5859160 DOI: 10.1038/s41598-018-23157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Mandar T Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02903, USA
| | - Mooseok Kang
- Department of Physics, Pusan National University, Busan, 46241, Korea
| | - Chun-Chen Ho
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Hsin Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yung-Lin Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Nandita M Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Szu-Huan Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, 35053, Taiwan.
| | - Tai-Huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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Naik MT, Kang M, Ho CC, Liao PH, Hsieh YL, Naik NM, Wang SH, Chang I, Shih HM, Huang TH. Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction. Sci Rep 2017; 7:17391. [PMID: 29234076 PMCID: PMC5727262 DOI: 10.1038/s41598-017-17465-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/27/2017] [Indexed: 11/09/2022] Open
Abstract
The negatively charged amino acid-dependent sumoylation motif (NDSM) carries an additional stretch of acidic residues downstream of the consensus Ψ-K-x-E/D sumoylation motif. We have previously shown that acetylation of the SUMO E2 conjugase enzyme, Ubc9, at K65 downregulates its binding to the NDSM and renders a selective decrease in sumoylation of substrates with the NDSM motif. Here, we provide detailed structural, thermodynamic, and kinetics results of the interactions between Ubc9 and its K65 acetylated variant (Ac-Ubc9K65) with three NDSMs derived from Elk1, CBP, and Calpain2 to rationalize the mechanism beneath this reduced binding. Our nuclear magnetic resonance (NMR) data rule out a direct interaction between the NDSM and the K65 residue of Ubc9. Similarly, we found that NDSM binding was entropy-driven and unlikely to be affected by the negative charge by K65 acetylation. Moreover our NMR, mutagenesis and molecular dynamics simulation studies defined the sequence of the NDSM as Ψ-K-x-E/D-x1-x2-(x3/E/D)-(x4/E/D)-xn and determined that K74 and K76 were critical Ubc9 residues interacting with the negatively charged residues of the NDSM.
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Affiliation(s)
- Mandar T Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02903, USA
| | - Mooseok Kang
- Department of Physics, Pusan National University, Busan, 46241, Korea
| | - Chun-Chen Ho
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Hsin Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yung-Lin Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Nandita M Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Szu-Huan Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, 35053, Taiwan.
| | - Tai-Huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CCH, Lin SY, Chen RH, Chang KS, Huang TH, Shih HM. Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation. Mol Cell 2011; 42:62-74. [PMID: 21474068 DOI: 10.1016/j.molcel.2011.02.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 12/02/2010] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation and interaction are increasingly associated with various cellular processes. However, little is known about the cellular signaling mechanisms that regulate proteins for distinct SUMO paralog conjugation and interactions. Using the transcriptional coregulator Daxx as a model, we show that SUMO paralog-selective binding and conjugation are regulated by phosphorylation of the Daxx SUMO-interacting motif (SIM). NMR structural studies show that Daxx (732)E-I-I-V-L-S-D-S-D(740) is a bona fide SIM that binds to SUMO-1 in a parallel orientation. Daxx-SIM is phosphorylated by CK2 kinase at residues S737 and S739. Phosphorylation promotes Daxx-SIM binding affinity toward SUMO-1 over SUMO-2/3, causing Daxx preference for SUMO-1 conjugation and interaction with SUMO-1-modified factors. Furthermore, Daxx-SIM phosphorylation enhances Daxx to sensitize stress-induced cell apoptosis via antiapoptotic gene repression. Our findings provide structural insights into the Daxx-SIM:SUMO-1 complex, a model of SIM phosphorylation-enhanced SUMO paralog-selective modification and interaction, and phosphorylation-regulated Daxx function in apoptosis.
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Affiliation(s)
- Che-Chang Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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Naik MT, Chang CC, Naik NM, Kung CCH, Shih HM, Huang TH. NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx. Biomol NMR Assign 2011; 5:75-77. [PMID: 20927612 DOI: 10.1007/s12104-010-9271-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 09/24/2010] [Indexed: 05/30/2023]
Abstract
Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4. Death-associated protein-6, Daxx, is a 740 residue important transcription corepressor known to represses transcriptional potential of several sumolyted transcription factors. Daxx also plays important role in apoptosis. Both terminals of Daxx harbor separate SUMO Interaction Motifs (SIM), which mediate its interaction with SUMO and hence the sumolyted transcription factors. The C-terminal SIM of Daxx preferentially binds SUMO-1. Practically complete (1)H, (13)C and (15)N resonance assignments for the complex between SUMO-1 and 20 residue Daxx C-terminal SIM peptide are reported here.
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Affiliation(s)
- Mandar T Naik
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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