1
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Wong NACS, Garcia-Petit C, Dangoor A, Andrew N. A literature review and database of how the primary KIT/PDGFRA variant of a gastrointestinal stromal tumour predicts for sensitivity to imatinib. Cancer Genet 2022; 268-269:46-54. [PMID: 36155382 DOI: 10.1016/j.cancergen.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/18/2022] [Accepted: 09/05/2022] [Indexed: 01/25/2023]
Abstract
It is well recognized that the primary KIT or PDGFRA variant of a gastrointestinal stromal tumour (GIST) can predict sensitivity to imatinib. However, these data are currently spread across a wide range of publications and have not been collated as one reference. A broad-ranging literature search was therefore performed to assemble such a database which should help optimize imatinib-based management of GIST patients henceforth. Having excluded wild type GISTs and results for imatinib used as adjuvant therapy, 79 publications (dated August 2001 to March 2022) underwent data extraction. These data on imatinib sensitivity were either derived from in vitro studies, predicted by in silico analysis or based on in vivo clinical patient response. Data interpretation carried some caveats: there was a potential for replication of patient-derived data between older and new publications; only predicted protein sequences were presented; the criteria used to record clinical response were not uniform across all publications; and imatinib dosage could vary between different clinical publications. However, these data showed broad agreement of imatinib sensitivity amongst similar subtypes of KIT or PDGFRA variant. There was also agreement between in vivo versus in vitro/in silico derived sensitivity data for most variants when both data types were available.
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Affiliation(s)
- Newton A C S Wong
- Department of Cellular Pathology, Southmead Hospital, Bristol, United Kingdom, BS10 5NB.
| | - Christel Garcia-Petit
- East of Scotland Regional Genetic Service, Ninewells Hospital, Dundee, United Kingdom, DD1 9SY
| | - Adam Dangoor
- Bristol Haematology and Oncology Centre, University Hospitals Bristol & Weston NHS Trust, Bristol, United Kingdom, BS2 8ED
| | - Nicola Andrew
- East of Scotland Regional Genetic Service, Ninewells Hospital, Dundee, United Kingdom, DD1 9SY
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2
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Rahman J, Rahmanuddin S, Sham S, Sonawane S. Extensive Degenerative Change Masquerading Histomorphology in a Giant Cystic Gastrointestinal Stromal Tumor With Rare PDGFRA Mutation. Cureus 2020; 12:e10772. [PMID: 33042650 PMCID: PMC7538027 DOI: 10.7759/cureus.10772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most frequent type of mesenchymal tumors of the gastrointestinal (GI) tract, and most of the time they acquire the mutation of special kinds of genes. GISTs may be familial or inherited and affect several family members of the family or can be sporadic. The risk of GIST is increased in people with mutations in the receptor tyrosine kinase (KIT) and platelet-derived growth factor receptor alpha (PDGFRA) genes. In this report, we present a case of a large GIST with extensive cystic and degenerative change in a 76-year-old female patient with a rare Asp842-His845 deletion mutation detected in PDGFRA exon 18, that required subtotal gastrectomy with en bloc resection.
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Affiliation(s)
- Jawaria Rahman
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, USA
| | - Syed Rahmanuddin
- Department of Radiology, City of Hope Comprehensive Cancer Center, Duarte, USA
| | - Sunder Sham
- Department of Pathology, Lenox Hill Hospital Northwell Health, New York, USA
| | - Snehal Sonawane
- Department of Pathology, South Bend Medical Foundation, South Bend, USA
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3
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Laurini E, Marson D, Aulic S, Fermeglia M, Pricl S. Computational Alanine Scanning and Structural Analysis of the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Complex. ACS NANO 2020; 14:11821-11830. [PMID: 32833435 PMCID: PMC7448377 DOI: 10.1021/acsnano.0c04674] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The recent emergence of the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent for the coronavirus disease 2019 (COVID-19), is causing a global pandemic that poses enormous challenges to global public health and economies. SARS-CoV-2 host cell entry is mediated by the interaction of the viral transmembrane spike glycoprotein (S-protein) with the angiotensin-converting enzyme 2 gene (ACE2), an essential counter-regulatory carboxypeptidase of the renin-angiotensin hormone system that is a critical regulator of blood volume, systemic vascular resistance, and thus cardiovascular homeostasis. Accordingly, this work reports an atomistic-based, reliable in silico structural and energetic framework of the interactions between the receptor-binding domain of the SARS-CoV-2 S-protein and its host cellular receptor ACE2 that provides qualitative and quantitative insights into the main molecular determinants in virus/receptor recognition. In particular, residues D38, K31, E37, K353, and Y41 on ACE2 and Q498, T500, and R403 on the SARS-CoV-2 S-protein receptor-binding domain are determined as true hot spots, contributing to shaping and determining the stability of the relevant protein-protein interface. Overall, these results could be used to estimate the binding affinity of the viral protein to different allelic variants of ACE2 receptors discovered in COVID-19 patients and for the effective structure-based design and development of neutralizing antibodies, vaccines, and protein/protein inhibitors against this terrible new coronavirus.
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Affiliation(s)
- Erik Laurini
- Molecular Biology
and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Domenico Marson
- Molecular Biology
and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Suzana Aulic
- Molecular Biology
and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology
and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology
and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127 Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental
Protection, University of Lodz, 90-136 Lodz, Poland
- Phone: +39 040 558 3750.
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4
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Molecular modelling evaluation of exon 18 His845_Asn848delinsPro PDGFRα mutation in a metastatic GIST patient responding to imatinib. Sci Rep 2019; 9:2172. [PMID: 30778083 PMCID: PMC6379366 DOI: 10.1038/s41598-018-38028-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023] Open
Abstract
Platelet-Derived Growth Factor Receptor Alpha (PDGFRA) mutations occur in approximately 5-7% of gastrointestinal stromal tumours (GIST). Over half of all PDGFRA mutations are represented by the substitution at position 842 in the A-loop of an aspartic acid (D) with a valine (V), recognized as D842V, conferring primary resistance to imatinib in vitro and in clinical observations due to the conformation of the kinase domain, which negatively affects imatinib binding. The lack of interaction between imatinib and the D842V PDGFRA mutated model has been established and widely confirmed in vivo. However, for the other PDGFRA mutations, the correlation between pre-clinical and clinical data is still unclear. An in silico evaluation of the p.His845_Asn848delinsPro mutation involving exon 18 of PDGFRA in a metastatic GIST patient responding to first-line imatinib has been provided. Docking analyses were performed, and the ligand-receptor interactions were evaluated with the jCE algorithm for structural alignment. The docking simulation and structural superimposition analysis show that PDGFRA p.His845_Asn848delinsPro stabilizes the imatinib binding site with the residues that are conserved in KIT. The in vivo evidence that PDGFRA p.His845_Asn848delinsPro is sensitive to imatinib was confirmed by the molecular modelling, which may represent a reliable tool for the prediction of clinical outcomes and treatment selection in GIST, especially for rare mutations.
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5
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Boonstra PA, Gietema JA, Suurmeijer AJH, Groves MR, de Assis Batista F, Schuuring E, Reyners AKL. Tyrosine kinase inhibitor sensitive PDGFRΑ mutations in GIST: Two cases and review of the literature. Oncotarget 2017; 8:109836-109847. [PMID: 29312652 PMCID: PMC5752565 DOI: 10.18632/oncotarget.22663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal malignancies of the gastrointestinal tract. Most GISTs harbor a c-KIT (80%) or a PDGFRα (10%) mutation that leads to constitutive activation of the tyrosine kinase receptor. Response to treatment with tyrosine kinase inhibitors (TKIs) is dependent on mutational status of the tumor. The most common mutation in PDGFRα, D842V, is known to be imatinib resistant. Almost all other PDGFRα mutations are imatinib sensitive. We describe two patients with a PDGFRα exon 18 mutated GIST responding to treatment with TKIs. One of these patients has a p.M844_S847 deletion, not previously described in relation with TKI treatment response. Mutations in circulating tumor DNA were detectable with digital droplet PCR in serial plasma samples taken during treatment and correlated with treatment response of both patients. Computer 3D-modeling of the PDGFRα kinase domain of these two variants revealed no direct interference in imatinib or sunitinib binding and no effect in its activity in contrast to the reported structure of the imatinib resistant D842V mutation. An overview is given of the literature regarding the evidence of patients with different PDGFRα mutated GISTs on response to TKIs. The findings emphasize the use of mutational analysis in GIST to provide patients personalized treatment. Detection of mutations in plasma is feasible and can provide real-time information concerning treatment response. We suggest to register GIST patients with these uncommon mutations in a prospective international database to understand the tumor biology and obtain more evidence of such mutations to predict treatment response.
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Affiliation(s)
- Pieter A Boonstra
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
| | - Jourik A Gietema
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
| | - Albert J H Suurmeijer
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein, Groningen, The Netherlands
| | - Matthew R Groves
- University of Groningen, Faculty of Science and Engineering, Antonius Deusinglaan, Groningen, The Netherlands
| | - Fernando de Assis Batista
- University of Groningen, Faculty of Science and Engineering, Antonius Deusinglaan, Groningen, The Netherlands
| | - Ed Schuuring
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein, Groningen, The Netherlands
| | - Anna K L Reyners
- University of Groningen, University Medical Center Groningen, Department of Medical Oncology, Hanzeplein, Groningen, The Netherlands
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6
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Colombo C, Belfiore A, Paielli N, De Cecco L, Canevari S, Laurini E, Fermeglia M, Pricl S, Verderio P, Bottelli S, Fiore M, Stacchiotti S, Palassini E, Gronchi A, Pilotti S, Perrone F. β-Catenin in desmoid-type fibromatosis: deep insights into the role of T41A and S45F mutations on protein structure and gene expression. Mol Oncol 2017. [PMID: 28627792 PMCID: PMC5664003 DOI: 10.1002/1878-0261.12101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Desmoid‐type fibromatosis (DF) is a rare mesenchymal lesion with high risk of local recurrence. Specific β‐catenin mutations (S45F) appeared to be related to this higher risk compared to T41A‐mutated or wild‐type (WT). We explored the influence of both mutations and WT on structure stability and affinity of β‐catenin for α‐catenin and the pattern of gene expression that may influence DF behavior. Using 33 surgically resected primary DFs harboring T41A (n = 14), S45F (n = 10), or WT (n = 9), we performed a comparative molecular analysis by protein/protein interaction modeling, gene expression by DASL microarrays, human inflammation gene panel, and assessment of immune system‐based biomarkers by immunohistochemistry. Mutated proteins were more stable than WT and formed a weaker complex with α‐catenin. Consensus unsupervised gene clustering revealed the presence of two DF group‐mutated (T41A + S45F) and WT (P = 0.0047). The gene sets ‘Inflammatory‐Defense‐Humoral Immune Response’ and ‘Antigen Binding’ were significantly enriched in T41A. The deregulation of 16 inflammation‐related genes was confirmed. Low numbers of T cells and tumor‐associated macrophages (TAM) infiltrating the tumors and low/absent PD‐1/PD‐L1 expression were also identified. We demonstrated that mutated DFs (T41A or S45F) and WT are two distinct molecular subgroups with regard to β‐catenin stability, α‐catenin affinity, and gene expression profiling. A different inflammation signature characterized the two mutated groups, suggesting mediation either by T41A or by S45F. Finally, all mutated cases showed a low number of TIL and TAM cells and a low or absent expression of PD‐1 and PD‐L1 consistent with β‐catenin activation insensitive to checkpoint blockade.
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Affiliation(s)
- Chiara Colombo
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Antonino Belfiore
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Nicholas Paielli
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Loris De Cecco
- Functional Genomics and Bioinformatics, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Canevari
- Functional Genomics and Bioinformatics, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, University of Trieste, Italy
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Stefano Bottelli
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Marco Fiore
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvia Stacchiotti
- Adult Mesenchymal Tumor Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Elena Palassini
- Adult Mesenchymal Tumor Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandro Gronchi
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvana Pilotti
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Federica Perrone
- Laboratory of Experimental Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
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7
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Perfetti V, Laurini E, Aulić S, Fermeglia M, Riboni R, Lucioni M, Dallera E, Delfanti S, Pugliese L, Latteri FS, Pietrabissa A, Pricl S. Molecular and functional characterization of a new 3' end KIT juxtamembrane deletion in a duodenal GIST treated with neoadjuvant Imatinib. Oncotarget 2017; 8:56158-56167. [PMID: 28915580 PMCID: PMC5593551 DOI: 10.18632/oncotarget.19341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/28/2017] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. GISTs express the receptor tyrosine kinase KIT, and the majority of GISTs present KIT gain-of-function mutations that cluster in the 5′ end of the receptor juxtamembrane domain. On the other hand, little information is known about GISTs carrying mutations in the 3′ end of the KIT juxtamembrane domain. Here we report and discuss a clinical case of localized duodenal GIST whose molecular characterization revealed the presence of a new 21 nucleotide/7 amino acid deletion in the 3′ end of KIT juxtamembrane domain (Δ574–580). The patient was treated with Imatinib at standard regimen dose (400 mg/day), and responded well as the original tumor mass reduced, ultimately allowing conservative surgery. In line with these clinical evidences computer simulations, biophysical techniques and in vitro experiments demonstrated that the receptor tyrosine kinase KIT carrying the Δ574–580 mutation displays constitutive phosphorylation, which can be switched-off upon Imatinib treatment. In addition, results from this study showed that a clinical useful procedure, neoadjuvant treatment, can occasionally be of value for the understanding of the molecular pathogenesis of GIST.
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Affiliation(s)
- Vittorio Perfetti
- Internal Medicine, Ospedale SS Annunziata-ASST Pavia and Department of Molecular Medicine University of Pavia, 27100 Pavia, Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, Pharmaceutical and Molecular Biology Division, DEA, University of Trieste, 34127 Trieste, Italy
| | - Suzana Aulić
- Molecular Simulation Engineering (MOSE) Laboratory, Pharmaceutical and Molecular Biology Division, DEA, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, Pharmaceutical and Molecular Biology Division, DEA, University of Trieste, 34127 Trieste, Italy
| | - Roberta Riboni
- Department of Molecular Medicine and Anatomic Pathology Section, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Lucioni
- Department of Molecular Medicine and Anatomic Pathology Section, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Elena Dallera
- Department of Molecular Medicine and Anatomic Pathology Section, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Sara Delfanti
- Department of Oncology and Hematology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Luigi Pugliese
- Department of Surgery, General Surgery II, University of Pavia and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | | | - Andrea Pietrabissa
- Department of Surgery, General Surgery II, University of Pavia and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, Pharmaceutical and Molecular Biology Division, DEA, University of Trieste, 34127 Trieste, Italy
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8
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Zick A, Peretz T, Lotem M, Hubert A, Katz D, Temper M, Rottenberg Y, Uziely B, Nechushtan H, Meirovitz A, Sonnenblick A, Sapir E, Edelman D, Goldberg Y, Lossos A, Rosenberg S, Fried I, Finklstein R, Pikarsky E, Goldshmidt H. Treatment inferred from mutations identified using massive parallel sequencing leads to clinical benefit in some heavily pretreated cancer patients. Medicine (Baltimore) 2017; 96:e6931. [PMID: 28514312 PMCID: PMC5440149 DOI: 10.1097/md.0000000000006931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular portraits of numerous tumors have flooded oncologists with vast amounts of data. In parallel, effective inhibitors of central pathways have shown great clinical benefit. Together, this promises potential clinical benefits to otherwise end-stage cancer patients. Here, we report a clinical service offering mutation detection of archived samples using the ion Ampliseq cancer panel coupled with clinical consultation.A multidisciplinary think tank consisting of oncologists, molecular-biologists, genetic counselors, and pathologists discussed 67 heavily pretreated, advanced cancer patient cases, taking into account mutations identified using ion Ampliseq cancer panel, medical history, and relevant literature.The team generated a treatment plan, targeting specific mutations, for 41 out of 64 cases. Three patients died before results were available. For 32 patients, the treating oncologists chose not to include the panel recommendation in the treatment plan for various reasons. Nine patients were treated as recommended by the panel, 5 with clinical benefit, and 4 with disease progression.This study suggests that routine use of massive parallel tumor sequencing is feasible and can judiciously affect treatment decisions when coupled with multidisciplinary team-based decision making. Administration of personalized based therapies at an earlier stage of disease, expansion of genetic alterations examined, and increased availability of targeted therapies may lead to further improvement in the clinical outcome of metastatic cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Alexander Lossos
- Leslie and Michael Gaffin Center for Oncology, Departments of Oncology and Neurology, Hebrew University-Hadassah Medical Center
| | - Shai Rosenberg
- Leslie and Michael Gaffin Center for Oncology, Departments of Oncology and Neurology, Hebrew University-Hadassah Medical Center
| | - Iris Fried
- Department of Pediatrics, Hadassah Medical Center, Division of Pediatric Hematology and Oncology
| | - Ruth Finklstein
- Lautenberg Center for Immunology, IMRIC, The Hebrew University-Hadassah Medical School
| | - Eli Pikarsky
- Lautenberg Center for Immunology, IMRIC, The Hebrew University-Hadassah Medical School
- Department of Pathology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Hanoch Goldshmidt
- Department of Pathology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
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9
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Zampieri D, Laurini E, Vio L, Fermeglia M, Pricl S, Wünsch B, Schepmann D, Mamolo MG. Improving selectivity preserving affinity: new piperidine-4-carboxamide derivatives as effective sigma-1-ligands. Eur J Med Chem 2015; 90:797-808. [PMID: 25528334 DOI: 10.1016/j.ejmech.2014.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/19/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
We report the design, synthesis and binding evaluation against σ1 and σ2 receptors of a series of new piperidine-4-carboxamide derivatives variously substituted on the amide nitrogen atom. Specifically, we assessed the effects exerted on σ receptor affinity by substituting the N-benzylcarboxamide group present on a series of compounds previously synthesized in our laboratory with different cyclic or linear moieties. The synthesized compounds 2a-o were tested to estimate their affinity and selectivity toward σ1 and σ2 receptors. Very high σ1 affinity (Ki = 3.7 nM) and Kiσ2/Kiσ1 selectivity ratio (351) were found for the tetrahydroquinoline derivative 2k, featuring a 4-chlorobenzyl moiety linked to the piperidine nitrogen atom.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy.
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Luciano Vio
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DI3, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy; National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste, Italy.
| | - Bernhard Wünsch
- Department of Pharmaceutical and Medicinal Chemistry, Corrensstrasse 48, 48149 Münster, Germany
| | - Dirk Schepmann
- Department of Pharmaceutical and Medicinal Chemistry, Corrensstrasse 48, 48149 Münster, Germany
| | - Maria Grazia Mamolo
- Department of Chemistry & Pharmaceutical Sciences, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
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10
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Smoothened (SMO) receptor mutations dictate resistance to vismodegib in basal cell carcinoma. Mol Oncol 2014; 9:389-97. [PMID: 25306392 DOI: 10.1016/j.molonc.2014.09.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 11/21/2022] Open
Abstract
Basal cell carcinomas (BCCs) and a subset of medulloblastomas are characterized by loss-of-function mutations in the tumor suppressor gene, PTCH1. PTCH1 normally functions by repressing the activity of the Smoothened (SMO) receptor. Inactivating PTCH1 mutations result in constitutive Hedgehog pathway activity through uncontrolled SMO signaling. Targeting this pathway with vismodegib, a novel SMO inhibitor, results in impressive tumor regression in patients harboring genetic defects in this pathway. However, a secondary mutation in SMO has been reported in medulloblastoma patients following relapse on vismodegib to date. This mutation preserves pathway activity, but appears to confer resistance by interfering with drug binding. Here we report for the first time on the molecular mechanisms of resistance to vismodegib in two BCC cases. The first case, showing progression after 2 months of continuous vismodegib (primary resistance), exhibited the new SMO G497W mutation. The second case, showing a complete clinical response after 5 months of treatment and a subsequent progression after 11 months on vismodegib (secondary resistance), exhibited a PTCH1 nonsense mutation in both the pre- and the post-treatment specimens, and the SMO D473Y mutation in the post-treatment specimens only. In silico analysis demonstrated that SMO(G497W) undergoes a conformational rearrangement resulting in a partial obstruction of the protein drug entry site, whereas the SMO D473Y mutation induces a direct effect on the binding site geometry leading to a total disruption of a stabilizing hydrogen bond network. Thus, the G497W and D473Y SMO mutations may represent two different mechanisms leading to primary and secondary resistance to vismodegib, respectively.
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11
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Rossi D, Pedrali A, Gaggeri R, Marra A, Pignataro L, Laurini E, Dal Col V, Fermeglia M, Pricl S, Schepmann D, Wünsch B, Peviani M, Curti D, Collina S. Chemical, Pharmacological, and in vitro Metabolic Stability Studies on Enantiomerically Pure RC‐33 Compounds: Promising Neuroprotective Agents Acting as σ
1
Receptor Agonists. ChemMedChem 2013; 8:1514-27. [DOI: 10.1002/cmdc.201300218] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Alice Pedrali
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Raffaella Gaggeri
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Annamaria Marra
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
| | - Luca Pignataro
- Dipartimento di Chimica, Università degli Studi di Milano, Istituto di Scienze e Tecnologie Molecolari (ISTM) del CNR, Via Golgi 19, 20133 Milan (Italy)
| | - Erik Laurini
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
| | - Valentina Dal Col
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
| | | | - Sabrina Pricl
- MOSE‐DEA, University of Trieste, Via Valerio 10, 34127 Trieste (Italy)
- National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE‐DEA, University of Trieste, Trieste (Italy)
| | - Dirk Schepmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster (Germany)
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, Correnstrasse 48, 48149 Münster (Germany)
| | - Marco Peviani
- Department of Biology and Biotechnology “L. Spallanzani”, Laboratory of Cellular and Molecular Neuropharmacology, University of Pavia, Via Ferrata 9, 27100 Pavia (Italy)
| | - Daniela Curti
- Department of Biology and Biotechnology “L. Spallanzani”, Laboratory of Cellular and Molecular Neuropharmacology, University of Pavia, Via Ferrata 9, 27100 Pavia (Italy)
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia (Italy)
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12
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Rossi D, Marra A, Picconi P, Serra M, Catenacci L, Sorrenti M, Laurini E, Fermeglia M, Pricl S, Brambilla S, Almirante N, Peviani M, Curti D, Collina S. Identification of RC-33 as a potent and selective σ1 receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells. Part 2: g-scale synthesis, physicochemical characterization and in vitro metabolic stability. Bioorg Med Chem 2013; 21:2577-86. [PMID: 23498917 DOI: 10.1016/j.bmc.2013.02.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 02/14/2013] [Indexed: 11/18/2022]
Abstract
Strong pharmacological evidences indicate that σ1 receptors are implicated in the pathophysiology of all major CNS disorders. In the last years our research group has conducted extensive studies aimed at discovering novel σ1 ligands and we recently selected (R/S)-RC-33 as a novel potent and selective σ1 receptor agonist. As continuation of our work in this field, here we report our efforts in the development of this new σ1 receptor agonist. Initially, we investigated the binding of (R) and (S) enantiomers of RC-33 to the σ1 receptor by in silico experiments. The close values of the predicted affinity of (R)-RC-33 and (S)-RC-33 for the protein evidenced the non-stereoselective binding of RC-33 to the σ1 receptor; this, in turn, supported further development and characterization of RC-33 in its racemic form. Subsequently, we set-up a scaled-up, optimized synthesis of (R/S)-RC-33 along with some compound characterization data (e.g., solubility in different media and solid state characterization by thermal analysis techniques). Finally, metabolic studies of RC-33 in different biological matrices (e.g., plasma, blood, and hepatic S9 fraction) of different species (e.g., rat, mouse, dog, and human) were performed. (R/S)-RC-33 is generally stable in all examined biological matrices, with the only exception of rat and human liver S9 fractions in the presence of NADPH. In such conditions, the compound is subjected to a relevant oxidative metabolism, with a degradation of approximately 65% in rat and 69% in human. Taken together, our results demonstrated that (R/S)-RC-33 is a highly potent, selective, metabolically stable σ1 agonist, a promising novel neuroprotective drug candidate.
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Affiliation(s)
- Daniela Rossi
- Medicinal Chemistry Laboratory, Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section (MCPTS), University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
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13
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Laurini E, Da Col V, Wünsch B, Pricl S. Analysis of the molecular interactions of the potent analgesic S1RA with the σ1 receptor. Bioorg Med Chem Lett 2013; 23:2868-71. [PMID: 23582276 DOI: 10.1016/j.bmcl.2013.03.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 10/27/2022]
Abstract
The highly selective σ1 receptor antagonist S1RA is endowed with a surprisingly high affinity for its target protein given a missing fundamental hydrophobic pharmacophoric requirement. Here we show that, with respect to other potent σ1 ligands, S1RA is able to compensate this loss by fulfilling all other pharmacophoric requirements and by gaining in solvation energy.
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Affiliation(s)
- Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory - DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
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14
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Conca E, Miranda C, Dal Col V, Fumagalli E, Pelosi G, Mazzoni M, Fermeglia M, Laurini E, Pierotti MA, Pilotti S, Greco A, Pricl S, Tamborini E. Are two better than one? A novel double-mutant KIT in GIST that responds to Imatinib. Mol Oncol 2013; 7:756-62. [PMID: 23567324 DOI: 10.1016/j.molonc.2013.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 12/18/2022] Open
Abstract
Gastrointestinal stromal tumors carry in about 85% of the cases activating mutations in KIT gene. Generally only one KIT mutation is found in primary tumors and the majority of mutations affecting KIT exon 11 is sensitive to Imatinib. We report upon a GIST case harboring a double-mutant KIT gene at exon 11, which expresses a receptor bearing the known activating W557G mutation and a newly discovered missense Y578C alteration. The relative affinities for ATP and Imatinib of each single (W557G, Y578C) and double (W557G/Y578C) mutant KITs were predicted by in silico studies (computer-based molecular simulations), and compared with those obtained for known Imatinib sensitive and resistant KIT mutants. In parallel, biochemical analysis of the single and double KIT mutants expressed in mammalian cells was performed. Both the in-silico/in-vitro investigations showed constitutive activation and sensitivity to Imatinib of the yet mentioned Y578C mutation as well as of the double mutant, providing evidence that the concomitant presence of the W557G and Y578C mutations does not affect Imatinib response compare to the single mutations, in line with what observed in Imatinib treated patient.
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Affiliation(s)
- Elena Conca
- Laboratory of Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Via Venezian 1, 20133 Milan, Italy
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15
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Laurini E, Marson D, Dal Col V, Fermeglia M, Mamolo MG, Zampieri D, Vio L, Pricl S. Another brick in the wall. Validation of the σ1 receptor 3D model by computer-assisted design, synthesis, and activity of new σ1 ligands. Mol Pharm 2012; 9:3107-26. [PMID: 23020867 DOI: 10.1021/mp300233y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Originally considered an enigmatic polypeptide, the σ(1) receptor has recently been identified as a unique ligand-regulated protein. Many studies have shown the potential of σ(1) receptor ligands for the treatment of various diseases of the central nervous system (CNS); nevertheless, almost no information about the 3D structure of the receptor and/or the possible modes of interaction of the σ(1) protein with its ligands have been unveiled so far. With the present work we validated our σ(1) 3D homology model and assessed its reliability as a platform for σ(1) ligand structure-based drug design. To this purpose, the 3D σ(1) model was exploited in the design of 33 new σ(1) ligands and in their ranking for receptor affinity by extensive molecular dynamics simulation-based free energy calculations. Also, the main interactions involved in receptor/ligand binding were analyzed by applying a per residue free energy deconvolution and in silico alanine scanning mutagenesis calculations. Subsequently, all compounds were synthesized in our laboratory and tested for σ(1) binding activity in vitro. The agreement between in silico and in vitro results confirms the reliability of the proposed σ(1) 3D model in the a priori prediction of the affinity of new σ(1) ligands. Moreover, it also supports and corroborates the currently available biochemical data concerning the σ(1) protein residues considered essential for σ(1) ligand binding and activity.
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Affiliation(s)
- Erik Laurini
- Molecular Simulation Engineering Laboratory, Department of Industrial Engineering and Information Technology, University of Trieste, Via Valerio 10, 34127 Trieste, Italy
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16
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Meyer C, Schepmann D, Yanagisawa S, Yamaguchi J, Dal Col V, Laurini E, Itami K, Pricl S, Wünsch B. Pd-catalyzed direct C-H bond functionalization of spirocyclic σ1 ligands: generation of a pharmacophore model and analysis of the reverse binding mode by docking into a 3D homology model of the σ1 receptor. J Med Chem 2012; 55:8047-65. [PMID: 22913577 DOI: 10.1021/jm300894h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To explore the hydrophobic binding region of the σ(1) receptor protein, regioisomeric spirocyclic thiophenes 9-11 were developed as versatile building blocks. Regioselective α- and β-arylation using the catalyst systems PdCl(2)/bipy/Ag(2)CO(3) and PdCl(2)/P[OCH(CF(3))(2)](3)/Ag(2)CO(3) allowed the introduction of various aryl moieties at different positions in the last step of the synthesis. The increasing σ(1) affinity in the order 4 < 5/6 < 7/8 indicates that the positions of the additional aryl moiety and the S atom in the spirocyclic thiophene systems control the σ(1) affinity. The main features of the pharmacophore model developed for this class of σ(1) ligands are a positive ionizable group, a H-bond acceptor group, two hydrophobic moieties, and one hydrophobic aromatic group. Docking of the ligands into a σ(1) 3D homology model via molecular mechanics/Poisson-Boltzmann surface area calculations led to a very good correlation between the experimentally determined and estimated free energy of receptor binding. These calculations support the hypothesis of a reverse binding mode of ligands bearing the aryl moiety at the "top" (compounds 2, 3, 7, and 8) and "left" (compounds 4, 5, and 6) positions, respectively.
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Affiliation(s)
- Christina Meyer
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Hittorfstrasse 58-62, D-48149 Münster, Germany
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Cassier PA, Fumagalli E, Rutkowski P, Schöffski P, Van Glabbeke M, Debiec-Rychter M, Emile JF, Duffaud F, Martin-Broto J, Landi B, Adenis A, Bertucci F, Bompas E, Bouché O, Leyvraz S, Judson I, Verweij J, Casali P, Blay JY, Hohenberger P. Outcome of patients with platelet-derived growth factor receptor alpha-mutated gastrointestinal stromal tumors in the tyrosine kinase inhibitor era. Clin Cancer Res 2012; 18:4458-64. [PMID: 22718859 DOI: 10.1158/1078-0432.ccr-11-3025] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Platelet-derived growth factor receptor-alpha (PDGFRA) mutations are found in approximately 5% to 7% of advanced gastrointestinal stromal tumors (GIST). We sought to extensively assess the activity of imatinib in this subgroup. EXPERIMENTAL DESIGN We conducted an international survey among GIST referral centers to collect clinical data on patients with advanced PDGFRA-mutant GISTs treated with imatinib for advanced disease. RESULTS Fifty-eight patients were included, 34 were male (59%), and median age at treatment initiation was 61 (range, 19-83) years. The primary tumor was gastric in 40 cases (69%). Thirty-two patients (55%) had PDGFRA-D842V substitutions whereas 17 (29%) had mutations affecting other codons of exon 18, and nine patients (16%) had mutation in other exons. Fifty-seven patients were evaluable for response, two (4%) had a complete response, eight (14%) had a partial response, and 23 (40%) had stable disease. None of 31 evaluable patients with D842V substitution had a response, whereas 21 of 31 (68%) had progression as their best response. Median progression-free survival was 2.8 [95% confidence interval (CI), 2.6-3.2] months for patients with D842V substitution and 28.5 months (95% CI, 5.4-51.6) for patients with other PDGFRA mutations. With 46 months of follow-up, median overall survival was 14.7 months for patients with D842V substitutions and was not reached for patients with non-D842V mutations. CONCLUSIONS This study is the largest reported to date on patients with advanced PDGFRA-mutant GISTs treated with imatinib. Our data confirm that imatinib has little efficacy in the subgroup of patients with D842V substitution in exon 18, whereas other mutations appear to be sensitive to imatinib.
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Abstract
Elucidation of the genetic processes leading to neoplastic transformation has identified cancer-promoting molecular alterations that can be selectively targeted by rationally designed therapeutic agents. Protein kinases are druggable targets and have been studied intensively. New methodologies--including crystallography and three-dimensional modeling--have allowed the rational design of potent and selective kinase inhibitors that have already reached the clinical stage. However, despite the clinical success of kinase-targeted therapies, most patients that respond eventually relapse as a result of acquired resistance. Darwinian-type selection of secondary mutations seems to have a major role in this resistance. The emergence and/or expansion of tumor clones containing new mutations in the target kinase and that are drug-insensitive have been observed after chronic treatment. The resistance mechanisms to tyrosine kinase inhibitors, in particular secondary resistant mutations as a consequence of treatment, will be discussed in detail. In particular, this Review will focus on KIT and PDGFRA mutations, which are involved in the pathogenesis of gastrointestinal stromal tumors. Harnessing the selection of mutated variants developed to overcome these resistance mechanisms is an ongoing goal of current research and new strategies to overcome drug resistance is being envisaged.
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