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Mühlenberg T, Falkenhorst J, Schulz T, Fletcher BS, Teuber A, Krzeciesa D, Klooster I, Lundberg M, Wilson L, Lategahn J, von Mehren M, Grunewald S, Tüns AI, Wardelmann E, Sicklick JK, Brahmi M, Serrano C, Schildhaus HU, Sievers S, Treckmann J, Heinrich MC, Raut CP, Ou WB, Marino-Enriquez A, George S, Rauh D, Fletcher JA, Bauer S. KIT ATP-Binding Pocket/Activation Loop Mutations in GI Stromal Tumor: Emerging Mechanisms of Kinase Inhibitor Escape. J Clin Oncol 2024; 42:1439-1449. [PMID: 38408285 DOI: 10.1200/jco.23.01197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 02/28/2024] Open
Abstract
PURPOSE Imatinib resistance in GI stromal tumors (GISTs) is primarily caused by secondary KIT mutations, and clonal heterogeneity of these secondary mutations represents a major treatment obstacle. KIT inhibitors used after imatinib have clinical activity, albeit with limited benefit. Ripretinib is a potent inhibitor of secondary KIT mutations in the activation loop (AL). However, clinical benefit in fourth line remains limited and the molecular mechanisms of ripretinib resistance are largely unknown. PATIENTS AND METHODS Progressing lesions of 25 patients with GISTs refractory to ripretinib were sequenced for KIT resistance mutations. Resistant genotypes were validated and characterized using novel cell line models and in silico modeling. RESULTS GISTs progressing on ripretinib were enriched for secondary mutations in the ATP-binding pocket (AP), which frequently occur in cis with preexisting AL mutations, resulting in highly resistant AP/AL genotypes. AP/AL mutations were rarely observed in a cohort of progressing GIST samples from the preripretinib era but represented 50% of secondary KIT mutations in patients with tumors resistant to ripretinib. In GIST cell lines harboring secondary KIT AL mutations, the sole genomic escape mechanisms during ripretinib drug selection were AP/AL mutations. Ripretinib and sunitinib synergize against mixed clones with secondary AP or AL mutants but do not suppress clones with AP/AL genotypes. CONCLUSION Our findings underscore that KIT remains the central oncogenic driver even in late lines of GIST therapy. KIT-inhibitor combinations may suppress resistance because of secondary KIT mutations. However, the emergence of KIT AP/AL mutations after ripretinib treatment calls for new strategies in the development of next-generation KIT inhibitors.
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Affiliation(s)
- Thomas Mühlenberg
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Johanna Falkenhorst
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tom Schulz
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Benjamin S Fletcher
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alina Teuber
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Dawid Krzeciesa
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Isabella Klooster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Meijun Lundberg
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Lydia Wilson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jonas Lategahn
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Margaret von Mehren
- Department of Hematology and Oncology, Fox Chase Cancer Center, Temple Health System, University, Philadelphia, PA
| | - Susanne Grunewald
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alicia Isabell Tüns
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Eva Wardelmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, CA
- Department of Pharmacology, Moores Cancer Center, University of California San Diego, San Diego, CA
| | - Mehdi Brahmi
- Centre Leon Berard, Medical Oncology, Lyon, France
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Hans-Ulrich Schildhaus
- University Hospital Essen, Institute of Pathology, Essen, Germany
- Current affiliation: Discovery Life Sciences Biomarker Services & Institute of Pathology Nodhessen, Kassel, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jürgen Treckmann
- University of Duisburg-Essen, Medical School, Department of Visceral and Transplantation Surgery, Essen, Germany
| | - Michael C Heinrich
- Portland VA Health Care System and OHSU Knight Cancer Institute, Portland, OR
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Boston, MA
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Wen-Bin Ou
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Suzanne George
- Dana-Farber Cancer Institute, Medical Oncology, Boston, MA
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Dortmund, Germany
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Sebastian Bauer
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany
- DKTK partner site Essen, German Cancer Consortium (DKTK), Heidelberg, Germany
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Teuber A, Schulz T, Fletcher BS, Gontla R, Mühlenberg T, Zischinsky ML, Niggenaber J, Weisner J, Kleinbölting SB, Lategahn J, Sievers S, Müller MP, Bauer S, Rauh D. Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA. Nat Commun 2024; 15:63. [PMID: 38167404 PMCID: PMC10761696 DOI: 10.1038/s41467-023-44376-8] [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: 07/11/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Avapritinib is the only potent and selective inhibitor approved for the treatment of D842V-mutant gastrointestinal stromal tumors (GIST), the most common primary mutation of the platelet-derived growth factor receptor α (PDGFRA). The approval was based on the NAVIGATOR trial, which revealed overall response rates of more than 90%. Despite this transformational activity, patients eventually progress, mostly due to acquired resistance mutations or following discontinuation due to neuro-cognitive side effects. These patients have no therapeutic alternative and face a dismal prognosis. Notable, little is known about this drug's binding mode and its medicinal chemistry development, which is instrumental for the development of the next generation of drugs. Against this background, we solve the crystal structures of avapritinib in complex with wild-type and mutant PDGFRA and stem cell factor receptor (KIT), which provide evidence and understanding of inhibitor binding and lead to the identification of a sub-pocket (Gα-pocket). We utilize this information to design, synthesize and characterize avapritinib derivatives for the determination of key pharmacophoric features to overcome drug resistance and limit potential blood-brain barrier penetration.
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Grants
- BA 5214/1-2 Deutsche Forschungsgemeinschaft (German Research Foundation)
- This work was co-funded by the German Research Foundation (DFG; BA 5214/1-2 (SB) | RA 1055/3-2 (DR)), the State of North Rhine-Westphalia (NRW), the European Union (European Regional Development Fund: Investing In Your Future) (EFRE-800400), DDHD (Drug Discovery Hub Dortmund, (DR)), the German Federal Ministry of Education and Research (InCa (01ZX2201B, (DR)), the Mercator Research Center Ruhr (MERCUR), IGNITE (Ex-2021-0033, (DR and SB)) and was supported by the "Netzwerke 2021" program, an initiative of the Ministry of Culture and Science of the State of North Rhine-Westphalia (CANcer TARgeting, NW21-062C, (DR and SB)). This work was supported by the Swiss Light Source of the Paul Scherrer Institute (SLS, Villingen, Switzerland) and The European Synchrotron Radiation Facility (ESRF, Grenoble, France, proposal MX-2391, DOI: 10.15151/ESRF-ES-744176088 and DOI: 10.15151/ESRF-ES-925653639, (DR and MPM)).
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Affiliation(s)
- A Teuber
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - T Schulz
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - B S Fletcher
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - R Gontla
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - T Mühlenberg
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - M-L Zischinsky
- Lead Discovery Center GmbH, Department for in vitro ADME and PK, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - J Niggenaber
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - J Weisner
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S B Kleinbölting
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - J Lategahn
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - M P Müller
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S Bauer
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - D Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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Mühlenberg T, Falkenhorst J, Schulz T, Fletcher BS, Teuber A, Krzeciesa D, Klooster I, Lategahn J, Ou WB, Lundberg M, von Mehren M, Grunewald S, Tüns AI, Brahmi M, Heinrich MC, Serrano C, Schildhaus HU, Sievers S, Treckmann J, Wilson L, Raut CP, Marino-Enriquez A, George S, Rauh D, Fletcher JA, Bauer S. Abstract 3887: ATP-binding pocket substitutions as secondary or tertiary in-cis mutations are major on-target ripretinib resistance mechanisms in gastrointestinal stromal tumor. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3887] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Ripretinib (Rip) is a kinase inhibitor with broad preclinical activity against mutant KIT. Based on the INVICTUS trial, Rip was approved for patients with Gastrointestinal Stromal Tumors (GIST) after treatment with 3 or more kinase inhibitors. Most patients in this ≥4th-line setting progress on Rip within one year. Here, we characterized Rip-progressing GIST samples to identify resistance mechanisms.
Methods: Progressing lesions in 25 patients were analyzed by NGS after Rip failure. KIT mutations (muts) were recapitulated by gene editing. Activities of Rip, sunitinib (SU), and novel TKIs were characterized by cell viability assays and immunoblot. Mutagenesis experiments were performed using ENU. SU- and Rip-resistant cell lines were pooled and treated with various regimens, with clonal composition deconvoluted by cDNA-based amplicon sequencing.
Results: 19/25 Rip-progressing GISTs displayed muts in the ATP-binding pocket (ATP-BP; e13/14). Four of these had pre-existing muts in the activation loop (AL; e17/18), which were confirmed to be in-cis with the primary and ATP-BP muts (triple in cis; TIC). Mutagenesis screens using a double KIT-mutant GIST line (e11 + AL) as a starting point confirmed that TIC-muts are a predominant escape mechanism when treated with Rip. A GIST subline (T1-triple) with TIC-muts in e11, e18 (A829P), and e13 (V654A) was highly resistant to Rip (GR50 > 2µM). Structural analyses of ATP-BP muts suggest steric interference and loss of van der Waals interactions that impede Rip binding and thereby confer Rip resistance. Another 3/25 Rip-progressing GISTs harbored pathogenic KIT muts in e9 only. A novel GIST cell line with primary KIT e9 mut (T1-e9) was 14-fold less sensitive to Rip than isogenic e11-driven cells (GR50 = 115 vs 8nM). Notably, adding a typical AL mut to T1-e9 (T1-e9-N822K) sensitized the cells to Rip (GR50 = 20nM). Immunoblots showed >95% inhibition of phospho-KIT in AL-mutant cell lines at Rip 100nM, whereas inhibition was weaker in T1-e9 (77%) and T1-V654A (46%), and absent in T1-triple. A compound screen of FDA-approved kinase inhibitors identified Nintedanib (NIN) as the most active compound against T1-triple. Clonal outgrowth assays of mixed cultures revealed SU (93% inhibition), and a weekly switch between Rip and either SU (96%) or NIN (79%) as the most effective inhibitors of pooled cell growth.
Conclusions: KIT e9 primary muts and e13/14 (ATP-BP) secondary muts are enriched in post-progression biopsies following Rip treatment. KIT TIC-muts are novel frequent events driving GIST clinical progression and confer a high degree of resistance. Strategies to overcome resistance may include combinations or sequences of approved drugs, and novel drugs that more efficiently inhibit TIC-mutant KIT.
Citation Format: Thomas Mühlenberg, Johanna Falkenhorst, Tom Schulz, Benjamin S. Fletcher, Alina Teuber, Dawid Krzeciesa, Isabella Klooster, Jonas Lategahn, Wen-Bin Ou, Meijun Lundberg, Margaret von Mehren, Susanne Grunewald, Alicia I. Tüns, Mehdi Brahmi, Michael C. Heinrich, Cesar Serrano, Hans-Ulrich Schildhaus, Sonja Sievers, Jürgen Treckmann, Lydia Wilson, Chandrajit P. Raut, Adrian Marino-Enriquez, Suzanne George, Daniel Rauh, Jonathan A. Fletcher, Sebastian Bauer. ATP-binding pocket substitutions as secondary or tertiary in-cis mutations are major on-target ripretinib resistance mechanisms in gastrointestinal stromal tumor. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3887.
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Affiliation(s)
| | | | - Tom Schulz
- 2Technical University Dortmund, Dortmund, Germany
| | | | - Alina Teuber
- 2Technical University Dortmund, Dortmund, Germany
| | | | | | | | - Wen-Bin Ou
- 3Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | - Michael C. Heinrich
- 6Portland VA Health Care System and OHSU Knight Cancer Institute, Portland, OR
| | - Cesar Serrano
- 7Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | | | - Sonja Sievers
- 8Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | | | | | | | - Daniel Rauh
- 2Technical University Dortmund, Dortmund, Germany
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Opel N, Redlich R, Kaehler C, Grotegerd D, Dohm K, Heindel W, Kugel H, Thalamuthu A, Koutsouleris N, Arolt V, Teuber A, Wersching H, Baune BT, Berger K, Dannlowski U. Prefrontal gray matter volume mediates genetic risks for obesity. Mol Psychiatry 2017; 22:703-710. [PMID: 28348383 DOI: 10.1038/mp.2017.51] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/18/2022]
Abstract
Genetic and neuroimaging research has identified neurobiological correlates of obesity. However, evidence for an integrated model of genetic risk and brain structural alterations in the pathophysiology of obesity is still absent. Here we investigated the relationship between polygenic risk for obesity, gray matter structure and body mass index (BMI) by the use of univariate and multivariate analyses in two large, independent cohorts (n=330 and n=347). Higher BMI and higher polygenic risk for obesity were significantly associated with medial prefrontal gray matter decrease, and prefrontal gray matter was further shown to significantly mediate the effect of polygenic risk for obesity on BMI in both samples. Building on this, the successful individualized prediction of BMI by means of multivariate pattern classification algorithms trained on whole-brain imaging data and external validations in the second cohort points to potential clinical applications of this imaging trait marker.
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Affiliation(s)
- N Opel
- Department of Psychiatry, University of Münster, Münster, Germany
| | - R Redlich
- Department of Psychiatry, University of Münster, Münster, Germany
| | - C Kaehler
- Department of Psychiatry, University of Münster, Münster, Germany.,Department of Mathematics and Computer Science, University of Münster, Münster, Germany
| | - D Grotegerd
- Department of Psychiatry, University of Münster, Münster, Germany
| | - K Dohm
- Department of Psychiatry, University of Münster, Münster, Germany
| | - W Heindel
- Department of Clinical Radiology, University of Münster, Münster, Germany
| | - H Kugel
- Department of Clinical Radiology, University of Münster, Münster, Germany
| | - A Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - N Koutsouleris
- Department of Psychiatry, University of Munich, Munich, Germany
| | - V Arolt
- Department of Psychiatry, University of Münster, Münster, Germany
| | - A Teuber
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - H Wersching
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - B T Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - K Berger
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - U Dannlowski
- Department of Psychiatry, University of Münster, Münster, Germany
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Wenclawiak B, Rathmann C, Teuber A. Supercritical-fluid extraction of soil samples and determination of polycyclic aromatic hydrocarbons (PAHs) by HPLC. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf00323750] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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